title: C26-N4

description:
HI.4193.007.Index_15.C26-N4
processed data file: Apiary_Nurses_Logcpm.txt

value: Nurse

value: Apiary

value: Unexposed


title: 4hpf_DMSO_Aebp2_ChIP_rep3

status: Public on Jan 04 2022

type: SRA

city: Salt Lake City

first: Graham

middle: James McGuire

last: Hickey

state: UT

address: 2000 Circle of Hope Drive

department: Oncological Sciences

country: USA

institute: University of Utah

description:
15987X22
Zebrafish
Aebp2_DMSO__4hpf_ChIP.narrowPeak
Aebp2_DMSO_4hpf_ChIP.bw

library_source: genomic

data_processing:
ChIP-seq Fastq files were aligned to Zv10 using Novocraft Novoalign (v3.8) with the following settings: -o SAM -r Random.
SAM files were processed to BAM format, sorted, and indexed using Samtools (v1.8).
MACS2 (v2.2.5) was utilized for peak calling with the following settings: -B -q 0.01 --SPMR. BAM files of ChIP replicates and input were provided to MACS2 in a single execution under the -t and -c flags, respectively.
Bedgraph output files from MACS2 were used to produce bigwig files with UCSC bedGraphToBigWig (v4).
Genome_build: zv10
Supplementary_files_format_and_content: *.narrowPeak: The narrowPeak files contain peaks that were called by MACS2 with a q value cutoff of 0.01.
Supplementary_files_format_and_content: *bw: The bigwig files are the treatment fragment pileups produced by MACS2 and are normalized by signal per million reads.

molecule: genomic DNA

organism: Danio rerio

source_name: WT Tubingen

growth_protocol: Standard zebrafish growth conditions.

extract_protocol:
Approximately 1.5 million cells were used for each ChIP replicate. Embryos were allowed to progress to the desired developmental stage and then transferred to 1.5 ml microcentrifuge tubes (~200 embryos per tube). Chorions were removed enzymatically by treatment with pronase 1.25mg/ml in PBS). Dechorionated embryos were gently washed twice with PBS to remove pronase. Samples were fixed with 1% formaldehyde (Electron Microscopy Sciences, Cat# 15712) for 10 minutes at room temperature with end over end rotation. Fixation was quenched with 130 mM glycine for five minutes at room temperature. Samples were centrifuged for five minutes at 500 x g at 4oC. Supernatant was discarded and cell pellets were washed twice with ice cold PBS. Cell pellets were frozen with liquid nitrogen and stored at -80ºC. 1 ml of Mild Cell Lysis Buffer (10 mM Tris-HCl pH 8.1, 10 mM NaCl, 0.5 NP-40, 2X proteinase inhibitors) was applied to cell pellets from 1000 embryos and rotated at 4ºC for 10 minutes. Samples were centrifuged at 1300 X g for 5 minutes at 4ºC. Supernatant was discarded and nuclei pellets were resuspended in 1 ml Nuclei Wash Buffer (50 mM Tris-HCl pH 8.0, 100 mM NaCl, 10 mM EDTA, 1% SDS, 2X protease inhibitors) and rotated at room temperature for 10 minutes. Samples were centrifuged at 1300 X g for 5 minutes at 4ºC to pellet nuclei. Supernatant was discarded and nuclei pellets were resuspended in 100 µl of Nuclei Lysis Buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1% SDS, 2X proteinase inhibitors). Samples were incubated on ice for 10 minutes. 900 µl of IP Dilution Buffer (16.7mM Tris-HCl pH 8.1, 167mM NaCl, 1.2mM EDTA, 0.01% SDS, 1.1% Triton X-100, 2X proteinase inhibitors) was added to samples. Nuclear lysates were sonicated with a Branson Digital Sonifier with the following settings: 10 second duration (0.9 seconds ON, 0.1 seconds OFF), 30% amplitude. 7 sonication cycles were performed. Samples were placed in an ice bath for at least 1 minute between each sonication cycle. Sonicated samples were centrifuged at 14,000 rpm, 4ºC, for 10 minutes to pellet insoluble material. Supernatants were transferred to new tubes. A portion of the sample was set aside to confirm optimal chromatin shearing by agarose gel electrophoresis. 20 µl of Dynabeads (Invitrogen) were blocked with 0.5mg/ml BSA in PBS. Blocked Dynabeads were subsequently applied to each sonicated sample and rotated for 1 hour at 4ºC. Samples were placed on a magnet stand for 1 minute and precleared supernatant was transferred to a new tube. 5% of the sample was removed and stored at -80ºC as input. Antibody and fresh 1X protease inhibitors were added to each sample. Samples were rotated overnight at 4ºC. Samples were centrifuged at 14,000 rpm, 4ºC, for 5 minutes to pellet insoluble material. Supernatants were transferred to new tubes. 50 µl of Dynabeads (Invitrogen) were blocked with BSA 5mg/ml in PBS. Blocked Dynabeads were subsequently applied to each sample and rotated for 6 hours at 4ºC. All wash buffers were kept ice cold during stringency washes. Samples were washed 8 times with RIPA Buffer (10 mM Tris-HCl pH 7.5, 140 mM NaCl, 1mM EDTA, 0.5 mM EGTA, 1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate, 2X protease inhibitors), 2 times with LiCl Buffer (10mM Tris-HCl pH 8.0, 1 mM EDTA, 250 mM LiCl, 0.5% NP-40, 0.5% sodium deoxycholate, 2X protease inhibitors), 2 times with TE Buffer (10mM Tris-HCl pH 8.0, 1 mM EDTA, 2X protease inhibitors). 100 µl of Elution Buffer (10 mM Tris-HCl pH8.0, 5 mM EDTA, 300 mM NaCl, 0.1% SDS) was added to beads. 2ul of RNase A (Thermo Fisher, Cat #EN531) was added to each ChIP and input sample and incubated at 37ºC for 30 minutes with gentle agitation. 10 µl of Proteinase K (Thermo Fisher, Cat # 25530049) was added to each sample and incubated at 37ºC for 1 hour with gentle agitation. Crosslinks were reversed overnight at 65ºC with gentle agitation. ChIP DNA was purified with a Qiagen MinElute PCR Purification kit (Cat #28004).
ChIP seq libraries were prepared using NEBNext ChIP-Seq Library Prep Reagent Set for Illumina (New England BioLabs, Cat # E6240).

treatment_protocol: Untreated or embryo media was supplemented with 150 μM PRT4165 (or DMSO) from when the embryos were at the 1-cell stage until the embryos were harvested.

tag: strain

value: Tubingen

tag: genotype

value: WT

tag: developmental stage

tag: tissue

value: Whole body (embryo)

tag: treatment

value: DMSO

tag: chip antibody


title: Monocytes+LPS (0.5ug/ml)_2

type: RNA

city: Houston

first: JEHAN

last: ALAM

state: TEXAS

address: Baylor One Plaza

institute: Baylor College of Medicine

hyb_protocol: One hundred nanograms of total RNA were hybridized with the Nanostring Technologies nCounter Mouse Immunology Panel and Nanostring Technologies nCounter Gene Expression Mouse Myeloid Innate Immunity Panel codeset (NS_MM_Myeloid_V2.0+Pls) containing 770 Unique pairs of 35-50bp reporter probes, 12 custom probe pairs and biotin-labeled capture probes, including internal refereance controls. overnight hybridization occured for 20hours at 65C.

scan_protocol: The cartridge containing immobilized sample was transferred to the nCounter Digital Analyzer (Software v3.0.1.4) and scanned at 555 field of view (FOV).

data_processing:
Data was processed using ROSALIND (https://app.rosalind.bio)
Data was analyzed by ROSALIND® (https://rosalind.bio/), with a HyperScale architecture developed by ROSALIND, Inc. (San Diego, CA). Read Distribution percentages, violin plots, identity heatmaps, and sample MDS plots were generated as part of the QC step. Normalization, fold changes and p-values were calculated using criteria provided by Nanostring. ROSALIND® follows the nCounter® Advanced Analysis protocol of dividing counts within a lane by the geometric mean of the normalizer probes from the same lane. Housekeeping probes to be used for normalization are selected based on the geNorm algorithm as implemented in the NormqPCR R library1. Abundance of various cell populations is calculated on ROSALIND using the Nanostring Cell Type Profiling Module. ROSALIND performs a filtering of Cell Type Profiling results to include results that have scores with a p-Value greater than or equal to 0.05. Fold changes and pValues are calculated using the fast method as described in the nCounter® Advanced Analysis 2.0 User Manual. P-value adjustment is performed using the Benjamini-Hochberg method of estimating false discovery rates (FDR). Clustering of genes for the final heatmap of differentially expressed genes was done using the PAM (Partitioning Around Medoids) method using the fpc R library2 that takes into consideration the direction and type of all signals on a pathway, the position, role and type of every gene, etc. Hypergeometric distribution was used to analyze the enrichment of pathways, gene ontology, domain structure, and other ontologies. The topGO R library3, was used to determine local similarities and dependencies between GO terms in order to perform Elim pruning correction. Several database sources were referenced for enrichment analysis, including Interpro4, NCBI5, MSigDB6,7, REACTOME8, WikiPathways9. Enrichment was calculated relative to a set of background genes relevant for the experiment.

molecule: total RNA

organism: Mus musculus

source_name: in vitro cultured Purified Monocytes

label_protocol: The samples were labeled according to the condition

growth_protocol: C57B/6 Mice were purchased from Jackson lab AND Pinkie mice were inhouse breed and maintained at BCM animal facilities until use

extract_protocol:
RNA was extracted from cultured cells
Whole cornea was surgically removed or the in vitro cultured Immune cells were spun down and the RNA was extracted using the standard protocol provided by the manufacturer, we use the Qiagen RNA preparation kit

treatment_protocol: Mice colonies were maintained at Baylor college of Medicne vivarium under the standard protocol

tag: experimental group

value: Monocytes +LPS (0.5ug/ml)

value: LPS (0.5ug/ml)

tag: Sex

value: Female

tag: age

tag: cell type

value: in vitro cultured Purified Monocytes


title: PEA2 R 24Hr rep1

city: Seattle

first: Amanda

last: Paulovich

state: WA

address: 1100 Fairview Ave. N.

institute: Fred Hutchinson Cancer Research Center

description: PEA2 p25

library_source: transcriptomic

data_processing:
Illumina Bcl2fastq v2.18
Genome_build: UCSC hg19
Supplementary_files_format_and_content: .csv

organism: Homo sapiens

source_name: Human Ovarian Cancer cell line (platinum resistant)

growth_protocol: Cells were grown in RPMI1640 (Corning 10-040-CV) medium supplemented with L-glutamine and 10% fetal bovine serum (heat Inactivated FBS, Atlanta Biologicals S10250)

extract_protocol:
Total RNA was extracted from cell pellets with the miRNeasy Kit (Qiagen, cat#217504).
Purified total RNA samples were evaluated for quality and quantity by Agilent Bioanalzyer using RNA 6000 Nano chip and reagents (cat#5067-1511). Sequencing libraries were prepared using Illumina TruSeq stranded Total RNA sample preparation kit (cat# 20020597) from 200ng of RNA according to manufacturer’s protocol. The finished libraries were quantified by Qubit fluorometer, Agilent TapeStation 2200 D1000 screentape (cat#5067-5582), and RT-qPCR using the Roche Kapa Biosystems library quantification kit (cat#KK4854) according to manufacturer’s protocols. Whole genome libraries for copy number analysis were sequenced with >25M 75bp read pairs and RNAseq libraries were sequenced with >50M 75bp read pairs by the Molecular Biology Core Facilities at Dana-Farber Cancer Institute.

