title: 4C_HEC-1-B_a12_REV-FWD_rep2

value: RF insertion


title: P-WT-Rep2

status: Public on Mar 11 2020

type: SRA

city: Hangzhou

first: Li

last: Shen

state: Zhejiang Province

address: 866 Yuhangtang Road

country: China

institute: Life Sciences Institute, Zhejiang University

library_source: transcriptomic

data_processing:
RNA‐seq was performed with biological replicates for all samples. Raw reads were trimmed to 50 bp and mapped to the mouse genome (mm9) with TopHat (v2.1.1) with default parameters. Uniquely mapped reads were subsequently assembled into transcripts guided by reference annotation (University of California at Santa Cruz [UCSC] gene models) with Cufflinks (v2.2.1). The expression level of each gene was quantified as fragments per kilobase of transcript per million mapped reads (FPKM) and FPKM values of replicates were averaged. Only expressed genes (FPKM > 1 in at least one sample) were considered in all analyses.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values of all RNA-seq samples

molecule: total RNA

organism: Mus musculus

source_name: Pachytene spermatocytes

growth_protocol: All mice have a C57BL/6J genetic background, and were maintained under specific pathogen-free conditions in a controlled environment of 20–22 oC, with a 12/12 h light/dark cycle, 50–70% humidity, and food and water provided ad libitum

extract_protocol:
Spermatocytes at different stages were collected from indicated genotypes (500 cells per sample) using FACS sorting. Each sample was directly lysed with 4 μl lysis buffer (0.2% Triton X-100, RNase inhibitor, dNTPs, oligo-dT primers) and immediately used for cDNA synthesis using the Smart-seq2 method
Sequencing libraries were constructed from 500 pg of amplified cDNA using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD503) according to manufacturer's instructions

treatment_protocol: Testes were prepared from adult male mice

tag: cell type

value: Pachytene spermatocytes

tag: background strain

tag: genotype

value: WT


title: Mp1

city: Wuhan

first: Bang

address: No. 1 SHizishan St

institute: Huazhong Agricultural University

description: Mp _abundance measurements.txt

data_processing:
Illumina Casava 1.8 software was used for basecalling
sequenced reads were trimmed  for adaptor sequence, reads containing ploy-N and low quality reads. Then clean reads were mapped to Sus scrofa or Toxoplasma  reference genome by  using TopHat v2.0.12.
Genome_build: Sus scrofa reference genone for  alignment: ftp://ftp.ensembl.org/pub/current_fasta/sus_scrofa/dna/ ;  Me49 reference genome for alignment: ftp://ftp.ensemblgenomes.org/pub/release-23/protists//fasta/toxoplasma gondii/dna/
Supplementary_files_format_and_content: tab-delimited text files include reads counts values for each sample

organism: Sus scrofa

source_name: porcine alveolar macrophages

growth_protocol: the cells (porcine alveolar macrophages and HFF cells)  and Me49 tachyzoites were cultured in DMEM with 10% or 2% FBS, 2 mM L-glutamine, 100 U/ml penicillin and 100 μg/ml streptomycin, respectively. Both maintained in incubator with 5% CO₂ and kept 37℃.

extract_protocol:
At indicated time, the samples were collected and  total RNA was harvested using Trizol reagent.   NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA)  was used with 3 µg total RNA per sample for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: the purified Me49 tachyzoites from HFFs were counted and used to infect porcine alveolar macrophages (MOI=5) for 1 h, the extracellualr parasites were washed away with PBS. The infected porcine alveolar macrophages were cultured for further 15 h. the porcine alveolar macrophages and Me49 controls were maintained under same conditions.

value: porcine alveolar macrophages

tag: cell line

tag: parasite strain

tag: culture time

value: at 70-80 percent confluency in T25 tissue culture flask, about 36 h


title: 4C_HEC-1-B_a12_REV-FWD_rep1

city: Shanghai

first: Xiao

last: Ge

address: No. 800 Dongchuan Road

institute: Shanghai JiaoTong University

library_source: genomic

data_processing:
Library strategy: 4C-seq
Sequenced reads were trimmed for adaptor sequence and the bait sequence, then aligned to the reference human genome (GRCh37/hg19) using the Bowtie program (version 1). The reads per million (RPM) value was calculated using the r3Cseq program (version 1.20) in the R package (version 3.3.3).
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph files: the reads per million (RPM) value in 4C-seq experiments.

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: Human endometrial HEC-1-B cells (ATCC) were cultured in MEM medium (Hyclone), supplemented with 10% (v/v) FBS (Gibco), 2 mM glutamine (Gibco), 1 mM sodium pyruvate (Sigma), and 1× penicillin-streptomycin (Gibco). Human K562 cells (ATCC) were cultured in DMEM medium (Hyclone) supplemented with 10% (v/v) FBS and 1× penicillin-streptomycin. Cells were maintained at 37 °C in a humidified incubator containing 5% (v/v) of CO2, and were passaged every three days.

extract_protocol:
After cross-linking with 2% formaldehyde, cells were lysed twice with cold lysis buffer, digested with DpnII, ligated with T4 DNA ligase.
4C libraries were generated by PCR.

value: human endometrial adenocarcinoma

tag: genotype/variation

tag: restriction enzyme

value: DpnII


title: H3K27ac_ChIPSeq_BPA 23_D70

city: Houston

first: Cheryl

middle: L

last: Walker

state: TX

address: 1 Baylor Plaza

department: Center for Precision Environmental Health

country: USA

institute: Baylor College of Medicine

data_processing:
The data quality was assessed using FastQC and low quality basepairs were removed using TrimGalore.
ChIP-Seq reads were mapped to the rat genome build UCSC rn6 using bowtie2 and duplicate reads were removed.
ChIP-Seq tracks were prepared using bedtools, normalized to reads per million reads mapped (rpm).
Differential regions were determined using the diffReps software using the G-test with significance achieved for a fold change > 2 and an FDR-adjusted q-value < 0.01.
Genome_build: rn6
Supplementary_files_format_and_content: ChIP-Seq tracks represented normalized to reads per million mapped in WIG and TDF format

organism: Rattus norvegicus

source_name: Rat liver

extract_protocol:
Frozen liver tissue was pulverized, followed by cross-linking of proteins to DNA with 37% formaldehyde, and then incubation with 10X glycine to stop the reaction. Cross-linked tissue was homogenized, and centrifuged at 1,500 rpm for 5 min at 4°C. The cell pellet was resuspended with cell lysis buffer (PBS with 0.5 mM EDTA and 0.05% Triton X-100), incubated on ice for 15 min, followed by centrifiugation at 5,000 rpm for 5 min at 4°C. The cell pellet was then resuspended with nuclear lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl at pH 8.1) and incubated on ice for 10 min. Chromatin was sonicated with a bioruptor (Diagenode, Denville, NJ) to obtain fragment sizes of 100-300 bp for ChIP-seq. ChIP was performed by incubating sheared chromatin with Magna ChIPTM Protein A+G magnetic beads, and antibodies against H3K4me3, H3K4me1, H3K27ac or H3K27me3 overnight at 4°.The next day, the beads were washed with low salt wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8, and 150 mM NaCl) high salt wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8, and 500 mM NaCl), lithium chloride wash buffer (0.25 M LiCl, 1% IGEPAL CA630, 1% sodium deoxycholate, 1 mM EDTA, and 10 mM Tris-HCl pH 8), and TE buffer (20 mM Tris-HCl pH 8 and 1 mM EDTA) for 5 minutes each at 4°. Immunoprecipitated DNA was recovered from the beads by incubation with ChIP elution buffer (1% SDS, 1 mM EDTA, 50 mM NaHCO3, and 50 mM Tris-HCl pH 8) and proteinase K for 2 hours at 62° with shaking, followed by incubation at 95° for 10 minutes. DNA was purified using the QIAquick PCR Purification kit (Qiagen) and DNA concetration was measured using a NanoDrop spectrophotometer (Thermo Scientific).
Sequencing librairies were prepared using Bioo Kit Option 2 protocol using 1.7-10 ng of DNA per sample.

treatment_protocol: Neonatal rats were treated with vehicle (VEH; sesame oil) or bisphenol A (BPA; 50 µg/kg dissolved in sesame oil) orally via pipette tip on post-natal days 1, 3, and 5. Littermates of the same sex were randomly assigned to the treatment groups. BPA was obtained from the National Instutite of Environmental Health Sciences (NIEHS). The dose and route of administration recapitulates human exposure to BPA. Rats were fasted overnight prior to tissue collection.Liver tissue was harvested on post-natal day 5 at 6 hours after treatment (PND5), and on day 70 (D70). Tissue was snap-frozen in liquid nitrogen for downstream epigenomic analyses.

tag: chip antibody

value: H3K27ac (Abcam, ab4729)

tag: strain

value: Sprague Dawley

tag: treatment

value: 50 microg/kg Bisphenol A (BPA)


title: P-WT-Rep1


title: H4K16ac 2h recovery rep2

city: West Haven

first: Matthew

middle: D

last: Simon

state: CT

address: 600 West Campus Dr. MIC312

department: Molecular Biophysics & Biochemistry

institute: Yale University Chemical Biology Instiute

data_processing:
Adaptor sequences were removed using Cutadapt -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT -m 3
Reads were aligned to reference genome using bowtie2
Aligned reads were filtered for MAPQ > 2 woth samtools
Sample enrichment over input was calcualted using MACS2
Enrichment bedgraph files were converted to bigWig format
Genome_build: dm6
Supplementary_files_format_and_content: bigWig files contain track of sample enrichemnt over input

organism: Drosophila melanogaster

source_name: S2 cell line

growth_protocol: S2 cells were grown in Schneider media supplemented with 1% penicillin/straptomycin and 10% heat-inactivated FBS at 27˚C until density of 4 million cells/ml.

extract_protocol:
Cells were washed with PBS and crosslinked with 1% formaldehyde for 5 min. Formaldehyde was quenched with glycine and incubated for 5 min. Cells were lysed and centrifuged to isolate nuclei. Nuclei were lysed and sheared with Covaris S220 to ~300 bp fragment sizes. SDS was quenched with Triton X-100 and extract was cleared by centrifugation. For IP, 2 µg of anti-H4K16ac Ab (Millipore, 07-329) was added per 1 ml of extract and incubated over night Complexes were captured on Protein G DynaBeads and washed with Low salt, High salt, LiCl and TE buffer. Complexes were eluted with proteinase K treatment followed by over night decrosslinking at 65˚C. DNA was isolated using PCR purification kit (Quiagen).
Libraries were constructed according to Bowman et al. (2012, BMC Genomics)

treatment_protocol: Control: Cells were incubated at 27˚C; Heat shock: Cells were incubated 1 h at 37˚C;  2h recovery: Cells were incubated 1 h at 37˚C. Then cold medium was added to decrease the temperature to 27˚C and cells were incubated for 2 h at 27˚C.

