title: KO1_H3K27

first: Dan

last: Lu

address: #38 Xueyuan Rd

institute: Peking University

data_processing:
Basecalls performed using CASAVA version 1.4
All reads produced by ChIP-seq of acetyl-H3K27 were aligned to the mm10 mouse genome using Bowtie2 version 2.3.5. with the following configurations…
Data were filtered using the following specifications…
peaks were called using MACS2 software version 2.1.2 with the following setting: ChIP threshold (0.05).
Genome_build: mm10
Supplementary_files_format_and_content: BED and BW files

source_name: CD8+ T cells

growth_protocol: Wild-type and PAC1-/- CD8+ T cells were isolated from mice infected with LCMV Cl13 for 30-day and subsequently sorted by flow cytometry.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: CD8+ T cells

value: spleen

tag: antibody

value: anti-H3K27-ac (Abcam, catalog number:ab4729, Lot number:GR3251519-2)


title: WT2_H3K27

status: Public on Dec 22 2019

type: SRA

city: Beijing

country: China

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: cell type

tag: tissue

tag: strain

tag: genotype

value: WT


title: KO2_In


title: WT2_In


title: KO1_In


title: KO2_H3K27


title: WT1_In


title: pam3_da_2

city: Nanjing

first: Yuqing

last: Wu

address: 101 Longmian Road

institute: Nanjing Medical University

library_source: transcriptomic

data_processing:
Basecalls performed using BGISEQ-500
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38.p5 whole genome using bowtie v2.2.5 with parameters -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200
Data were filtered using SOAPnuke version v1.5.2 with parameters -l 15 -q 0.2 -n 0.05
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

molecule: total RNA

source_name: BMDMs treated with Pam3CSK6 and DA

growth_protocol: For isolation of BMDMs, tibias and femurs were removed from wild-type mice by sterile techniques and the bone marrow was flushed with fresh medium. BMDMs were plated in DMEM supplemented with 10% FBS in the presence of 10% L929 conditioned medium for 4–6 d at 37 °C in a humidified atmosphere of 5% CO2.

extract_protocol:
RNA isolation were performed on a BGISEQ-500 (Beijing Genomic Institution, BGI)
RNA libraries were prepared for sequencing using standard BGISEQ-500 protocols

treatment_protocol: BMDMs treated for 2h with DA and then stimulated with Pam3CSK4 for 6h

tag: age

value: 8 weeks


title: siFOXD3 rep1

city: Shanghai

first: Ji

middle: Xiang

last: jun

state: Shanghai

address: 500 Dongchuan Rd

department: the Institute of Biomedical Sciences and School of Life Sciences

institute: East China Normal University

data_processing:
Sequencing tags were mapped to the human (Homo sapiens) genome (version hg19) using the software TopHat
Transcript abundance was estimated using Cufflinks
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

organism: Homo sapiens

source_name: lung cancer cell line

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: lung cancer cell line


title: pam3_da_3

source_name: BMDMs treated with Pam3CSK7 and DA


title: pam3_da_1

source_name: BMDMs treated with Pam3CSK5 and DA


title: urinary_HC_rep2

type: RNA

city: Kanazawa

first: Shin-ichi

last: Horike

state: Ishikawa

address: 13-1 Takaramachi

department: Research Center for Experimental Modeling of Human Disease

country: Japan

institute: Kanazawa University

description: Gene expression in urine from healthy controls.

hyb_protocol: Cy3-labeled miRNA samples were hybridized in a reaction volume of 45 µl containing 1x Hi-PRM hybridization buffer and 1x GE blocking agent following the manufacturer's instructions. The mixed samples were hybridized to Agilent Human miRNA Microarrays (G4872A) for 20 hours at 55°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 5 minute at room temperature with Gene Expression Wash Buffer 1 (Agilent) and 5 minute with 37°C GE Wash buffer 2 (Agilent), then dried.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2539A) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters (protocol AgilentHD_miRNA and Grid: 070156_D_F_20141006) to obtain background subtracted and spatially detrended Processed Signal intensities.
Data were normalized and filtered wtih two filters with GeneSpring software 13 (Agilent Technologies). In brief, raw data were normalized with their 75 percentile values. In the first filter, when the value of a probe was lower than  20 percentile value in any samples, the probe was excluded. In the second filter, when the flag of a probe was compromised in any samples, the probe was exluded. After flitering, control probes were excluded, and log scale values were transformed into normal scale.

source_name: urinary_005, collected from healthy controls, replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from urinary RNA using the miRNA Complete Labeling and Hyb Kit (Agilent) according to the manufacturer's instructions. T4 RNA ligase and Cy-3-pCp were used for labeling the miRNA samples.

extract_protocol: miRNA was extracted with miRNeasy Serum/Plasma Kit (Qiagen, Valencia, CA)  according to the manufacturer's instructions.

tag: sample type

value: urine sample


title: shEXOSC10-r1

city: San Francisco

first: Hani

last: Goodarzi

state: CA

department: Biochemistry and Biophysics

country: USA

institute: UCSF

data_processing:
STAR (v. 2.5) was used to map the reads to the human transcriptome (build hg19).
HTSeq-count (v.0.7) was then used to count reads in each gene and DESeq2 was used to compare samples.
Genome_build: hg19
Supplementary_files_format_and_content: Gene count files

growth_protocol: Cells were grown in DMEM-based media supplemented with 10% FBS, 1% L-glutamine, 1% Sodium Pyruvate, and 1% Pen/Strep.

extract_protocol:
RNA samples were collected using total RNA Purification Kit (Norgen Biotek).
Libraries were generated using QuantSeq 3’ mRNA-Seq library prep kit fwd (Lexogen) and run on an HiSeq 4000 Instrument.

treatment_protocol: EXOSC10 and XRN2 knockdown cells, along with shControl cells, in biological replicates were used for this experiment.

tag: replicate

tag: shRNA


title: siNC  rep3

value: wild type


title: pam3_3

source_name: BMDMs treated with Pam3CSK4


title: urinary_HC_rep3

source_name: urinary_006, collected from healthy controls, replicate 3


title: WT1_H3K27


title: shContrl-r2

value: shContrl


title: urinary_HC_rep1

source_name: urinary_004, collected from healthy controls, replicate 1


title: siNC  rep2


title: pam3_2


title: urinary_GC_rep3

description: Gene expression in urine from GC patients.

source_name: urinary_003, collected from GC patients, replicate 3


title: shContrl-r1


title: siNC  rep1


title: pam3_1


title: Dam-Pros∆N7

status: Public on Dec 21 2019

first: Yan

last: Song

state: 北京

address: No.5 Yiheyuan Road

description: GMR71C09-Gal4_ProsΔN7-vs-Dam-averaged.bedgraph

data_processing:
Library strategy: DamID-seq
FASTQ files were processed with damidseq_pipeline.
Biological replicates in gatc.bedgraph format were averaged,
The averaged binding tracks used for further analysis.
Genome_build: DMBDGP6
Supplementary_files_format_and_content: gatc.bedgraph files were generated using the damidseq_pipeline software, at GATC fragment resolution. Score represents the normalised log2(Dam-fusion/Dam) enrichment. Processed files are provided as both raw data and scaled data. Microsoft excel file was generated using the find_peaks pipeline sofware.

organism: Drosophila melanogaster

source_name: dissected 3rd instar larval brain

extract_protocol:
DNA was extracted from whole fly larvae brain via Qiagen Blood and Tissue kits as per manufacturers' instructions, digested with DpnI, DamID adaptors ligated, digested with DpnII and amplified via PCR.
DNA was sonicated to an average size of 300bp using a Diagenode Bioruptor and DamID adaptors removed via either AlwI digestion. Sonnicated material was end-repaired, A-tailed, sequencing adaptors ligated and PCR amplified.

value: brain

tag: developmental stage

value: 3rd instar larvae


title: Dam-HP1a

description: GMR71C09-Gal4_HP1a-vs-Dam-averaged.bedgraph


title: Dam-ProsFL

description: GMR71C09-Gal4_ProsFL-vs-Dam-averaged.bedgraph


title: urinary_GC_rep2

source_name: urinary_002, collected from GC patients, replicate 2


title: Rab11_KD_3

city: Worcester

first: Dr Yvonne

last: Edwards

state: MA

address: 373 Plantation Street

department: Program in Molecular Medicine

institute: University of Massachusetts Medical School

data_processing:
Using FASTX toolkit Ion torrent sequences are trimmed with min quality score of 17 and min read length of 35 bases
The trimmed sequences (from Ion Torrent and Illumina) are mapped to the reference genome Drosophila melanogaster Ensembl BDGP5 (Adam MD et al 2000) using the aligner STAR (version 2.4.2a) (Dobin A et al 2013).
The STAR package has an in-built count functionality HTseq-count (version 0.6.1) (Anders S et al 2015) to count uniquely mapped reads at the gene level.
DESEQ2 (Love MI et al 2014) is used to perform statistical analysis to determine differentially expressed genes between the control samples and the knockdown samples.
Genome_build: Drosophila melanogaster Ensembl BDGP5
Supplementary_files_format_and_content: mergedCounts.txt reports the HTseq-counts of uniquely mapped reads at the gene level
Supplementary_files_format_and_content: DESEQ2 reports significantly differentially expressed genes  between the two conditions (padj value < 0.1 )

source_name: midgut

growth_protocol: flies were raised at RT with low yeast, agar, cornmeal, molasses medium, shifted to 29 degree for 5days after 5days post enclosure.

extract_protocol:
midguts were dissected from control and Rab11_KD flies and total RNA isolation with TriReagent
Ion Torrent and Illumina protocols

value: enterocyte

value: adult

tag: genotype/variation

value: Rab11 KD


title: urinary_GC_rep1

source_name: urinary_001, collected from GC patients, replicate 1


title: WT_3


title: Dam-ctr


title: 91

city: New York

first: Jennifer

last: Downs

address: 1300 York Ave.

institute: Weill Cornell Medicine

data_processing:
Illumina bcl2fastq2 v2.17 was used for basecalling.
Sequenced reads were trimmed for low-quality bases and for adapter sequences using cutadapt; then mapped to the human hg19 reference genome using tophat v2.0.11.
Read counts were calculated using HTSeq-count v0.6.1.
Genome_build: hg19
Supplementary_files_format_and_content: txt file, raw read counts

source_name: cervical cytobrushes

extract_protocol:
RNA extraction via RNA mini kit (Qiagen) according to manufacturer's instructions.
Libraries were prepared using Illumina TruSeq RNA Sample Preparation (Non-stranded and Poly-A selection).

tag: schisto status

value: cervical mucus


title: 87


title: 96


title: A12 NET-seq Rep 1

city: Birmingham

first: Andrew

middle: Martin

last: Clarke

state: Al

address: 720 20th street S

department: Biochemistry and Molecular Genetics

institute: University of Alabama at Birmingham

description: NET-seq reads for Sample 4

data_processing:
Basecalls were converted to fastq files using Illumina’s bcl2fastq software (ver. 2.18.0.012)
The first two nucleotides were clipped from the 5’ end of each read and the 3’ adapter sequence CTGTAGGCACCAT was removed from each read via trim galore (ver. 0.4.1)
The sequences were aligned to the Saccharomyces cerevisiae genome assembly 3 via BWA MEM (ver 0.6) with a minimum alignment score of 20. All other parameters are default
Output files were converted to .bed files using samtools (ver 1.3.1)
Genome_build: SacCer 3
Supplementary_files_format_and_content: Bed files indicate full read. 5’ end of reads correspond to 3’ ends of nascent transcripts.