treatment_protocol: Cells were plated in 150-mM tissue culture plates and cultured for 48 hours, at which point they were approximately 50% confluent. The cultures were then treated with vehicle or 80 µM carboplatin (S1215, Selleckchem US) for 8 or 24 hours

value: 80uM carboplatin

tag: time of treatment

tag: cell line and catalog #

value: PEA2 MilliporeSigma 10032307-1VL/ ECACC 10032307


title: Monocytes+LPS (0.5ug/ml)_1


title: 4hpf_DMSO_Aebp2_ChIP_rep2

description:
15987X21
Zebrafish
Aebp2_DMSO__4hpf_ChIP.narrowPeak
Aebp2_DMSO_4hpf_ChIP.bw


title: 4hpf_DMSO_Aebp2_ChIP_rep1

description:
15987X20
Zebrafish
Aebp2_DMSO__4hpf_ChIP.narrowPeak
Aebp2_DMSO_4hpf_ChIP.bw


title: C26-N1

city: Toronto

first: Amro

last: Zayed

state: Ontario

address: 4700 Keele Street

department: Biology

country: Canada

institute: York University

description:
HI.4193.007.Index_13.C26-N1
processed data file: Apiary_Nurses_Logcpm.txt

data_processing:
We used Trimmomatic v0.36 to remove removes adapters, low quality bases (leading and trailing 20), and low quality reads (reads shorter than 50 bases and when the average quality per base drops below 25 for a 20 base window).
Field and Apiary data were analyzed seperatly
The RNA sequences were aligned and gene expression quantified with the amel 4.5 Apis mellifera genome assembly and Official Gene Set v3.2 using Spliced Transcripts Alignment to a Reference (STAR) v2.7
The gene expression counts were then processed using EdgeR in R version 3.6.3
Any genes that had an expression count lower than 1 count per million (cpm) in less than two samples were filtered out
The remaining counts were normalized using the default trimmed mean of M-values (TMM) method
Genome_build: Amel_4.5
Supplementary_files_format_and_content: Matrix tables with normalized gene counts in log(cpm) for every gene in Apiary Foragers, Apiary Nurses, Field Foragers, or Field Nurses

organism: Apis mellifera

extract_protocol:
RNeasy Mini Kit (Qiagen) following manufacturer instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: caste

tag: experiment

value: Brain


title: PEA1 S 24Hr rep1

source_name: Human Ovarian Cancer cell line (platinum sensitive)

value: PEA1 MilliporeSigma 10032306-1VL/ ECACC 10032306


title: PEO23 R 08Hr rep1

value: PEO23 MilliporeSigma 10032313-1VL/ ECACC 1003213


title: Monocytes Control_3

value: Monocytes +vehicle

value: vehicle


title: C26-F1

description:
HI.4193.006.Index_25.C26-F1
processed data file: Apiary_Foragers_Logcpm.txt

value: Forager

value: Apiary


title: C26-F3

description:
HI.4193.006.Index_27.C26-F3
processed data file: Apiary_Foragers_Logcpm.txt

value: Unexposed


title: Monocytes Control_2


title: Monocytes Control_1


title: postZGA_Jarid2_Input

description:
Jarid2_4.3hpf_ChIP.bw
Jarid2_4.3hpf_ChIP.narrowPeak

data_processing:
ChIP-seq Fastq files were aligned to Zv10 using Novocraft Novoalign (v3.8) with the following settings: -o SAM -r Random.
SAM files were processed to BAM format, sorted, and indexed using Samtools (v1.8).
MACS2 (v2.2.5) was utilized for peak calling with the following settings: -B -q 0.01 --SPMR. BAM files of ChIP replicates and input were provided to MACS2 in a single execution under the -t and -c flags, respectively.
Bedgraph output files from MACS2 were used to produce bigwig files with UCSC bedGraphToBigWig (v4).
Genome_build: zv10
Supplementary_files_format_and_content: narrowPeak and bigwig file formats. The narrowPeak files contain peaks that were called by MACS2 with a q value cutoff of 0.01. The bigwig files are the treatment fragment pileups produced by MACS2 and are normalized by signal per million reads.

value: Tubingen

value: WT

value: 4.3 hpf

value: Untreated


title: 4hpf_DMSO_Aebp2_input_3

description:
15987X19
Zebrafish

value: Whole body (embryo)

value: DMSO


title: S3

city: Canterbury

first: Rebecca

middle: Anne

last: Hall

address: Giles Lane

department: School of Biosciences

country: United Kingdom

institute: University of Kent

description: Oestrogen 3

data_processing:
Trim reads, CLC Genomics Workbench 11.0.1
Reads alignement, CLC Genomics Workbench 11.0.1
Genome_build: Candida genome database : http://www.candidagenome.org/ Sequences available here: http://www.candidagenome.org/download/sequence/C_albicans_SC5314/Assembly21/current/, C_albicans_SC5314_version_A21-s02-m09-r10
Supplementary_files_format_and_content: TPM

organism: Candida albicans

source_name: Liquid culture

growth_protocol: Cells were grown in YPD supplemented or not with 10 µM oestrogen at 37c, 200 rpm.

extract_protocol:
RNeasy kit (Qiagen)
RNA libraries were produced using the Biomek FxP (Beckman Coulter A31842) with NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolab E7420L) and NEBnext Multiplex Oligos for Illumina Dual Index Primers (New England Biolabs E7600S)

tag: spike-in

value: 10 microM oestrogen in ethanol

tag: replicate


title: C26-F2

description:
HI.4193.006.Index_23.C26-F2
processed data file: Apiary_Foragers_Logcpm.txt


title: PEO14 S 08Hr rep1

value: 80uM carboplatin

value: PEO14 MilliporeSigma 10032311-1VL/ ECACC 10032311


title: PEO4 R 08Hr rep1

value: PEO4 MilliporeSigma 10032309-1VL/ ECACC 10032309


title: 4hpf_DMSO_Aebp2_input_2

description:
15987X18
Zebrafish


title: S2

description: Oestrogen 2


title: 4hpf_DMSO_Aebp2_input_1

description:
15987X17
Zebrafish


title: C27-F10

description:
HI.4193.007.Index_14.C27-F10
processed data file: Apiary_Foragers_Logcpm.txt

value: Brain


title: PEO1 S 08Hr rep1

value: PEO1 MilliporeSigma 10032308-1VL/ ECACC 10032308


title: C26-F10

description:
HI.4193.006.Index_21.C26-F10
processed data file: Apiary_Foragers_Logcpm.txt


title: postZGA_Rnf2_ChIP_rep2

description:
15987X12
Zebrafish
Rnf2_4.3hpf_ChIP.narrowPeak
Rnf2_4.3hpf_ChIP.bw


title: PEA2 R 08Hr rep1

description: PEA2 p25

value: PEA2 MilliporeSigma 10032307-1VL/ ECACC 10032307


title: C3

description: Control 3


title: C25-N4

description:
HI.4193.006.Index_20.C25-N4
processed data file: Apiary_Nurses_Logcpm.txt

value: Nurse


title: PEO23 R 00Hr rep3

value: untreated

value: PEO23 MilliporeSigma 10032313-1VL/ ECACC 1003213


title: C2

description: Control 2


title: C1

description: Control 1


title: postZGA_Rnf2_input

description:
15987X9
Zebrafish


title: PEO14 S 00Hr rep3


title: C25-N3

description:
HI.4193.006.Index_11.C25-N3
processed data file: Apiary_Nurses_Logcpm.txt

value: Apiary

value: Unexposed


title: postZGA_H2Aub1_ChIP_rep3

description:
15987X8
Zebrafish
H2Aub1_4.3hpf_ChIP.narrowPeak
H2Aub_4.3hpf_ChIP.bw

value: Tubingen

value: WT


title: PEO4 R 00Hr rep3


title: postZGA_H2Aub1_ChIP_rep1

description:
15987X6
Zebrafish
H2Aub1_4.3hpf_ChIP.narrowPeak
H2Aub_4.3hpf_ChIP.bw

value: Untreated


title: PEO1 S 00Hr rep3


title: postZGA_H2Aub1_ChIP_rep2

description:
15987X7
Zebrafish
H2Aub1_4.3hpf_ChIP.narrowPeak
H2Aub_4.3hpf_ChIP.bw

value: Whole body (embryo)


title: Neut1um1h-2

city: Tianjin

first: Shan

last: Jiang

address: Tianjin NanjingRoad

country: China

institute: Public Union Medical College

data_processing:
A propriety Sub-pixel Registration algorithm developed by MGI was used for base call.
This project uses the filtering software SOAPnuke developed by BGI independently for filtering. The specific steps are as follows:  1) Remove the reads containing the adaptor(adaptor pollution);  2) Remove reads whose N content is greater than 5%;  3) Remove low-quality reads (we define reads with bases with a quality score less than 10 as the proportion of total bases in the reads that are greater than 20% as low-quality reads).  The filtered "Clean Reads" are saved in FASTQ format.
Bowtie2 was used to map the clean reads to the reference gene sequence (transcriptome), and then RSEM was used to calculate the gene expression level of each sample.
The DEseq2 was used to perform differential expression analysis.DESeq2: Qvalue (Adjusted Pvalue) <= 0.05
Genome_build: GCF_000001635.26_GRCm38.p6
Supplementary_files_format_and_content: tab-delimited text files include FPKM values, TPM values and raw gene counts for each Sample

source_name: Neutrophils

growth_protocol: Neutrophils were extracted from mouse bone marrow with a purity of more than 95%. They were cultured in 1640 medium containing 20%FBS for 1 h, collected and lysed

extract_protocol:
RNA from neutrophils was collected using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Neutrophils were treated with 1um Ruxolitinib or vehicle (80% glucose +20%PEG300) for 1h

value: Bone marrow derived neutrophils

value: Ruxolitinib 0.1uM


title: C25-F4

description:
HI.4193.005.Index_9.C25-F4
processed data file: Apiary_Foragers_Logcpm.txt

value: Forager


title: Neut1h-2

value: vehicle


title: C25-N5

description:
HI.4193.006.Index_22.C25-N5
processed data file: Apiary_Nurses_Logcpm.txt


title: S1

description: Oestrogen 1

value: 10 microM oestrogen in ethanol


title: C23-N5

description:
HI.4193.005.Index_5.C23-N5
processed data file: Apiary_Nurses_Logcpm.txt

value: Exposed

value: Brain


title: postZGA_H2Aub1_input

description:
15987X5
Zebrafish


title: postZGA_Rnf2_ChIP_rep1

description:
15987X11
Zebrafish
Rnf2_4.3hpf_ChIP.narrowPeak
Rnf2_4.3hpf_ChIP.bw


title: PEA2 R 00Hr rep3

description: PEA2 p24

value: PEA2 MilliporeSigma 10032307-1VL/ ECACC 10032307


title: PEA1 S 08Hr rep1

value: 80uM carboplatin

value: PEA1 MilliporeSigma 10032306-1VL/ ECACC 10032306


title: Neut1h


title: 3T3-bulk

city: Xiamen

first: Li

last: Lin

state: Fujian

address: 422 Road, Siming District,  Xiamen, China

institute: Xiamen University

description:
the gene expression matirx (txt file)
3T3-bulk_raw_dge.txt.gz

data_processing:
Well-paired-seq sequencing libraries produced paired-end reads: read 1 contains a cell barcode (12 bases) and a UMI (8 bases); read 2 contains the sequence of the transcript.
Data preprocessing and read alignment were implemented by using the Drop-seq core computational program (https://github.com/broadinstitute/Drop-seq/releases/tag/v2.3.0).
Briefly, the program extracted cell barcodes and UMIs from raw reads, filtered out low-quality reads, trimmed unusable read 2 sequences, performed the read alignment, added gene tags, repaired cell barcodes, and generated a digital gene expression matrix.
Reads filtration aimed to remove reads where the cell barcode or UMI had at least 1 base with quality lower than 10. At least five contiguous bases of the adapter and at least six contiguous bases of A with no mismatch were hard clipped off the read 2. After trimming, the reads were aligned to the hg19 or hg19_mm10 reference genome using STAR version 2.7.1a33 with default parameters. Thus, a gene tag “GE” was added to each read and multi-mapping reads were discarded.
Cell barcodes correlation, including detection and repairing of substitution errors and indel synthesis errors, were then carried out. UMIs for a gene with one edit distance were merged together. The total number of unique UMIs for each gene were counted as the number of transcripts of that gene for a given cell to generate digital gene expression.
Genome_build: hg19, mm10
Supplementary_files_format_and_content: digital gene expression and sample annotation in text file

source_name: embryonic fibroblast cells

extract_protocol:
Cells were lyzed and mRNA captured on barcoded beads were reverse transcripted and amplified using PCR.
RNA libraries were prepared for sequencing using standard TruePrep® DNA Library Prep Kit V2 for Illumina® (Vazyme, cat#TD502) according to the manufacturer’s protocols

treatment_protocol: Drug-treated group was treated by vorinostat at 0, 0.1, 1, or 10 µM for 36 hours


title: C23-N4

description:
HI.4193.005.Index_4.C23-N4
processed data file: Apiary_Nurses_Logcpm.txt

value: Nurse


title: C25-N2

description:
HI.4193.006.Index_10.C25-N2
processed data file: Apiary_Nurses_Logcpm.txt

value: Apiary


title: PEA1 S 00Hr rep3

value: untreated


title: C25-N1

description:
HI.4193.005.Index_8.C25-N1
processed data file: Apiary_Nurses_Logcpm.txt

value: Unexposed


title: Neut1um1h


title: postZGA_Aebp2_ChIP_rep2

description:
15987X3
Zebrafish
Aebp2_4.3hpf_ChIP.narrowPeak
Aebp2_4.3hpf_ChIP.bw

value: Tubingen

value: WT


title: C25-F3

description:
HI.4193.005.Index_3.C25-F3
processed data file: Apiary_Foragers_Logcpm.txt


title: Well-paired-seq_3T3_single_cells

description:
the gene expression matirx (txt file)
Well-paired-seq_3T3_single_cells_raw_dge.txt.gz


title: WT_testis_rep3

city: Chicago

first: Manyuan

last: Long

state: IL

address: 5801 S. Ellis Ave.