tag: heat shock

value: yes

tag: recovery

tag: antibody


title: 4C_HEC-1-B_a12_REV-FWD_mut_rep1

value: RF mutation


title: H4K16ac Heat shock rep2

value: no


title: 4C_HEC-1-B_a12_REV-FWD_mut_rep2


title: 4C_HEC-1-B_a12_FWD_rep2

value: F insertion


title: H3K4me3_ChIPSeq_BPA 14_D70

value: H3K4me3 (Active Motif, 39915)


title: H3K27me3_ChIPSeq_BPA 14_D70

value: H3K27me3 (Active Motif, 39155)


title: H3K4me1_ChIPSeq_BPA 14_D70

value: H3K4me1 (Abcam, ab8895)


title: H4K16ac Heat shock rep1


title: 4C_HEC-1-B_a12_FWD_rep1


title: H3K27ac_ChIPSeq_BPA 14_D70


title: 4C_HEC-1-B_a12_FWD_mut_rep1

value: F mutation


title: H4K16ac Control rep2


title: H4K16ac Control rep1


title: Input S2 cell line


title: H3K27me3_ChIPSeq_BPA 3_PND5


title: H3K27me3_ChIPSeq_BPA 2_PND5


title: Tg_Mp3

description: for infection samples, the reads were aligned to either Sus scrofa or Me49 reference genome, and the abundance measurements were recorded in Mp _abundance measurements.txt  or Tg _abundance measurements.txt

organism:
Toxoplasma gondii
Sus scrofa

source_name: porcine alveolar macrophages/Me49

value: Me49-Infected porcine alveolar cells

value: Cultured in T25 tissue culture flask for 15 h post Me49 infection


title: 4C_HEC-1-B_a12_2REV-2FWD_rep1

value: RRFF insertion


title: H3K27me3_ChIPSeq_VEH 4_PND5

value: Sesame oil (VEH)


title: Tg_Mp2


title: 4C_HEC-1-B_a12_2REV-2FWD_mut_rep2

value: human endometrial adenocarcinoma

value: RRFF mutation


title: H4K16ac 2h recovery rep1


title: H3K27me3_ChIPSeq_VEH 3_PND5


title: 4C_HEC-1-B_a12_2REV-2FWD_mut_rep1

value: DpnII


title: hnf4 RNAi replicate 3

city: Dallas

first: George

last: Wendt

address: 6001 Forest Park Road, ND7.300

department: Pharmacology

institute: University of Texas Southwestern Medical Center

data_processing:
Illumina Casava1.9 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the Schistosoma mansoni genome (v7) using STAR (version 020201).
Pairwise comparisons of differential gene expression were performed with DESeq2 (version 1.12.2).
Genome_build: Schistosoma mansoni v7
Supplementary_files_format_and_content: comma separated values file containing analysis of data generated from three replicates of control RNAi samples and 3 replicates of hnf4 RNAi samples. Statistical significance determined by the Wald test in DESeq2 (version 1.12.2)

molecule: polyA RNA

organism: Schistosoma mansoni

source_name: adult male parasites

extract_protocol:
Parasites were flash frozen on dry ice, and RNA was harvested using Trizol reagent. IlluminaTruSeq Stranded mRNA Library Prep (Cat# 20020594)  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: hnf4 RNAi

value: Puerto Rico

tag: tissue

value: whole parasite

tag: age

value: 6 weeks + 17 days culture

tag: gender

value: male


title: H3K27ac_ChIPSeq_BPA 4_PND5

value: H3K27ac (Abcam, ab4729)

value: Sprague Dawley

value: 50 microg/kg Bisphenol A (BPA)


title: hnf4 RNAi replicate 2


title: 4C_HEC-1-B_a12_2FWD_rep2

tag: cell type

value: FF insertion


title: H3K27me3_ChIPSeq_BPA 4_PND5

value: H3K27me3 (Active Motif, 39155)


title: 4C_HEC-1-B_a12_FWD_mut_rep2

value: F mutation


title: hnf4 RNAi replicate 1


title: control RNAi replicate 3

value: control RNAi


title: H3K27ac_ChIPSeq_BPA 3_PND5


title: H3K27ac_ChIPSeq_VEH 3_PND5


title: 4C_HEC-1-B_a12_2FWD_mut_rep1

value: FF mutation


title: 4C_HEC-1-B_a12_2FWD-2REV_rep4

value: FFRR insertion


title: H3K27ac_ChIPSeq_VEH 4_PND5

value: Sesame oil (VEH)


title: 4C_HEC-1-B_a12_2REV-2FWD_rep2

value: human endometrial adenocarcinoma

value: RRFF insertion


title: control RNAi replicate 1


title: 4C_HEC-1-B_a12_2FWD_mut_rep2

value: DpnII


title: H3K27ac_ChIPSeq_VEH 2_PND5


title: 4C_HEC-1-B_a12_2FWD-2REV_rep2


title: H3K4me1_ChIPSeq_BPA 4_PND5

value: H3K4me1 (Abcam, ab8895)


title: tao RNAi d6 replicate 3

first: James

middle: Joseph

last: Collins

state: Texas

address: 6001 Forest Park Rd

value: Puerto Rico

value: whole adult male parasite

value: 6 weeks + 6 days culture


title: 4C_HEC-1-B_a12_2FWD_rep1


title: H3K27ac_ChIPSeq_BPA 2_PND5

value: H3K27ac (Abcam, ab4729)


title: Tg_Mp1

value: Me49-Infected porcine alveolar cells

value: Cultured in T25 tissue culture flask for 15 h post Me49 infection


title: 4C_HEC-1-B_a12_2FWD-2REV_rep3


title: H3K27me3_ChIPSeq_VEH 2_PND5

value: Sprague Dawley


title: tao RNAi d6 replicate 2


title: tao RNAi d6 replicate 1


title: 4C_HEC-1-B_a12_2FWD-2REV_mut_rep4

value: FFRR mutation


title: control RNAi replicate 2

value: whole parasite

value: 6 weeks + 17 days culture

value: male


title: H3K4me1_ChIPSeq_BPA 2_PND5

value: 50 microg/kg Bisphenol A (BPA)


title: 4C_HEC-1-B_a12_2FWD-2REV_rep1

value: FFRR insertion


title: mock RNAi d6 replicate 2


title: H3K4me3_ChIPSeq_BPA 3_PND5

value: H3K4me3 (Active Motif, 39915)


title: 4C_HEC-1-B_a12_2FWD-2REV_mut_rep1

value: human endometrial adenocarcinoma


title: stk RNAi d9 replicate 3

value: 6 weeks + 9 days culture


title: AS-DC_vitro_2

city: London

first: Kristine

last: Vaivode

address: CIBCI, First Floor, New Hunt's House, Great Maze Pond

department: Centre for Inflammation Biology and Cancer Immunology

country: United Kingdom

institute: King's College London

data_processing:
Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mis-match was allowed for index sequence identification.
After investigating the quality of the raw data, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the the human reference genome using STAR aligner (v2.5.3a).
Raw read counts matrix made also with STAR (using the parameter --quantMode GeneCounts).
The read counts matrix was imported in Rstudio Version 1.2.5033 with  R version 3.6.1.
Dataset was processed using DESeq2 R package (version 1.24.0) functions.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text file (.txt) with raw data values for each sample

source_name: In vivo cord blood HSPC derived mononuclear phagocytes

growth_protocol:
For in vitro experiments, CD34+ hematopoietic progenitors isolated from human cord blood were differentiated in vitro by culturing them with engineered mesenchymal stromal cells expressing human transmembrane FLT3L, SCF and soluble CXCL12 (MS5_FS12) for 14 days.
For in vivo experiments, CD34+ hematopoietic progenitors isolated from human cord blood were differentiated in vivo in subcutaneous Matrigel organoids containing engineered mesenchymal stromal cells expressing human transmembrane FLT3L, SCF and soluble CXCL12 (MS5_FS12) in NSG mice for 12 days.

extract_protocol:
In vitro and in vivo differentiated cells were FACS sorted in in 1.5ml Eppendorf tubes (100-1000 cells/tube) containing Trizol
RNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked with Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA). RNA library preparations, sequencing reactions, and initial bioinformatics analysis were conducted at GENEWIZ, LLC. (South Plainfield, NJ, USA). The SMART-Seq v4 Ultra Low Input Kit for Sequencing was used for full-length cDNA synthesis and amplification (Clontech, Mountain View, CA) as per manufacturer’s protocol. Illumina Nextera XT library was used for library preparation. Briefly, cDNA was fragmented, and adaptor was added using Transposase, followed by limited-cycle PCR to enrich and add index to the cDNA fragments. Final libraries were analyzed on the Agilent TapeStation for library sizing and quantified using the Qubit dsDNA HS Assay Kit and by qPCR using the KAPA Library Quantification Kit. The sequencing libraries were multiplexed and clustered on four lanes of a flowcell. After clustering, the flowcell was loaded on the Illumina HiSeq instrument according to manufacturer’s instructions. The samples were sequenced using a 2x150 Paired End (PE) configuration.

value: In vitro differentiated cells

tag: donor

value: CD45RA+CD123+Siglec6+Axl+ cells

tag: culture conditions

value: Co-cultured with MS5_FS12


title: stk RNAi d9 replicate 2

value: Puerto Rico

value: whole adult male parasite


title: 4C_HEC-1-B_a12_2FWD-2REV_mut_rep3

tag: cell line

value: DpnII


title: H3K4me3_ChIPSeq_BPA 2_PND5


title: H3K4me3_ChIPSeq_BPA 4_PND5


title: mock RNAi d6 replicate 1

value: 6 weeks + 6 days culture


title: mock RNAi d9 replicate 3


title: H3K4me1_ChIPSeq_VEH 3_PND5

value: H3K4me1 (Abcam, ab8895)

value: Sprague Dawley

value: Sesame oil (VEH)


title: H3K4me3_ChIPSeq_VEH 3_PND5


title: H3K4me1_ChIPSeq_VEH 4_PND5


title: H3K4me1_ChIPSeq_VEH 2_PND5


title: AS-DC_vitro_3


title: pDC_vitro_3

value: CD45RA+CD123+Siglec6-Axl- cells


title: 4C_HEC-1-B_a12_2FWD-2REV_mut_rep2

value: FFRR mutation


title: H3K4me3_ChIPSeq_VEH 2_PND5


title: pDC_vitro_2


title: stk RNAi d9 replicate 1


title: mock RNAi d9 replicate 2


title: AS-DC_vitro_1


title: Mid Stage Developing Seed Whole Seed_5

city: Denton

first: Drew

last: Sturtevant

state: TEXAS

address: 155 Union Circle #305220

department: BioDiscovery Institute

institute: University of North Texas

description:
processed data file: Seed_tissues_countdata.txt
processed data file: Seed_tissues_normalized_countstable.csv
MD_WS5

data_processing:
Reads were trimmed using Trimmomatic to remove remaining adaptor sequences, the remaining settings were default
Trimmed reads were mapped to the reference using STAR and the default settings
Expression analysis was completed using DESeq2
Genome_build: GWHAASQ00000000, http://bigd.big.ac.cn/gwh
Supplementary_files_format_and_content: "countdata.txt" files are output from salmon; "normalized_countstable.csv" are output normalized counts from DESeq2

organism: Simmondsia chinensis

source_name: Jojoba Mid Stage Developing Seed Whole Seed

extract_protocol:
RNA was extracted using a hot-borate extraction method
TrueSeq Stranded mRNA kKit

tag: germplasm resources information network number (grin)

value: PARL# 940

value: Mid Stage Developing Seed Whole Seed


title: mock RNAi d9 replicate 1


title: mock RNAi d6 replicate 3


title: pDC_vitro_1


title: H3K4me3_ChIPSeq_VEH 4_PND5

value: H3K4me3 (Active Motif, 39915)


title: DC2_vitro_3

value: CD1c+ cells


title: Mid Stage Developing Seed Whole Seed_2

description:
processed data file: Seed_tissues_countdata.txt
processed data file: Seed_tissues_normalized_countstable.csv
MD_WS2


title: Mid Stage Developing Seed Whole Seed_1

description:
processed data file: Seed_tissues_countdata.txt
processed data file: Seed_tissues_normalized_countstable.csv
MD_WS1


title: DC2_vitro_2


title: Mid Stage Developing Seed Whole Seed_4

description:
processed data file: Seed_tissues_countdata.txt
processed data file: Seed_tissues_normalized_countstable.csv
MD_WS4


title: AS-DC_vivo_1

value: In vivo differentiated cells

value: Co-cultured in matrigel with MS5_FS12


title: DC2_vivo_3


title: LKB1 KO biological rep 5

type: RNA

city: Rehovot

first: Avraham

last: Yaron

address: Herzl st. 234

country: Israel

institute: Weizmann Institute of Science

description: Gene expression data

hyb_protocol: 5.5ug ss cDNA in 130 ul were hybridized to a Mouse Gene 1.0 ST array using Affymetrix hybridization kit materials and hybridized for 17 hours at 45° at 60rpm. Post-hyb washes were done with Affymetrix wash solutions on the FS450 station using FS450_0002 protocol.

scan_protocol: Arrays were scanned on the Affymetrix GeneChip Scanner 3000 7G

data_processing: The data were analyzed with Partek Genomics Suite, ver. 6.6, using RMA background correction and quantile normalization.