organism: Saccharomyces cerevisiae

source_name: yeast

growth_protocol: Three liters per sample of each specified strain were grown to A600 = 0.3 in YEPD with nutation and collected via filtration

extract_protocol:
Cells were lysed via 10 1 minute grinds at maximum amplitude in a mikro dismembrator II. The grinding cup was chilled in liquid nitrogen for 1 minute between each grind.
NET-seq libraries were prepared as in Clarke, et. al., NETSeq reveals heterogeneous nucleotide incorporation by RNA polymerase I, PNAS, 2018. 115 (50), E11633-E11641. In brief,  Pol I elongation complexes were isolated from the cell lysate via immunoprecipitation with anti-HA magnetic beads. Associated RNA transcripts were then isolated using an acidic phenol-chloroform extraction. The RNA transcripts were then 3’ appended with a DNA linker and reverse transcribed to produce complementary DNAs (cDNAs). The cDNAs were circularized and amplified by PCR to produce high-throughput sequencing libraries.
NET-seq

value: rpa12 deletion


title: WT NET-seq Rep 2

description: NET-seq reads for Sample 2


title: WT NET-seq Rep 1

description: NET-seq reads for Sample 1


title: 94

value: S. mansoni


title: 93


title: 88


title: WT NET-seq Rep 3

description: NET-seq reads for Sample 3


title: 92


title: 95


title: 97


title: 89


title: 90


title: A12 NET-seq Rep 2

description: NET-seq reads for Sample 5


title: 86


title: 85


title: 83


title: 84


title: 79


title: 81


title: 80


title: 78


title: A12 NET-seq Rep 3

description: NET-seq reads for Sample 6


title: 77


title: 74


title: 73


title: 69


title: 71


title: 65


title: 62


title: 59


title: 64


title: 61


title: 72


title: 63


title: 82


title: 67


title: 68


title: 66


title: 58


title: 50


title: 55


title: 57


title: 52

value: S. haematobium


title: 53


title: 54


title: 56


title: 76


title: 49


title: 51


title: 47


title: 75


title: 48


title: 70


title: 60


title: 45


title: 46


title: 44


title: 43


title: 40


title: 38


title: 35


title: 37


title: 36


title: 34


title: 41


title: 32


title: 25


title: 30


title: 29


title: 31


title: 26


title: 28


title: 23


title: 27


title: 22


title: 20


title: 19


title: 24


title: 21


title: 18


title: 17


title: 42


title: 39


title: 16


title: 15


title: 33


title: 12


title: 13


title: 10


title: 9


title: 8


title: 5


title: 7


title: 2


title: 6


title: 4


title: microglia, TREM2 +/+, young IL9_M

city: South San Francisco

first: Thomas

last: Sandmann

email: genomics@dnli.com, sandmann@dnli.com

state: California

address: 161 Oyster Point Blvd

institute: Denali Therapeutics

description:
microglia, TREM2 +/+, young
IL9_M

data_processing:
Sequencing adapters were trimmed using skewer (Jiang et al., 2014; version 0.2.2) with default parameters. Unique molecular identifiers (UMIs) were extracted from each read with the umi2index tool (Lexogen). Quality control of the trimmed reads was performed using FastQC (version 0.11.5: www.bioinformatics.babraham.ac.uk/projects/fastqc).
Reads were aligned to an index of the mouse genome (version GRCm38_p6) A STAR index (Dobin et al., 2013; version 2.5.3a) was built with the --sjdbOverhang=50 argument. Splice junctions from Gencode gene models (release M17) were provided via the --sjdbGTFfile argument. STAR alignments were generated with the following parameters: --outFilterType BySJout --quantMode TranscriptomeSAM --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMstrandField intronMotif --outSAMattributes NH HI AS nM MD XS --outSAMunmapped Within. Alignments sharing the same UMI and genomic coordinate were deduplicated using the collapse_UMI_bam tool (Lexogen). Post-alignment quality control reports were generated using MultiQC (Ewels et al., 2016; version 1.0).
The raw gene expression matrix was constructed from the 'forward' column of STAR's ReadsPerGene.out.tab output files using R (version 3.4.3). Gene symbols and Entrez gene identifiers were mapped using Ensembl (version 91) via the biomaRt R package (Durinck et al, 2009; version 2.34.0).
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited, gzip-compressed text file with matrix of raw counts results from deduplicated UMIs for each sample.

source_name: Cd11b+ microglia isolated from whole brain

growth_protocol: Mice were housed on a 12hr/12hr light dark cycle. All mouse husbandry and experimental procedures were approved by Denali's Institutional Animal Care and Use Committee.

extract_protocol:
Mice were perfused with PBS, brain were removed and dissociated with the Adult Brain Dissociation Kit (Miltenyi). Cells were fluorescence-activated cell sorted for viability, then microglia (Cd11b+) and astrocytes (ACSA-2+) were collected for RNA extaction using the RNeasy Plus Micro kit (Qiagen)
Libraries were prepared using the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina with the unique-molecular identifier add-on kit (Lexogen), following the ‘low-input’ procedure defined by the manufacturer.

treatment_protocol: Trem2-WT and homozygous knockout mice were aged for 2 months (young) or 16-18 months (old), respectively.

value: TREM2 +/+

value: microglia

tag: Sex

value: female

value: months

tag: rin


title: astrocyte, TREM2 -/-, old IL8_A

description:
astrocyte, TREM2 -/-, old
IL8_A

source_name: ACSA-2+ astrocytes isolated from whole brain

value: TREM2 -/-

value: astrocyte


title: astrocyte, TREM2 +/+, young IL9_A

description:
astrocyte, TREM2 +/+, young
IL9_A


title: MGE cells, CSE74J

city: Durham

first: Debra

last: Silver

state: North Carolina

address: 224 CARL Building

department: Molecular Genetics and Microbiology

institute: Duke University School of Medicine

data_processing:
TrimGalore toolkit1 was used which employs Cutadapt2 to trim low-quality bases and Illumina sequencing adapters from the 3’ end of the reads
Only reads that were 20nt or longer after trimming were kept for further analysis.
Reads were mapped to the GRCm38v73 version of the mouse genome and transcriptome3 using the STAR RNA-seq alignment tool4. Reads were kept for subsequent analysis if they mapped to a single genomic location.
Gene counts were compiled using the HTSeq tool5.  Only genes that had at least 10 reads in any given library were used in subsequent analysis.
Normalization and differential expression was carried out using the DESeq26 Bioconductor7 package with the R statistical programming environment8. The false discovery rate was calculated to control for multiple hypothesis testing.
Genome_build: mm10
Supplementary_files_format_and_content: Normalized counts, Raw counts

source_name: MGE E11.5

extract_protocol:
RNA was extracted using the RNAeasy kit (Qiagen 74034).
Libraries were prepared using NuGEN mRNA Seq with AnyDeplete Globin (AnyDeplete step was skipped during the library preparation protocol).

treatment_protocol:
Plug dates were defined as embryonic day (E)0.5 on the morning the plug was identified. Dams were sacrificed at E11.5 and embryonic tissue harvested
E11.5 Nkx2.1-cre;tdTomato positive telencephalon was fluorescently activated cell sorting (FACs) using a B-C Astrios cell sorter directly into RLT buffer (Qiagen RNAeasy kit; Qiagen 74034) and frozen at -80.

value: MGE cells


title: MGE cells, CSE71H


title: microglia, TREM2 +/+, old IL7_M

description:
microglia, TREM2 +/+, old
IL7_M


title: MGE cells, CSE70B

value: Magoh lox/+; Nkx2.1-Cre; ROSAloxSTOPloxTdTomato


title: MGE cells, CSE70E


title: zmknl1-Rep1

city: Wuhan

first: Handong

last: Su

state: Hubei

address: No.1,Shizishan Street · Hongshan District

institute: Huazhong Agricultural University

data_processing:
Sequenced reads were trimmed using Trimmomatic (version: 0.36)
The quaility control reads were mapped to B73 RefGen_v3.31 using hisat2 (version: 2.0.1-beta).
Htseq-count was used to count reads of all the annotated genes.
Significant DEGs were identified using DESeq2 package as those with threshold (q value < 0.05, log2(fold change) > 1.5).
Genome_build: Maize B73 RefGen_v3.31
Supplementary_files_format_and_content: Htseq-count was used to count reads of all the annotated genes.

organism: Zea mays

source_name: maize

growth_protocol: Suitable materials were planted in the field for RNA-seq experiments.

extract_protocol:
Total RNA was extracted using TRIzol reagent. The cDNA libraries were constructed following Illumina standard protocols and sequenced with Illumina HiSeq 2500 by Berry Genomics Co. Ltd, China.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: kernels at 14 DAP

value: zmknl1 mutant


title: 11


title: microglia, TREM2 -/-, young IL6_M

description:
microglia, TREM2 -/-, young
IL6_M

value: brain


title: zmknl1-Rep2


title: microglia, TREM2 +/+, young IL5_M

description:
microglia, TREM2 +/+, young
IL5_M


title: 1


title: astrocyte, TREM2 +/+, young IL5_A

description:
astrocyte, TREM2 +/+, young
IL5_A


title: 3


title: MGE cells, CSE71L


title: 14


title: MGE cells, CSE77C


title: astrocyte, TREM2 -/-, old IL4_A

description:
astrocyte, TREM2 -/-, old
IL4_A


title: astrocyte, TREM2 +/+, old IL7_A

description:
astrocyte, TREM2 +/+, old
IL7_A


title: microglia, TREM2 -/-, old IL8_M

description:
microglia, TREM2 -/-, old
IL8_M


title: astrocyte, TREM2 +/+, old IL3_A

description:
astrocyte, TREM2 +/+, old
IL3_A


title: microglia, TREM2 -/-, old IL28_M

description:
microglia, TREM2 -/-, old
IL28_M


title: microglia, TREM2 +/+, old IL3_M

description:
microglia, TREM2 +/+, old
IL3_M


title: WT-Rep2

value: wild type


title: E18.5

city: St. Louis

first: Farshid

last: Guilak

state: MO

address: 4515 McKinley Ave

institute: Washington University in St. Louis

data_processing:
The Cell Ranger Single Cell Software Suite v2 was used to perform sample demultiplexing, barcode processing, and single cell 3’ gene counting (http://software.10xgenomics.com/single-cell/overview/welcome).
The gene/barcode matrix was imported to Seurat (https://github.com/satijalab/seurat, v2.3.4) and filtering was performed to exclude cells with less than 200 or more than 6,000 genes. Cells with more than 10% unique molecular identifier (UMI) counts associated with mitochondrial genes were also excluded. The data was log-normalized and library size and mitochondrial UMI counts were regressed.
The cell cycle stage of each cell was assigned as S, G1, or G2/M based on a pre-determined list of cell cycle markers [Tirosh et al. 2016] and the difference between the G2/M and S scores was calculated and variance-corrected.
Cluster analysis was performed via t-distributed stochastic neighbor embedding (tSNE) at each time point to examine cellular heterogeneity and cell types present in hindlimb tissues
Genome_build: mm10
Supplementary_files_format_and_content: gene list (_genes.tsv) and cell barcodes (xbarcodes.tsv) as well as gene/barcode matrices (xmatrix.mtx) are provided for each time point

source_name: hindlimb

extract_protocol:
Murine hindlimbs were manually dissected at 4 time points during embryonic joint development, including points marking formation of the limb bud (E11.5), formation of cartilaginous condensations (E13.5), joint cavitation (E15.5), and joint morphogenesis (E18.5). Embryonic pups (7-9/litter) were removed by caesarean section from a timed-pregnant female C57BL/6 mouse per time point (The Jackson Laboratory, Bar Harbor, ME) and euthanized. Hindlimbs from 6-7 pups/litter were digested with collagenase (Type II, Worthington-biochem, Lakewood, NJ) and pronase (EMD Millipore, Billerica, MA) in 15-minute increments with agitation at 37°C for up to one hour. Every 15 minutes, mechanical dissociation was applied by pipetting up and down. Following digestion, cells from each litter (time point) were pooled, strained through a 100um cell strainer, pelleted, resuspended at 1 x 10^6 cells per 500ml in freeze media (80% FBS, 10% DMEM, 10% DMSO), and stored in liquid nitrogen until single cell capture.
Cells in freeze media were rapidly thawed in a 37°C water bath, and resuspended in 1X PBS and 0.04% bovine serum albumin. Dead cells were removed using magnetic bead-bound antibodies against apoptotic and necrotic cells (Dead cell removal kit, Miltenyi Biotec) and cells were washed twice. Single cell capture was performed with the 10x Chromium Controller (10x Genomics, Pleasanton, CA). Briefly, single cell suspensions were brought to a concentration of 1,000 cells/ml and approximately 6,000 cells per time point (4 samples total) were loaded into the 8-channel microfluidic chip that encapsulates thousands of cells in gel beads in emulsion (GEMs). Cell capture, cDNA generation, and library preparation were performed using Chromium Single Cell 3’ v2 Reagent kit, following the manufacturer’s instructions. To test the reliability of single-cell capture, a 1:1 mixture of E18.5 mouse hindlimb cells and human 293T cells was sequenced and the multiplet rate was determined by the fraction of mouse reads in human barcodes and vice versa. Single cell RNA-seq libraries were pooled and run on the Illumina NovaSeq S1 flow cell with 26x98bp reads to generate ~500 million reads per library (time point).