institute: University of Chicago

data_processing:
Through assessing the quality of original raw sequencing data, good base-wise quality was revealed in average in all samples, indicating a high confidence on the base call. Adapter/primer sequences are absent from reads; therefore, trimming of sequencing reads was skipped prior to downstream RNA-seq analysis. Overall, around 94.89% of reads were successfully mapped to the fruit fly genome model in RNA-seq data. All RNA samples were used for further downstream identification of differentially expressed (DE) mRNA genes in individual pairwise comparison.
Several commonly used tools (DESeq2, edgeR, and limma) were utilized for the identification of DE mRNA between pairwise groups. Using the criteria of fold change no less than 1.5 and FDR (False Discovery Rate) less than 0.1). Pairwise comparison, KO-Zeus/KO-Ctrl, were conducted. Overall, we find Zeus regulated the expression of 661 differentially expressed genes (DEGs) based on combination of three tools. Venn diagram was further depicted to present the consensus/overlapped DE gene sets detected across different methods.

organism: Drosophila melanogaster

source_name: whole testis from adult fly

growth_protocol: All the flies were feeded by the food from the fly kitchen from University of Chicago; with 12h/12h day/night condition at 25℃ under ~60% humidity

extract_protocol:
Using the ArcturusTM PicoPureTM RNA Isolation kit (Applied Biosystems, LOT 00665884)
poly(A) mRNA was purified from total RNA, using oligo(dT)-attached magnetic beads; reverse-transcribed to double-stranded cDNA with random primers; end-repaired; and ligated with NEB adaptors for Illumina sequencing (HiSeq 4000, University of Chicago Genomics Core Facility)

treatment_protocol: Each replicate was stored in PBS for1-2 days. This is a common sample storage reagent.

value: whole testis from adult fly


title: PEO14 S 00Hr rep2

value: PEO14 MilliporeSigma 10032311-1VL/ ECACC 10032311


title: postZGA_Aebp2_ChIP_rep1

description:
15987X2
Zebrafish
Aebp2_4.3hpf_ChIP.narrowPeak
Aebp2_4.3hpf_ChIP.bw

value: Whole body (embryo)

value: Untreated


title: postZGA_Aebp2_input

description:
15987X1
Zebrafish


title: C25-F1

description:
HI.4193.005.Index_12.C25-F1
processed data file: Apiary_Foragers_Logcpm.txt

value: Forager


title: C25-F2

description:
HI.4193.005.Index_1.C25-F2
processed data file: Apiary_Foragers_Logcpm.txt


title: WT_testis_rep2


title: ZGA_H3K4me1_input

description:
16259X6
Zebrafish


title: PEO4 R 00Hr rep2

value: PEO4 MilliporeSigma 10032309-1VL/ ECACC 10032309


title: WT_testis_rep1


title: postZGA_Aebp2_ChIP_rep3

description:
15987X4
Zebrafish
Aebp2_4.3hpf_ChIP.narrowPeak
Aebp2_4.3hpf_ChIP.bw


title: PEO1 S 00Hr rep2

value: PEO1 MilliporeSigma 10032308-1VL/ ECACC 10032308


title: ZGA_H3K4me1_ChIP_rep2

description:
16259X4
Zebrafish
H3K4me1_3.5hpf_ChIP.narrowPeak
H3K4me1_3.5hpf_ChIP.bw


title: PEA2 R 00Hr rep2

description: PEA2 p24


title: C21-N9

description:
HI.4193.004.Index_6.C21-N9
processed data file: Apiary_Nurses_Logcpm.txt

value: Exposed

value: Brain


title: C23-F8

description:
HI.4193.004.Index_7.C23-F8
processed data file: Apiary_Foragers_Logcpm.txt


title: PEA1 S 00Hr rep2


title: ZGA_H3K4me1_ChIP_rep1

description:
16259X3
Zebrafish
H3K4me1_3.5hpf_ChIP.narrowPeak
H3K4me1_3.5hpf_ChIP.bw


title: Zeus_KO_testis_rep3

value: Zeus-KO mutant


title: C21-N7

description:
HI.4193.004.Index_2.C21-N7
processed data file: Apiary_Nurses_Logcpm.txt


title: PEO23 R 00Hr rep2

value: PEO23 MilliporeSigma 10032313-1VL/ ECACC 1003213


title: C25-F10

description:
HI.4193.005.Index_19.C25-F10
processed data file: Apiary_Foragers_Logcpm.txt


title: PEO23 R 00Hr rep1


title: Zeus_KO_testis_rep1


title: C23-N1

description:
HI.4193.004.Index_18.C23-N1
processed data file: Apiary_Nurses_Logcpm.txt

value: Nurse


title: ZGA_H2Az_ChIP_rep2

description:
16259X2
Zebrafish
H2Az_3.5hpf_ChIP.narrowPeak
H2Az_3.5hpf_ChIP.bw


title: ZGA_H2Az_input

description:
16259X5
Zebrafish


title: PEO14 S 00Hr rep1


title: C23-N3

description:
HI.4193.004.Index_16.C23-N3
processed data file: Apiary_Nurses_Logcpm.txt

value: Apiary


title: KO18

city: Oslo

first: Kuan

last: Yang

address: Sognsvannsveien 20

department: Research Institute of Internal Medicine

country: Norway

institute: Oslo University Hospital

data_processing:
Raw files were trimmed with Fastp (v0.20.0) in paired-end mode to remove contaminated adapters and reads with phred quality scores below 30.
Filtered reads were mapped to mouse cDNA (GRCm38.p6, Ensembl release 98) by Kallisto (v0.46.0) with 200 bootstrap iterations
sleuth (v0.30.0) was used to obtain deferentially expressed transcripts with Wald test from HDF5 file outputed by kallisto.
Genome_build: GRCm38.p6, Ensembl release 98
Supplementary_files_format_and_content: HDF5 (.h5) binary file which contains estimated counts, TPM, effective lenght of main quantification and boostraps as well as run info

source_name: Macrophages

extract_protocol:
Total RNA of bone marrow-derived macrophages was isolated under RNase‐free conditions using RNeasy spin columns according to manufacture's manual
Library was constructed by using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® according to manufacture's protocol.

value: EndoV knockout

tag: background

value: Bone marrow-derived macrophages


title: PEO4 R 00Hr rep1

value: untreated


title: KO17


title: C23-F1

description:
HI.4193.004.Index_15.C23-F1
processed data file: Apiary_Foragers_Logcpm.txt


title: D28_NEC

city: Singapore

first: Wharton

middle: O Y

last: Chan

state: Singapore

address: 8 College Road

department: Emerging Infectious Disease

country: Singapore

institute: Duke-NUS Medical School

description: Single Cell RNA Counts

data_processing:
Cellranger-5.0.0
Genome_build: GRCh38
Supplementary_files_format_and_content: sparse matrix count table (cellranger standard output)
Supplementary_files_format_and_content: list of genes tsv (cellranger standard output)
Supplementary_files_format_and_content: list of cell barcodes tsv (cellranger standard output)

source_name: Human Nasal Epithelial Cells

growth_protocol: Fully differentiated Human Nasal Epithelial Cells

extract_protocol: 10X 3’ Single Cell Library

treatment_protocol: Uninfected, or infected with SARS-CoV-2 wild-type at MOI of 0.1 for indicated period

value: Donor-derived Nasal Epithelial Cells in Airway Liquid Interface Culture

value: Infected (Day 28)


title: PEO1 S 00Hr rep1


title: KO16


title: C23-N2

description:
HI.4193.004.Index_14.C23-N2
processed data file: Apiary_Nurses_Logcpm.txt


title: ZGA_H2Az_ChIP_rep1

description:
16259X1
Zebrafish
H2Az_3.5hpf_ChIP.narrowPeak
H2Az_3.5hpf_ChIP.bw

tag: strain

value: Tubingen

value: WT


title: D3_NEC

description: Single Cell RNA Counts

value: Infected (Day 3)


title: PEA2 R 00Hr rep1

description: PEA2 p23

value: PEA2 MilliporeSigma 10032307-1VL/ ECACC 10032307


title: WT15

tag: genotype

value: Wild Type


title: PEA1 S 00Hr rep1

value: PEA1 MilliporeSigma 10032306-1VL/ ECACC 10032306


title: WT14


title: Zeus_KO_testis_rep2

value: whole testis from adult fly


title: D0_NEC

description: Single Cell RNA Counts

value: Uninfected


title: WT13


title: C21-N3

description:
HI.4193.003.Index_27.C21-N3
processed data file: Apiary_Nurses_Logcpm.txt

value: Exposed

value: Brain


title: single-cell RNA-seq of lung orthotopic tumor

city: New York City

first: Alireza

last: Khodadadi-Jamayran

state: NY

address: 550 1st Ave, MSB 304

department: Division of Advanced Research Technologies (DART)

institute: New York University, NYU Langone Medical Center

description:
hashtag 1 = KP_STINGa
hashtag 2 = KP_Vehicle
hashtag 4 = KPK_STINGa
hashtag 5 = KPK_vehicle

data_processing:
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
Additional cell-level demultiplexing and alignment was performed with 10x Cell Ranger software. Demultiplexing for hashtag oligos is done using iCellR and sample names are included in the metadata file.
Genome_build: mm10
Supplementary_files_format_and_content: gene-barcode matrix and metadata (one file including all samples with sample/hashtag identifiers).

molecule: polyA RNA

source_name: lung orthotopic tumor

growth_protocol: lung orthotopic tumor

extract_protocol:
standard RNA extraction protocol
Single Cell 3’ Reagent Kits v2: Chromium™ Single Cell 3’ Library & Gel Bead Kit v2, PN-120237; Single Cell 3’ Chip Kit v2 PN-120236 and i7 Multiplex Kit PN-120262" (10x Genomics)

treatment_protocol: STING agonist DMXAA (STINGa)

tag: condition

value: multiplexed sample:pool of KP_STINGa, KP_vehicle, KPK_STINGa, KPK_vehicle

value: lung

value: immune cell (CD45+ PI neg)

tag: disease state

value: lung adenocarcinoma


title: C21-F3

description:
HI.4193.003.Index_25.C21-F3
processed data file: Apiary_Foragers_Logcpm.txt

value: Forager

value: Apiary

tag: treatment

tag: tissue


title: postMBT_ATAC-seq_rep2

description:
Zebrafish
11766X6
postmbt_atac_noChrM_3lanes_120_220.log2FE.bw
postmbt_atac_noChrM_3lanes_120_220.narrowPeak

data_processing:
Fastq files were aligned to Zv10 using novoalign (version 3.8) with the following parameters: -r Random -o SAM.
SAM files were converted to BAM format and sorted with Samtools. Bam files for technical replicates were merged using Samtools merge.
Bam files were processed using Multi-Replica Macs ChIPSeq Wrapper (version 12, https://github.com/HuntsmanCancerInstitute/MultiRepMacsChIPSeq) with the following parameters: --species zebrafish --pe --min 120 --max 220 --nodup --cutoff 2 --tdep N, where N represents the lowest observed sequencing depth in millions.
Genome_build: zv10
Supplementary_files_format_and_content: *.narrowPeak: The narrowPeak files are the identified peaks of enrichment at a threshold of q-value 0.01.
Supplementary_files_format_and_content: *.bw: The bigWig files are log2-scaled Fold Enrichment of ATAC-seq signal over Input signal.

extract_protocol:
Approximately 300 embryos/tube of a 4hpf embryo was lysed with TN5 Lysis buffer (10mM Tris-CL, pH 7.4, 10mM NaCl, 3 mM MgCl2, 0.1% Igepal CA 630 + 1% protease inhibitor). Nuclei was isolated by removing. Chorion, yolk and cell membrane by physical disruption utilizing a 3mL syringe/20G needle while kept on ice. Nuclei was washed 2 times at room temperature for 10mins with nuclei wash buffer (50mM Tris-HCL pH 8.0, 100mM NaCl, 10mM EDTA + 1% protease inhibitor).
The ATAC-seq library was made using Nextera DNA Flex Library Prep Kit (Illumina, 20018704) according to kit specifications. Proper sizing of tagmentation was determined by DNA acrylamide gels utilizing Typhoon imager (GE Healthcare) for each lot of enzyme used.

treatment_protocol: Untreated

tag: developmental stage

value: Whole body (embryo)

value: Untreated


title: C21-F5

description:
HI.4193.003.Index_23.C21-F5
processed data file: Apiary_Foragers_Logcpm.txt


title: postMBT_ATAC-seq_rep1

description:
Zebrafish
11766X5
postmbt_atac_noChrM_3lanes_120_220.log2FE.bw
postmbt_atac_noChrM_3lanes_120_220.narrowPeak

value: Tubingen

value: WT


title: dLN_WT_2

city: Boston

first: Lifei

last: Hou

state: MA

address: 300 Longwood Ave

institute: Boston Children's Hospital

data_processing: The resulting 4.5 Gb/genotype of raw data was trimmed, and 20 million reads were mapped. Of the ≥ 24,000 genes evaluated in the resulting 2-way data sets, the 9,600 genes that had expression levels (FPKM) ≥1.0 were analyzed for differential expression.