label: biotin

source_name: E13.5 embryo

label_protocol: 250ng Total RNA were used. cDNA samples were generated and labeled using Ambion WT Expression kit

extract_protocol: RNA was isolated using Trizol

value: E13.5 DRG

tag: genotype/variaton

value: LKB1 KO


title: DC2_vitro_1

value: In vitro differentiated cells

value: Co-cultured with MS5_FS12


title: AS-DC_vivo_2

value: CD45RA+CD123+Siglec6+Axl+ cells


title: Mid Stage Developing Seed Whole Seed_3

description:
processed data file: Seed_tissues_countdata.txt
processed data file: Seed_tissues_normalized_countstable.csv
MD_WS3


title: wild-type biological rep 5

description: Gene expression data

value: wild type


title: Mid Stage Developing Seed Seed Coat_5

description:
processed data file: Seed_tissues_countdata.txt
processed data file: Seed_tissues_normalized_countstable.csv
MD_SC5

source_name: Jojoba Mid Stage Developing Seed Seed Coat

value: Mid Stage Developing Seed Seed Coat


title: pDC_vivo_2


title: Mid Stage Developing Seed Seed Coat_4

description:
processed data file: Seed_tissues_countdata.txt
processed data file: Seed_tissues_normalized_countstable.csv
MD_SC4


title: Mid Stage Developing Seed Seed Coat_2

description:
processed data file: Seed_tissues_countdata.txt
processed data file: Seed_tissues_normalized_countstable.csv
MD_SC2


title: pDC_vivo_1


title: wild-type biological rep 3

description: Gene expression data


title: Mid Stage Developing Seed Seed Coat_1

description:
processed data file: Seed_tissues_countdata.txt
processed data file: Seed_tissues_normalized_countstable.csv
MD_SC1


title: LKB1 KO biological rep 4

description: Gene expression data


title: DC2_vivo_2


title: LKB1 KO biological rep 3

description: Gene expression data


title: wild-type biological rep 2

description: Gene expression data


title: Mid Stage Developing Seed Seed Coat_3

description:
processed data file: Seed_tissues_countdata.txt
processed data file: Seed_tissues_normalized_countstable.csv
MD_SC3


title: DC2_vivo_1


title: Mid Stage Developing Seed Embryonic Axis_5

description:
processed data file: Seed_tissues_countdata.txt
processed data file: Seed_tissues_normalized_countstable.csv
MD_EA5

source_name: Jojoba Mid Stage Developing Seed Embryonic Axis


title: wild-type biological rep 1

description: Gene expression data


title: LKB1 KO biological rep 1

description: Gene expression data


title: Mid Stage Developing Seed Embryonic Axis_4

description:
processed data file: Seed_tissues_countdata.txt
processed data file: Seed_tissues_normalized_countstable.csv
MD_EA4


title: F_DC2_CD206_d3

data_processing:
Base-calling was performed on Illumina bcl2fastq v2.19.1.403
The raw sequencing data was initially processed using open source, web-based platform Galaxy (version 18.05.rc1).
Reads were filtered for quality with more than 80% of the sequence having quality score > 33 using FastQC tool.
Mapping against reference genome was performed with Hisat2 v2.1.0 to the hg38 human genome.
Adapter sequences were detected automatically with TrimGalore!. Reads under 20bp were discarded.
All processed sequencing files were imported in Partek® Flow® software (Partek Inc., build 7.0.18.0514) and the gene count data was normalised using FPKM.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file with FPKM values for each sample

source_name: Cord blood HSPC derived  mononuclear phagocytes

growth_protocol: CD34+ hematopoietic progenitors isolated from human cord blood were differentiated in vitro by culturing them with engineered mesenchymal stromal cells expressing human transmembrane FLT3L, SCF and soluble CXCL12 (MS5_FS12) for 14 days.

extract_protocol:
in vitro differentiated cells and human PBMCs isolated from healthy donors were FACS sorted in 96-well plates (100 cells/well) containing lysis buffer (RLT).
RNA-seq libraries were prepared using Labcyte Echo 525 contactless liquid handling system (Labcyte Inc). In brief, ERCC mix (Thermo Fisher) was added to each sample and first strand full length cDNA was generated with a modified protocol of the SMARTseq v4 Ultra Low Input RNA Kit (Takara Clontech) using poly dT primers and a template switching oligo. Full length cDNA was amplified using SeqAmp™ DNA Polymerase (Takara Clontech). 12 ng of amplified cDNA from each sample was used to generate non-stranded RNA libraries using a modified protocol of the Ovation Ultralow System V2 1-96 kit (NuGEN). In brief, amplified cDNA was fragmented through sonication on Covaris E220 (Covaris Inc), repaired and polished followed by ligation of indexed adapters. Adapter ligated cDNA were pooled before final amplification to add flow cell primers. Libraries were sequenced on HiSeq2500 (Illumina Cambridge) for 100 cycles PE in Rapid mode.

tag: donor status

value: healthy donor

value: CD1c+ CD206+ cells

tag: culture condition


title: wild-type biological rep 4

description: Gene expression data


title: Mid Stage Developing Seed Embryonic Axis_3

description:
processed data file: Seed_tissues_countdata.txt
processed data file: Seed_tissues_normalized_countstable.csv
MD_EA3


title: F_DC2_CD206_d2


title: F_DC2_CD206_d1


title: Mid Stage Developing Seed Embryonic Axis_2

description:
processed data file: Seed_tissues_countdata.txt
processed data file: Seed_tissues_normalized_countstable.csv
MD_EA2


title: F_DC2_d3

value: CD1c+ CD206- cells


title: Mid Stage Developing Seed Embryonic Axis_1

description:
processed data file: Seed_tissues_countdata.txt
processed data file: Seed_tissues_normalized_countstable.csv
MD_EA1


title: F_DC2_d2


title: Mid Stage Developing Seed Cotyledons_5

description:
processed data file: Seed_tissues_countdata.txt
processed data file: Seed_tissues_normalized_countstable.csv
MD_C5

source_name: Jojoba Mid Stage Developing Seed Cotyledons

value: Mid Stage Developing Seed Cotyledons


title: Mid Stage Developing Seed Cotyledons_4

description:
processed data file: Seed_tissues_countdata.txt
processed data file: Seed_tissues_normalized_countstable.csv
MD_C4

value: PARL# 940


title: F_DC1_d3

value: Clec9A+CD141+ cells


title: F_DC1_d2


title: Mid Stage Developing Seed Cotyledons_3

description:
processed data file: Seed_tissues_countdata.txt
processed data file: Seed_tissues_normalized_countstable.csv
MD_C3


title: Mid Stage Developing Seed Cotyledons_1

description:
processed data file: Seed_tissues_countdata.txt
processed data file: Seed_tissues_normalized_countstable.csv
MD_C1


title: F_DC1_d1


title: B_DC2_d3

source_name: Peripheral blood mononuclear phagocytes

value: Blood

value: CD1c+ cDC2


title: 140478A_JjianB10: Jujian' kernel_October_rep1

city: Changsha

last: Jiang

state: Hunan

address: 88 Shaoshan Road

description: gene expression in Camellia oleifera  'Jujian' seed during fruit swelling period ( October)

hyb_protocol: DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm at 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: Scanned on an Agilent G2565CA scanner.

data_processing: Feature Extraction v10.7 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and genespring software was used to analyze the raw data, which are normalized by percentile normalization.

organism: Camellia oleifera

source_name: elite varieties 'Jujian' kernels,October,replicate1

label_protocol: cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. This procedure has been previously described, and the procedure has been improved by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio) for producing higher yields of labeled cDNA.

growth_protocol: All organisms were mantained from the C. oleifera resource nursery of Central South University of Forestry and Technology in East town, Wangcheng Country, Changsha city, Hunan Province, China (N 28°30'23.36'', E 112°48'43.03'', altitude of 34.5 m). Ten plants with good growth of each variety were selected, and the fruit (containing the seeds needed for the experiment) were randomly picked each sampling time.

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: Kernels of the seeds in fruit of each C. oleifera variety were stripped, wrapped in aluminum foil and transferred  immediately to liquid nitrogen each sampling time, Then stored in ultra-low temperature refrigerator (-80 °C) in the laboratory for total RNA isolation .

tag: cultivar

value: Jujian

value: kernel (embryo free of seed coat)

tag: developmental stage

value: seed mature period (October)


title: Dry Seed_6

description:
processed data file: Developmental_seed_timecourse_countdata.txt
processed data file: Developmental_seed_timecourse_normalized_countstable.csv
S6

source_name: Jojoba Dry Seed

value: Dry Seed


title: 140478A_HshuoB10: Huashuo' kernel_October_rep1

institute: Central South University of Forestry and Technology

description: gene expression in Camellia oleifera  'Huashuo' seed during fruit swelling period ( October)

source_name: elite varieties 'Huashuo' kernels,October,replicate1

value: Huashuo


title: 140478A_HJinB10: Huajin' kernel_October_rep1

description: gene expression in Camellia oleifera  'Huajin' seed during fruit swelling period ( October)

source_name: elite varieties 'Huajin' kernels,October,replicate1

value: Huajin


title: 140478A_HXinB10: Huaxin' kernel_October_rep1

description: gene expression in Camellia oleifera  'Huaxin' seed during fruit swelling period ( October)

source_name: elite varieties 'Huaxin' kernels,October,replicate1

value: Huaxin


title: F_DC2_d1

value: In vitro differentiated cells

value: Co-cultured with MS5_FS12


title: Mid Stage Developing Seed Cotyledons_2

description:
processed data file: Seed_tissues_countdata.txt
processed data file: Seed_tissues_normalized_countstable.csv
MD_C2


title: 140478A_JjianA10: Jujian' kernel_October_rep1


title: B_DC2_d2

value: healthy donor


title: Dry Seed_5

description:
processed data file: Developmental_seed_timecourse_countdata.txt
processed data file: Developmental_seed_timecourse_normalized_countstable.csv
S5


title: B_DC1_d3

value: Clec9A+CD141+ cDC2


title: Male 3

data_processing:
Illumina Casava1.9 software used for basecalling.
Illumina bcl files were further processed using Cell Ranger (10x Genomics) according to the manufacturer's protocol
Outputs from Cell Ranger were analyzed using Seurat (v3.0) as described in the associated manuscript
Genome_build: Schistosoma mansoni v7
Supplementary_files_format_and_content: Excel spreadsheet (.xlsx) with cluster markers determined by Seurat as described in the associated manuscript
Supplementary_files_format_and_content: R object (.rds) of combined dataset that was used to perform clustering and other single-cell analyses in the associated manuscript

extract_protocol:
Parasites were dissociated and FACS sorted as described in the associated manuscript
single-cell RNAseq libraries were prepared using a 10x genomics Chromium Controller according to the manufacturer's protocol
RNA-Seq (8bp index, 28bp barcode, 58bp insert)

tag: strain

value: Puerto Rico

tag: Stage

value: adult male

value: 6 weeks


title: Dry Seed_4

description:
processed data file: Developmental_seed_timecourse_countdata.txt
processed data file: Developmental_seed_timecourse_normalized_countstable.csv
S4

value: PARL# 940


title: B_DC1_d2

value: Blood

value: Clec9A+CD141+ cDC1


title: 10X E12.5 VT 02

city: Cincinnati

first: Mike

last: Adam

state: Ohio

address: 240 Albert Sabin Way

department: CBDI

institute: Cincinnati Children's Hospital Research Foundation

data_processing:
Raw sequencing data was processed through 10X Genomics CellRanger v3.0.2 using default parameters to obtain the gene expression matrices
Genome_build: mm10
Supplementary_files_format_and_content: mtx matrix files

source_name: brain

extract_protocol:
Single-cell suspensions were processed through Chromium 10X to generate single-cell cDNA libraries attached to microbeads
Microbeads were counted, and amplified by PCR, and the 3' end of the cDNA prepared for sequencing using a modified Nextera XT protocol

value: Lateral ganglionic eminence


title: Male 2


title: 10X E12.5 VT 01


title: B_DC1_d1


title: Dry Seed_2

description:
processed data file: Developmental_seed_timecourse_countdata.txt
processed data file: Developmental_seed_timecourse_normalized_countstable.csv
S2


title: Male 1


title: Dry Seed_1

description:
processed data file: Developmental_seed_timecourse_countdata.txt
processed data file: Developmental_seed_timecourse_normalized_countstable.csv
S1


title: B_DC2_d1

value: CD1c+ cDC2


title: 140478A_HshuoA10: Huashuo' kernel_October_rep1

value: kernel (embryo free of seed coat)

value: seed mature period (October)


title: 140478A_JjianB8: Jujian' kernel_August_rep1

description: gene expression in Camellia oleifera  'Jujian' seed during fruit swelling period ( August)

source_name: elite varieties 'Jujian' kernels,August,replicate1

value: Jujian

value: nutrition high-speed synthesis period (August)


title: 140478A_HJinB8: Huajin' kernel_August_rep1

description: gene expression in Camellia oleifera  'Huajin' seed during fruit swelling period ( August)

source_name: elite varieties 'Huajin' kernels,August,replicate1

value: Huajin


title: 140478A_HXinA10: Huaxin' kernel_October_rep1

value: Huaxin


title: IM3

source_name: adult virgin female parasites

value: adult virgin female


title: Late Stage Developing Seed_6

description:
processed data file: Developmental_seed_timecourse_countdata.txt
processed data file: Developmental_seed_timecourse_normalized_countstable.csv
Sc-LD6