value: embryonic day 18.5

value: hindlimb


title: astrocyte, TREM2 +/+, old IL27_A

description:
astrocyte, TREM2 +/+, old
IL27_A


title: E15.5

value: embryonic day 15.5


title: astrocyte, TREM2 -/-, young IL26_A

description:
astrocyte, TREM2 -/-, young
IL26_A


title: microglia, TREM2 -/-, young IL26_M

description:
microglia, TREM2 -/-, young
IL26_M


title: E13.5

value: embryonic day 13.5


title: microglia, TREM2 +/+, young IL25_M

description:
microglia, TREM2 +/+, young
IL25_M


title: astrocyte, TREM2 -/-, old IL28_A

description:
astrocyte, TREM2 -/-, old
IL28_A


title: astrocyte, TREM2 +/+, young IL25_A

description:
astrocyte, TREM2 +/+, young
IL25_A


title: astrocyte, TREM2 -/-, young IL6_A

description:
astrocyte, TREM2 -/-, young
IL6_A


title: microglia, TREM2 +/+, old IL27_M

description:
microglia, TREM2 +/+, old
IL27_M


title: astrocyte, TREM2 +/+, old IL23_A

description:
astrocyte, TREM2 +/+, old
IL23_A


title: microglia, TREM2 -/-, young IL22_M

description:
microglia, TREM2 -/-, young
IL22_M


title: microglia, TREM2 -/-, old IL24_M

description:
microglia, TREM2 -/-, old
IL24_M


title: WT-Rep1

value: kernels at 14DAP


title: Pooled microglia cells from two Trem2 -/- animals after 12 weeks on cuprizone diet

data_processing:
The fastq files from each dataset were individually processed using Cell Ranger (v2.1.1). The "raw_gene_bc_matrices" directories from these runs served as the starting point for all subsequent quality control, filtering, and downstream analyses. These steps were performed using a combination of the DropletUtils, scater (McCarthy et al., 2017) and scran (Lun et al., 2016) Bioconductor (v3.8) packages. Experiments were independently quality controlled and filtered by removing low quality droplets. First, droplets containing only ambient levels of RNA were removed. We then calculate per cell: (i) the number of UMIs; (ii) number of genes detected; (iii) fraction of reads that map to ribosomal proteins; and (iv) fraction of reads that map to the mitochondrial genome. Cells that are outliers in any of these metrics (> 2-3 median absolute deviations too low for (i) and (ii), too high for (iii) and (iv)) are removed. Read counts were normalized using a deconvolution strategy for scaling normalization of sparse count data (Lun et al., 2016). All downstream analyses were perform using the 4,895 genes that were identified with positive components of biological variance (i.e., higher variance than the assumed technical Poisson noise) as implemented in the "decomposeVar" method in the scran package.
Genome_build: mm10
Supplementary_files_format_and_content: three csv-delimited text files with 1) the matrix of raw quantitation results for each cell, 2) cell annotations and 3) gene annotations, respectively (more details in the READ.txt)

source_name: TREM2-/- microglia, cuprizone diet

extract_protocol:
Mice were perfused with PBS, brains were removed and dissociated with the Adult Brain Dissociation Kit (Miltenyi). 30,000 live CD11b+ CD45low microglia were sorted from each hemibrain and two hemibrains per condition were pooled into PBS + 0.5% BSA to generate 4 total sequencing groups. Microglia were counted and diluted to 500,000 cells/mL in 70μL and viability was verified to be >70%.
Single cell libraries were barcoded and prepared using the Chromium Single Cell 3' Library Kit with v2 chemistry (10X Genomics, product #120267) with a Chromium Controller (10X Genomics) at the Stanford Functional Genomics Facility. The libraries were sequenced using a NovaSeq S4 (Illumina) at the UCSF Center for Advanced Technology.

treatment_protocol: Trem2-WT, heterozyogus knockout, and homozygous knockout mice were fed a control or 0.2% cuprizone diet for 12 weeks.

value: male

value: 12-14 months

value: Trem2 -/-

tag: diet

value: cuprizone

tag: timepoint

value: 12 weeks


title: astrocyte, TREM2 +/+, young IL21_A

description:
astrocyte, TREM2 +/+, young
IL21_A

value: TREM2 +/+

value: astrocyte

value: female

value: months


title: astrocyte, TREM2 -/-, old IL20_A

description:
astrocyte, TREM2 -/-, old
IL20_A

value: TREM2 -/-


title: microglia, TREM2 +/+, young IL21_M

description:
microglia, TREM2 +/+, young
IL21_M

value: brain

value: microglia


title: astrocyte, TREM2 -/-, young IL22_A

description:
astrocyte, TREM2 -/-, young
IL22_A


title: Pooled microglia cells from two Trem2 +/- animals after 12 weeks on cuprizone diet

source_name: TREM2+/- microglia, cuprizone diet

value: Trem2 +/-


title: microglia, TREM2 +/+, old IL23_M

description:
microglia, TREM2 +/+, old
IL23_M


title: ACKR4ko 2 Tail

city: Hannover

first: Nadine

last: Eckert

state: Lower Saxony

address: Carl-Neuberg-Straße 1

department: Immunology

country: Germany

institute: Hannover Medical School

description:
common_S550Nr1_S550Nr3.vcf
unique_S550Nr3_vars.annotated.vcf

data_processing:
Library strategy: DNA-seq
demultiplexing (Illumina bcl2fastq 2.19)
adapter trimming (Skewer, 0.2.2)
alignment to the murine reference genome (mm10) with Burrows-Wheeler Aligner (BWA-mem 0.7.2-cegat), Reads aligned to multiple sides with the same mapping score were discarded
duplicate removal with with SAMtool 0.1.18
Genetic variants were identified with Verscan 2.4.2-cegat (26) and variants with a frequency of ≥ 2% were annotated with SnpEff (version 4.2 with GRCm38.75 )
Genome_build: mm10
Supplementary_files_format_and_content: VCF files contain the information on which position the samples deviate from the reference genome mm10. Point mutations are listed in the snps files and and insertions/deletions in the indels files. Annotated variant lists are in the files named with .annotated. Comparisions between WT (S550Nr1) and Ackr4-/- samples (S550Nr2 and S550Nr3) are labelled with common_ for the shared variants or with unique_ for the variants found in only one sample.

source_name: Tail

growth_protocol: Mice were bred in the Central Animal Facility of the Hannover Medical School, Germany under SPF conditions, controlled day-night cycles and with food and water ad libidum.

extract_protocol:
Genomic DNA from tail tissue was isolated with QIAamp DNA Mini Kit (Qiagen, Hilden, Germany). DNA amount and purity was determined with Qubit dsDNA BR Assay Kit (Thermo Fischer Scientific).
1 µg DNA was used for library preparation with Agilent SureSelect XT Mouse All Exon Kit.

value: tail

tag: gender


title: WT tail

description:
unique_S550Nr1-2_vars.annotated.vcf
unique_S550Nr1-3_vars.annotated.vcf


title: ACKR4ko 1 Tail

description:
common_S550Nr1_S550Nr2.vcf
unique_S550Nr2_vars.annotated.vcf


title: microglia, TREM2 -/-, young IL2_M

description:
microglia, TREM2 -/-, young
IL2_M


title: Pooled microglia cells from two Trem2 +/+ animals after 12 weeks on cuprizone diet

source_name: WT microglia, cuprizone diet

value: Trem2 +/+


title: microglia, TREM2 -/-, old IL4_M

description:
microglia, TREM2 -/-, old
IL4_M


title: astrocyte, TREM2 -/-, young IL2_A

description:
astrocyte, TREM2 -/-, young
IL2_A


title: Pooled microglia cells from two Trem2 +/+ animals after 12 weeks on control diet

source_name: WT microglia, control diet

value: control


title: astrocyte, TREM2 +/+, old IL19_A

description:
astrocyte, TREM2 +/+, old
IL19_A


title: microglia, TREM2 +/+, old IL19_M

description:
microglia, TREM2 +/+, old
IL19_M


title: E11.5

value: embryonic day 11.5

value: hindlimb


title: microglia, TREM2 -/-, young IL18_M

description:
microglia, TREM2 -/-, young
IL18_M


title: RD rep3

first: Haibo

last: Zhou

address: No.160, Pujian Road

department: Department of Rheumatology

institute: Renji Hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using HISAT2 (Kim et al., 2015;Pertea et al., 2016).
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using StringTie(Pertea et al., 2016).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

source_name: monocyte derived dendritic cell

growth_protocol: Cells were cultured in RPMI 1640 medium (Gibco) with 10% fetal bovine serum (FBS, Gibco) and 1% Penicillin-Streptomycin (Gibco) at 37°C and 5% CO2 or collected directly for subsequent experiments. To obtain moDCs, mouse monocytes were isolated from BM with the Mouse Monocyte Isolation Kit (BM) according to the technical manual (Miltenyi, Germany). Cells were cultured with 100ng/mL GM-CSF (Peprotech) and 50ng/mL IL-4 (Peprotech) for 7 days and then sorted by Flow cytometry (FACSAriaTM III, BD).

extract_protocol:
Total RNA was extracted by Trizol reagent (Invitrogen) and determined by Bioanalyzer 4200 (Agilent, Santa Clara, CA, USA).
Next-generation libraries of mRNA-seq were prepared using VAHTS mRNA-seq v2 Library Prep Kit for Illumina® (Vazyme, Nanjing, China). The Library quality was determined by Bioanalyzer 4200 (Agilent, Santa Clara, CA, USA).

treatment_protocol: Mouse monocyte derived dendritic cells were primed with interferon α for 24 hours, and then cultured with R837, together with or without spermidine for 18 hours.

value: Bone marrow

value: monocyte derived dendritic cell

tag: treatment

value: R837+Spermidine stimulated


title: microglia, TREM2 -/-, old IL20_M

description:
microglia, TREM2 -/-, old
IL20_M


title: microglia, TREM2 +/+, young IL17_M

description:
microglia, TREM2 +/+, young
IL17_M


title: RD rep2

tag: cell type


title: astrocyte, TREM2 -/-, old IL16_A

description:
astrocyte, TREM2 -/-, old
IL16_A

tag: tissue


title: astrocyte, TREM2 +/+, young IL17_A

description:
astrocyte, TREM2 +/+, young
IL17_A


title: RD rep1

tag: strain


title: microglia, TREM2 +/+, old IL15_M

description:
microglia, TREM2 +/+, old
IL15_M

tag: genotype


title: R rep3

value: R837 stimulated


title: astrocyte, TREM2 +/+, old IL15_A

description:
astrocyte, TREM2 +/+, old
IL15_A

value: TREM2 +/+

tag: age


title: microglia, TREM2 -/-, old IL16_M

description:
microglia, TREM2 -/-, old
IL16_M


title: R rep2


title: astrocyte, TREM2 +/+, young IL13_A

description:
astrocyte, TREM2 +/+, young
IL13_A

value: astrocyte


title: astrocyte, TREM2 -/-, young IL14_A

description:
astrocyte, TREM2 -/-, young
IL14_A

value: female


title: microglia, TREM2 +/+, young IL13_M

description:
microglia, TREM2 +/+, young
IL13_M

value: months


title: R rep1


title: microglia, TREM2 -/-, young IL14_M

description:
microglia, TREM2 -/-, young
IL14_M

value: TREM2 -/-


title: microglia, TREM2 -/-, old IL12_M

description:
microglia, TREM2 -/-, old
IL12_M

value: brain


title: Ctrl rep2

value: No stimulation


title: astrocyte, TREM2 -/-, old IL12_A

description:
astrocyte, TREM2 -/-, old
IL12_A


title: microglia, TREM2 -/-, young IL10_M

description:
microglia, TREM2 -/-, young
IL10_M

value: microglia


title: astrocyte, TREM2 +/+, old IL11_A

description:
astrocyte, TREM2 +/+, old
IL11_A


title: astrocyte, TREM2 -/-, young IL10_A

description:
astrocyte, TREM2 -/-, young
IL10_A


title: astrocyte, TREM2 -/-, young IL18_A

description:
astrocyte, TREM2 -/-, young
IL18_A


title: Ctrl rep1


title: microglia, TREM2 +/+, young IL1_M

description:
microglia, TREM2 +/+, young
IL1_M


title: Ctrl rep3


title: astrocyte, TREM2 +/+, young IL1_A

description:
astrocyte, TREM2 +/+, young
IL1_A


title: Colon mesenchyme 2B (C2B)

city: New Haven

first: Richard

last: Flavell

state: CT

address: 300 Cedar Street, TAC S-569

department: Department of Immunobiology

institute: Yale University

data_processing:
Drop-seq preprocessing was performed using DropSeq tools (https://anaconda.org/bioconda/dropseq_tools).
The alignment was peformed using STAR (2.6)
Bead synthesis error was detected using DetectBeadSynthesisErrors in DropSeq tools.
Read counts per cell were generated using BAMTagHistogram in DropSeq tools.
Visualization was done using ggplot2 R package.
Genome_build: mm10
Supplementary_files_format_and_content: Gzipped text file which includes gene-by-cell count matrix

molecule: polyA RNA

source_name: Colon mesenchyme

growth_protocol: Standard mouse housing conditions, freshly isolated cells

extract_protocol:
Epithelial depletion with EDTA and DTT. Mesenchymal cell isolation with Collagenase XI and Dispase
Drop-seq protocol

treatment_protocol: No treatment of mice. No treatement of cells.