source_name: dLN

extract_protocol:
Cells were freshly sorted and RNA was harvested using QIAGEN RNeasy Plus Mini kits and quantified by optical density at 260/280/230nm. TruSeq RNA V2 kits were used to construct transcript-5 specific libraries that were sequenced on Illumina HiSeq2500
RNA libraries were prepared for sequencing using standard Illumina protocols

value: dLN

value: wild type


title: C21-F2

description:
HI.4193.003.Index_22.C21-F2
processed data file: Apiary_Foragers_Logcpm.txt


title: dLN_WT_1


title: C21-F4

description:
HI.4193.003.Index_21.C21-F4
processed data file: Apiary_Foragers_Logcpm.txt


title: CNS_WT_2

source_name: CNS

value: CNS


title: CNS_WT_1


title: MBT_ATAC-seq_rep1

description:
Zebrafish
11766X3
mbt_atac_noChrM_3lanes_120_220.log2FE.bw
mbt_atac_noChrM_3lanes_120_220.narrowPeak


title: preMBT_ATAC-seq_rep2

description:
Zebrafish
11766X2
prembt_atac_noChrM_3lanes_120_220.log2FE.bw
prembt_atac_noChrM_3lanes_120_220.narrowPeak


title: C21-F1

description:
HI.4193.003.Index_20.C21-F1
processed data file: Apiary_Foragers_Logcpm.txt


title: 2J7-N

description:
HI.4193.003.Index_11.2J7-N
processed data file: Field_Nurses_Logcpm.txt

value: Nurse

value: Field

value: Unexposed


title: C21-N8

description:
HI.4193.004.Index_13.C21-N8
processed data file: Apiary_Nurses_Logcpm.txt

value: Exposed

value: Brain


title: G4_Terc-/-_rep3

city: tianjin

first: nannan

last: zhao

state: --- Select a state ---

address: nankai

institute: nankai university

data_processing:
The quality control with the software FastQC v0.11.9
Clean reads were aligned to the mouse mm10 genome with the STAR 2.5.3a software
The counts of the retrotransposons were counted by the featureCounts software

source_name: ESC

extract_protocol:
Feeder were removed, flash frozen on dry ice, and RNA was harvested using RNA kit(QIAGEN,74134). 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: ESC

tag: phenotype

value: Terc-/-

tag: group


title: preMBT_ATAC-seq_rep1

description:
Zebrafish
11766X1
prembt_atac_noChrM_3lanes_120_220.log2FE.bw
prembt_atac_noChrM_3lanes_120_220.narrowPeak


title: 2J7-F

description:
HI.4193.003.Index_10.2J7-F
processed data file: Field_Foragers_Logcpm.txt


title: G4_Terc-/-_rep2


title: model brain after BHD intervention Replicate 1

city: Changsha

first: Bo-wei

last: CHEN

address: No. 95 Shaoshan Middle Road

institute: Hunan University of Chinese Medicine

description: Biological replicate 4 of 4. middle cerebral artery embolization model rat hippocampus after BHD intervention.7days.

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent  G2505C scanner. Images were quantified using Agilent Feature Extraction Software (version A.10.7.1.1).

data_processing: Agilent Feature Extraction Software (v 10.7.1.1) was used for background subtraction and LOWESS normalization.

organism: Rattus norvegicus

source_name: brain,BHD intervention 7days

label_protocol: 10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label

growth_protocol: Drink and eat freely

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

value: brain

value: male


title: model brain after BHD intervention Replicate 3


title: 2J6-F

description:
HI.4193.002.Index_9.2J6-F
processed data file: Field_Foragers_Logcpm.txt

value: Forager


title: model brain after BHD intervention Replicate 2


title: Control sample of Lingual Nerve

city: Wakayama

first: Takashi

last: Nakanishi

state: Wakayama

address: Kimiidera 811-1

department: Oral and Maxillofacial Surgery

country: Japan

institute: Wakayama Medical University

description: Gene expression in the margin of the lingual nerve removed the unaffected side of the removed tongue with cancer.

hyb_protocol: Hybridization was performed at 45ºC for 16 h.

scan_protocol: After washing, fluorescence intensity was assayed using a scanner (GeneChip® Scanner 3000 7G; Affymetrix).

data_processing: The signal intensities were quantified and analyzed by subtracting background fluorescence using Expression Console™ Software (Affymetrix).

label_protocol: Using a Nano Drop One (Thermo Fisher Scientific Inc., Shanghai, China), and the 260:280 nm absorbance ratios (A260/280) of the RNA samples were measured. RNA samples with A260/280 ratios greater than 2.0 were used.   Equal amounts of RNA (100 µg) from three traumatic neuroma samples were combined. The quality of the combined RNA sample was assessed using an Agilent 2100 Bioanalyzer with an RNA 6000 Nano Kit (Agilent Technologies, Palo Alto, CA, USA). Samples with RNA Integrity Number (RIN) scores over 7.5 were used.

extract_protocol: Total RNA from the lingual nerve was extracted with the RNeasy Mini Kit (QIAGEN, Germany).

treatment_protocol: The samples of traumatic neuroma were collected from the patients with lingual nerve injury at removing the neuroma in microneurosurgery. RNA samples were fixed by RNAlater® (Thermo Fisher Scientific, Japan)

value: lingual nerve

tag: state

value: control


title: G4_Terc-/-_rep1


title: Traumatic Neuroma

description: Gene expression in the traumatic neuroma of the human lingual nerve

value: traumatic neuroma


title: 4hpf_DMSO_H3K27me3_ChIP_rep2

description:
15569X11
Zebrafish
H3K27me3_4hpf_DMSO_ChIP.narrowPeak
H3K27me3_4hpf_DMSO_ChIP.bw

data_processing:
ChIP-seq Fastq files were aligned to Zv10 using Novocraft Novoalign (v3.8) with the following settings: -o SAM -r Random.
SAM files were processed to BAM format, sorted, and indexed using Samtools (v1.8).
MACS2 (v2.2.5) was utilized for peak calling with the following settings: -B -q 0.01 --SPMR. BAM files of ChIP replicates and input were provided to MACS2 in a single execution under the -t and -c flags, respectively.
Bedgraph output files from MACS2 were used to produce bigwig files with UCSC bedGraphToBigWig (v4).
Genome_build: zv10
Supplementary_files_format_and_content: *.narrowPeak: The narrowPeak files contain peaks that were called by MACS2 with a q value cutoff of 0.01.
Supplementary_files_format_and_content: *bw: The bigwig files are the treatment fragment pileups produced by MACS2 and are normalized by signal per million reads.

value: Tubingen

value: WT

value: Whole body (embryo)

value: DMSO

tag: chip antibody


title: 4hpf_DMSO_H3K27me3_ChIP_rep3

description:
15569X12
Zebrafish
H3K27me3_4hpf_DMSO_ChIP.narrowPeak
H3K27me3_4hpf_DMSO_ChIP.bw


title: model brain Replicate 4

description: Biological replicate 4 of 4. middle cerebral artery embolization model rat hippocampus.7days.

source_name: brain,model 7days


title: 2J6-N

description:
HI.4193.002.Index_8.2J6-N
processed data file: Field_Nurses_Logcpm.txt

value: Nurse


title: model brain Replicate 2

description: Biological replicate 2 of 4. middle cerebral artery embolization model rat hippocampus.7days.


title: G1_Terc-/-_rep3


title: MBT_ATAC-seq_rep2

description:
Zebrafish
11766X4
mbt_atac_noChrM_3lanes_120_220.log2FE.bw
mbt_atac_noChrM_3lanes_120_220.narrowPeak

value: Untreated


title: model brain Replicate 3

description: Biological replicate 3 of 4. middle cerebral artery embolization model rat hippocampus.7days.


title: model brain Replicate 1

description: Biological replicate 1 of 4. middle cerebral artery embolization model rat hippocampus.7days.


title: 4hpf_DMSO_H3K27me3_ChIP_rep1

description:
15569X10
Zebrafish
H3K27me3_4hpf_DMSO_ChIP.narrowPeak
H3K27me3_4hpf_DMSO_ChIP.bw


title: model brain after BHD intervention Replicate 4


title: G1_Terc-/-_rep2


title: Control brain Replicate 4

description: Biological replicate 4 of 4. Control rat hippocampus.

source_name: brain ,normal


title: 2J3-F

description:
HI.4193.002.Index_4.2J3-F
processed data file: Field_Foragers_Logcpm.txt

value: Field


title: G1_Terc-/-_rep1


title: 2J3-N

description:
HI.4193.002.Index_5.2J3-N
processed data file: Field_Nurses_Logcpm.txt

value: Exposed


title: 2J5-N

description:
HI.4193.002.Index_3.2J5-N
processed data file: Field_Nurses_Logcpm.txt

value: Brain


title: 4hpf_DMSO_H3K27me3_input3

description:
15569X9
Zebrafish

source_name: WT Tubingen


title: 2J4-N

description:
HI.4193.002.Index_19.2J4-N
processed data file: Field_Nurses_Logcpm.txt


title: Control brain Replicate 3

description: Biological replicate 3 of 4. Control rat hippocampus.

source_name: brain,normal


title: 4hpf_DMSO_H3K27me3_input2

description:
15569X8
Zebrafish


title: WT_rep3

value: ESC


title: 4hpf_PRT4165_H3K27me3_ChIP_rep3

description:
15569X6
Zebrafish
H3K27me3_4hpf_PRT4165_ChIP.narrowPeak
H3K27me3_4hpf_PRT4165_ChIP.bw


title: uIRIx30min-24h, rep2

city: Beijing

first: Jianwen

last: Chen

state: Beijing

address: 28th, Fu Xing road, Hai Dian district

institute: First Medical Center of Chinese PLA General Hospital

data_processing:
A propriety Sub-pixel Registration algorithm developed by MGI was used for base call.
This project uses the filtering software SOAPnuke developed by BGI independently for filtering. The specific steps are as follows:  1) Remove the reads containing the adaptor(adaptor pollution);  2) Remove reads whose N content is greater than 5%;  3) Remove low-quality reads (we define reads with bases with a quality score less than 10 as the proportion of total bases in the reads that are greater than 20% as low-quality reads).  The filtered "Clean Reads" are saved in FASTQ format.
Bowtie2 was used to map the clean reads to the reference gene sequence (transcriptome), and then RSEM was used to calculate the gene expression level of each sample.
The DEseq2 was used to perform differential expression analysis.DESeq2: Qvalue (Adjusted Pvalue) <= 0.05
Genome_build: GCF_000001635.26_GRCm38.p6,The platform is DNBSEQ-MGI2000 (Mus musculus)
Supplementary_files_format_and_content: fpkm.anno_Ischemia_different_min_data.csv

extract_protocol:
Unilateral clamping of the left renal pedicle plus contralateral nephrectomy was performed. Briefly, mice were anesthetized, right kidney was exciced. The left kidney was clamped for indicated minutes (0min for sham-24h group, 16min for uIRIx16min-24h group, 18minfor uIRIx18min-24h group, 20min for uIRIx20min-24h group, 22min for uIRIx22min-24h group, 24min for uIRIx24min-24h group, 26min for uIRIx26min-24h group, 28min for uIRIx28min-24h group, 30min for uIRIx30min-24h group). Mice were placed on 37°C heating platform while operation, ischemia and before awakening. At 24h after ischemia, mice were anesthetized and blood was taken to detect creatinine, kidney was harvest for PAS staining and mRNA seq.
RNA libraries were prepared for sequencing using standard DNBSEQ-G400 (Mus musculus) protocols

value: kidney

value: unilateral ischemia-reperfusion injury (UIRI)

tag: time


title: uIRIx30min-24h, rep3


title: WT_rep2


title: 2J5-F

description:
HI.4193.002.Index_1.2J5-F
processed data file: Field_Foragers_Logcpm.txt

tag: caste


title: WT_rep1


title: Control brain Replicate 2

scan_protocol: Scanned on an Agilent G2505C scanner.Images were quantified using Agilent Feature Extraction Software (version A.10.7.1.1).

value: brain

value: male


title: MRL_uninj_6 (Tendon MRL uninjured rep 4)

city: Rochester

first: Hani

middle: A

last: Awad

address: 601 Elmwood Avenue

department: Biomedical Engineering

institute: University of Rochester

data_processing:
bcltofastq-2.19.0
Trimmomatic-0.36 "TRAILING:13 LEADING:13 ILLUMINACLIP:adapters.fasta:2:30:10 SLIDINGWINDOW:4:20 MINLEN:15"
STAR_2.5.2b "--twopassMode Basic --runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical"
subread-1.5.0p3, featurecounts, Unique "-s 0 -t exon -g gene_name"
Differential expression analysis was performed using DESeq2-1.14.1
Genome_build: GRCm38.p5 + Gencode-M12 Annotation
Supplementary_files_format_and_content: raw gene counts

source_name: Flexor Tendon

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

treatment_protocol: Partial (50%) laceration of the deep digital flexor tendon in the third digit of the hind paw.