source_name: Jojoba Late Stage Developing Seed

value: Late Stage Developing Seed


title: 140478A_HJinA10: Huajin' kernel_October_rep1

description: gene expression in Camellia oleifera  'Huajin' seed during fruit swelling period (October)


title: Dry Seed_3

description:
processed data file: Developmental_seed_timecourse_countdata.txt
processed data file: Developmental_seed_timecourse_normalized_countstable.csv
S3

value: Dry Seed


title: 140478A_HJinA8: Huajin' kernel_August_rep1


title: 140478A_JjianA8: Jujian' kernel_August_rep1


title: 140478A_HXinB8: Huaxin' kernel_August_rep1

description: gene expression in Camellia oleifera  'Huaxin' seed during fruit swelling period ( August)

source_name: elite varieties 'Huaxin' kernels,August,replicate1


title: 140478A_HXinA8: Huaxin' kernel_August_rep1


title: 140478A_HshuoB8: Huashuo' kernel_August_rep1

description: gene expression in Camellia oleifera  'Huashuo' seed during fruit swelling period ( August)

source_name: elite varieties 'Huashuo' kernels,August,replicate1

value: Huashuo


title: PGE2-2

city: Tokyo

first: Taro

last: Hiromi

state: Not required for this country

address: 6-1-1, shinjyuku, shinjyuku-ku

country: Japan

institute: Tokyo Medical University

description: Gene expression after 24 h of PGE2 treatment

hyb_protocol: .6 μg of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE 8x60K Microarray Ver2.0 (Agilent Technologies) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent Technologies) and 1 minute with 37°C GE Wash buffer 2 (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 12.0.3.1 (Agilent Technologies) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities

label_protocol: Cyanine3 (Cy3) labeled cRNA was prepared from 0.1 μg Total RNA using the Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: Adult mouse aortic smooth muscle cells were obtained by the explant method

extract_protocol: RNA was prepared using the Versagene Blood RNA Purification kit (Gentra Systems, Minneapolis MN) following the manufacturer's recommendations.

treatment_protocol: maintain with 10% DMEM

tag: genotype

value: aortic VSMCs


title: Late Stage Developing Seed_4

description:
processed data file: Developmental_seed_timecourse_countdata.txt
processed data file: Developmental_seed_timecourse_normalized_countstable.csv
Sc-LD4


title: IM1

value: Puerto Rico

value: 6 weeks


title: LKB1 KO biological rep 2

description: Gene expression data

source_name: E13.5 embryo

value: E13.5 DRG

value: LKB1 KO


title: 140478A_HshuoA8: Huashuo' kernel_August_rep1


title: Late Stage Developing Seed_5

description:
processed data file: Developmental_seed_timecourse_countdata.txt
processed data file: Developmental_seed_timecourse_normalized_countstable.csv
Sc-LD5

value: PARL# 940


title: Late Stage Developing Seed_3

description:
processed data file: Developmental_seed_timecourse_countdata.txt
processed data file: Developmental_seed_timecourse_normalized_countstable.csv
Sc-LD3


title: Control-2

description: Gene expression after 24 h without any treaments

source_name: control


title: 140478A_JjianA6: Jujian' kernel_June_rep1

description: gene expression in Camellia oleifera  'Jujian' seed during fruit swelling period ( June)

source_name: elite varieties 'Jujian' kernels,June,replicate1

value: fruit swelling period ( June)


title: PGE2-1


title: Tg_3

description: Tg _abundance measurements.txt

organism: Toxoplasma gondii

value: Me49 tachyzoites

tag: parasite strain

tag: culture time

value: maintained in HFFs in T25 tissue culture flask, about 48 h


title: Female 1

source_name: adult sexually mature female parasites

value: adult sexually mature female

tag: age


title: H3K4me1_ChIPSeq_BPA 3_PND5

source_name: Rat liver

tag: chip antibody

value: H3K4me1 (Abcam, ab8895)

value: Sprague Dawley

tag: treatment

value: 50 microg/kg Bisphenol A (BPA)


title: Female 3

source_name: adult sexually mature female parasites amputated anterior to the vitellaria


title: Tg_2

description: Tg _abundance measurements.txt

tag: cell type


title: Late Stage Developing Seed_1

description:
processed data file: Developmental_seed_timecourse_countdata.txt
processed data file: Developmental_seed_timecourse_normalized_countstable.csv
Sc-LD1

tag: tissue


title: zebrafish_1dpf_quantSeq

city: Vienna

first: Stefan

middle: Ludwig

last: Ameres

address: Dr.-Bohr-Gasse 3

country: Austria

institute: Institute of Molecular Biotechnology

description: 3' end sequencing data from zebrafish 1dpf

data_processing:
3' end sequencing data was processed using 3'GAmES
metadata for all the priming sites obtained as an intermediate from 3'GAmES was integrated using custom R scripts.
Genome_build: GRCz11
Supplementary_files_format_and_content: bed files containing information for all priming sites which have been used for the analysis and the final counting windows

organism: Danio rerio

source_name: 1 day post fertilization embryo

growth_protocol: Zebrafish (Danio rerio) were raised according to standard protocols (28°C water temperature; 14/10 hour light/dark cycle) until 1 day post fertilization (time-point of sample collection).

extract_protocol:
Total RNA was isolated using the standard TRIzol (Invitrogen) protocol, and genomic DNA was removed by TURBO-DNase treatment followed by phenol/chloroform extraction.
3ʹ end sequencing libraries were prepared using QuantSeq, Lexogen

value: embryo

value: 1 day post fertilization


title: Mid Stage Developing Seed_6

description:
processed data file: Developmental_seed_timecourse_countdata.txt
processed data file: Developmental_seed_timecourse_normalized_countstable.csv
Sc-MD6

source_name: Jojoba Mid Stage Developing Seed

value: Mid Stage Developing Seed


title: IM2

value: adult virgin female


title: mycelial mat, mY_T3

city: Beijing

first: Yingbin

last: Li

address: No.2 Yuanmingyuan West Road, Haidian District

department: plant protection college

institute: China Agricultural University

description: mRNA sequencing

data_processing:
Illumina Casava1.8 software used for basecalling.
A cDNA library constructed by technology from the pooled RNA  was sequenced run with Illumina sequence platform. Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20) were removed.
We aligned reads of samples to the reference genome using HISAT package.
The mapped reads of each sample were assembled using StringTie. Then, all transcriptomes from Samples were merged to reconstruct a comprehensive transcriptome using perl scripts. After the final transcriptome was generated, StringTie and edgeR was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM.
Genome_build: Fusarium solani FSSC 5 v1.0
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample

organism: Fusarium solani

source_name: mycelial mat

growth_protocol: WT and ∆FsYvc1-17 fungi were cultured on PDA medium (covered with cellophane) at 25ºC for 60 h (~ 2.5 cm diameter)

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
Poly(A) RNA is purified from total RNA(5ug) using poly-T oligo-attached magnetic beads using two rounds of purification. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the TruSeq RNA Sample Preparation v2 (Cat. RS-122-2001,RS-122-2002) (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing ( 2 x 150 bp) on an Illumina Novaseq 6000 at the (LC Sceiences,USA) following the vendor’s recommended protocol.

treatment_protocol: treated with 4.8 μg/mL AITC for 3 h

tag: culture protocol

value: PDA medium,  25ºC, 60 h, (~ 2.5 cm diameter)

value: mycelial mat

value: treated with AITC at 4.8 μg/mL for 3 hours

tag: replicate


title: RNASeq_VEH 13_D240_Western diet

data_processing:
The data quality was assessed using FastQC and low quality basepairs were removed using TrimGalore.
After trimming samples were aligned to Rn6 using HISAT2
Features were quantified using featureCounts and the Gencode gene model
Differential gene expression was inferred after RUVSeq normalization using DESeq2; significance was achieved for fold change exceeding 1.25x and FDR-adjusted q-value<0.1
Genome_build: rn6
Supplementary_files_format_and_content: Gene expression as read counts for all samples.

extract_protocol:
RNA from frozen liver tissue of D70 (n = 3 per treatment group) and of D240 (n = 3 per treatment group) male rats was prepared using the Qiagen RNeasy kit (cat no. 74101), including optional on-column DNase digestion, according to the manufacturer’s instructions. RNA concentration was measured using Thermo Scientific’s Nanodrop and then sent to the Next Generation Sequencing Core at the University of Texas MD Anderson Cancer Center Science Park for RNA quality analysis, library prep and sequencing. RNA quality control was performed with the Agilent 2100 Bioanalyzer. The RNA Integrity Number (RIN) was determined for every sample and all samples used for sequencing libraries had RIN values >8.4.
Seqeuncing libraries were prepared using the Illumina Truseq stranded total RNA kit using 1000 ng of RNA per sample.

treatment_protocol: Neonatal rats were treated with vehicle (VEH; sesame oil) or bisphenol A (BPA; 50 µg/kg dissolved in sesame oil) orally via pipette tip on post-natal days 1, 3, and 5. Littermates of the same sex were randomly assigned to the treatment groups. BPA was obtained from the National Instutite of Environmental Health Sciences (NIEHS). The dose and route of administration recapitulates human exposure to BPA. Rats were fasted overnight prior to tissue collection.Liver tissue was harvested on post-natal day 5 at 6 hours after treatment (PND5), and on day 70 (D70). Tissue was snap-frozen in liquid nitrogen for downstream transcriptomic analyses.

tag: post natal day

tag: diet

value: Western diet

value: Vehicle


title: 140478A_JjianB6 : Jujian' kernel_June_rep1

value: Jujian

value: kernel (embryo free of seed coat)


title: Mid Stage Developing Seed_5

description:
processed data file: Developmental_seed_timecourse_countdata.txt
processed data file: Developmental_seed_timecourse_normalized_countstable.csv
Sc-MD5

tag: germplasm resources information network number (grin)

value: PARL# 940


title: Female 2

value: Puerto Rico

value: 6 weeks


title: mycelial mat, mY_T2

description: mRNA sequencing


title: 140478A_HXinB6: Huaxin' kernel_June_rep1

description: gene expression in Camellia oleifera  'Huaxin' seed during fruit swelling period ( June)

source_name: elite varieties 'Huaxin' kernels,June,replicate1

tag: cultivar

value: Huaxin

value: fruit swelling period ( June)


title: 140478A_HJinA6: Huajin' kernel_June_rep1

description: gene expression in Camellia oleifera  'Huajin' seed during fruit swelling period ( June)

source_name: elite varieties 'Huajin' kernels,June,replicate1

value: Huajin

tag: developmental stage


title: 140478A_HshuoB6: Huashuo' kernel_June_rep1

description: gene expression in Camellia oleifera  'Huashuo' seed during fruit swelling period ( June)

source_name: elite varieties 'Huashuo' kernels,June,replicate1

value: Huashuo


title: 140478A_HJinB6: Huajin' kernel_June_rep1


title: RNASeq_VEH 29_D70

value: Normal chow


title: ES_LESB_surf_6

city: Burnaby

first: Travis

last: Blimkie

state: British Columbia

address: 8888 University Drive

department: MBB

country: Canada

institute: Simon Fraser University

data_processing:
Base-calling and de-multiplexing were done using built-in software on the Illumina HiSeq2500
Fastq file quality control was performed using FastQC v0.11.7 and MultiQC v1.0
Fastq files were aligned to the LESB58 genome using STAR v2.6.1a
Read count tables were generated using htseq-count v0.11.2
Genome_build: LESB58 125 (GCF_000026645.1)
Supplementary_files_format_and_content: read count table containing uniquely mapped reads per gene (https://www.pseudomonas.com/) for each sample

organism: Pseudomonas aeruginosa LESB58

growth_protocol: Surfing motility on KB and SCFM 0.3% agar supplemented with 0.4% porcine stomach mucin. Strains were adjusted in KB medium to an OD600 of 0.1 and incubated for 48 h at 37°C as previously described

extract_protocol:
RNA stabilized using RNAprotect Bacteria (Qiagen), extracted using Rneasy Mini Kit (Qiagen), DNAase treated using TURBO DNA-free kit (Thermo Fisher), rRNA depletion conducted with Ribozero Bacteria kit (Illumina - USA)
cDNA libraries were constructed for sequencing using a KAPA Stranded Total RNA Kit (Kapa Biosystems)