value: Colon mesenchyme

value: 10 weeks


title: astrocyte, TREM2 -/-, old IL24_A

description:
astrocyte, TREM2 -/-, old
IL24_A


title: Colon mesenchyme 2A (C2A)


title: Microglia cells from Trem2 -/- animal 981 after 12 weeks on cuprizone diet

data_processing:
Sequencing adapters were trimmed using skewer (Jiang et al., 2014; version 0.2.2) with default parameters. Quality control of the trimmed reads was performed using FastQC (version 0.11.5: www.bioinformatics.babraham.ac.uk/projects/fastqc).
Reads were aligned to an index of the mouse genome (version GRCm38_p6) A STAR index (Dobin et al., 2013; version 2.5.3a) was built with the --sjdbOverhang=50 argument. Splice junctions from Gencode gene models (release M17) were provided via the --sjdbGTFfile argument. STAR alignments were generated with the following parameters: --outFilterType BySJout --quantMode TranscriptomeSAM --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMstrandField intronMotif --outSAMattributes NH HI AS nM MD XS --outSAMunmapped Within. Post-alignment quality control reports were generated using MultiQC (Ewels et al., 2016; version 1.0).
The raw gene expression matrix was constructed from the 'forward' column of STAR's ReadsPerGene.out.tab output files using R (version 3.4.3). Gene symbols and Entrez gene identifiers were mapped using Ensembl (version 91) via the biomaRt R package (Durinck et al, 2009; version 2.34.0).
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited, gzip-compressed text file with matrix of raw quantitation results for each sample.

source_name: Microglia isolated from whole brain

extract_protocol:
Mice were perfused with PBS, brain were removed and dissociated with the Adult Brain Dissociation Kit (Miltenyi). Cells were fluorescence-activated cell sorted for viability, then microglia (Cd11b+) and all other cells were collected for RNA extaction using the RNeasy Plus Micro kit (Qiagen)
Libraries were prepared using the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen), following the ‘low-input’ procedure defined by the manufacturer.

treatment_protocol: Trem2-WT, heterozyogus knockout, and homozygous knockout mice were fed a control or 0.2% cuprizone diet for 5 weeks or 12 weeks.

value: Trem2 -/-

value: cuprizone

value: weeks


title: Non-microglia cells from Trem2 +/- animal 9546 after 5 weeks on control diet

source_name: Non-microglia isolated from whole brain

value: Trem2 +/-

value: other

value: control


title: Microglia cells from Trem2 +/- animal 9546 after 5 weeks on control diet


title: Non-microglia cells from Trem2 -/- animal 9542 after 12 weeks on cuprizone diet

value: male


title: Non-microglia cells from Trem2 -/- animal 981 after 12 weeks on cuprizone diet


title: Microglia cells from Trem2 -/- animal 9542 after 12 weeks on cuprizone diet


title: microglia, TREM2 +/+, old IL11_M

description:
microglia, TREM2 +/+, old
IL11_M

value: TREM2 +/+


title: Colon mesenchyme 2C (C2C)


title: Colon mesenchyme 1B (C1B)


title: Non-microglia cells from Trem2 -/- animal 9470 after 5 weeks on control diet


title: Non-microglia cells from Trem2 +/- animal 9469 after 12 weeks on cuprizone diet


title: Microglia cells from Trem2 +/- animal 9469 after 12 weeks on cuprizone diet


title: Non-microglia cells from Trem2 -/- animal 9467 after 12 weeks on control diet


title: Colon mesenchyme 1A (C1A)


title: Microglia cells from Trem2 -/- animal 9467 after 12 weeks on control diet


title: Non-microglia cells from Trem2 +/- animal 9463 after 12 weeks on control diet


title: Ptger4 epithelial knock-out-3 (V2)

source_name: Ptger4 knock-out crypt cells

extract_protocol:
Crypt isolation from the small intestine with EDTA and dissociation with trypsin
Drop-seq protocol

value: Ptger4 knock-out crypt cells

value: Small intestine, freshly isolated crypts


title: Microglia cells from Trem2 +/- animal 9463 after 12 weeks on control diet

value: female


title: Non-microglia cells from Trem2 -/- animal 945 after 5 weeks on control diet


title: Non-microglia cells from Trem2 +/- animal 944 after 12 weeks on control diet


title: Ptger4 flox-2 (F1B)

source_name: Ptger4 flox crypt cells

value: Ptger4 flox crypt cells


title: Ptger4 flox-3 (F2)


title: Ptger4 epithelial knock-out-2 (V1B)


title: Non-microglia cells from Trem2 +/- animal 943 after 12 weeks on control diet

value: brain


title: Microglia cells from Trem2 +/- animal 944 after 12 weeks on control diet


title: Microglia cells from Trem2 +/- animal 943 after 12 weeks on control diet


title: Non-microglia cells from Trem2 +/+ animal 9145 after 12 weeks on control diet

value: Trem2 +/+


title: Microglia cells from Trem2 +/+ animal 9144 after 5 weeks on cuprizone diet

value: microglia


title: Non-microglia cells from Trem2 +/+ animal 9144 after 5 weeks on cuprizone diet


title: Microglia cells from Trem2 -/- animal 8635 after 12 weeks on control diet


title: Microglia cells from Trem2 -/- animal 9470 after 5 weeks on control diet


title: Microglia cells from Trem2 -/- animal 8485 after 5 weeks on cuprizone diet


title: Ptger4 epithelial knock-out-1 (V1A)


title: BR_TvL_18 sample 5

city: Leiden

first: Tim

middle: Marijn

last: van Leeuwe

address: Sylviusweg 72

country: Netherlands

institute: Leiden University

data_processing:
Filtered reads were mapped to the NRRL3 transcriptome annotation version 20140311 using Salmon v.0.14.1
Differential gene expression was assessed via pairwise comparisons using DESeq2 v1.24.0 using the design ~ biomass + mutation
Supplementary_files_format_and_content: tab-delimited text files include read values for each gene in each Sample

organism: Aspergillus niger

source_name: mycelial biomass

growth_protocol: Controlled batch fermentations for A. niger strains MA234.1 and TLF39 were performed in 6.6L BioFlo bioreactors (New Brunswick Scientific), as previously described (Jørgensen et al., 2010). A batch of 21 L MM (as described by Arentshorst et al., 2012) containing 0.75% D-glucose was made by adding 1 L filter-sterilized (0.2 µm pore) glucose (15.75% w/v) solution to a freshly autoclaved volume of 20 L MM (no carbon source) as described above. Allowing 1 day of dissolving and a check for contamination, 5 L MM 0.75% glucose was added to each bioreactor directly after autoclaving. Temperature, acidity and stir speed were set to and kept at 30°C, pH 3 and 250 rpm, respectively. The pH was controlled by addition of titrants (2M NaOH and 1M HCl). Sparger aeration of 1 L/min was left on to allow oxygen saturation of the medium prior to inoculation. Next, aeration was set to headspace only and 1.5 mL 10% w/v Yeast Extract was added to the medium to promote homogeneous germination for the to-be-added spores. Subsequently, a total of 5x10e9 (106 sp/mL) spores were added to the medium using a concentrated spore solution. Germination time of approximately 4-5h was maintained, preceding the addition of polypropyleneglycol P2000 anti-foam agent, increasing agitation to 750 rpm and changing aeration from headspace to sparger only (1 L/min). Oxygen, base and acid consumption were monitored and samples were taken at regular intervals to obtain biomass, culture filtrate and microscopy samples. Biomass was harvested by applying a vacuum over Whatman™ Glass Microfiber Filter (GF/C™) (diameter 47 mm, CAT No.1822-047, Buckinghamshire, UK). Samples were all quickly frozen in liquid nitrogen prior to storage at -80°C. Biomass accumulation through time was gravimetrically determined by lyophilizing designated samples from the corresponding broth culture mass.

extract_protocol:
RNA was isolated from mycelial biomass samples obtained from batch cultivated A. niger strains MA234.1 and TLF39, using TRIzol (Invitrogen). RNA was purified afterwards with NucleoSpin RNA Clean-up kit (Macherey-Nagel) with DNase treatment. Concentration and quality of the RNA was determined using a NanoDrop 2000 spectrophotometer (Thermo Scientific) and by gel-electrophoresis, respectively
RNA libraries were prepared for sequencing using standard Illumina protocols

value: wild type

tag: percentage of maximum biomass

tag: biological replicate


title: BR_TvL_17 sample 11

value: <delta>crhA-G


title: BR_TvL_18 sample 9


title: Non-microglia cells from Trem2 -/- animal 8485 after 5 weeks on cuprizone diet

value: Trem2 -/-


title: BR_TvL_16 sample 10


title: BR_TvL_17 sample 7


title: Microglia cells from Trem2 -/- animal 945 after 5 weeks on control diet


title: Non-microglia cells from Trem2 +/- animal 8042 after 5 weeks on cuprizone diet

value: cuprizone


title: Non-microglia cells from Trem2 -/- animal 8635 after 12 weeks on control diet

value: weeks


title: BR_TvL_16 sample 7


title: Non-microglia cells from Trem2 +/+ animal 743 after 5 weeks on cuprizone diet


title: Non-microglia cells from Trem2 +/- animal 7674 after 12 weeks on control diet

value: Trem2 +/-


title: Microglia cells from Trem2 +/- animal 8042 after 5 weeks on cuprizone diet


title: BR_TvL_15 sample 6


title: Microglia cells from Trem2 +/+ animal 9145 after 12 weeks on control diet


title: Microglia cells from Trem2 +/+ animal 743 after 5 weeks on cuprizone diet


title: Non-microglia cells from Trem2 +/- animal 6296 after 12 weeks on cuprizone diet

value: other


title: Non-microglia cells from Trem2 +/+ animal 8043 after 12 weeks on cuprizone diet


title: Microglia cells from Trem2 +/+ animal 5512 after 5 weeks on control diet

value: control


title: Microglia cells from Trem2 +/- animal 6296 after 12 weeks on cuprizone diet


title: Non-microglia cells from Trem2 +/- animal 4352 after 5 weeks on control diet


title: Non-microglia cells from Trem2 +/+ animal 5512 after 5 weeks on control diet

value: male


title: Microglia cells from Trem2 +/- animal 4352 after 5 weeks on control diet


title: Microglia cells from Trem2 +/+ animal 8043 after 12 weeks on cuprizone diet


title: Non-microglia cells from Trem2 +/+ animal 3917 after 12 weeks on cuprizone diet


title: Microglia cells from Trem2 +/+ animal 3917 after 12 weeks on cuprizone diet


title: Non-microglia cells from Trem2 -/- animal 310 after 5 weeks on cuprizone diet


title: Microglia cells from Trem2 -/- animal 310 after 5 weeks on cuprizone diet


title: Non-microglia cells from Trem2 -/- animal 2478 after 5 weeks on cuprizone diet


title: Microglia cells from Trem2 +/- animal 7674 after 12 weeks on control diet


title: Microglia cells from Trem2 +/+ animal 309 after 5 weeks on control diet


title: Non-microglia cells from Trem2 +/+ animal 309 after 5 weeks on control diet


title: Microglia cells from Trem2 -/- animal 2478 after 5 weeks on cuprizone diet


title: Non-microglia cells from Trem2 +/- animal 2476 after 12 weeks on cuprizone diet


title: BR_TvL_15 sample 1


title: Microglia cells from Trem2 +/- animal 2476 after 12 weeks on cuprizone diet


title: Non-microglia cells from Trem2 +/+ animal 2474 after 5 weeks on cuprizone diet


title: phyA-strong_shade24_rep2

city: Xiamen

first: Yi

last: Tao

address: South Xiangan Rd.

department: School of LIfe Sciences

institute: Xiamen University

hyb_protocol: 12.5 ug fragmented cRNAs were hybridized for 16 hr at 45C using Hybridization Oven 640.The GeneChip (#900720) HWS Kit was used for hybridization, washing and staining.

scan_protocol: Gene chips were scanned using GeneChip® Scanner 3000,

data_processing: The data was analysed using RMA in the affy Bioconductor package in R, using the v14.0.0 Arabidopsis CustomCDF from http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF

label: biotin

organism: Arabidopsis thaliana

source_name: mutant_seedlings_strong shade 24hr

label_protocol: Ambion #1792 MessageAmp™ Premier RNA Amplification Kit was used to synthesis biotin-labeled cRNA.