value: MRL/MpJ

value: tendon

tag: time-point

value: Uninjured


title: 4hpf_PRT4165_H3K27me3_ChIP_rep1

city: Salt Lake City

first: Graham

last: Hickey

address: 2000 Circle of Hope Drive

institute: University of Utah

description:
15569X4
Zebrafish
H3K27me3_4hpf_PRT4165_ChIP.narrowPeak
H3K27me3_4hpf_PRT4165_ChIP.bw

extract_protocol:
Approximately 1.5 million cells were used for each ChIP replicate. Embryos were allowed to progress to the desired developmental stage and then transferred to 1.5 ml microcentrifuge tubes (~200 embryos per tube). Chorions were removed enzymatically by treatment with pronase 1.25mg/ml in PBS). Dechorionated embryos were gently washed twice with PBS to remove pronase. Samples were fixed with 1% formaldehyde (Electron Microscopy Sciences, Cat# 15712) for 10 minutes at room temperature with end over end rotation. Fixation was quenched with 130 mM glycine for five minutes at room temperature. Samples were centrifuged for five minutes at 500 x g at 4oC. Supernatant was discarded and cell pellets were washed twice with ice cold PBS. Cell pellets were frozen with liquid nitrogen and stored at -80ºC. 1 ml of Mild Cell Lysis Buffer (10 mM Tris-HCl pH 8.1, 10 mM NaCl, 0.5 NP-40, 2X proteinase inhibitors) was applied to cell pellets from 1000 embryos and rotated at 4ºC for 10 minutes. Samples were centrifuged at 1300 X g for 5 minutes at 4ºC. Supernatant was discarded and nuclei pellets were resuspended in 1 ml Nuclei Wash Buffer (50 mM Tris-HCl pH 8.0, 100 mM NaCl, 10 mM EDTA, 1% SDS, 2X protease inhibitors) and rotated at room temperature for 10 minutes. Samples were centrifuged at 1300 X g for 5 minutes at 4ºC to pellet nuclei. Supernatant was discarded and nuclei pellets were resuspended in 100 µl of Nuclei Lysis Buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1% SDS, 2X proteinase inhibitors). Samples were incubated on ice for 10 minutes. 900 µl of IP Dilution Buffer (16.7mM Tris-HCl pH 8.1, 167mM NaCl, 1.2mM EDTA, 0.01% SDS, 1.1% Triton X-100, 2X proteinase inhibitors) was added to samples. Nuclear lysates were sonicated with a Branson Digital Sonifier with the following settings: 10 second duration (0.9 seconds ON, 0.1 seconds OFF), 30% amplitude. 7 sonication cycles were performed. Samples were placed in an ice bath for at least 1 minute between each sonication cycle. Sonicated samples were centrifuged at 14,000 rpm, 4ºC, for 10 minutes to pellet insoluble material. Supernatants were transferred to new tubes. A portion of the sample was set aside to confirm optimal chromatin shearing by agarose gel electrophoresis. 20 µl of Dynabeads (Invitrogen) were blocked with 0.5mg/ml BSA in PBS. Blocked Dynabeads were subsequently applied to each sonicated sample and rotated for 1 hour at 4ºC. Samples were placed on a magnet stand for 1 minute and precleared supernatant was transferred to a new tube. 5% of the sample was removed and stored at -80ºC as input. Antibody and fresh 1X protease inhibitors were added to each sample. Samples were rotated overnight at 4ºC. Samples were centrifuged at 14,000 rpm, 4ºC, for 5 minutes to pellet insoluble material. Supernatants were transferred to new tubes. 50 µl of Dynabeads (Invitrogen) were blocked with BSA 5mg/ml in PBS. Blocked Dynabeads were subsequently applied to each sample and rotated for 6 hours at 4ºC. All wash buffers were kept ice cold during stringency washes. Samples were washed 8 times with RIPA Buffer (10 mM Tris-HCl pH 7.5, 140 mM NaCl, 1mM EDTA, 0.5 mM EGTA, 1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate, 2X protease inhibitors), 2 times with LiCl Buffer (10mM Tris-HCl pH 8.0, 1 mM EDTA, 250 mM LiCl, 0.5% NP-40, 0.5% sodium deoxycholate, 2X protease inhibitors), 2 times with TE Buffer (10mM Tris-HCl pH 8.0, 1 mM EDTA, 2X protease inhibitors). 100 µl of Elution Buffer (10 mM Tris-HCl pH8.0, 5 mM EDTA, 300 mM NaCl, 0.1% SDS) was added to beads. 2ul of RNase A (Thermo Fisher, Cat #EN531) was added to each ChIP and input sample and incubated at 37ºC for 30 minutes with gentle agitation. 10 µl of Proteinase K (Thermo Fisher, Cat # 25530049) was added to each sample and incubated at 37ºC for 1 hour with gentle agitation. Crosslinks were reversed overnight at 65ºC with gentle agitation. ChIP DNA was purified with a Qiagen MinElute PCR Purification kit (Cat #28004).
ChIP seq libraries were prepared using NEBNext ChIP-Seq Library Prep Reagent Set for Illumina (New England BioLabs, Cat # E6240).

value: Tubingen


title: uIRIx28min-24h, rep3


title: uIRIx28min-24h, rep2


title: 2J4-F

description:
HI.4193.002.Index_12.2J4-F
processed data file: Field_Foragers_Logcpm.txt

data_processing:
We used Trimmomatic v0.36 to remove removes adapters, low quality bases (leading and trailing 20), and low quality reads (reads shorter than 50 bases and when the average quality per base drops below 25 for a 20 base window).
Field and Apiary data were analyzed seperatly
The RNA sequences were aligned and gene expression quantified with the amel 4.5 Apis mellifera genome assembly and Official Gene Set v3.2 using Spliced Transcripts Alignment to a Reference (STAR) v2.7
The gene expression counts were then processed using EdgeR in R version 3.6.3
Any genes that had an expression count lower than 1 count per million (cpm) in less than two samples were filtered out
The remaining counts were normalized using the default trimmed mean of M-values (TMM) method
Genome_build: Amel_4.5
Supplementary_files_format_and_content: Matrix tables with normalized gene counts in log(cpm) for every gene in Apiary Foragers, Apiary Nurses, Field Foragers, or Field Nurses

value: Forager

tag: experiment


title: MRL_uninj_4 (Tendon MRL uninjured rep 2)


title: 4hpf_PRT4165_H3K27me3_ChIP_rep2

description:
15569X5
Zebrafish
H3K27me3_4hpf_PRT4165_ChIP.narrowPeak
H3K27me3_4hpf_PRT4165_ChIP.bw

value: WT

value: Whole body (embryo)


title: uIRIx30min-24h, rep1


title: 4hpf_PRT4165_H3K27me3_input3

description:
15569X3
Zebrafish


title: 2J1-F

description:
HI.4193.001.Index_7.2J1-F
processed data file: Field_Foragers_Logcpm.txt


title: 4hpf_DMSO_H3K27me3_input1

description:
15569X7
Zebrafish

value: DMSO


title: MRL_uninj_5 (Tendon MRL uninjured rep 3)


title: 4hpf_PRT4165_H3K27me3_input2

description:
15569X2
Zebrafish


title: 4hpf_PRT4165_H3K27me3_input1

description:
15569X1
Zebrafish


title: Control brain Replicate 1

scan_protocol: Scanned on an Agilent G2505C scanner. Images were quantified using Agilent Feature Extraction Software (version A.10.7.1.1).


title: uIRIx28min-24h, rep1


title: uIRIx26min-24h, rep3


title: 2J2-N

description:
HI.4193.001.Index_16.2J2-N
processed data file: Field_Nurses_Logcpm.txt

value: Nurse


title: MRL_uninj_1 (Tendon MRL uninjured rep 1)


title: uIRIx26min-24h, rep2


title: C57_uninj_5 (Tendon C57 uninjured rep 3)


title: C57_uninj_6 (Tendon C57 uninjured rep 4)


title: 2J10-N

description:
HI.4193.001.Index_15.2J10-N
processed data file: Field_Nurses_Logcpm.txt

value: Field

value: Unexposed


title: 2J10-F

description:
HI.4193.001.Index_6.2J10-F
processed data file: Field_Foragers_Logcpm.txt

value: Brain


title: ZGA_H2Aub1_ChIP_rep1

description:
14341X1
Zebrafish
H2Aub1_ZGA_ChIP.narrowPeak
H2Aub_3.5_ChIP.bw

value: Untreated


title: ZGA_H2Aub1_input

description:
14341X3
Zebrafish


title: uIRIx24min-24h, rep3

value: kidney


title: 1J7-F

description:
HI.4193.001.Index_2.1J7-F
processed data file: Field_Foragers_Logcpm.txt


title: uIRIx26min-24h, rep1

value: unilateral ischemia-reperfusion injury (UIRI)


title: 2J2-F

description:
HI.4193.001.Index_14.2J2-F
processed data file: Field_Foragers_Logcpm.txt

value: Exposed


title: C57_uninj_4 (Tendon C57 uninjured rep 2)


title: C57_uninj_3 (Tendon C57 uninjured rep 1)


title: preZGA_H2Aub1_ChIP_rep2

description:
14450X13
Zebrafish
H2Aub1_preZGA_ChIP.narrowPeak
H2Aub_2.5hpf_ChIP.bw


title: 1J7-N

description:
HI.4193.001.Index_13.1J7-N
processed data file: Field_Nurses_Logcpm.txt


title: uIRIx24min-24h, rep2


title: uIRIx24min-24h, rep1


title: C21-N4

description:
HI.4184.008.Index_7.C21-N4
processed data file: Apiary_Nurses_Logcpm.txt

value: Apiary


title: 2J1-N

description:
HI.4193.001.Index_18.2J1-N
processed data file: Field_Nurses_Logcpm.txt


title: preZGA_H2Aub1_input

description:
14450X11
Zebrafish


title: BI-274

value: MRL/MpJ

value: 7 days post injury


title: BI-275

value: tendon


title: BI-272


title: uIRIx22min-24h, rep3


title: C23-F3

description:
HI.4184.008.Index_6.C23-F3
processed data file: Apiary_Foragers_Logcpm.txt


title: uIRIx22min-24h, rep2


title: ZGA_Rnf2_input

description:
15529X12
Zebrafish

value: Tubingen


title: C27-N10

description:
HI.4184.008.Index_2.C27-N10
processed data file: Apiary_Nurses_Logcpm.txt


title: ZGA_H2Aub1_ChIP_rep2

description:
14341X2
Zebrafish
H2Aub1_ZGA_ChIP.narrowPeak
H2Aub_3.5_ChIP.bw


title: BI-270


title: BI-185


title: uIRIx20min-24h, rep3


title: 1J9-F

description:
HI.4184.008.Index_18.1J9-F
processed data file: Field_Foragers_Logcpm.txt

value: Forager


title: uIRIx20min-24h, rep2


title: ZGA_Rnf2_rep2

description:
15529X10
Zebrafish
Rnf2_3.5hpf_ChIP.narrowPeak
Rnf2_3.5hpf_ChIP.bw

value: WT


title: uIRIx22min-24h, rep1


title: ZGA_Rnf2_rep1

description:
15529X9
Zebrafish
Rnf2_3.5hpf_ChIP.narrowPeak
Rnf2_3.5hpf_ChIP.bw

value: Whole body (embryo)


title: BI-184


title: BI-183


title: preZGA_Rnf2_input

description:
15637X4
Zebrafish


title: uIRIx20min-24h, rep1


title: preZGA_H2Aub1_ChIP_rep1

description:
14450X12
Zebrafish
H2Aub1_preZGA_ChIP.narrowPeak
H2Aub_2.5hpf_ChIP.bw


title: C23-F2

description:
HI.4184.008.Index_13.C23-F2
processed data file: Apiary_Foragers_Logcpm.txt


title: preZGA_Rnf2_ChIP_rep3

description:
15637X3
Zebrafish
Rnf2_2.5hpf_ChIP.narrowPeak
Rnf2_2.5hpf_ChIP.bw


title: preZGA_Rnf2_ChIP_rep2

description:
15637X2
Zebrafish
Rnf2_2.5hpf_ChIP.narrowPeak
Rnf2_2.5hpf_ChIP.bw


title: BM-WT-TIRAP-3

city: Vancouver

first: Aly

last: Karsan

state: British Columbia

address: 675 West 10th Avenue

institute: BC Cancer

data_processing:
Reads aligned and repositioned using JAGuaR v2.0.3
Cram file generated by the compression of bam files uisng samtools (v1.9)
Reads Per Kilobase of transcript, per Million mapped reads (RPKM) were calculated using sailfish (v0.6.2)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file including gene id, chormosome, start, end, strand, gene symbol, biotype gene description and  RPKM values for each sample