tag: genotype/variation

value: wild type

tag: growth condition

value: surfing colony

tag: molecule subtype

value: ribosomally depleted RNA


title: 140478A_HXinA6: Huaxin' kernel_June_rep1


title: Mid Stage Developing Seed_3

description:
processed data file: Developmental_seed_timecourse_countdata.txt
processed data file: Developmental_seed_timecourse_normalized_countstable.csv
Sc-MD3

value: Mid Stage Developing Seed


title: mycelial mat, mY_CK3

description: mRNA sequencing

tag: strain

value: PDA medium,  25ºC, 60 h, (~ 2.5 cm diameter)

value: mycelial mat

value: Untreated with AITC

tag: genotype


title: Tg_1

description: Tg _abundance measurements.txt

data_processing:
Illumina Casava 1.8 software was used for basecalling
sequenced reads were trimmed  for adaptor sequence, reads containing ploy-N and low quality reads. Then clean reads were mapped to Sus scrofa or Toxoplasma  reference genome by  using TopHat v2.0.12.
Genome_build: Sus scrofa reference genone for  alignment: ftp://ftp.ensembl.org/pub/current_fasta/sus_scrofa/dna/ ;  Me49 reference genome for alignment: ftp://ftp.ensemblgenomes.org/pub/release-23/protists//fasta/toxoplasma gondii/dna/
Supplementary_files_format_and_content: tab-delimited text files include reads counts values for each sample

extract_protocol:
At indicated time, the samples were collected and  total RNA was harvested using Trizol reagent.   NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA)  was used with 3 µg total RNA per sample for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Me49 tachyzoites

tag: cell line

tag: parasite strain

tag: culture time

value: maintained in HFFs in T25 tissue culture flask, about 48 h


title: RNASeq_VEH 27_D70

tag: treatment

value: Vehicle


title: Mid Stage Developing Seed_2

description:
processed data file: Developmental_seed_timecourse_countdata.txt
processed data file: Developmental_seed_timecourse_normalized_countstable.csv
Sc-MD2

value: PARL# 940

tag: tissue


title: RNASeq_VEH 26_D70


title: RNASeq_BPA 25_D70

value: BPA


title: ES_LESB_surf_5


title: mycelial mat, mY_T1

description: mRNA sequencing

tag: culture protocol

value: treated with AITC at 4.8 μg/mL for 3 hours


title: ES_LESB_relspo_surf_6

value: relA-spoT double knockout


title: ES_LESB_surf_2


title: Mid Stage Developing Seed_1

description:
processed data file: Developmental_seed_timecourse_countdata.txt
processed data file: Developmental_seed_timecourse_normalized_countstable.csv
Sc-MD1


title: Early Stage Developing Seed_6

description:
processed data file: Developmental_seed_timecourse_countdata.txt
processed data file: Developmental_seed_timecourse_normalized_countstable.csv
Sc-ED6

source_name: Jojoba Early Stage Developing Seed

value: Early Stage Developing Seed


title: Mid Stage Developing Seed_4

description:
processed data file: Developmental_seed_timecourse_countdata.txt
processed data file: Developmental_seed_timecourse_normalized_countstable.csv
Sc-MD4


title: RNASeq_BPA 14_D240_Western diet

value: Western diet


title: RNASeq_BPA 22_D70

value: Normal chow


title: ES_LESB_relspo_surf_5


title: mycelial mat, WT_T3

description: mRNA sequencing

tag: replicate

value: wild type


title: mycelial mat, mY_CK2

description: mRNA sequencing


title: mycelial mat, mY_CK1

description: mRNA sequencing


title: ES_LESB_relspo_surf_2

value: surfing colony


title: Early Stage Developing Seed_4

description:
processed data file: Developmental_seed_timecourse_countdata.txt
processed data file: Developmental_seed_timecourse_normalized_countstable.csv
Sc-ED4


title: mycelial mat, WT_T1

description: mRNA sequencing


title: Early Stage Developing Seed_5

description:
processed data file: Developmental_seed_timecourse_countdata.txt
processed data file: Developmental_seed_timecourse_normalized_countstable.csv
Sc-ED5


title: RNASeq_VEH 18_D240_Western diet

tag: post natal day


title: mycelial mat, WT_T2

description: mRNA sequencing


title: Early Stage Developing Seed_3

description:
processed data file: Developmental_seed_timecourse_countdata.txt
processed data file: Developmental_seed_timecourse_normalized_countstable.csv
Sc-ED3


title: RNASeq_BPA 13_D240_Western diet

tag: diet


title: RNASeq_VEH 15_D240_Western diet


title: Early Stage Developing Seed_2

description:
processed data file: Developmental_seed_timecourse_countdata.txt
processed data file: Developmental_seed_timecourse_normalized_countstable.csv
Sc-ED2

tag: germplasm resources information network number (grin)


title: RNASeq_BPA 24_D70


title: 140478A_HshuoA6: Huashuo' kernel_June_rep1

tag: cultivar

value: Huashuo

value: kernel (embryo free of seed coat)

value: fruit swelling period ( June)


title: mycelial mat, WT_CK1

description: mRNA sequencing

value: PDA medium,  25ºC, 60 h, (~ 2.5 cm diameter)

value: mycelial mat


title: IVLT-2B_11

city: San Francisco

middle: Gregory

last: Jones

state: CA

institute: UCSF

data_processing:
10x cellranger v2.0.1
Target Site analysis with Cassiopeia
Phylogenetic inference with Cassiopeia
Genome_build: "dummy" build
Supplementary_files_format_and_content: All .bam files are possorted_genome_bam's produced with Cell Ranger. IVLT-2B.alleleTable.txt is the allele table resulting from Cassiopeia's pre-processing pipeline, summarzing the allele information for all cells from the lineage tracing experiment. *.nwk files are reconstructed trees, in newick format.

source_name: A549 lung adenocarcinoma cell line

growth_protocol: A549 cells (human lung adenocarcinoma line, ATCC CCL-185) were maintained in Dulbecco’s modified eagle medium (DMEM, Gibco) supplemented with 10% FBS (VWR Life Science Seradigm), 2 mM glutamine, 100 units/mL penicillin, and 100 µg/mL streptomycin.

extract_protocol:
Cells were washed with PBS with 0.04% w/v bovine serum albumin (BSA, New England Biolabs), filtered through 40 µm FlowMi filter tips filter tips (Bel-Art), and counted according to the 10x Genomics protocol. Approximately 14,000 cells per sample were loaded into the 10x Genomics Chromium Single Cell 3' Library and Gel Bead Kit v2, and  cDNA was reverse-transcribed, amplified, and purified according to the manufacturer’s protocol. Resulting cDNA libraries were quantified by BioAnalyzer, yielding  the expected size distribution described in the manufacturer’s protocol.
To prepare the Target Site amplicon sequencing library, resulting amplified  cDNA libraries were further amplified with custom, Target Site-specific primers containing P5/P7 Illumina adapters and sample indices. PCR amplification was performed using Kapa HiFi HotStart ReadyMix, as in ] according to the following program: melting at 95C for 3 minutes, then 14 cycles at 98C for 15 seconds and 70C for 20 seconds. Approximately 12 fmol of template cDNA were used per reaction; amplification was performed in quadruplicate to avoid PCR-induced library biases, such as jack-potting. PCR products were re-pooled and purified by SPRI bead selection at 0.9x ratio and quantified by BioAnalyzer

treatment_protocol: To construct the lineage tracing-competent cell line, A549 cells were transduced by serial lentiviral infection with the three lineage tracing components: (1) Cas9, (2) Target Site, and (3) triple-sgRNAs. First, A549 cells were transduced by Cas9 (mCherry) lentivirus and mCherry+ cells were selected to purity by fluorescenceactivated cell sorting on the BD FACS Aria II. Second, A549-Cas9 cells were transduced by concentrated Target Site (GFP) lentivirus and GFP+ cells were selected by FACS; after sorting, Target Site infection and sorting were repeated two more times for a total of three serial lentiviral transfections, sorting for cells with progressively higher GFP signal after each infection. This strategy of serial transfection with concentrated lentivirus yielded cells with high copy numbers of the Target Site, which were confirmed by quantitative PCR. Third, A549 cells with Cas9 and Target Site were transduced by titered triple-sgRNA (BFP-PuroR) lentivirus and selected

tag: cell type

tag: plate


title: mycelial mat, WT_CK2

description: mRNA sequencing

value: Untreated with AITC


title: IVLT-2B_10


title: IVLT-2B_00


title: IVLT-2B_01


title: RNASeq_BPA 12_D240_Western diet


title: mycelial mat, WT_CK3

description: mRNA sequencing


title: Early Stage Developing Seed_1

description:
processed data file: Developmental_seed_timecourse_countdata.txt
processed data file: Developmental_seed_timecourse_normalized_countstable.csv
Sc-ED1


title: 0112_NAM

status: Public on Mar 10 2020

city: New York

first: Joseph

middle: C

last: Devlin

state: NY

address: 430 East 29th Street

department: Microbiology

institute: New York University Langone Health

data_processing:
Trimmomatic v0.32 was used to remove adapter sequences and bases with base quality lower than three from the ends.
Also using sliding window methods, bases of reads that did not qualify for window size 4 and mean quality 15 were trimmed and reads with length shorter than 36 bp were dropped.
The quality of the data was assessed before and after trimming using FastQC v0.10.0.
Trimmed reads were mapped to reference genome (gencode.mm10) with TopHat v.2.0.13 and bowtie2 v.2.2.3 and –G option on Cufflinks v.2.2.1 was used for transcript assembly and FPKM quantification.
Data was normalized using log2 transformation with 1 was added to the raw signal (FPKM+1) followed by quantile normalization using the preprocessCore package in R
Genome_build: mm10
Supplementary_files_format_and_content: FPKM table of gene expression values from Cufflinks

source_name: Lung

growth_protocol: Single cell suspensions from naïve lung tissues were processed with Liberase TM as indicated previously.  For sorting, following surface staining, the cell pellet was directly resuspended in 1X phosphate-buffered saline (PBS) with 1mM EDTA and 2%FBS. Cells were sorted on Becton-Dickinson FacsAria II instrument.

extract_protocol:
RNAeasy Plus Microkit (Qiagen, Valencia, CA) was used to extract total RNA from the sorted cells.
RNA-Sequencing libraries were prepared using the Illumina TruSeq Stranded mRNA library kit and the individual libraries were pooled together
The samples were run over four lanes on the Illumina HiSeq2500 with 101 paired end reads

treatment_protocol: For cell sorting, lung tissue was treated in the same way without fixation. After staining, cell pellet was directly resuspended in 1xPBS with 1mM EDTA and 2%FBS. Cells were sorted on Becton-Dickinson FacsAria II instrument

value: nerve- and airway-associated macrophages


title: 0218_AM

value: alveolar macrophages


title: Control-1

description: Gene expression after 24 h without any treaments

value: aortic VSMCs


title: 0218_NAM


title: X1415.1091

city: Bar Harbor

first: Ron

last: Korstanje

state: ME

address: 600 Main St

institute: The Jackson Laboratory

data_processing:
Expectation-Maximization algorithm for Allele Specific Expression (EMASE) and Genotyping by RNAseq (GBRS, http://churchill-lab.github.io/gbrs)
Supplementary_files_format_and_content: TPM

source_name: Kidney RNA

extract_protocol:
Kidney's were flash frozen and ground into a powder on dry ice.  RNA was extracted using  miRNA Easy kit from Qiagen
TruSeq RNA library prep kit v2 from illumina

tag: Sex

value: F

tag: generation


title: X1415.1088

value: M

tag: strain


title: X1415.1054


title: X1415.1095


title: X1415.1051


title: X1415.1084


title: X1415.1056


title: 0112_AM


title: X1415.1043


title: X1415.1117


title: X1415.1036


title: X1415.1122


title: X1415.1035


title: Anti-Ago2 ChIP KD cells

first: Bernett

last: Lee

address: 8A Biomedical Grove #03-06 Immunos

country: Singapore

institute: Singapore Immunology Network

description:
A833_06_Ago2_ZIP_181a
Gene expression from Anti-Ago2 ChIP KD cells

hyb_protocol: 3.8 μg of fragmented and labeled sense-strand cDNA were hybridized for 16 h at 45°C on GeneChip Human Gene 2.0 ST microarrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 (performed at an Affymetrix Service Provider and Core Facility, “KFB - Center of Excellence for Fluorescent Bioanalytics” (Regensburg, Germany; www.kfb-regensburg.de).