growth_protocol: Seeds were surfice sterilized and sown on 1/2MS. They were imbibed at 4 degree for 2 days and then germinated under continuous white light at 22 degree. All seedlings were first grown in continuous white light at 22 degree for 5 days before treatments. Whole seedlings were used for total RNA extraction

extract_protocol: Total RNAs were isolated using Tripure (Roche) according to the manufacturer's instructions

treatment_protocol: Seedlings were treated with continuous white light (about 45 µmolm-2sec-1), shade (LED light, red:13 µmolm-2sec-1, blue: 3.5 µmolm-2sec-1, and far-red light:21 µmolm-2sec-1, R:FR=0.7), or strong shade(LED light, red:3 µmolm-2sec-1, blue: 3.5 µmolm-2sec-1, and far-red light:30 µmolm-2sec-1, R:FR=0.1) for 24 hours before extraction

tag: ecotype background

value: phyA-211 (null phyA mutant)

value: 5-day old

value: whole seedlings

tag: exposed to

value: simulated shade (R:FR=0.1) for 24 hrs


title: phyA-strong_shade24_rep1

tag: genotype/variation


title: Col-strong_shade24_rep3

source_name: WT_seedlings_strong shade 24hr


title: Microglia cells from Trem2 +/+ animal 1930 after 5 weeks on control diet

value: female


title: Microglia cells from Trem2 +/+ animal 1932 after 12 weeks on control diet

value: brain


title: Non-microglia cells from Trem2 +/+ animal 1932 after 12 weeks on control diet

value: Trem2 +/+


title: phyA-strong_shade24_rep3


title: Col-strong_shade24_rep2


title: Ptger4 flox-1 (F1A)

value: Ptger4 flox crypt cells

value: 10 weeks

value: Small intestine, freshly isolated crypts


title: Microglia cells from Trem2 +/+ animal 2474 after 5 weeks on cuprizone diet

value: microglia


title: Non-microglia cells from Trem2 +/+ animal 1930 after 5 weeks on control diet


title: phyA-shade24_rep3

source_name: mutant_seedlings_shade 24hr

value: simulated shade (R:FR=0.7) for 24 hrs


title: Non-microglia cells from Trem2 -/- animal 1748 after 12 weeks on cuprizone diet

value: Trem2 -/-

value: cuprizone

value: weeks


title: Microglia cells from Trem2 -/- animal 1748 after 12 weeks on cuprizone diet


title: Microglia cells from Trem2 +/- animal 1745 after 5 weeks on control diet

value: Trem2 +/-

value: control


title: phyA-shade24_rep2

value: phyA-211 (null phyA mutant)


title: Microglia cells from Trem2 +/+ animal 1746 after 12 weeks on cuprizone diet


title: Non-microglia cells from Trem2 +/+ animal 1746 after 12 weeks on cuprizone diet

value: other


title: Col-strong_shade24_rep1

value: wild type

value: 5-day old

value: whole seedlings


title: Non-microglia cells from Trem2 +/- animal 1745 after 5 weeks on control diet

value: brain

value: male


title: Non-microglia cells from Trem2 -/- animal 1744 after 12 weeks on control diet

value: female


title: Col-shade24_rep2

source_name: WT_seedlings_shade 24hr


title: Microglia cells from Trem2 -/- animal 1744 after 12 weeks on control diet


title: Non-microglia cells from Trem2 +/- animal 1108 after 5 weeks on cuprizone diet


title: Col-shade24_rep3


title: Col-shade24_rep1


title: Col-wc_rep2

source_name: WT_seedlings_continuous light 24hr

value: continous white light for 24 hrs


title: Microglia cells from Trem2 +/- animal 1108 after 5 weeks on cuprizone diet


title: Non-microglia cells from Trem2 +/- animal 1106 after 5 weeks on cuprizone diet


title: phyA-wc_rep2

source_name: mutant_seedlings_continuous light 24hr


title: phyA-shade24_rep1


title: Non-microglia cells from Trem2 -/- animal 1104 after 5 weeks on control diet


title: Microglia cells from Trem2 +/- animal 1106 after 5 weeks on cuprizone diet


title: 2_Nj

city: Olsztyn

first: Jan

middle: Pawel

last: Jastrzebski

state: Wa-Ma

address: ul. Oczapowskiego 1A

department: Biology and Biotechnology

country: Poland

institute: University of Warmia and Mazury in Olsztyn

data_processing:
Sequencing - Illumina SBS technology utilizes a proprietary reversible terminator-based method that detects single bases as they are incorporated into DNA template strands
Generation of Raw Data - The Illumina sequencer generates raw images utilizing sequencing control software for system control and base calling through an integrated primary analysis software called RTA (Real Time Analysis). The BCL (base calls) binary is converted into FASTQ utilizing illumina package bcl2fastq.
Trimming - Trimmomatic
Mapping - STAR
Counting: Stringtie
Genome_build: Meleagris_gallopavo.UMD2.91
Supplementary_files_format_and_content: coma-delimited text files include COUNTS values for all Samples together

organism: Meleagris gallopavo

source_name: Epididymis

extract_protocol:
Total RNA was extracted from the samples using a Total RNA Mini kit (A&A Biotechnology, Gdynia, Poland) according to the manufacturer’s protocol.
TruSeq Stranded mRNA Sample Preparation Guide, Part # 15031047 Rev. E

treatment_protocol: Males were photostimulated at 26 wk of age (14 h light to 10 h darkness)

value: Male

value: Epididymis

value: 38 weeks


title: 2_Ns

source_name: Ductus deferens

value: Ductus deferens


title: phyA-wc_rep1


title: 2_Jd

source_name: Testis

value: Testis


title: 16_Jd


title: Non-microglia cells from Trem2 +/- animal 1040 after 12 weeks on cuprizone diet

value: cuprizone

value: weeks


title: Microglia cells from Trem2 +/- animal 1040 after 12 weeks on cuprizone diet

value: Trem2 +/-

value: microglia


title: Col-wc_rep1


title: R613_16-51-5

city: Milano

first: Cinzia

last: Parolini

address: via Balzaretti 9

country: Italy

institute: Università degli Studi di Milano

description: Hepatic gene expression

hyb_protocol: Fluorescently labelled cRNA was hybridized to whole mouse genome expression microarrays following the manufacturer’s protocol (Affymetrix GeneChip Mouse Gene ST system).

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner.

data_processing: Normalization of gene expression data and filtering of probe sets by expression levels, flags, and errors were performed using GeneSpring software. Significant differences in gene expression among the two mouse lines were analysed by analysis of variance. Genes exhibiting expression changes between the two mouse lines were detected by Tukey’s significant difference test.

source_name: A-I(M)

label_protocol: RNA was labelled with cyanine 3 dye using the QuickAmp Labelling Kit (Agilent Technologies). RNA concentration, dye incorporation, and quality were analysed using a UV–VIS spectrophotometer.

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

value: liver

value: A-I k-in


title: 16_Ns


title: R613_16-50-4

description: Hepatic gene expression


title: R613_16-48-2

description: Hepatic gene expression

source_name: A-I(F)


title: TAZ-KO+Flag-TAZ

city: Berkeley

first: Kunxin

last: Luo

address: 375E Li Ka Shing Center for Biomedical and Health Sciences

department: Department of Molecular and Cell Biology

institute: University of California, Berkeley

data_processing:
Illumina Casava1.7 software used for basecalling.
Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Indexes of the reference genome was built using STAR and paired-end clean reads were aligned to the reference genome using STAR (v2.5). STAR used the method of Maximal Mappable Prefix(MMP) which can generate a precise mapping result for junction reads.
HTSeq v0.6.1 was used to count the read numbers mapped of each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Prior to differential gene expression analysis, for each sequenced library, the read counts were adjusted by edgeR program package through one scaling normalized factor. Differential expression analysis of two conditions was performed using the edgeR R package (3.16.5). The P values were adjusted using the Benjamini & Hochberg method. Corrected P-value of 0.05 and absolute foldchange of 1 were set as the threshold for significantly differential expression.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include read counts and fpkm

extract_protocol:
Total cellular RNAs were extracted using TRIzol
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tag

value: cell


title: YAP-KO

source_name: YKO


title: TAZ-KO

source_name: TKO


title: TAZ-KO+Flag-TAZ-deltaCC


title: WT

source_name: WT


title: 28 hpf miR-34a-/- treated with 1μM CPT rep3

city: Ottawa

first: Sergey

last: Prykhozhij

state: ON

address: Room 318/319 | CAREG, 20 Marie-Curie Private

country: Canada

institute: CHEO Research Institute/University of Ottawa

data_processing:
Read trimming: the raw reads had the adapters “ATCACCGAC” removed and filtered by the quality of 20 with the Trim Galore (v0.4.4).
Read mapping: The reads passed through the two-step mapping for RNA-Seq data from Ion proton: first with STAR (v2.7) and then mapping the unmapped reads from the first alignment using bowtie2. The two mapped files were merged with Picard tools (v2.5.0).
Read counting: The counts were extracted using HTSeq (V0.9.1).
Genome_build: danRer11
Supplementary_files_format_and_content: read counts

organism: Danio rerio

source_name: whole embryo

growth_protocol: Zebrafish experiments and husbandry follows standard protocols in accordance with the standards of the University of Ottawa Animal Care Committee (approval number: CHEOe-3168-A1). Zebrafish embryos were maintained at 28.5 °C during development and as adults. Embryos were grown in egg water (1x E3 prepared from 60x E3 stock).

extract_protocol:
Each total RNA sample was extracted from 30-50 zebrafish embryos by homogenizing them in 500 µL Trizol reagent (Thermo Fisher Scientific, 15596026) using 1 mL syringe and 22G needle. Lysates were centrifuged at 12,000 g at 4ºC for 5 minutes and the supernatant was transferred to Phasemaker Tubes (Thermo Fisher Scientific, A33248) and RNA was purified according to the Phasemaker Tubes protocol manual.
Total RNA samples were measured and analyzed for integrity on Agilent Tape Station. Samples with RNA integration number ≥8 were selected for library preparation. Poly-A enrichment was performed from 20 µg of total RNA to enrich for mRNA (Dyna beads mRNA direct micro Kit). 100ng of poly-A enriched RNA was fragmented using RNase III and purified using magnetic bead clean up module (RNA Seq V2 kit, Life Technologies). The size distribution of the fragmented RNA was assessed on Agilent Tape Station using RNA HS screen tape assay and 50 ng of fragmented polyA-enriched RNA was used to prepare whole transcriptome library (RNA seq V2). Yield and size distribution of the library was analyzed on Agilent Tape Station using D1000 screen tape. Barcoded library was equally pooled and amplified onto Ion Sphere™ Particles (ISPs) from Ion Pi HiQ OT2 kit (Life Technologies). ISPs enriched with template library were loaded onto Ion PI chip V3 and sequenced on Ion Proton from Thermo Fisher.

treatment_protocol: Camptothecin (CPT) treatments were performed by adding either DMSO (control groups) or the 2 mM stock CPT solution in DMSO to fish water for 1 µM concentration and incubating embryos for 4 hours.

tag: Stage

value: 28 hpf

value: 4 hours with 1μM camptothecin


title: Microglia cells from Trem2 -/- animal 1104 after 5 weeks on control diet

source_name: Microglia isolated from whole brain

value: Trem2 -/-

value: brain

value: control

tag: Sex


title: 28 hpf miR-34a-/- treated with 1μM CPT rep2


title: 15_Ns

value: Male


title: R613_16-47-5

description: Hepatic gene expression

value: female


title: 15_Jd

value: 38 weeks


title: 15_Nj

value: Epididymis


title: 28 hpf miR-34a-/- treated with 1μM CPT rep1


title: Sorted cells cultured for 9 passages, biological rep 3

city: Auckland

first: Hilary

last: Sheppard

address: Symonds St

country: New Zealand

institute: Auckland University

hyb_protocol: 21.5 µl of biotin labelled sample was used in a 132 µl hybridisation cocktail containing added hybridisation controls. 130 µl of this cocktail was hybridised on arrays for 16 to 18 hours at 48°. Standard post hybridization wash and double-stain protocols were used on an Affymetrix GeneChip Fluidics Station 450.

scan_protocol: Arrays were scanned on an Affymetrix GeneChip scanner 3000 7G.