source_name: bone marrow over expressing TIRAP

extract_protocol:
Bone marrow was harvested by flushing the bones from mice that were injected with 5-FU 4 days prior to select for HSPC. The HSPC were transduced with TIRAP or control vectors. RNA was harvested from these transduced cells using Qiagen Rneasy kit. mRNA was prepared from 1ug of total RNA using the MultiMACS mRNA isolation kit and cDNA synthetised using the H Minus First Strand cDNA Synthesis Kit.
The paired-end RNA sequencing library was prepared following the BCCA Genome Sciences Center paired-end library preparation plate- based library construction protocol on a Biomek FX robot

value: Bone marrow

value: Adult

tag: Sex

value: Male

value: wild type

tag: cell type

value: hematopoeitic stem/progenitor cells (HSPC)


title: BM-WT-TIRAP-2

tag: strain


title: C28-N1

description:
HI.4184.007.Index_25.C28-N1
processed data file: Apiary_Nurses_Logcpm.txt

extract_protocol:
RNeasy Mini Kit (Qiagen) following manufacturer instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Nurse

value: Brain


title: uIRIx18min-24h, rep3

value: kidney

value: unilateral ischemia-reperfusion injury (UIRI)


title: uIRIx18min-24h, rep1


title: C28-N7

description:
HI.4184.007.Index_27.C28-N7
processed data file: Apiary_Nurses_Logcpm.txt

value: Apiary

value: Exposed


title: uIRIx18min-24h, rep2


title: BM-WT-TIRAP-1

tag: genotype


title: ZGA_Rnf2_rep3

description:
15529X11
Zebrafish
Rnf2_3.5hpf_ChIP.narrowPeak
Rnf2_3.5hpf_ChIP.bw

value: Untreated


title: 4hpf_DMSO_RNAseq_rep3

description:
15111X6
Zebrafish
4hpf_PRT4165_vs__DMSO_RNaseq_counts.txt
DMSO_control_4hpf.bw

data_processing:
RNA-seq fastq files were aligned to Zv10 using STAR (v2.5.4a) with the following settings: --runMode alignReads --twopassMode Basic --alignIntronMax 50000 --outSAMtype BAM SortedByCoordinate --outWigType bedGraph --outWigStrand Unstranded.
BAM files were subsequently indexed using Samtools (v1.8).
FeatureCounts (v1.5.1) was utilized to collect count data for zv10 Ensemble v90 genes via the following command: -T 16 -s 2 –largestOverlap.
Count data for all replicates across experimental conditions were combined into a single count matrix in R. The count matrix was subsequently used to identify differentially expressed genes with the R package DESeq2 (v1.18).
For generation of bigwig files, Bam files for a given condition were merged, sorted, and indexed with samtools. Subsequently deepTools bamCoverage (v2.5.4) was used with the --normlizeUsingRPKM option to produce bigwig files.
Genome_build: zv10
Supplementary_files_format_and_content: 4hpf_PRT4165_vs__DMSO_RNaseq_counts.txt: The count matrix contains data regarding the number of counts each experimental replicate has across zv10 Ensembl v90 transcripts.
Supplementary_files_format_and_content: *.bw: The bigWig files contain RNA-seq signal normalized by RPKM.

extract_protocol:
Total RNA was harvested from zebrafish embryos with a Qiagen Allprep kit (Cat #80204). The Invitrogen DNA-free DNA removal kit (Cat # AM1906 ) was subsequently used to remove contaminating DNA from RNA samples.
Intact poly(A) RNA was purified from total RNA samples (100-500 ng) with oligo(dT) magnetic beads and stranded mRNA sequencing libraries were prepared as described using the Illumina TruSeq Stranded mRNA Library Preparation Kit (RS-122-2101, RS-122-2102).

treatment_protocol: Embryo media was supplemented with 150 μM PRT4165 (or DMSO) from when the embryos were at the 1-cell stage until the embryos were harvested.

value: DMSO


title: C28-N2

description:
HI.4184.008.Index_15.C28-N2
processed data file: Apiary_Nurses_Logcpm.txt


title: preZGA_Rnf2_ChIP_rep1

description:
15637X1
Zebrafish
Rnf2_2.5hpf_ChIP.narrowPeak
Rnf2_2.5hpf_ChIP.bw

value: Tubingen


title: 4hpf_DMSO_RNAseq_rep2

description:
15111X5
Zebrafish
4hpf_PRT4165_vs__DMSO_RNaseq_counts.txt
DMSO_control_4hpf.bw


title: C28-N5

description:
HI.4184.007.Index_23.C28-N5
processed data file: Apiary_Nurses_Logcpm.txt


title: uIRIx16min-24h, rep1


title: BI-181

value: tendon

value: 7 days post injury


title: BM-WT-MIG-1

source_name: bone marrow overexpressing control vector


title: C28-F5

description:
HI.4184.007.Index_20.C28-F5
processed data file: Apiary_Foragers_Logcpm.txt

value: Forager


title: C28-F9

description:
HI.4184.007.Index_22.C28-F9
processed data file: Apiary_Foragers_Logcpm.txt


title: uIRIx16min-24h, rep3


title: C23-F9

description:
HI.4184.008.Index_14.C23-F9
processed data file: Apiary_Foragers_Logcpm.txt


title: 4hpf_PRT4165_RNAseq_rep2

description:
15111X2
Zebrafish
4hpf_PRT4165_vs__DMSO_RNaseq_counts.txt
PRT4165_treated_4hpf.bw

value: WT

value: Whole body (embryo)


title: E11.5 left lobe replicate 2

city: Princeton

first: Katharine

last: Goodwin

state: NJ

address: Hoyt Laboratory, 25 William St

department: Lewis-Sigler Institute for Integrative Genomics

institute: Princeton University

description: pooled cells from 3 lungs

data_processing:
Basecalls performed using RTA version 1.18.64.0
Concatenated fastq files from both lanes of flowcell
Demultiplexed reads using barcode_splitter 0.18.2 (https://bitbucket.org/princeton_genomics/barcode_splitter)
Single cell analysis (alignment, cell identification, gene counts, etc.) performed by CellRanger count version 2.0.1
Single cell analysis by Seurat (v3)
Genome_build: Mus musculus reference genome mm10-1.2.0
Supplementary_files_format_and_content: 10x Cell Ranger HDF5 formatted matrix files

source_name: E11.5 lung

extract_protocol:
Lungs were dissected from CD1 mouse embryos collected at E11.5 in cold PBS. Isolated left lobes were grouped by stage, placed in dispase, and mechanically dissociated with tungsten needles. After 10 minutes in dispase at room temperature, DMEM without HEPES and supplemented with 5% fetal bovine serum (FBS, Atlanta Biologicals) was added, and cell suspensions were passed through a filter with 40-µm-diameter pores. The resultant cell suspensions were then processed by the Princeton Genomics Core Facility. The two sample groups were processed separately. Cells were loaded and processed using the Chromium Single Cell 3’ Library and Gel Bead Kit v2 on the Chromium Controller (10X Genomics) following manufacturer protocols. Individual cells were encapsulated in droplets with single gel beads carrying unique barcoded primers and then lysed. Then cDNA fragments were synthesized, barcoded, and amplified by PCR.
Illumina sequencing libraries were prepared from the amplified cDNA from each sample group using the Nextra DNA library prep kit (Illumina). The v2 libraries were sequenced on Illumina HiSeq 2500 Rapid flowcells (Illumina) as paired-end 26 + 50 nucleotide reads following manufacturer protocols.

tag: strain background

value: left lobe of lungs

tag: biological replicate

value: replicate 2


title: 4hpf_PRT4165_RNAseq_rep1

description:
15111X1
Zebrafish
4hpf_PRT4165_vs__DMSO_RNaseq_counts.txt
PRT4165_treated_4hpf.bw

tag: treatment


title: Sham-24h, rep2

tag: tissue

value: control

value: Sham


title: Sham-24h, rep1


title: uIRIx16min-24h, rep2


title: E11.5 left lobe replicate 1

description: pooled cells from 4 lungs

tag: developmental stage

value: replicate 1


title: DAC-treated CT26 cells (WGBS)

status: Public on Jan 03 2022

city: Shanghai

first: Ganjun

last: Yu

state: Shanghai

address: 800 Xiangyin Road, Shanghai, China.

institute: National Key Laboratory of Medical Immunology & Institute of Immunology

data_processing:
Adapter were trimmed using TrimGalore! v0.6.6 and masked for low-complexity or low-quality sequence
Raw sequencing reads were aligned to the mouse genome (mm10) using bismark .
Methylation levels called using bismark.
The percentage of bisulfite converted cytosines (representing unmethylated cytosines) and non-converted cytosines (representing methylated cytosines) was calculated for each cytosine position in CpG, CHG, and CHH contexts (with H corresponding to A, C, or T nucleotides).
Genome_build: mm10
Supplementary_files_format_and_content: a comma-separated text file containing a matrix of methylation levels determined for CpG positions each Sample.

source_name: CT26 cells

extract_protocol:
Genomic DNA was isolated from the control and the DAC-treated CT26 cells and PDX tumors using a QIAamp genomic DNA Kit (Qiagen, Stockach, Germany) according to the instructions.
The bisulfite-treated DNA was purified on a spin column and used to prepare the sequencing library using an EpiGnome Kit (Epicentre, Wisconsin, USA).In this procedure,bisulfite-treated single-stranded DNA was random-primed using a polymerase able to read uracil nucleotides to synthesize DNA that contained a specific sequence tag. The 3′ ends of the newly synthesized DNA strands were then selectively tagged with a second specific sequence, which resulted in doubly tagged DNA molecules with known sequence tags at their 5′ and 3′ ends.

tag: cell line

value: CRC cell line CT26

value: DAC-treated


title: 4hpf_DMSO_RNAseq_rep1

description:
15111X4
Zebrafish
4hpf_PRT4165_vs__DMSO_RNaseq_counts.txt
DMSO_control_4hpf.bw


title: DAC-treated CT26 cells

data_processing:
Raw data (raw reads) were processed using Trim Galore and FastQC. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
Then the clean reads were mapped to mm10 reference genome using STAR(2.5.3a) software.
FPKM value of each gene was calculated using StringTie(v1.3.1c) and cufflinks.
DEGs were identified using the DESeq (2012) R package functions estimate Size Factors and nbinomTest.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include reads count values for each Sample.

extract_protocol:
The total RNA was isolated with TRIzol (Sigma, St Louis, US) according to the manufacturer’s instructions
RNA libraries were prepared for sequencing using standard Illumina protocols


title: Control groups were treated synchronously under the same conditions except for the absence of DAC

value: non DAC-treated


title: BM-WT-MIG-3

value: Bone marrow

value: Adult

value: Male

value: wild type

value: hematopoeitic stem/progenitor cells (HSPC)


title: 4hpf_PRT4165_RNAseq_rep3

description:
15111X3
Zebrafish
4hpf_PRT4165_vs__DMSO_RNaseq_counts.txt
PRT4165_treated_4hpf.bw

value: Tubingen


title: Sham-24h, rep3

value: kidney


title: C28-F3

city: Toronto

first: Amro

last: Zayed

address: 4700 Keele Street

institute: York University

description:
HI.4184.007.Index_10.C28-F3
processed data file: Apiary_Foragers_Logcpm.txt

value: Forager

value: Apiary

value: Exposed

value: Brain


title: methylation_U87MG-xray-rep2

type: genomic

city: Heidelberg

first: Wahyu

middle: Wijaya

last: Hadiwikarta

address: Im Neuenheimer Feld 280

country: Germany

institute: Deutsches Krebsforschungszentrum

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol.