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G (performed at an Affymetrix Service Provider and Core Facility, “KFB - Center of Excellence for Fluorescent Bioanalytics” (Regensburg, Germany; www.kfb-regensburg.de).

data_processing: Affymetrix CEL files were normalized using the Robust Multi-array Average (RMA) method in the xps bioconductor package running R version 3.1.2.

source_name: moDC precursor cell_IP

label_protocol: Ambion WT Expression Kit Protocol was used for the preparation of biotinylated sense-strand cDNA from 300ng of total RNA, followed by fragmentation and labeling according to the Affymetrix GeneChip WT Terminal Labeling and Hybridization User Manual (performed at an Affymetrix Service Provider and Core Facility, “KFB - Center of Excellence for Fluorescent Bioanalytics” (Regensburg, Germany; www.kfb-regensburg.de).

growth_protocol: Expanded human cord blood CD34 cells were cultured for 4-5 days using a protocol known to enrich for myeloid cell potential (Jurkin et al., 2010). These monocytic progenitors (moPs) were transduced with either miRZip scramble control or miRZip-181a anti-miR-181a (KD) lentiviral constructs, and FACS-sorted for transduced GFP positive cells.

extract_protocol: Ago-2 coimmunoprecipitated RNA samples and corresponding input control (total RNA) samples were extracted and precipitated using Phenol/Chloroform/ isopropyl alcohol. RNA was pelleted, dried, and treated with DNaseI (Fermentas) for 45 min at 37 degrees celcius, followed by thermal inactivation of DNaseI. RNA integrity was assessed using a Agilent 2100 Bioanalyzer (Agilent Technologies) prior to microarray hybridization.

treatment_protocol: FACS-sorted transduced monocytic progenitors (moPs) were incubated with dendritic cell lineaging GM-CSF (100ng/ml) and IL-4 (25ng/ml) cytokines (Peprotech) in complete RPMI medium for 24 hours. Cells were harvested, washed with PBS, and pellets snap frozen at -80 degrees. Scrambled control and miR-181a KD cell pellets from three different donors were pooled prior to cell lysis and Ago2-coimmunoprecipitation.

value: monocyte-derived dendritic cells (moDCs)

tag: knockdown

value: miR-181a knock down


title: Anti-Ago2 ChIP control cells

description:
A833_05_Ago2_ZIP_000
Gene expression from Anti-Ago2 ChIP control cells

value: miRZip scramble control


title: ChIP control KD cells

description:
A833_04_RBC_ZIP_181a
Gene expression from input KD cells

source_name: moDC precursor cell_IP_control


title: KD cells total RNA

description:
A833_02_Input_ZIP_181a
Gene expression from KD cells total RNA

source_name: moDC precursor cell_totalRNA


title: X1415.1029


title: Control cells total RNA

description:
A833_01_Input_ZIP_000
Gene expression from control cells total RNA


title: ChIP control cells

description:
A833_03_RBC_ZIP_000
Gene expression from input control cells


title: X1415.1023


title: X1415.1026


title: Late Stage Developing Seed_2

description:
processed data file: Developmental_seed_timecourse_countdata.txt
processed data file: Developmental_seed_timecourse_normalized_countstable.csv
Sc-LD2

source_name: Jojoba Late Stage Developing Seed

value: PARL# 940

value: Late Stage Developing Seed


title: Uterine epithelium from Sox17-heterozygous mutant sample #253 on day 4

first: Masami

last: Kanai-Azuma

address: 1-5-45 Yushima, Bunkyo-ku

institute: Tokyo Medical and Dental University

hyb_protocol: Fifteen micrograms of biotin-aRNA was enzymatically fragmented and hybridized to Mouse Genome 430 2.0 GeneChip arrays (Affymetrix).

scan_protocol: The DNA chip was then washed, stained with a Fluidics Station 450 instrument (Affymetrix), and scanned with a GeneChip scanner 3000 (Affymetrix).

data_processing: The data obtained were managed using GeneChip Operating Software  and normalized using the Robust Multiarray Average method using Expression Console Software (Affymetrix). Differences in expression levels between each probe across the samples were analyzed using the Transcriptome Analysis Console (Affymetrix).

source_name: Uterine epithelium from Sox17-heterozygous mutant sample on day 4 of pregnancy

label_protocol: 100 ng total RNA was reverse transcribed, amplified, and labeled with biotin.

growth_protocol: Day 1 (the day vaginal plug were found) and day 4 of pregnancy

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

treatment_protocol: The uterine epithelium was prepared by successively incubating uterine pieces in Hank’s balanced salt solution containing pancreatin (Sigma-Aldrich) and dispase (Thermo Fisher, MA, USA) for 1 h at 4°C, for 1 h at room temperature    (20-28°C), and for 15 min at 37°C

tag: genotype

value: Sox17-heterozygous mutant

tag: time

value: day 4 of pregnancy

value: Uterine epithelium

tag: gender

value: female


title: X1415.1019


title: Uterine epithelium from Sox17-heterozygous mutant sample #281 on day 4


title: Uterine epithelium from wild-type sample #302 on day 1

source_name: Uterine epithelium from wild-type sample on day 1 of pregnancy

value: wild type

value: day 1 of pregnancy


title: Uterine epithelium from wild-type sample #277 on day 4

source_name: Uterine epithelium from wild-type sample on day 4 of pregnancy


title: X1415.1016


title: X1415.1014


title: X1415.0971


title: Uterine epithelium from wild-type sample #284 on day 4


title: X1415.1009


title: Uterine epithelium from wild-type sample #303 on day 1


title: X1415.0949


title: X1415.0952


title: X1415.0914


title: X1415.0974


title: X1415.0968


title: X1415.0923


title: X1415.0911


title: X1415.0920


title: X1415.0980


title: X1415.0963


title: X1415.0898


title: X1415.0903


title: X1415.0905


title: X1415.0896


title: X1415.0977


title: X1415.0987


title: X1415.0888


title: X1415.0879


title: X1415.0873


title: X1415.0843


title: X1415.0864


title: X1415.0840


title: X1415.0891


title: X1415.0884


title: X1415.0870


title: X1415.0856


title: X1415.0885


title: X1415.0851


title: X1415.0861


title: X1415.0834


title: X1415.0826


title: X1415.0934


title: X1415.0736


title: X1415.0821


title: X1415.0819


title: X1415.0720


title: X1415.0817


title: X1415.0708


title: X1415.0713


title: X1415.0892


title: X1415.0732


title: X1415.0802


title: X1415.0807


title: X1415.0726


title: X1415.0717


title: X1415.0831


title: X1415.0707


title: X1415.0688


title: X1415.0700


title: X1415.0813


title: X1415.0663


title: X1415.0652


title: X1415.0658


title: X1415.0647


title: X1415.0674


title: X1415.0729


title: X1415.0678


title: X1415.0644


title: X1415.0622


title: X1415.0639


title: X1415.0617


title: X1415.0680


title: X1415.0667


title: X1415.0634


title: X1415.0606


title: X1415.0601


title: X1415.0599


title: X1415.0574


title: X1415.0578


title: X1415.0561


title: X1415.0691


title: X1415.0575


title: X1415.0571


title: X1415.0585


title: X1415.0557


title: X1415.0545


title: X1415.0540


title: X1415.0534


title: X1415.0488


title: X1415.0508


title: X1415.0531


title: X1415.0499


title: X1415.0483


title: X1415.0479


title: X1415.0472


title: X1415.0466


title: X1415.0476


title: X1415.0564


title: X1415.0455


title: X1415.0449


title: X1415.0457


title: X1415.0443


title: X1415.0550


title: X1415.0451


title: X1415.0484


title: X1415.0429


title: X1415.0422


title: X1415.0414


title: X1415.0413


title: X1415.0409


title: X1415.0406


title: X1415.0397


title: X1415.0401


title: DwC_11167_30mM (SC.139)

city: Chicago

first: Michael

last: Grassi

state: IL

address: 1855 West Taylor Street

department: Department of Ophthalmology and Visual Sciences

institute: University of Illinois at Chicago

hyb_protocol: Hybridizationwas done to Illumina HT12v4 microarrays (Catalog number: 4393543)

scan_protocol: Scanned on an Illumina HiScan scanner

data_processing: Analysis of the gene expression data was performed as follows. For a given individual Si (i= 1,…,22) and gene Gk (k= 1,...,15591), we calculated ∆i,k= HGi,k - SGi,k, where ∆ is response to glucose RG, HG is gene expression in high glucose culture, and SG is gene expression in standard glucose culture. All replicate data was fit using a mixed model that accounted for the correlation between repeated measures within individuals. We built a design matrix using the model.matrix function, and accounted for correlation between biological triplicates using limma’s duplicatecorrelation function. A mixed linear model was then fit that incorporates this correlation and ∆i,k (where ∆ is response to glucose, RG = HGi,k - SGi,k) using the lmFit function. The analysis was performed using the R package limma

source_name: Lymphoblastoid cell line

label_protocol: Samples were processed using the Illumina™ TotalPrep™-96 RNA Amplification Kit (ThermoFisher 4393543)

growth_protocol: Lymphoblastoid cell lines were thawed and cultured in RPMI and 10% FBS until they reached over 85% cell viability. Cells were seeded in a T25 flask. Two replicates were performed per cell line. Cells were counted every day or every other day for five to ten days and recorded.

extract_protocol: Quality control from RNA extraction was performed using the Agilent bio-analyzer.

treatment_protocol: All lymphoblastoid cell lines were maintained in conventional lymphocyte cell culture conditions of RPMI 1640 with 10% FBS in a 25-cm2 cell culture flask. The cells were incubated at 370C in 5% CO2 and the media was changed twice each week. Prior to the experiments (below), lymphoblastoid cells following serum starvation were passaged for a minimum of one week in either standard (SG) RPMI 1640 (11mM glucose) or high glucose (HG) RPMI media (30mM glucose)

tag: cell line

value: Lymphoblastoid cell line


title: X1415.0436


title: DwoC_21183_30mM (SC.136)


title: DwC_11167_normal (SC.137)


title: X1415.0393


title: X1415.0383


title: DwoC_18296_30mM (SC.143)


title: DwoC_16362_normal (SC.135)


title: DwC_17075_30mM (SC.144)


title: DwoC_18296_normal (SC.138)


title: DwC_26008_30mM (SC.140)


title: DwoC_2318_30mM (SC.132)


title: DwC_26008_normal (SC.130)


title: DwoC_16362_30mM (SC.141)


title: DwoC_2318_normal (SC.128)


title: DwC_26008_normal (SC.142)


title: DwC_26008_30mM (SC.125)


title: DwC_17075_normal (SC.133)


title: DwC_17075_normal (SC.131)


title: DwoC_21183_normal (SC.134)


title: DwoC_2318_30mM (SC.129)


title: NoD_14520_30mM (SC.127)


title: DwoC_2318_normal (SC.126)


title: X1415.0370


title: X1415.0372


title: X1415.0363


title: X1415.0361


title: DwC_17075_30mM (SC.123)


title: DwoC_2318_30mM (SC.124)


title: X1415.0378


title: X1415.0355


title: X1415.0358


title: X1415.0351


title: X1415.0347


title: X1415.0340


title: X1415.0348


title: X1415.0329


title: X1415.0334


title: X1415.0324


title: DwoC_2318_normal (SC.119)


title: X1415.0318


title: DwoC_6154_30mM (SC.120)


title: X1415.0308


title: NoD_14520_normal (SC.122)


title: DwC_6009_normal (SC.118)


title: X1415.0303


title: X1415.0302


title: DwC_13206_30mM (SC.114)


title: DwoC_2318_normal (SC.121)


title: DwC_26008_normal (SC.115)


title: DwoC_18296_30mM (SC.116)


title: DwoC_2318_30mM (SC.113)


title: DwoC_6154_normal (SC.117)


title: X1415.0300


title: DwC_6009_30mM (SC.112)


title: DwC_13206_normal (SC.109)


title: X1415.0291


title: X1415.0293


title: DwoC_18296_normal (SC.110)


title: X1415.0288


title: X1415.0281


title: DwC_17075_normal (SC.108)


title: X1415.0278


title: DwC_13206_30mM (SC.104)


title: DwC_26008_30mM (SC.111)


title: DwC_11167_30mM (SC.106)


title: DwoC_18296_normal (SC.105)


title: DwoC_16362_30mM (SC.107)


title: X1415.0274


title: X1415.0269


title: DwoC_16362_normal (SC.103)


title: X1415.0261


title: X1415.0258


title: X1415.0266


title: X1415.0259


title: X1415.0248


title: X1415.0256


title: DwoC_2318_normal (SC.98)


title: X1415.0243


title: X1415.0241


title: X1415.0235


title: X1415.0229


title: DwC_17075_30mM (SC.99)