data_processing: Data was normalised using Expression Console Software and Transcriptome Analysis Console (TAC) software (Thermofisher)

source_name: AdMSC ex-vivo

label_protocol: 100 ng total RNA was processed using the FlashTag Biotin HSR Kit (ThermoFisher) and hybridised to GeneChip miRNA 3.0 arrays (ThermoFisher) according to the manufacturer’s FlashTag Biotion HSR RNA Labelling Kit for GeneChip miRNA Array protocol.

growth_protocol: cells were grown in DMEM F-12 (Life Technologies) supplemented with 10 % Fetal Bovine Serum (FBS, Life Technologies), 1 % Penicillin-Streptomycin 10,000 U/mL (Invitrogen) and 1 × GlutaMAX (Invitrogen)

extract_protocol: RNA was isolated using a miRVANA kit from Ambion following the manufactures instructions (cat # AM1560)

treatment_protocol: cells were isolated using immunomagnetic beads and then grown for 0,3 or 28 days, or for 9 passages in standard tissue culture plates in medium as described above.

value: adipose derived mesenchymal stromal cells

value: cultured in DMEM+10% FBS for 9 passages


title: R613_15-42-4

description: Hepatic gene expression

source_name: A-IM(M)

value: A-IM k-in

value: male


title: Sorted cells cultured for 28 days, biological rep 3

value: cultured in DMEM+10% FBS for 28 days


title: 14_Jd

value: Testis


title: 16_Nj


title: R613_15-47-5

description: Hepatic gene expression

value: liver


title: 28 hpf miR-34a-/- DMSO control rep3

value: 4 hours with 0.005% DMSO


title: 14_Ns

value: Ductus deferens


title: R613_15-45-5

description: Hepatic gene expression

source_name: A-IM(F)


title: R613_15-42-3

description: Hepatic gene expression


title: Sorted cells cultured for 3 days, biological rep 3

value: cultured in DMEM+10% FBS for 3 days


title: 28 hpf miR-34a-/- DMSO control rep2

value: 28 hpf


title: 28 hpf miR-34a-/- DMSO control rep1


title: Freshly sorted cells, biological rep 3


title: 14_Nj


title: L3E2

city: District of Columbia

first: Lin

last: Yang

address: 111 Michigan Avenue NW

institute: Children's National Medical Center

data_processing:
Data processing, including read filtering, cell barcode identification, alignment and quantification, was performed using inDrop processing pipeline, provided by the inDrop paper (Klein et al Science 2015).
Genome_build: mm10
Supplementary_files_format_and_content: gene count matrix file

source_name: Primed mouse ESCs

growth_protocol: Naive mouse ESCs were cultured in 2i/LIF medium (1:1 DMEM/F12 (Gibco) and Neurobasal medium (Gibco) containing 1%(v/v) N2 and B27 supplements (Gibco), 1mM PD03259010（stem cell), 3mM CHIR99021 (stem cell), 1000u/ml mLIF (Peprotech), 1X L-glutamine (Gibco), 100mM 2-mercaptoethanol (Sigma) and 1% Penicillin Streptomycin (Gibco)）on 0.1% gelatin-coated dishes with MEF feeders

extract_protocol:
1CellBio inDrop protocol (Cell Barcoding by Co-Encapsulation to cDNA Synthesis)
Linear amplification by IVT (In Vitro Transcription)
1CellBio inDrop platform

value: mouse embryonic stem cells

tag: cell state

value: Primed


title: L3E1

source_name: Naïve mouse ESCs

value: Naïve


title: 28 hpf wild-type treated with 1μM CPT rep3

value: wild-type

value: 4 hours with 1μM camptothecin


title: Sorted cells cultured for 9 passages, biological rep 2


title: 12_Ns

value: Male

value: 38 weeks


title: 28 hpf wild-type treated with 1μM CPT rep2


title: L2E2


title: 12_Jd


title: 12_Nj

value: Epididymis


title: 28 hpf wild-type treated with 1μM CPT rep1


title: Freshly sorted cells, biological rep 2

value: adipose derived mesenchymal stromal cells


title: 11_Jd


title: L2E1


title: Sorted cells cultured for 3 days, biological rep 2


title: Sorted cells cultured for 9 passages, biological rep 1

value: cultured in DMEM+10% FBS for 9 passages


title: 28 hpf wild-type DMSO control rep3


title: 28 hpf wild-type DMSO control rep2


title: 11_Ns


title: 11_Nj


title: at-seed_6DAP-RNAseq_replicate3_col_dd25

city: Uppsala

first: Juan

middle: C

last: Santos-González

state: Uppsala

address: Almas Allé 5

department: Department of Plant Biology and Forest Genetics

country: Sweden

institute: SLU

data_processing:
Reads were mapped to the Arabidopsis (TAIR10) genome, masked for rRNA genes, using TopHat (v2.1.0 , Trapnell et al. 2009) with parameters adjusted as suggested in Rogers et al (2012) (-g 1 -a 10 -i 40 -I 5000 -F 0 -r 130). Mapped reads were counted and normalized to reads per kilobase per million mapped reads (RPKM) for genes using GFOLD (v1.1.4, Feng et al, 2012)
Genome_build: TAIR10
Supplementary_files_format_and_content: RNA-seq: expression levels (RPKM) are shown for genes  in TAIR10 for each condition and replicate.

source_name: F1-seed of transgenic Columbia-0 expressing DD25::IaaH

growth_protocol: All seeds were surface sterilized (70%, 30% ethanol 10min), stratified for 2 days at 4°C and germinated on half-strength Murashige and Skoog medium (1% sucrose) in long-day conditions (16 h light/8 h darkness; 21°C). Plants were transferred to soil after 10 to 12 days and grown under long day conditions.

extract_protocol:
For RNA sequencing, 6DAP seeds of WT Col-0 and DD25::IaaH plants were manually dissected out of the silique. RNA was extracted following the MagJET Plant RNA Purification Kit (Thermo Fsher Scientific). mRNA was subsequently purified using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB).
Samples were sequenced at the National Genomic Infrastructure (NGI) from SciLife Laboratory (Uppsala, Sweden) on an Illumina HiSeq2500 in paired-end 125bp read length. Differentially expressed genes were identified using the DESeq package

treatment_protocol: Material was generated by manually self pollinating WT Col-0 and DD25::IaaH plants.

value: 6 DAP seeds


title: siBsx 1

city: Bethesda

first: Steven

middle: L.

last: Coon

state: MD

address: 10 Center Dr; Room 8S261A

department: NICHD

institute: National Institutes of Health

description: Carstensen et al Table S1.xlsx

data_processing:
Illumina sequencer reads were processed initially using HCS v.2.2.68 and RTA v.1.18.66, and bases were called using bcl2fastq v.2.20.0.422.
The RNA-Seq data were aligned with RNA STAR (2.5.4a; Dobin et al., 2013) against RefSeq rn6. The mean alignment rate was 94% with 66% uniquely assigned to the transcriptome.
Read quantitation was performed using featureCounts of the Subread package (1.5.2; Liao et al., 2014) with Refseq rn6 gene definitions as the template. Of the total 28,341 genes in the database, 26,553 had at least one read mapped to them.
Differential expression analysis was performed using DESeq2 (v.1.16.1; Love et al, 2014) running Wald tests (Anders and Huber, 2010).
Genome_build: rn6
Supplementary_files_format_and_content: Normalization, counts and other columns in Excel files as per DESeq2 protocol.

organism: Rattus norvegicus

source_name: adult pinealocytes

growth_protocol: Pinealocyte primary cultures were prepared as described in Rohde et al., 2014 with 105 cells per sample. Briefly, isolated pinealocytes were prepared from newly dissected rat pineal glands by enzymatic digestion (Papain Dissociation System; Worthington Biochemicals Corp). The prepared pinealocytes were suspended in DMEM with 10% fetal bovine serum and antibiotic antimycotic solution (Sigma-Aldrich) and incubated at 37°C, 95% air, and 5% CO2.

extract_protocol:
RNA was extracted using TriZOL (Life Technologies) and purified with a Qiagen RNeasyR Micro Kit including DNase I treatment (Qiagen). RNA quality was determined on a Bioanalyzer 2100 (Agilent) with RIN‐values ranging from 7.7 to 8.9.
cDNA library preparation with ribosomal RNA depletion was performed with the SMARTer Stranded Total RNASeq Pico Input Mammalian Kit (Takara Bio) using 3.4 ng total RNA. Nine bar coded libraries were pooled and sequenced on one Flow Cell of a HiSeq2500 (Illumina) in Rapid Run Mode.

treatment_protocol: For knockdown experiments, pinealocytes were transfected with siRNA specifically targeting either Lhx4, (siLhx4; 40 nM; Stealth siRNA targeting position 1221‐1245 on NM_001108348.1; Thermo Fisher Scientific catalog #RSS323070), or Bsx (siBsx; 40 nM; Stealth siRNA targeting position 182-206 on NM_001191995.1; Thermo Fisher Scientific catalog #RSS1330001,) or non-targeting siRNA (siNT) (40 nM; Stealth RNAi siRNA negative control, Thermo Fisher Scientific catalog #12935300) using Lipofectamine RNAiMAX Reagent (Thermo Fisher Scientific). The medium was changed 24 hours after initiation of transfection. On the third day, cells were harvested, immediately frozen on crushed solid CO2 and stored at -80°C.

value: Sprague-Dawley

value: pineal gland

value: adult

tag: knockdown

value: siBsx


title: siBsx 2

description: Carstensen et al Table S1.xlsx


title: 28 hpf wild-type DMSO control rep1

value: 4 hours with 0.005% DMSO


title: siBsx 3

description: Carstensen et al Table S1.xlsx


title: Sorted cells cultured for 28 days, biological rep 2

value: cultured in DMEM+10% FBS for 28 days


title: Sorted cells cultured for 28 days, biological rep 1


title: Sorted cells cultured for 3 days, biological rep 1

value: cultured in DMEM+10% FBS for 3 days


title: Sample 12 (8 - ChIP 6): H4K5acK8acK12acK16ac_IAA

city: LA TRONCHE

first: Mohamed-ali

last: HAKIMI

state: Grenoble

address: Domaine de la Merci, Campus Santé

country: France

institute: CNRS

description: IAA treated

data_processing:
Data Analysis: After the sequencing platform generated the sequencing images, the stages of image analysis and base calling were performed using Off-Line Basecaller software (OLB V1.8). After passing Solexa CHASTITY quality filter, the clean reads were aligned to Toxoplasma gondii reference genome (Tgo) using BOWTIE (V2.1.0). Aligned reads were used for peak calling of the ChIP regions using MACS V1.4.0. Statistically significant ChIP-enriched regions (peaks) were identified by comparison of two samples, using a p-value threshold of 10-5. Then the peaks in each sample were annotated by the overlapped gene using the newest Toxoplasma gondii database. The EXCEL/BED format file containing the ChIP-enriched regions was generated for each sample.
Data visualization: The mapped 100 bp reads represent enriched DNA fragments by ChIP experiment. Any region of interest in the raw ChIP-seq signal profile can be directly visualized in genome browser. We use 10-bp resolution intervals (10-bp bins) to partition the stacked reads region, and count the number of reads in each bin.  All the 10 bp resolution ChIP-seq profiles of each sample are saved as UCSC wig format files, which can be visualized in Toxoplasma gondii Genome Browser (http://protists.ensembl.org/Toxoplasma_gondii/Info/ Index).
Genome_build: Toxoplasma gondii genome (ME49 strain) file "ToxoDB-13.0_TgondiiME49_Genome.fasta" to upload at ToxoDB website : http://toxodb.org/common/downloads/release-13.0/TgondiiME49/fasta/data/
Supplementary_files_format_and_content: Statistically significant ChIP-enriched regions (peaks) were identified by comparison of two samples, using a p-value threshold of 10-5. Then the peaks in each sample were annotated by the overlapped gene using the newest Toxoplasma gondii database. The EXCEL/BED format file containing the ChIP-enriched regions was generated for each sample. We use 10-bp resolution intervals (10-bp bins) to partition the stacked reads region, and count the number of reads in each bin.  All the 10 bp resolution ChIP-seq profiles of each sample are saved as UCSC wig format files, which can be visualized in Toxoplasma gondii Genome Browser (http://protists.ensembl.org/Toxoplasma_gondii/Info/ Index).

organism: Toxoplasma gondii

source_name: intracellular parasites

growth_protocol: Toxoplasma gondii type II strains Pruku80_MORC_HA and Pruku80_MORC_mAID_HA_KD were maintained by serial passage Human foreskin fibroblast (HFF) monolayer under tachyzoite conditions in DMEM (Life) supplemented with 10% (vol/vol) FBS (Life) and 25 mM Hepes buffer, pH 7.2.