scan_protocol: Microarrays were scanned using the Illumina iScan-Scanner according to "Standard Illumina Scanning Protocol"

data_processing:
The data were normalised for red and green channel separately using quantile normalisation with R using function normalize.quantiles from Bioconductor package "preprocessCore". Average ß values were calculated by considering the assay type of the feature. Illumina Methylation EPIC uses both Illumina Assay Type I and II. Refer to the following documentation: https://www.illumina.com/content/dam/illumina-support/documents/documentation/software_documentation/genomestudio/genomestudio-2011-1/genomestudio-methylation-v1-8-user-guide-11319130-b.pdf (last checked Dec. 2021)
matrix_signal_intensities.csv contains: Unmethylated and methylated signal intensities.  ID_REF is based on the IlmnID
matrix_processed.csv: Average Beta. ID_REF is based on the IlmnID

label: Cy3, Cy5

label_protocol: 104-500 ng genomic DNA from each sample was bisulfite converted using the EZ-96 DNA Methylation Kit (Zymo Research Corporation, Orange, US) according to the manufacturer recommendations. Each sample was whole genome amplified and enzymatically fragmented following the instructions in the Illumina Infinium HD Assay Methylation Protocol Guide

growth_protocol: Experiments were performed with established PC cell lines DU145, PC3 and LNCaP (ATCC), HNSCC cell lines FaDuDD, Cal33 (DSMZ), SAS, and UT-SCC-14 (JCRB), as well as GBM cell lines LN229 and U87MG (ATCC). All cells were cultured according to the manufacturer's recommendations in a humidified incubator supplemented with 5 % CO2 at 37°C. FaDu, Cal33, PC3 and DU145 cells were maintained in Dulbecco’s Modified Eagle Medium (DMEM, Sigma-Aldrich) and LNCaP in Roswell Park Memorial Institute (RPMI) 1640 Medium (Sigma-Aldrich) containing 10 % fetal bovine serum (FBS; PAA Laboratories), 1mM L-glutamine (Sigma-Aldrich), 1 % HEPES (1 M; PAA Laboratories), 1 % sodium pyruvate (100 mM; Sigma-Aldrich) and 1 % MEM non-essential amino acids (100x; Sigma-Aldrich). LN229 and U87MG were maintained in Minimum Essential Medium with Earle’s salts (MEM Earle’s; Sigma-Aldrich) containing 10 % FBS, 1 % penicillin/streptomycin (Sigma-Aldrich), and 1 % sodium pyruvate. The U87MG line from ATCC is of unknown origin (Allen et al., 2016). Normal cell line controls included immortalized prostate cell line RWPE-1 (ATCC) cultured in keratinocyte serum free medium (K-SFM, Invitrogen) containing bovine pituitary extract (BPE) and human recombinant epidermal growth factor (EGF) as well as the keratinocyte cell line HaCaT (CLS) propagated in DMEM media. All cell lines were genotyped using microsatellite polymorphism analysis to validate identity and were tested regularly for mycoplasma contamination. Cells were not further used above passage 20. The irradiated sublines (IR) from established PCa and HNSCC cell lines were irradiated with multiple fractions of 4 Gy irradiation and selected for clones with intrinsic and acquired radioresistance (RR). The molecular and functional characterization of these IR- and RR-sublines has been previously published (Cojoc et al., 2015; Kurth et al., 2015; Peitzsch et al., 2016).

extract_protocol: DNA was isolated with the Qiamp DNA Mini Kit (Qiagen) according to the manufacturer's protocol.

treatment_protocol: Photon irradiation was performed using 200 kV X-rays (Yxlon Y.TU 320; 0.5 mm copper filter) at a dose rate of 1.3 Gy/min at 20 mA. Proton irradiation was performed at the Research Facility of the University Proton Therapy Dresden (UPTD), with 150 MeV protons at a horizontal fixed-beam line with a dose rate of 3 Gy/min. Beam line, setup and dosimetry have been fully described in previous papers (Beyreuther et al., 2018; Suckert et al., 2020). A dedicated beam shaping system consisting of a double-scattering device and a ridge filter provided a laterally extended 10 x 10 cm2 field with a 2 cm spread-out Bragg peak (SOBP) (Helmbrecht et al., 2016). To assure positioning of the cells within the SOBP, resulting in a dose-averaged LET value of 3.7 keV/µm, monolayer culture plates or flasks were placed vertically to the beam axis at a 90° angle, whereas 3D cultures were positioned at a 42° angle. Daily dosimetry with a Markus ionization chamber and Unidos dosimeter (PTW) readout ensured consistent irradiation conditions. The proton beam at UPTD was only available for radiobiological experiments every 3-4 months, causing an increased biological variability between independent repeats. Physical doses of either radiation type ranged from 0 to 8 Gy.

tag: time after dose in days


title: BM-WT-MIG-2


title: Control groups were treated synchronously under the same conditions except for the absence of DAC (WGBS


title: methylation_Cal33-xray-rep2


title: methylation_Cal33-sham-rep2


title: methylation_FaDu-xray-rep2

source_name: FaDu

value: FaDu


title: methylation_FaDu-proton-rep2


title: methylation_PC3-xray-rep2


title: methylation_FaDu-sham-rep2


title: methylation_U87MG-proton-rep2


title: methylation_U87MG-sham-rep2


title: C28-N3

description:
HI.4184.007.Index_21.C28-N3
processed data file: Apiary_Nurses_Logcpm.txt

value: Nurse


title: methylation_LN229-proton-rep2


title: methylation_LN229-xray-rep2


title: methylation_Cal33-proton-rep2


title: methylation_LN229-sham-rep2


title: DBA/2J withdrawal saline mouse 6

city: Richmond

first: Michael

last: Miles

state: VA

department: Pharmacology and Toxicology

institute: Virginia Commonwealth Univ.

description:
Gene expression data from DBA/2J mouse delivered saline by minipump, minipump removed 24 hours before sacrifice
D2_WithdrawalSaline_Mouse6

hyb_protocol: RNA was labelled and hybridized according to instructions provided with the Affymetrix GeneChip WT cDNA Synthesis and Amplification and GeneChip WT Terminal labelling kits.

scan_protocol: Microarrays were scanned using Affymetrix GeneChip Operating Software.

data_processing: Array CEL files were processed using the GCSScore package for R (Harris GM, Abbas S, and Miles MF, BMC Genomics 22:96, 2021) to determine approximate significance of change between each drug/time group sample and their corresponding saline controls. S-scores are scaled as with Z-score. Significance Analysis of Microarrays (SAM) was then used for statistical analysis of group wise biological significance.

label: biotin

growth_protocol: Mice were were house 4 animals/cage with free access to food and water under a 12-hour light/dark cycle in a 21 °C environment.

extract_protocol: Nucleus accumbens tissue was dissected at time of sacrifice and snap frozen in liquid nitrogen. RNA was extracted using the Qiagen mRNeasy Mini Kit. RNA quality was assessed by Biorad Experion Automated Electrophoresis System. All samples had RNA integrity (RIN) numbers > 8.

treatment_protocol: Mice were implanted subcutaneously with osmotic minipumps for 14 days that delivered either (-)-Nicotine hydrogen tartrate [(-)-1-methyl-2-(3- pyridyl) pyrrolidine (þ)-bitartrate] dissolved in sterile saline, or saline alone. Minipumps delivered nicotine at 24 mg/kg/day.  Withdrawal mice had minipumps surgically removed 24 hours before sacrifice. Chronic mice were sacrificed without minipump removal.

tag: drug

value: Saline

value: withdrawal

value: male

value: Nucleus accumbens


title: DBA/2J withdrawal saline mouse 1

description:
Gene expression data from DBA/2J mouse delivered saline by minipump, minipump removed 24 hours before sacrifice
D2_WithdrawalSaline_Mouse1

label_protocol: RNA was labelled and hybridized according to instructions provided with the Affymetrix GeneChip WT cDNA Synthesis and Amplification and GeneChip WT Terminal labelling kits.


title: methylation_PC3-proton-rep2


title: methylation_PC3-sham-rep2


title: methylation_DU145-proton-rep2


title: methylation_DU145-xray-rep2


title: methylation_DU145-sham-rep2


title: DBA/2J chronic saline mouse 5

description:
Gene expression data from DBA/2J mouse delivered saline by minipump up to time of sacrifice
D2_ChronicSaline_Mouse5

value: chronic


title: DBA/2J chronic saline mouse 3

description:
Gene expression data from DBA/2J mouse delivered saline by minipump up to time of sacrifice
D2_ChronicSaline_Mouse3


title: DBA/2J chronic nicotine mouse 5

description:
Gene expression data from DBA/2J mouse delivered nicotine by minipump up to time of sacrifice
D2_ChronicNicotine_Mouse5

value: Nicotine


title: DBA/2J chronic saline mouse 1

description:
Gene expression data from DBA/2J mouse delivered saline by minipump up to time of sacrifice
D2_ChronicSaline_Mouse1


title: DBA/2J chronic nicotine mouse 4

description:
Gene expression data from DBA/2J mouse delivered nicotine by minipump up to time of sacrifice
D2_ChronicNicotine_Mouse4


title: DBA/2J withdrawal nicotine mouse 1

description:
Gene expression data from DBA/2J mouse delivered nicotine by minipump, minipump removed 24 hours before sacrifice
D2_WithdrawalNicotine_Mouse1


title: C28-F4

description:
HI.4184.007.Index_11.C28-F4
processed data file: Apiary_Foragers_Logcpm.txt


title: DBA/2J withdrawal saline mouse 4

description:
Gene expression data from DBA/2J mouse delivered saline by minipump, minipump removed 24 hours before sacrifice
D2_WithdrawalSaline_Mouse4


title: DBA/2J withdrawal saline mouse 3

description:
Gene expression data from DBA/2J mouse delivered saline by minipump, minipump removed 24 hours before sacrifice
D2_WithdrawalSaline_Mouse3


title: DBA/2J withdrawal nicotine mouse 4

description:
Gene expression data from DBA/2J mouse delivered nicotine by minipump, minipump removed 24 hours before sacrifice
D2_WithdrawalNicotine_Mouse4


title: DBA/2J withdrawal slaine mouse 5

description:
Gene expression data from DBA/2J mouse delivered saline by minipump, minipump removed 24 hours before sacrifice
D2_WithdrawalSaline_Mouse5


title: C57BL/6J withdrawal slaine mouse 6

description:
Gene expression data from C57BL/6J mouse delivered saline by minipump, minipump removed 24 hours before sacrifice
B6_WithdrawalSaline_Mouse6


title: C57BL/6J withdrawal slaine mouse 4

description:
Gene expression data from C57BL/6J mouse delivered saline by minipump, minipump removed 24 hours before sacrifice
B6_WithdrawalSaline_Mouse4


title: DBA/2J chronic saline mouse 2

description:
Gene expression data from DBA/2J mouse delivered saline by minipump up to time of sacrifice
D2_ChronicSaline_Mouse2


title: DBA/2J chronic nicotine mouse 1

description:
Gene expression data from DBA/2J mouse delivered nicotine by minipump up to time of sacrifice
D2_ChronicNicotine_Mouse1


title: DBA/2J chronic saline mouse 4

description:
Gene expression data from DBA/2J mouse delivered saline by minipump up to time of sacrifice
D2_ChronicSaline_Mouse4


title: C57BL/6J withdrawal slaine mouse 3

description:
Gene expression data from C57BL/6J mouse delivered saline by minipump, minipump removed 24 hours before sacrifice
B6_WithdrawalSaline_Mouse3


title: DBA/2J withdrawal nicotine mouse 3

description:
Gene expression data from DBA/2J mouse delivered nicotine by minipump, minipump removed 24 hours before sacrifice
D2_WithdrawalNicotine_Mouse3


title: DBA/2J withdrawal nicotine mouse 2

description:
Gene expression data from DBA/2J mouse delivered nicotine by minipump, minipump removed 24 hours before sacrifice
D2_WithdrawalNicotine_Mouse2


title: C57BL/6J withdrawal slaine mouse 1

description:
Gene expression data from C57BL/6J mouse delivered saline by minipump, minipump removed 24 hours before sacrifice
B6_WithdrawalSaline_Mouse1


title: DBA/2J withdrawal saline mouse 2

description:
Gene expression data from DBA/2J mouse delivered saline by minipump, minipump removed 24 hours before sacrifice
D2_WithdrawalSaline_Mouse2


title: C57BL/6J withdrawal nicotine mouse 6

description:
Gene expression data from C57BL/6J mouse delivered nicotine by minipump, minipump removed 24 hours before sacrifice
B6_WithdrawalNicotine_Mouse6


title: C57BL/6J withdrawal nicotine mouse 5

description:
Gene expression data from C57BL/6J mouse delivered nicotine by minipump, minipump removed 24 hours before sacrifice
B6_WithdrawalNicotine_Mouse5


title: C57BL/6J withdrawal slaine mouse 5

description:
Gene expression data from C57BL/6J mouse delivered saline by minipump, minipump removed 24 hours before sacrifice
B6_WithdrawalSaline_Mouse5


title: DBA/2J withdrawal nicotine mouse 5

description:
Gene expression data from DBA/2J mouse delivered nicotine by minipump, minipump removed 24 hours before sacrifice
D2_WithdrawalNicotine_Mouse5


title: DBA/2J chronic saline mouse 6

description:
Gene expression data from DBA/2J mouse delivered saline by minipump up to time of sacrifice
D2_ChronicSaline_Mouse6


title: DBA/2J chronic nicotine mouse 3

description:
Gene expression data from DBA/2J mouse delivered nicotine by minipump up to time of sacrifice
D2_ChronicNicotine_Mouse3


title: C57BL/6J withdrawal nicotine mouse 3

description:
Gene expression data from C57BL/6J mouse delivered nicotine by minipump, minipump removed 24 hours before sacrifice
B6_WithdrawalNicotine_Mouse3


title: C57BL/6J withdrawal slaine mouse 2

description:
Gene expression data from C57BL/6J mouse delivered saline by minipump, minipump removed 24 hours before sacrifice
B6_WithdrawalSaline_Mouse2


title: DBA/2J chronic nicotine mouse 2

description:
Gene expression data from DBA/2J mouse delivered nicotine by minipump up to time of sacrifice
D2_ChronicNicotine_Mouse2


title: C57BL/6J chronic saline mouse 6

description:
Gene expression data from C57BL/6J mouse delivered saline by minipump up to time of sacrifice
B6_ChronicSaline_Mouse6


title: C57BL/6J chronic nicotine mouse 5

description:
Gene expression data from C57BL/6J mouse delivered nicotine by minipump up to time of sacrifice
B6_ChronicNicotine_Mouse5