title: DwC_13206_normal (SC.97)


title: DwC_13206_normal (SC.96)


title: X1415.0226


title: DwC_13206_30mM (SC.93)


title: DwC_11167_normal (SC.100)


title: NoD_11985_normal (SC.92)


title: DwC_6009_30mM (SC.94)


title: DwC_21127_30mM (SC.95)


title: DwoC_2318_30mM (SC.101)


title: NoD_11985_30mM (SC.89)


title: X1415.0201


title: DwoC_21183_30mM (SC.90)


title: DwoC_18296_30mM (SC.102)


title: X1415.0212


title: DwC_21127_normal (SC.86)


title: X1415.0194


title: DwoC_16362_normal (SC.91)


title: DwoC_21183_normal (SC.87)


title: X1415.0183


title: X1415.0176


title: DwoC_16362_30mM (SC.88)


title: X1415.0174


title: X1415.0198


title: X1415.0170


title: X1415.0165


title: X1415.0163


title: X1415.0156


title: X1415.0155


title: DwC_6009_normal (SC.85)


title: DwoC_21183_normal (SC.81)


title: DwC_27141_normal (SC.84)


title: NoD_7344_30mM (SC.83)


title: DwoC_6154_normal (SC.82)


title: X1415.0145


title: X1415.0146


title: X1415.0139


title: DwC_27141_30mM (SC.79)


title: DwC_21127_normal (SC.78)


title: DwC_21127_30mM (SC.80)


title: NoD_7344_normal (SC.76)


title: DwC_11167_30mM (SC.77)


title: X1415.0136


title: X1415.0127


title: X1415.0134


title: X1415.0124


title: X1415.0152


title: DwoC_6154_30mM (SC.75)


title: X1415.0121


title: X1415.0120


title: DwC_21127_30mM (SC.71)


title: DwC_11167_normal (SC.73)


title: X1415.0108


title: X1415.0101


title: DwoC_21183_30mM (SC.74)


title: DwC_27141_30mM (SC.67)


title: DwC_27141_normal (SC.72)


title: DwoC_25224_30mM (SC.69)


title: DwoC_3395_30mM (SC.70)


title: DwoC_25224_normal (SC.65)


title: X1415.0092


title: DwC_6009_normal (SC.66)


title: X1415.0084


title: X1415.0111


title: X1415.0082


title: NoD_14381_normal (SC.64)


title: DwC_21127_normal (SC.68)


title: DwC_6009_30mM (SC.63)


title: X1415.0098


title: DwoC_3395_normal (SC.62)


title: DwC_1026_normal (SC.59)


title: NoD_14381_30mM (SC.61)


title: DwoC_3395_30mM (SC.58)


title: DwoC_25224_normal (SC.60)


title: E15.5_Retina_Ribo_rep1

city: Guangzhou

first: Hongwei

last: Wang

state: Guangdong

address: No 7 Jinsui Rd, Research Building, Rm 301

department: Zhongshan Ophthalmic Center

institute: Sun Yat-Sen University

description: processed data file: E15.5_Ribo-seq_exon_level_tpm.txt

data_processing:
Raw sequence reads were demultiplexed using CASAVA (version 1.8.2), and the 3'-end adapter was clipped using Cutadapt (version 1.8.1) (with the parameters '-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -match-read-wildcards -m 6').
Low-quality sequences were trimmed using Sickle (version 1.33) (with the parameters '-q 20').
The trimmed reads were filtered by length with the ranges [25, 34] for ribosome footprints and [20, 50] for mRNA.
The retained reads that mapped to reference mouse rRNA or tRNA were further removed. The remaining reads were then aligned to the mouse reference genome (download from GENCODE, Release M18: GRCm38.p6) using Tophat2 (version 2.0.14)] with the following command: ' tophat2 -g 20 -N 2 --transcriptome-index [index_file] -G [gtf_file] [fastq_file] -o [output_directory]'.
Only those uniquely mapped reads were extracted for gene expression determination. The total number of aligned count reads per gene was obtained using the Subread R package-featureCounts (version 1.6.2), and further converted to TPM value (Transcripts Per Kilobase Million).
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

extract_protocol:
Frozen tissue samples were lysed separately using 1 ml of mammalian lysis buffer (200 µl 5x Mammalian Polysome Buffer, 100 µl 10% Triton X-100, 10 µl DTT(100 mM), 10 µl DNase I (1U/µl), 2 µl Cycloheximide (50 mg/ml), 10 µl 10% NP-40 and 668 µl Nuclease-Free Water). After incubation for 20 min on ice, lysates were cleared by centrifugation at 10000 x g for 3 min at 4°C. Ribosomal RNA was depleted using the Ribo-Zero magnetic kit (Epicentre).
Sequencing libraries of ribosome protected fragments were generated using ARTseqTM Ribosome Profiling Kit according to the manufacturer's instructions. Sequencing libraries of poly(A)+ RNA were generated using VAHTSTM mRNA-seq v2 Library Prep Kit for Illumina according to the manufacturer's instructions.

tag: age

value: Embryonic day 15.5

tag: tissue

value: Retina


title: E15.5_Lung_Ribo_rep2

value: Lung


title: E15.5_Liver_Ribo_rep2

value: Liver


title: E15.5_Kidney_Ribo_rep1

value: Kidney


title: E15.5_Kidney_Ribo_rep2


title: E15.5_Heart_Ribo_rep2

value: Heart


title: E15.5_Heart_Ribo_rep1


title: E15.5_Lung_Ribo_rep1


title: DwC_27141_30mM (SC.56)


title: NoD_11985_30mM (SC.57)


title: E15.5_Liver_Ribo_rep1


title: E15.5_Brain_Ribo_rep2

value: Brain


title: E15.5_Retina_mRNA_rep2

description: processed data file: E15.5_RNA-seq_exon_level_tpm.txt


title: DwC_27141_normal (SC.50)


title: E15.5_Retina_Ribo_rep2


title: E15.5_Brain_Ribo_rep1


title: E15.5_Retina_mRNA_rep1


title: NoD_11985_normal (SC.53)


title: DwC_1026_30mM (SC.52)


title: NoD_14581_normal (SC.49)


title: DwoC_3395_normal (SC.55)


title: E15.5_Lung_mRNA_rep1


title: E15.5_Lung_mRNA_rep2


title: NoD_7012_30mM (SC.48)


title: NoD_14381_30mM (SC.46)


title: DwoC_25224_30mM (SC.51)


title: DwC_1026_normal (SC.47)


title: NoD_14569_30mM (SC.45)


title: E15.5_Liver_mRNA_rep2


title: DwC_1026_normal (SC.42)


title: E15.5_Liver_mRNA_rep1


title: NoD_7012_normal (SC.41)


title: E15.5_Kidney_mRNA_rep1


title: DwC_1026_30mM (SC.43)


title: E15.5_Kidney_mRNA_rep2


title: NoD_14381_normal (SC.40)


title: NoD_14569_normal (SC.39)


title: E15.5_Heart_mRNA_rep2


title: E15.5_Heart_mRNA_rep1


title: E15.5_Brain_mRNA_rep1


title: DwC_1026_30mM (SC.38)


title: DwC_1026_30mM (SC.37)


title: E15.5_Brain_mRNA_rep2


title: DwC_1026_normal (SC.44)


title: M0_ATF4_ChIP_rep1

city: Braunschweig

first: Andreas

last: Kloetgen

state: NI

address: Inhoffenstr 7

department: Department for Computational Biology of Infection Research

country: Germany

institute: Helmholtz Centre for Infection Research

description:
processed data file:
M0_ATF4.bw
M0_peaks.bed

data_processing:
Read alignment: Reads were aligned against the reference sequence mm10 with bowtie2 (version 2.3.1) with standard parameters and only uniquely mapped reads were kept with MAPQ > 20.
Deduplication: Aligned reads were filtered for duplicated reads using picard-tools version 2.6.0.
Peak-calling: Peak calling for Atf4 was performed using MACS2 (version 2.0.1) using narrow option (sepcial parameters: --no-model).
Differential binding: To identify differentially bound peaks, we performed diffBind (version 2.2.12) analysis, using the normalization option DBA_EDGER.
Bigwig: For visualization purposes, we generated fold-enrichment bigwig files by applying MACS2 (version 2.0.1) bdgcmp over input (-m FE)
Genome_build: mm10
Supplementary_files_format_and_content: bigwig, peak (bed)

growth_protocol: Bone marrow derived macrophages grown by adding M-CSF to culture medium for 5-7 days

extract_protocol:
Chromatin-IP was performed according to Cell Signaling ChIP kit # 9003 protocol
Libraries were prepared according to NEBNext® Ultra™ II DNA Library Prep Kit for Illumina kit instructions (NEB #E7103). Briefly, DNA was end-repaired, using NEBNext Ultrea II end prep Enzyme mix. The blunt, phosphorylated ends were treated with fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were size selected using Ampure AMPure XP. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on Illumina HiSeq/NextSeq.

treatment_protocol: Addition of IL-4 (40 ng/ml) overnight

tag: strain background

tag: genotype/variation

tag: treatment

value: m-CSF

tag: chip antibody

value: ATF4 antibody (D4B8, Cell Signaling Technology Cat. #11815)


title: NoD_7344_30mM (SC.36)


title: M2_ATF4_ChIP_rep1

description:
processed data file:
M2_ATF4.bw
M2_peaks.bed

value: m-CSF + IL-4


title: NoD_14581_normal (SC.35)


title: C57 middle ear mucosa 2

city: La Jolla

first: Chanond

middle: A

last: Nasamran

department: Center for Computational Biology and Bioinformatics

institute: University of California San Diego

description:
Total RNA
barcodes.tsv, genes.tsv, matrix.mtx; library_id = C57-controlMEM-1-Jun

data_processing:
Reads were aligned and quantified using the Cell Ranger v2.2.0 count function with default parameters
Reads from all samples were combined using the Cell Ranger v2.2.0 aggr function with default parameters
Genome_build: mm10
Supplementary_files_format_and_content: Standard output from Cell Ranger count function; barcodes.tsv, genes.tsv, and matrix.mtx that form a genes by cells count matrix.

source_name: Middle ear mucosa

extract_protocol:
Mucosal tissue was harvested from the bullae of three groups of six mice each.  The tissue from each group was pooled, enzymatically digested and triturated to produce single-cell suspensions.
A 10X Genomics Chromium Controller was used to generate bar-coded cDNA libraries from each sample.
The strategy was to produce three representative samples of the cells of the mucosa from the uninfected middle ear.

value: uninfected middle ear mucosal tissue


title: C57 middle ear mucosa 1

description:
Total RNA
barcodes.tsv, genes.tsv, matrix.mtx; library_id = C57-controlMEM-1-Apr


title: NoD_14569_normal (SC.32)


title: NoD_7344_normal (SC.34)


title: DwC_1026_30mM (SC.30)


title: NoD_14520_normal (SC.31)


title: C57 middle ear mucosa 3

description:
Total RNA
barcodes.tsv, genes.tsv, matrix.mtx; library_id = C57-controlMEM-2-Jun


title: NoD_14581_30mM (SC.54)


title: NoD_14569_30mM (SC.29)


title: NoD_14581_30mM (SC.28)


title: DwC_1026_normal (SC.26)


title: NoD_7012_30mM (SC.24)


title: NoD_14520_30mM (SC.25)


title: NoD_7012_normal (SC.33)


title: NoD_7012_30mM (SC.27)


title: WHO Z PBT2 2

city: Gold Coast

first: John

middle: Michael

last: Atack

state: QLD

address: Gold Coast Campus

department: Institute for Glycomics

country: Australia

institute: Griffith University

data_processing:
Illumina bcl2fastq  2.20.0.422 pipeline
bowtie aligner (2.3.3.1) was used to map reads to the WHO-Z genomic DNA sequence; accession number 070D30A8B4A67321F3393C618ED58032
edgeR version 3.18.1 was used to perform differential expression analysis.
Genome_build: GCF_900087715.2
Supplementary_files_format_and_content: .txt files - abundance measurements and expression differences DMSO vs PBT2

organism: Neisseria gonorrhoeae

source_name: WHO Z DMSO

growth_protocol: overnight cultures (16 hrs from mid-log) in GC broth supplemented with either DMSO or PBT2

extract_protocol:
RNA was isolated using Trizol according to manufacturer's protocol
RNA libraries were prepared for sequencing using standard Illumina TruSeq protocols

tag: agent

value: WHO Z


title: WHO Z PBT2 1


title: WHO Z DMSO 3

value: DMSO


title: WHO Z PBT2 3


title: DwoC_25224_30mM (SC.16)


title: WHO Z DMSO 2


title: WHO Z DMSO 1


title: DwoC_25224_normal (SC.20)


title: NoD_14520_normal (SC.12)


title: DwoC_3395_30mM (SC.15)


title: NoD_7344_30mM (SC.14)


title: S40_Lane_2

data_processing:
The Cell Ranger Single Cell Software Suite, version 1.3 was used to perform sample de-multiplexing, barcode and UMI processing, and single-cell 3′ gene counting.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files from 10X Cell Ranger Software Suite

growth_protocol: Single cell suspensions from naïve lung tissues were processed with Liberase TM as indicated previously.  For single cell sorting, following surface staining, the cell pellet was directly resuspended in 1X phosphate-buffered saline (PBS) with 1mM EDTA and 2%FBS. Cells were sorted on Sony biotechnology SY3200 sorter instrument. Cells were gated for Single, live, CD45+ cells. Then, MerTK+CD64+ cells were sorted for the single RNA-seq analysis.