extract_protocol:
Crosslinked chromatin was lysed in ice-cold lysis buffer (50mM HEPES KOH pH7.5, 140mM NaCl, 1mM EDTA, 10% glycerol, 0.5%NP-40, 0.125% triton X-100, protease inhibitor cocktail) and sheared in shearing buffer (1mM EDTA pH8.0, 0.5mM EGTA pH8.0, 10mM Tris pH8.0, protease inhibitor cocktail) by sonication using a Diagenode Biorupter. Samples were sonicated, for 16 cycles (30 seconds ON and 30 seconds OFF), to 200-500 base-pair average size. Immunoprecipitation was carried out using sheared chromatin, 5% BSA, protease inhibitor cocktail, 10% triton X-100, 10% deoxycholate, DiaMag Protein A-coated magnetic beads (Diagenode) and antibodies (H4K5acK8acK12acK16ac, H4K31me1, HDAC3, and HA). A rabbit IgG antiserum was used as a control mock. After overnight incubation at 4°C on rotating wheel, chromatin-antibody complexes were washed and eluted from beads by using iDeal ChIP-seq kit for Histones (Diagenode) according to the manufacturer’s protocol. Samples were decrosslinked by heating for 4 hours at 65°C. DNA was purified by using IPure kit (Diagenode) and quantified by using Qubit Assays (Thermo Fisher Scientific) according to the manufacturer's protocol. For ChIP-seq, purified DNA was used to prepare libraries and then sequenced by Arraystar (USA, http://www.arraystar.com/).
ChIP-Sequencing library preparation was performed according to Illumina’s protocol Preparing Samples for ChIP Sequencing of DNA. Library Preparation: 10 ng DNA of each sample was converted to phosphorylated blunt-ended with T4 DNA polymerase, Klenow polymerase and T4 polymerase (NEB); An ‘A’ base was added to the 3' end of the blunt phosphorylated DNA fragments using the polymerase activity of Klenow (exo minus) polymerase (NEB); Illumina's genomic adapters were ligated to the A tailed DNA fragments; PCR amplification was performed to enrich ligated fragments using Phusion High Fidelity PCR Master Mix with HF Buffer (Finnzymes Oy). The enriched product of ~200-700 bp was cut out from gel and purified. Sequencing:  The library was denatured with 0.1M NaOH to generate single-stranded DNA molecules, and loaded onto channels of the flow cell at 8pM concentration, amplified in situ using TruSeq Rapid SR cluster kit (#GD-402-4001, Illumina). Sequencing was carried out by running 100 cycles on Illumina HiSeq 4000 according to the manufacturer’s instructions.

treatment_protocol: HFF cells were grown to confluence and infected with Pruku80_MORC_HA or Pruku80_MORC_mAID_HA_KD strains. Genome-wide MORC and HDAC3 occupancy profiles in Pruku80_MORC_mAID_HA_KD left untreated (UT) and treated with IAA (indole-3-acetic acid) for 30 hours. Harvested intracellular parasites were crosslinked with formaldehyde (final concentration 1%) for 8 mins at room temperature and the crosslinking was stopped by addition of glycine (final concentration 0.125M) for 5 min at room temperature.

tag: chip antibody

value: H4K5acK8acK12acK16ac (Millipore)

tag: dev. stage

value: tachyzoites


title: Freshly sorted cells, biological rep 1

tag: cell type


title: at-seed_6DAP-RNAseq_replicate2_col_dd25

tag: tissue


title: at-seed_6DAP-RNAseq_replicate1_col_dd25


title: siLhx4 3

description: Hertz et al Table S1.xlsx

tag: strain


title: siLhx4 1

description: Hertz et al Table S1.xlsx


title: siLhx4 2

description: Hertz et al Table S1.xlsx


title: at-seed_6DAP-RNAseq_replicate2_col_wt

source_name: F1-seed of Columbia-0

value: wild type


title: Sample 11 (7 - ChIP 6): H4K5acK8acK12acK16ac_UT

description: untreated sample


title: Sample 10 (9 no FR - ChIP 5): H4K5acK8acK12acK16ac


title: Sample 9 (12 - ChIP 6): HDAC3_IAA

description: IAA treated

value: HDAC3 - Home made antibody


title: Pru_FR 7h-REP1

city: La Tronche

first: Alexandre

last: Bougdour

state: Isère

address: Domaine de la Merci, Campus santé

department: Prevention and Therapy of Chronic diseases

institute: Centre de Recherche Inserm U1209 / CNRS UMR5309 / UGA

description:
HFF and parasites
replicate 1

data_processing:
The RNA-Seq reads (FASTQ) were processed and analyzed using the Lasergene Genomics Suite version 15 (DNASTAR, Madison, WI, USA) using default parameters.
The paired-end reads were uploaded onto the SeqMan NGen (version 15, DNASTAR. Madison, WI, USA) platform for reference-based assembly using the Toxoplasma Type II ME49 strain (ToxoDB-40, ME49 genome) as reference template.
The ArrayStar module (version 15, DNASTAR. Madison, WI, USA) was used for normalization, differential gene expression and statistical analysis of uniquely mapped paired-end reads using the default parameters.
The expression data quantification and normalization were calculated using the RPKM (Reads Per Kilobase of transcript per Million mapped reads) normalization method.
Genome_build: Toxoplasma Type II ME49 strain (ToxoDB-40, ME49 genome)
Supplementary_files_format_and_content: xlsx format. The matrix table includes RPKM values of T. gondii transcripts for each sample. Mean values of  biological duplicates are also provided.

source_name: Human cells and T. gondii

growth_protocol: Cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM, Invitrogen) supplemented with 10% heat-inactivated FBS (Invitrogen), 10 mM HEPES buffer, pH 7.2, 2 mM L-glutamine, and 50 μg/ml penicillin and streptomycin (Thermo Fisher Scientific). Cells were incubated at 37°C in 5% CO2.

extract_protocol:
Total RNAs were extracted and purified using the RNeasy Plus Mini Kit (Qiagen). RNA quantity and quality were measured by NanoDrop 2000 (Thermo Scientific). RNA integrity was assessed by standard non-denaturing 1.2% TBE agarose gel electrophoresis. The ribosomal large subunits from Toxoplasma and the host cells was used to verify that the ratio between Toxoplasma RNA versus host RNA was equivalent between the different biological samples, thus indicating that the samples had equivalent infection rates.
RNA libraries were prepared using polyA selected RNAs for sequencing using standard Illumina protocols (Illumina TruSEQ RNA library prep).

treatment_protocol: Cells infected with the RH MORC KD strain were left untreated (UT) or treated with IAA for 7 or 24h before being harvested for RNA extraction. Cells infected with the Pru MORC KD strain were left untreated or treated with IAA for 24 or 48h before RNA extraction. Cells infected with the Pru strain were left unstimulated (US) or treated with FR235222 (FR) for 7 or 18h before being harvested for RNA extraction.

tag: t. gondii strain and genotype

tag: strain background

value: Prugniaud

tag: treatment


title: Pru_FR 18h-REP1

description:
HFF and parasites
replicate 1


title: Pru_FR 18h-REP2

description:
HFF and parasites
replicate 2


title: siNT 3

description: Hertz et al Table S1.xlsx

tag: age

value: siNT


title: siNT 2

description: Hertz et al Table S1.xlsx


title: Sample 7 (7 - ChIP 5): HDAC3


title: siNT 1

description: Hertz et al Table S1.xlsx


title: Pru_US-REP1

description:
HFF and parasites
replicate 1


title: RH MORC KD_IAA_24h-REP2

description:
HFF and parasites
replicate 2

value: RHku80 MORC KD, UPRT::OsTir1-(Ty)3, MORC-mAID-HA-DHFR

value: RH

value: IAA for 24h


title: Ptger4-ON co-culture

description: Drop-seq

source_name: intestinal fibroblast/crypt co-cultures in Organoid Growth Media with DMSO vehicle control (spheroid growth)

growth_protocol: Organoid Growth Media (OGM)

extract_protocol:
Co-culture dissociation with 1:2.5 0.25% Trypsin/EDTA in DMEM
Drop-seq protocol

treatment_protocol: DMSO vehicle or ONO-AE3-208 Ptger4 (EP4) inhibitor (Cayman, 14522) dissolved in DMSO, added to the co-cultures every second day at a final concentration of 10 uM

value: intestinal fibroblast/crypt co-cultures

tag: growth

value: 10 weeks

value: Small intestine


title: Sample 6 (10 - ChIP 6): MORC_HA_IAA

description: IAA treated

value: HA antibody (Cell Signaling)


title: Ptger4-OFF co-culture

description: Drop-seq

source_name: intestinal fibroblast/crypt co-cultures in Organoid Growth Media with ONO-AE3-208 Ptger4 inhibitor (budding organoid growth)


title: HELA_WT4

city: Martinsried

first: Martha

last: Smets

address: Großhaderner Str. 2

department: Department Biology II

institute: Ludwig-Maximilians University Munich

data_processing:
base-calls were performed with Illumina bcl2fastq
demultiplexing was done using the assignRG package
cDNA reads were mapped to the hg19 genome assembly using NGM (v.4.12) Sedlazeck et al. 2013 and minimum sequence identity of 0.9
reads were assigned to gene features using the Rsubread package Liao et al. 2014
Genome_build: hg19
Supplementary_files_format_and_content: .txt gene-wise read-counts per sample

source_name: HeLa cell line

growth_protocol: HeLa cells were cultured in DMEM (Sigma) supplemented with 10% fetal calf serum (Biochrom) and 50 µg/ml gentamycine (PAA).

extract_protocol:
Total RNA was isolated from HeLa cells in biological quadruplicates using the nucleospin triprep kit (Macherey-Nagel).
Smart-seq2 (Picelli et al. 2013) from 5ng of RNA

tag: cell line

value: HeLa

tag: genotype

value: wt

tag: sequencing

value: single-end


title: Sample 5 (9 - ChIP 6): MORC_HA_UT

description: untreated sample


title: RH MORC KD_IAA_24h-REP1

description:
HFF and parasites
replicate 1


title: Pru_FR 7h-REP2

description:
HFF and parasites
replicate 2


title: at-seed_6DAP-RNAseq_replicate3_col_wt

tag: ecotype background

tag: genotype/variation

value: 6 DAP seeds


title: WT_2

city: Worcester

first: Dr Yvonne

last: Edwards

address: 373 Plantation Street

institute: University of Massachusetts Medical School

data_processing:
Using FASTX toolkit Ion torrent sequences are trimmed with min quality score of 17 and min read length of 35 bases
The trimmed sequences (from Ion Torrent and Illumina) are mapped to the reference genome Drosophila melanogaster Ensembl BDGP5 (Adam MD et al 2000) using the aligner STAR (version 2.4.2a) (Dobin A et al 2013).
The STAR package has an in-built count functionality HTseq-count (version 0.6.1) (Anders S et al 2015) to count uniquely mapped reads at the gene level.
DESEQ2 (Love MI et al 2014) is used to perform statistical analysis to determine differentially expressed genes between the control samples and the knockdown samples.
Genome_build: Drosophila melanogaster Ensembl BDGP5
Supplementary_files_format_and_content: mergedCounts.txt reports the HTseq-counts of uniquely mapped reads at the gene level
Supplementary_files_format_and_content: DESEQ2 reports significantly differentially expressed genes  between the two conditions (padj value < 0.1 )

source_name: midgut

growth_protocol: flies were raised at RT with low yeast, agar, cornmeal, molasses medium, shifted to 29 degree for 5days after 5days post enclosure.

extract_protocol:
midguts were dissected from control and Rab11_KD flies and total RNA isolation with TriReagent
Ion Torrent and Illumina protocols

value: enterocyte

tag: developmental stage

value: adult

value: WT


title: HELA_WT3


title: HELA_WT2


title: Sample 8 (11 - ChIP 6): HDAC3_UT

description: untreated sample

value: HDAC3 - Home made antibody

value: tachyzoites


title: Pru_US-REP2

description:
HFF and parasites
replicate 2

value: Prugniaud


title: at-seed_6DAP-RNAseq_replicate1_col_wt

value: wild type


title: RH MORC KD_IAA_7h-REP1

description:
HFF and parasites
replicate 1

value: RHku80 MORC KD, UPRT::OsTir1-(Ty)3, MORC-mAID-HA-DHFR

value: RH

value: IAA for 7h


title: WT_1


title: HELA_WT1


title: Sample 3 (5D - ChIP 4): MORC_HA_Rep1


title: Rab11_KD_2

value: Rab11 KD


title: RH MORC KD_UT-REP2

description:
HFF and parasites
replicate 2


title: Rab11_KD_1


title: RH MORC KD_UT-REP1

description:
HFF and parasites
replicate 1


title: ZNF599_KO4


title: Sample 1 (5 - ChIP 6): H4K31me1_UT

description: untreated sample

value: H4K31me1 - Home made antibody


title: SEC28˚C_rep2

first: Miyuki

last: Nakamura

address: Ulls Grand1

institute: Swedish University of Agricultural Sciences

description: small RNA

data_processing:
3' adapter (5′ -AGATCGGAAGAGCACACGTCT-3′) sequences were trimmed after removing low quality reads by fastq_quality_filter (-q 20 -p 80 -Q 33). Transfer RNA-, ribosomal RNA-, and small nuclear (nucleoar) RNA-derived sequences were subtracted using bowtie with allowing maximum 1 mismatch. 17–28 nt length reads were extracted and scored.
Genome_build: Pabies1.0-genome-gene-only
Supplementary_files_format_and_content: tab-delimited text files (column1:sequence, column2:read count)

organism: Picea abies

source_name: Embryonic callus 28˚C

growth_protocol: Needles were harvested in May and August. Pollen was harvested in May. Embryonic calli were grown in dark 22˚C.