title: C57BL/6J chronic saline mouse 2

description:
Gene expression data from C57BL/6J mouse delivered saline by minipump up to time of sacrifice
B6_ChronicSaline_Mouse2


title: DBA/2J chronic nicotine mouse 6

description:
Gene expression data from DBA/2J mouse delivered nicotine by minipump up to time of sacrifice
D2_ChronicNicotine_Mouse6


title: C57BL/6J withdrawal nicotine mouse 1

description:
Gene expression data from C57BL/6J mouse delivered nicotine by minipump, minipump removed 24 hours before sacrifice
B6_WithdrawalNicotine_Mouse1


title: C57BL/6J chronic saline mouse 1

description:
Gene expression data from C57BL/6J mouse delivered saline by minipump up to time of sacrifice
B6_ChronicSaline_Mouse1


title: C57BL/6J chronic saline mouse 5

description:
Gene expression data from C57BL/6J mouse delivered saline by minipump up to time of sacrifice
B6_ChronicSaline_Mouse5


title: C57BL/6J chronic saline mouse 3

description:
Gene expression data from C57BL/6J mouse delivered saline by minipump up to time of sacrifice
B6_ChronicSaline_Mouse3


title: C57BL/6J withdrawal nicotine mouse 2

description:
Gene expression data from C57BL/6J mouse delivered nicotine by minipump, minipump removed 24 hours before sacrifice
B6_WithdrawalNicotine_Mouse2


title: C57BL/6J chronic saline mouse 4

description:
Gene expression data from C57BL/6J mouse delivered saline by minipump up to time of sacrifice
B6_ChronicSaline_Mouse4


title: Zymosan 2

city: Palo Alto

first: Gregory

last: Scherrer

state: CA

address: 1050 Arastradero Rd

department: Anesthesiology

institute: Stanford University

data_processing:
Reads were mapped to reference genome rn6 via the Galaxy platform (http://usegalaxy.org) using HISAT2 version 2.0.5.1.
FPKM (fragments per kilobase of transcript sequence per million mapped fragments) values were obtained using Cufflinks version 2.2.1.
Reads were quantified using featureCounts version 1.4.6.p5
Differential analysis was conducted in R with DESeq2
Genome_build: rn6
Supplementary_files_format_and_content: tab-delimited text file including FPKM for all samples
Supplementary_files_format_and_content: excel spreadsheet with Deseq2 output for all groups

source_name: Cortical Microglia

growth_protocol: Brains were extracted from perfused male 21 day old rats and the cerebellum of each brain was discarded. Brains were mechanically dissociated to a single-cell suspension and passed through a density gradient to remove myelin and cellular debris. Myeloid cells were isolated by CD11b-immunopanning and plated in serum-free medium

extract_protocol:
After treatment cells were washed twice before lysis and RNA purification using the RNeasy Micro kit
Libraries were prepared using Smart-Seq2 and modified for sequencing using the Nextera XT DNA Sample Preparation Kit (Illumina)

treatment_protocol: After 5 days, cell were stimulated with TLR ligands LPS (1 ng/mL), PAM3CSK4 (1 ng/mL), or zymosan (100 ug/mL) or morphine (1 uM or 10 uM) by introducing the drug in a 50% medium change.

value: Cortical Microglia

value: Sprague-Dawley

tag: age

value: 21 days

value: Zymosan  (100 ug/mL)


title: Zymosan 4


title: PAM3CSK4 3

value: PAM3CSK4 (1 ng/mL)


title: Zymosan 1


title: C57BL/6J withdrawal nicotine mouse 4

description:
Gene expression data from C57BL/6J mouse delivered nicotine by minipump, minipump removed 24 hours before sacrifice
B6_WithdrawalNicotine_Mouse4

tag: time


title: RAW CM KO 3

city: MILANO

first: BIANCA

last: CIONI

state: MI

address: Via Antonio Amadeo 42

department: Research

country: Italy

institute: IRCCS Istituto Nazionale Tumori

description: RAW264.7 cells cultured in conditioned medium of JMJD6-KO PyMT-41C cells

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard Affymetrix scanning protocol on GeneChip Scanner 3000 7G

data_processing:
Gene-level signal were derived from CEL files using sst-RMA algorithm implemente in Affymetrix Expression Console software
MTA-1_0.r3.pgf
MTA-1_0.na35.mm10.transcript.csv

source_name: RAW264.7 in JMJD6-KO conditioned medium 3

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

growth_protocol: RAW264.7 cells were grown for 24 hrs in 50:50 normal RPMI supplemented with 10% FBS and conditioned medium of JMDJ6-KO, SCR PyMT-41C cells alone or in combination with CSH.

extract_protocol: Total RNA was extracted using Qiazol reagent and purified with the RNeasy kit on a QIAcube automated station (Qiagen) according to the manufacturers’ instructions

treatment_protocol: not applicable

value: macrophage


title: C57BL/6J chronic nicotine mouse 4

description:
Gene expression data from C57BL/6J mouse delivered nicotine by minipump up to time of sacrifice
B6_ChronicNicotine_Mouse4


title: RAW CM SCR+CSH 1

description: RAW264.7 cells cultured in conditioned medium of SCR PyMT-41C cells with addition of the ANXA-1 receptor blockade, CSH

source_name: RAW264.7 in SCR+CSH conditioned medium 1


title: PAM3CSK4 1


title: LPS 3

value: LPS (1 ng/mL)


title: LPS 4


title: C57BL/6J chronic nicotine mouse 1

description:
Gene expression data from C57BL/6J mouse delivered nicotine by minipump up to time of sacrifice
B6_ChronicNicotine_Mouse1


title: C57BL/6J chronic nicotine mouse 3

description:
Gene expression data from C57BL/6J mouse delivered nicotine by minipump up to time of sacrifice
B6_ChronicNicotine_Mouse3


title: RAW CM SCR+CSH 4

source_name: RAW264.7 in SCR+CSH conditioned medium 4


title: C57BL/6J chronic nicotine mouse 2

description:
Gene expression data from C57BL/6J mouse delivered nicotine by minipump up to time of sacrifice
B6_ChronicNicotine_Mouse2


title: RAW CM SCR 1

description: RAW264.7 cells cultured in conditioned medium of SCR PyMT-41C cells

source_name: RAW264.7  in SCR conditioned medium 1


title: RAW NM 3

description: RAW264.7 cells cultured in normal medium

source_name: RAW264.7  in normal medium 3


title: PAM3CSK4 4


title: RAW NM 2

source_name: RAW264.7  in normal medium 2


title: PAM3CSK4 2


title: LPS 1


title: RAW NM 4

source_name: RAW264.7  in normal medium 4


title: RAW CM SCR+CSH 2

source_name: RAW264.7 in SCR+CSH conditioned medium 2


title: RAW CM KO 1

source_name: RAW264.7 in JMJD6-KO conditioned medium 1


title: Morphine 4

value: Morphine (1uM)


title: RAW CM KO 2

source_name: RAW264.7 in JMJD6-KO conditioned medium 2


title: LPS 2


title: PBS 4

value: PBS


title: Morphine 2


title: Morphine 1


title: PBS 3


title: Morphine 3


title: PBS 2


title: PBS 1


title: NRG1 2 -  2h

city: Cambridge

first: Julie

last: Takagi

address: 70 Massachusetts Ave, 56-230

institute: MIT

data_processing:
Reads were mapped to the C. albicans SC5314 haplotype A genome, version A22-s05-m05-r03, retrieved from the Candida Genome Database (www.candidagenome.org) using RNA STAR (Galaxy Version 2.7.8a+galaxy0).
Read summarization was performed on the gene level using featureCounts (Galaxy Version 2.0.1+galaxy2) with annotations from a modified version of C. albicans SC5314 haplotype A
Multimapping read pairs, read pairs mapping across more than one gene, and read pairs in which ends mapped to different chromosomes were removed from downstream analyses.
Differential expression analysis was performed using DESEQ2 (Galaxy Version 2.11.40.7+galaxy1). Genes were considered differentially expressed when P <0.05 after the false-discovery rate was controlled.
Genome_build: Candida albicans SC5314
Supplementary_files_format_and_content: abundance measurements

source_name: Planktonic fungal cultures

growth_protocol: Batch cultivation of Candida albicans was carried out shaking at 37 °C in RPMI media. Overnight cultures of WT or an NRG1 mutant strain were diluted 1:100 in RPMI medium with or without (0.1%) MUC5AC-glycans and grown for 2 or 8 h at 37 °C in a round bottom 96-well microtiter plate.

extract_protocol:
Total RNA was extracted using the MasterPure RNA Purification kit (Lucigen) and residual DNA was removed using the Turbo DNA-free kit (Ambion). The integrity of the total RNA was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies). rRNA were removed using the Ribo-Zero Magnetic Kit (Epicentre).
Gene expression analysis was conducted via Illumina RNA sequencing (RNA-seq). Libraries were produced using the KAPA RNA HyperPrep kit (Kapa Biosystems). Libraries were sequenced using the Illumina HiSeq platform with a single-end protocol and read lengths of 40 nt or 52 nt.

value: media

value: 2 hours

tag: culture type

value: planktonic


title: WT SG 1 - 2h

value: media + 0.1% MUC5AC glycans


title: WT SG 2 - 2h


title: WT 2 - 2h


title: WT SG 3 -8h

value: 8 hours


title: WT SG 2 -8h


title: WT 1 - 2h


title: WT SG 1 - 8h


title: Zymosan 3

value: male


title: NRG1 SG 1 - 2h


title: NRG1 SG 2 - 2h


title: NRG1 1 - 2h


title: WT 2 - 8h


title: WT 1 - 8h


title: KO_IFN_CD40L_24 [58]

city: Ridgefield

first: Li

last: Li

state: Connecticut

address: PO Box 368

institute: Boehringer Ingelheim Pharmaceuticals, Inc.

data_processing:
Illumina HiSeq2000 sequencer to generate 101x2 pair-end reads
Sequenced reads were examined by fastqc, then mapped to mouse reference genome  Mouse GRCm39/mm39 using STAR, followed by Rsubread to generate raw counts, followed by data normalization by EdgeR. Differentially expressed genes (DEGs) and biological pathway were determined by LIMMA-Voom.
Genome_build: mm39
Supplementary_files_format_and_content: Normalized_data.csv

growth_protocol: Monocytes from NFAM1+/+ and NFAM1-/- mice  were resuspended in cell culture media comprised of RPMI, 10% fetal bovine serum and 1% Penicillin/streptomycin. Monocytes were cultured in a 96 well tissue culture plate  at a concentration of 20,000 cells per well and either left untreated or pretreated for one hour with 100 ug/mL of mouse IFN-γ and subsequently stimulated with MegaCD40L for 6 and 24 hours.

extract_protocol:
RNA was isolated using an RNeasy Plus Mini kit .
Library construction and sequencing were performed at Beijing Genomics Institute as follows. RNA was then fragmented and cDNA was synthesized using the Illumina Truseq polyA mRNA library preparation protocol (non-stranded). RNA-sequencing was performed on an Illumina HiSeq2000 sequencer to generate 101x2 pair-end reads.

treatment_protocol: To better understand the impact of NFAM1 deletion of monocyte activation, monocytes isolated from human PBMCs were nucleofected with CRISPR ribonucleoprotein (RNP) complexes using an Amaxa 4D nucleofection system according to manufacturer’s instructions (Lonza). Knockout efficiency was assessed by western blot detection of NFAM1 protein or sanger sequencing of PCR amplified target genomic loci. We performed whole transcriptome analysis on monocytes that were cultured in the presence or absence of IFN-γ plus CD40L for 6 and 24 hours. NFAM1+/+ and NFAM1-/- monocytes were left unstimulated, or stimulated with IFN-γ plus 1 ug/mL MegaCD40L. 6 or 24 hours later, supernatant was removed, cells were resuspended in RNAlater, and RNA was isolated using an RNeasy Plus Mini kit. Library construction and sequencing were performed at Beijing Genomics Institute as follows. RNA was then fragmented and cDNA was synthesized using the Illumina Truseq polyA mRNA library preparation protocol (non-stranded). RNA-sequencing was performed on an Illumina HiSeq2000 sequencer to generate 101x2 pair-end reads.

tag: agent

value: IFN-γ plus 1 ug/mL MegaCD40L

value: PBL Monocyte

value: wild type


title: WT_IFN_CD40L_24 [56]


title: KO_IFN_CD40L_24 [55]


title: WT_NoStm_6 [1]


title: KO_NoStim_24 [46]


title: KO_IFN_CD40L_6 [12]


title: KO_NoStm_6 [4]


title: WT_IFN_CD40L_6 [10]


title: KO_IFN_CD40L_6 [11]


title: KO_NoStim_24 [43]


title: WT_NoStm_6 [2]


title: WT_NoStim_24 [44]


title: WT_IFN_CD40L_6 [26]


title: KO_NoStm_6 [3]


title: WT 3 - 8h