extract_protocol:
The sorted cellular suspensions were loaded on a 10x Genomics Chromium instrument to generate single-cell gel beads in emulsion (GEMs). 10.5K cells were loaded per channel with an expected yield of 6000 cells.
Single-cell RNA-Seq libraries were prepared using the following 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), and following the Single Cell 3’ Reagent Kits v2 User Guide (Manual Part # CG00052 Rev A). Libraries were run on two lanes of a NovaSeq 6000.


title: DwoC_6154_30mM (SC.10)


title: NoD_14569_normal (SC.11)


title: NoD_11985_30mM (SC.8)


title: DwoC_25224_30mM (SC.13)


title: NoD_7344_normal (SC.18)


title: NoD_14581_30mM (SC.2)


title: NoD_14520_30mM (SC.4)


title: DwoC_6154_norm (SC.1)


title: NoD_14381_normal (SC.9)


title: DwoC_25224_normal (SC.19)


title: NoD_14581_normal (SC.6)


title: NoD_14381_30mM (SC.5)


title: DwoC_3395_normal (SC.21)


title: S40_Lane_1


title: NoD_11985_normal (SC.3)


title: 9w - replicate 3

city: Huddinge

first: Simon

last: Joost

address: Blickagången 16

department: BioNut

country: Sweden

institute: Karolinska Institutet

description:
barcodes_9w.tsv
genes_9w.tsv
matrix_9w.mtx

data_processing:
Processed data: The 10x demux pipeline (now deprecated) was used to demultiplex the flowcells. Count data were subsequently generated using CellRanger(v1.1.0) pooling replicates from each time point. In particular, 5w replicates were pooled from lanes 1-3, while 9w replicates were pooled from lanes 4-6. Later during data analysis, it became apparent that data in 9w - replicate 3 (lane 6) was of low quality. Barcodes linked to this replicate were retroactively removed using the following file: assigned_barcodes.txt
Fastq files: Fastq files were demultiplexed using mkfastq included in CellRanger(v1.2.1).
Genome_build: mm10
Supplementary_files_format_and_content: 'matrix_Xw.mtx':mtx file containing unnormalized count data; 'barcodes_Xw.tsv':list of single-cell barcodes corresponding to count matrix; 'genes_Xw.tsv':list of genes corresponding to count matrix

source_name: Skin

extract_protocol:
After sacrifice, the back of the mice was shaved and the dorsal skin was isolated and floated on HBSS + 0.04% BSA. The skin was then cut into smaller pieces (around 1 mm in width) and incubated in 0.2% collagenase at 37°C for one hour. The partly digested skin was placed in a 70 µm cell strainer, smashed with a piston and rinsed three times with HBSS + 0.04% BSA. The flow-through was saved on ice, while the undigested tissue remaining in the cell strainer was incubated in 0.05% trypsin-EDTA for 15 minutes at 37°C. The trypsin-digested tissue was smashed once more and then passed through a 70 µm cell strainer. The flow-through of the collagenase digestion (containing mainly stromal cells) and the flow-through of the trypsin digestion (containing mainly epidermal cells) were pooled, spun down and subsequently filtered through a 40 µm cell strainer. The viability of the cell suspension was determined using trypan blue.
Single-cell cDNA libraries were prepared using the Chromium Single Cell 3’ kit (version1, 10X Genomics) according to the manufacturer’s instruction. The prepared libraries were sequenced on an Illumina HiSeq2500 at one lane per replicate.

treatment_protocol: All experiments were performed on female C57BL/6 mice. The mice were fed ad libitum, and handled and housed under standard conditions in the animal facility of Karolinska University Hospital Huddinge. All mouse experiments were performed in accordance to Swedish legislation and approved by the Stockholm South Animal Ethics Committee. Mice were sacrificed by cervical dislocation either during second anagen at 5 weeks of age or during second telogen at 9 weeks of age. Single-cell transcriptomes from n = 3 anagen and n = 2 telogen mice were included in the final dataset.

value: Skin

tag: time point

value: 9w - telogen


title: S39_Lane_2


title: 9w - replicate 2


title: NoD_7012_normal (SC.22)


title: 5w - replicate 3

description:
barcodes_5w.tsv
genes_5w.tsv
matrix_5w.mtx

value: 5w - anagen


title: S39_Lane_1


title: 5w - replicate 2


title: 9w - replicate 1


title: S38_Lane_2


title: S38_Lane_1


title: KOM2

city: Fayetteville

first: Jeong Hoon

last: Pan

state: Arkansas

address: 987 W. Maple St.

institute: University of Arkansas

description: Raw reads_Normalized_JKKIM

data_processing:
Sequenced reads were performed quality assessment using FastQC.
Sequenced reads were then aligend to GRCm38.p5 reference genome using ArrayStar
Raw read counts then obtained from ArrayStar were then analyzed using JMP Genomics.
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: Test files include raw read counts for each sample and a tab of raw read counts filtered for detected transcripts.

source_name: Idh2-/- Male #2

extract_protocol:
Total RNA from liver tissues was isolated using the RNeasy Plus Mini Kit (Qiagen, Hilden, Germany) and then the quality of isolated RNA was first assessed using the conventional A260/280 ratio and A260/230 ratio measurement (SpectraMax i3x; Molecular Devices, Sunnyvale, CA, USA) which were all satisfactory. In addition, RNA Integrity Number (also known as RIN) was assessed using the RNA R6K assay for the Agilent 2200 TapeStation (Agilent Technology, Santa Clara, CA, USA) in which RINs ranged between 8.5 and 9.5 hence satisfactory.
Illumina TruSeq RNA Library Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.

value: male


title: 5w - replicate 1


title: S37_Lane_2


title: MOLM-13, 6h stenodactylin, rep 6

city: Bologna

first: Daniele

last: Mercatelli

address: Via Irnerio 45

department: Pharmacy and Biotechnology

country: Italy

institute: University of Bologna

description: replicate 6

hyb_protocol: Biotin-labeled cRNA (750 ng) was hybridized to the The Illumina Sentrix BeadChip according to Manufacturer's instructions.

scan_protocol: Transcriptome analysis was performed using the Illumina iScan, which is based upon fluorescence detection of biotin-labeled cRNA following Manufacturer's instructions.

data_processing: Bead summary data was imported into GenomeStudio to remove control probes and to produce a text file containing the signal and detection p-values per probe for all samples. The text file was imported into J-Express Pro 2012 (http://jexpress.bioinfo.no), and signal intensity values were quantile normalized (Bolstad et al., 2003) and log2 transformed.

source_name: MOLM-13 cell line

label_protocol: Using the Illumina TotalPrep RNA Amplification Kit (version 280508, Applied Biosystems/Ambion, USA), 300 ng of total RNA from each sample were reversely transcribed, amplified and Biotin-16-UTP–labeled.

growth_protocol: MOLM-13 cells were maintained in RPMI 1640 medium (Sigma-Aldrich Co., St Louis, MO, USA) containing 10% heat-inactivated fetal bovine serum (FBS), 2 mM L-glutamine, 100U/ml penicillin and 100 µg/ml streptomycin (Sigma-Aldrich), hereafter named complete medium. All the cultures were kept under standard incubation conditions (humidified atmosphere, 5 % CO2, 37 °C) and passed from two to three times a week to keep them in logarithmic growth phase.

extract_protocol: Total RNA was extracted using the RNeasy Plus Minikit (Qiagen, Germany), following manufacturer’s instructions

treatment_protocol: Cells were treated with stenodactylin 10-9M for 2, 4, and 6 hours.

value: treated with stenodactylin for 6 hours


title: KOF3

description: Raw reads_Normalized_JKKIM

source_name: Idh2-/- Female #3

value: Female


title: MOLM-13, 6h stenodactylin, rep 4

description: replicate 4


title: MOLM-13, 6h stenodactylin, rep 5

description: replicate 5


title: S37_Lane_1


title: MOLM-13, 6h stenodactylin, rep 2

description: replicate 2


title: validation - 9w - replicate 3

data_processing:
Main data: The 10x demux pipeline (now deprecated) was used to demultiplex the flowcells. Count data were subsequently generated using CellRanger(v1.1.0) pooling replicates from each time point. In particular, 5w replicates were pooled from lanes 1-3, while 9w replicates were pooled from lanes 4-6. Later during data analysis, it became apparent that data in 9w - replicate 3 (lane 6) was of low quality. Barcodes linked to this replicate were retroactively removed using the following file: assigned_barcodes.txt. Validation data: Count data was generated using CellRanger(v3.0.2)
Fastq files: Fastq files were demultiplexed using mkfastq included in CellRanger.
Genome_build: mm10
Supplementary_files_format_and_content: 'matrix_Xw.mtx':mtx file containing unnormalized count data; 'barcodes_Xw.tsv':list of single-cell barcodes corresponding to count matrix; 'genes_Xw.tsv':list of genes corresponding to count matrix. '10X_19_0XX_filtered_feature_bc_matrix.h5': h5 file containing gene x barcode count matrix (CellRanger filtered, unnormalised) of validation data.

extract_protocol:
After sacrifice, the back of the mice was shaved and the dorsal skin was isolated and floated on HBSS + 0.04% BSA. The skin was then cut into smaller pieces (around 1 mm in width) and incubated in 0.2% collagenase at 37°C for one hour. The partly digested skin was placed in a 70 µm cell strainer, smashed with a piston and rinsed three times with HBSS + 0.04% BSA. The flow-through was saved on ice, while the undigested tissue remaining in the cell strainer was incubated in 0.05% trypsin-EDTA for 15 minutes at 37°C. The trypsin-digested tissue was smashed once more and then passed through a 70 µm cell strainer. The flow-through of the collagenase digestion (containing mainly stromal cells) and the flow-through of the trypsin digestion (containing mainly epidermal cells) were pooled, spun down and subsequently filtered through a 40 µm cell strainer. The viability of the cell suspension was determined using trypan blue.
Single-cell cDNA libraries were prepared using the 10X Genomics Chromium Single Cell 3’ kit (main dataset: version1; validation dataset: version 3) according to the manufacturer’s instruction. The prepared libraries were sequenced on an Illumina HiSeq2500 (main dataset) or Illumina NovaSeq 6000 (validation dataset) respectively.

treatment_protocol: All experiments were performed on female C57BL/6 mice. The mice were fed ad libitum, and handled and housed under standard conditions in the animal facility of Karolinska University Hospital Huddinge. All mouse experiments were performed in accordance to Swedish legislation and approved by the Stockholm South Animal Ethics Committee. Mice were sacrificed by cervical dislocation either during second anagen at 5 weeks of age or during second telogen at 9 weeks of age. Single-cell transcriptomes from n = 3 anagen and n = 2 telogen mice were included in the final dataset (main dataset). In addition, a validation dataset from n = 3 anagen and n = 2 telogen mice was created.


title: WTF3

description: Raw reads_Normalized_JKKIM

source_name: Wild type Female #3

value: wild type


title: KOF1

description: Raw reads_Normalized_JKKIM

source_name: Idh2-/- Female #1

value: Liver


title: WTF2

description: Raw reads_Normalized_JKKIM

source_name: Wild type Female #2


title: WTM2

description: Raw reads_Normalized_JKKIM

source_name: Wild type Male #2


title: KOM1

description: Raw reads_Normalized_JKKIM

source_name: Idh2-/- Male #1


title: WTM3

description: Raw reads_Normalized_JKKIM

source_name: Wild type Male #3


title: validation - 9w - replicate 1