extract_protocol:
Total RNAs were extracted as previously described in Gambino et al., 2008. Subsequently, sRNAs were separated from high molecular weight RNAs by PEG8000 as previously described in Peng et al. 2014
Libraries were constructed using the Illumina NEBNext® Small RNA Library Prep Set according to the manufacturer's protocol.

treatment_protocol: Embryonic calli were treated in each temperature for 3 weeks and then immediately frozen by liquid nitrogen.

tag: location

value: Embryonic callus

tag: temperature


title: Pru MORC KD_IAA_48h-REP2

description:
HFF and parasites
replicate 2

value: Pruku80 MORC KD, UPRT::OsTir1-(Ty)3, MORC-mAID-HA-DHFR

value: IAA for 48h


title: BS-Lo-6b

city: Madison

first: Francisco

last: Peñagaricano

state: Wisconsin

address: 1675 Observatory Drive

department: Animal and Dairy Sciences

institute: University of Wisconsin-Madison

description: bisulfite converted genomic DNA

data_processing:
The quality of the sequencing reads was evaluated using FastQC software, and if necessary, sequencing reads were trimmed using the software Trim Galore (version: 0.4.4).
Reads were mapped to the lastest bovine reference genome (ARS-UCD1.2) using the software package Bismark (version 0.20.1).
Duplicate alignments were removed using the tool deduplicate_bismark (version 0.20.1).
Methylation calling and extraction were performed using Bismark methylation extractor (version 0.20.1).
Genome_build: Cow genome assembly: ARS-UCD1.2
Supplementary_files_format_and_content: Tab-delimited text files including chromosome, genomic start position, genomic end position, percentage of methylation at that position, number of Cs methylated, and number of Cs non-methylated

organism: Bos taurus

source_name: Sperm

extract_protocol:
Sperm DNA was extracted using a phenol/chloroform extraction protocol. Sample quality was checked via gel electrophoresis and Nanodrop ND1000 spectrophotometer.
Bisulfite treatment, library preparation and subsequent whole-genome sequencing were performed by CD Genomics (New York, NY, USA).

value: Sperm

tag: breed

value: Holstein

value: low fertility


title: ZNF599_KO3

value: HeLa

value: single-end


title: ZNF599_KO2


title: SEC28˚C_rep1

description: small RNA


title: BS-Lo-4

description: bisulfite converted genomic DNA


title: ZNF599_KO1


title: Pru MORC KD_IAA_24h-REP2

description:
HFF and parasites
replicate 2

value: IAA for 24h


title: BS-Lo-3

description: bisulfite converted genomic DNA


title: RH MORC KD_IAA_7h-REP2

description:
HFF and parasites
replicate 2


title: SEC4˚C_rep2

description: small RNA

source_name: Embryonic callus 4˚C


title: SEC4˚C_rep1

description: small RNA


title: Pru MORC KD_IAA_48h-REP1

description:
HFF and parasites
replicate 1


title: BS-Lo-2

description: bisulfite converted genomic DNA


title: F3-600

city: Wuhan

first: Handong

last: Su

address: No.1,Shizishan Street · Hongshan District

institute: Huazhong Agricultural University

data_processing:
Basecalls performed using Illumina CASAVA.
Raw reads from ChIP-seq data were mapped to the B73 RefGen_v4 genome using bwa mem with the default parameters.
The mapped reads with MAPQ values >= 20 as uniquely mapping for further analysis.
RPM values were calculated with 10 kb windows along the genome to make it comparable between different samples.
Genome_build: Maize B73 RefGen_v4
Supplementary_files_format_and_content: BED files contains the positions of mapped reads of the ChIP-seq.

source_name: maize

growth_protocol: Suitable materials were planted in the greenhouse or in the field for RNA-seq and ChIP-bisulfite experiments.

extract_protocol:
Extracted nuclei were digested with micrococcal nuclease (Sigma-Al drich) for ChIP experiments using the maize CENH3 antibody.The ChIP-enriched DNAs of B73, F3-152 and F3-600 were performed Illumina sequencing. The maize CENH3 is a rabbit polyclonal antiserum and was raised against the peptides: C-RPGTVALREIRKYQKS; STSATPERAAGTGGR-C. Keyhole limpet hemocyanin (KLH)-conjugated peptide was used to immunize rabbits.
ChIP libraries were prepared according to standard Illumina's instructions.180-400 bp fragments (contained the joint) were selected by gel extraction.

value: young leaves

tag: chip antibody


title: Pru MORC KD_IAA_24h-REP1

description:
HFF and parasites
replicate 1

value: Prugniaud


title: Sample 2 (6 - ChIP 6): H4K31me1_IAA

description: IAA treated

tag: dev. stage

value: tachyzoites


title: BS-Lo-1

description: bisulfite converted genomic DNA

tag: tissue


title: SEC22˚C_rep2

description: small RNA

source_name: Embryonic callus 22˚C


title: B73

value: control


title: BS-Hi-5

description: bisulfite converted genomic DNA

value: high fertility


title: Pru MORC KD_UT-REP1

description:
HFF and parasites
replicate 1

tag: t. gondii strain and genotype


title: SEC_22˚C_rep1

description: small RNA


title: BS-Hi-4

description: bisulfite converted genomic DNA


title: BS-Hi-3

description: bisulfite converted genomic DNA


title: Pollen_rep1

description:
small RNA
location: 59°48'47.7"N, 17°38'20.6"E

source_name: Pollen

value: Pollen


title: Needle_rep2

source_name: Needles

value: Needles


title: BS-Hi-2

description: bisulfite converted genomic DNA


title: Needle_rep1


title: BS-Hi-1

description: bisulfite converted genomic DNA


title: Pru MORC KD_UT-REP2

description:
HFF and parasites
replicate 2

tag: strain background


title: PAO1_neg_2

status: Public on Dec 20 2019

city: Zurich

first: Julian

last: Trouillon

address: Otto-Stern-Weg 3

department: Institute of Molecular Systems Biology

country: Switzerland

institute: ETH Zurich

description: adaptor-ligated sheared genomic DNA

data_processing:
Library strategy: DAP-seq
Read trimming using Trimmomatic
Alignment using Bowtie2
Peak calling using MACS2
closest features called with BEDtools
Genome_build: IHMA879472, PAO1b, PA23, CHA0, KT2440
Supplementary_files_format_and_content: excel table, MACS2 analysis results with closest features

organism: Pseudomonas aeruginosa

source_name: purified genomic DNA from liquid cultures

extract_protocol:
Purified proteins bound to magnetic beads were incubated with adaptor-ligated sheared genomic DNA. After washes and isolation of bead-protein-DNA complexes, the bound DNA regions were eluted by heating and then used for library preparation.
DNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: erfa origin


title: PAO1_Erf_I_2

description:
adaptor-ligated sheared genomic DNA
PAO1_processed.xlsx

value: P. aeruginosa


title: PAO1_neg_3

description: adaptor-ligated sheared genomic DNA


title: F3-152


title: PAO1_Erf_I_1


title: PAO1_Erf_I_3


title: Pollen_rep2


title: IHMA_Erf_chlo_1

description:
adaptor-ligated sheared genomic DNA
I_E_chlo_processed.xlsx

value: P. chlororaphis


title: IHMA_Erf_chlo_2


title: IHMA_Erf_chlo_3


title: IHMA_Erf_I_1

description:
adaptor-ligated sheared genomic DNA
I_E_I_processed.xlsx


title: IHMA_Erf_I_3


title: Sample 3 (5 no FR - ChIP 5): MORC_HA_Rep2

value: HA antibody (Cell Signaling)


title: IHMA_neg_1

description: adaptor-ligated sheared genomic DNA


title: IHMA_neg_3

description: adaptor-ligated sheared genomic DNA


title: IHMA_neg_2

description: adaptor-ligated sheared genomic DNA


title: 180126 Ackr4ko 3 B cells

city: Hannover

first: Nadine

last: Eckert

address: Carl-Neuberg-Straße 1

institute: Hannover Medical School

description: Gene expression after 3d stimulation-MACS purified B cells

hyb_protocol: cRNA fragmentation, hybridization and washing steps were carried-out as recommended: ‘One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling Protocol V6.7’.

scan_protocol: Slides were scanned on the Agilent Micro Array Scanner G2565CA (pixel resolution 3 µm, bit depth 20)

data_processing: Data extraction was performed with the ‘Feature Extraction Software V10.7.3.1’ using the extraction protocol file ‘GE1_107_Sep09.xml’. Measurements of on-chip replicates (quadruplicates) were averaged using the geometric mean of processed intensity values of the green channel, ‘gProcessedSignal’ (gPS) to retrieve one resulting value per unique non-control probe. Single Features were excluded from averaging, if they i) were manually flagged, ii) were identified as Outliers by the Feature Extraction Software, iii) lay outside the interval of ‘1.42 x interquartile range‘ regarding the normalized gPS distribution of the respective on-chip replicate population, or, iv) showed a coefficient of variation of pixel intensities per Feature that exceeded 0.5.   Averaged gPS values were normalized by quantile normalization first, followed by global linear scaling. For the latter approach, all quantile normalized gPS values of one sample were multiplied by an array-specific scaling factor. This factor was calculated by dividing a ‘reference 75th Percentile value’ (set as 1500 for the whole series) by the 75th Percentile value of the particular (quantile normalized) Microarray to be finally normalized (‘Array i’ in the formula shown below). Accordingly, finally normalized gPS values for all samples (microarray data sets) were calculated by the following formula:   finally normalized gPSArray i = quantile normalized gPSArray i  x (1500 / 75th PercentileArray i)

source_name: spleen, 3d, Ackr4ko

label_protocol: 50 ng of total RNA were used as input. Synthesis of Cy3-labeled cRNA was performed in ¾ reaction volumes with the ‘Low Input Quick Amp Labeling Kit One-Color’ (#5190-2305, Agilent Technologies) according to the manufacturer’s recommendations.

extract_protocol: RNA was prepared using the RNeasy Micro Kit (Qiagen, Hilden, Germany) following the manufacturer's recommendations.  The protocol includes DNA removal via column.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: MACS-purified B cells from splenocytes from C57BL/6 and Ackr4-deficient mice were activated in culture with 10µg/ML anti-IgM and 10µg/mL anti-CD40 (clone FGK4.5) in IMDM medium supplemented with 10% heat-inactivated fetal bovine serum, 1% Pen/Strep, 1% L-glutamine and beta-mercapthethanol.   The B cells were activated for 3 days at 37 ºC in a humidified incubator with 5% CO2.

value: spleen

tag: cell type

value: B cells

tag: gender

value: male

tag: age

tag: time

value: day 3 of activation


title: 180115 Ackr4ko 2 B cells

tag: genotype


title: 180115 WT 4 B cells

source_name: spleen, 3d, C57BL/6

value: WT


title: 180126 WT 4 B cells


title: PAO1_derfA_2 RNAseq

description: rRNA-depleted RNA

data_processing:
Read trimming using Trimmomatic
Alignment using Bowtie2
Feature count using htseq-count
Differential expression analysis using DESeq2
Genome_build: IHMA879472, PAO1F
Supplementary_files_format_and_content: excel table, DESeq2 analysis results

source_name: LB liquid culture at OD=1

growth_protocol: LB liquid culture at OD=1

extract_protocol:
Hot Phenol RNA Extraction
RNA were treated with Dnase I, then rRNA were depleted using the Illumina RiboZero kit. Libraries were constructed using the NEBNext Ultra II Directional RNA lib prep kit from NEB.


title: PAO1_derfA_1 RNAseq

description: rRNA-depleted RNA