title: H1_FOXA1_2_Exon_Deletion_GT.ChIP-Seq.H3K4me1.replicate.1

description: Histone marker


title: H1_FOXA1_2_Exon_Deletion_PP2.ChIP-Seq.H3K27ac.replicate.1

status: Public on Oct 18 2021

type: SRA

city: La Jolla

first: Maike

last: Sander

state: CA

address: 2880 Torrey Pines Scenic Dr.

country: USA

institute: UC San Diego

description: Histone marker

library_source: genomic

data_processing:
For RNA-seq: Sequence fragments were aligned to the hg19 genome build with STAR using the parameters: --runThreadN 16. Only the reads aligned uniquely to one genomic location were retained for subsequent analysis. Fragment per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cufflinks
For ChIP-seq: Sequence fragments were aligned to the hg19 genome build using bwa. Only the reads aligned uniquely to one genomic location were retained for subsequent analysis. Fragments were normalized to 1e7 bases of library size using Homer.
For ATAC-seq: adaptors were trimmed from ATAC-Seq reads using the trim_galore package. Reads were mapped to human reference genome hg19 using bwa. Mapped reads were filtered by Samtools, skipping alignment for reads with MAPQ smaller than 30, removing duplicate and mitochondrial reads. Peaks were called using mac2, with the parameters: --nomodel --shift -100 --extsize 200 -B --broad --keep-dup all --nolambda
Genome_build: Genome_build: hg19
Supplementary_files_format_and_content: Supplementary_files_format_and_content: bigWig files were generated

molecule: genomic DNA

organism: Homo sapiens

source_name: H1 FOXA1/2 Exon Deletion

growth_protocol: CyT49 hESCs were maintained and differentiated as previously described (Kroon et al., 2008; Schulz et al., 2012). H1 cells were maintained and differentiated as previously described (Jin et al. 2019). iAEC2 cells were maintained and differentiatied as previously described (Hurley et al 2020)

extract_protocol:
ChIP-seq was performed using the ChIP-IT High-Sensitivity kit (Active Motif) according to the manufacturer’s instructions. Briefly, for each cell stage and condition analyzed, 5-10 x 10e6 cells were harvested and fixed for 15 min in an 11.1% formaldehyde solution. Cells were lysed and homogenised using a Dounce homogeniser and the lysate was sonicated in a Bioruptor® Plus (Diagenode), on high for 3 x 5 min (30 sec on, 30 sec off). Between 10 and 30 µg of the resulting sheared chromatin was used for each immunoprecipitation.
Libraries were prepared using the KAPA DNA Library Preparation Kits for Illumina® Kit
Libraries were prepared using the TruSeq® Stranded mRNA Library Prep Kit (RNA-seq) and the KAPA DNA Library Preparation Kits for Illumina® KAPA Kit (ChIP-seq)

tag: cell line

tag: cell type

value: differentiated hESCs

tag: developmental stage

value: Late pancreatic progenitor

tag: chip antibody

value: Rabbit anti-H3K27ac

tag: antibody manufacturer

value: Active Motif

tag: antibody catalog number


title: H1_WT_PP2.ChIP-Seq.H3K4me1.replicate.1

description: Histone marker

source_name: H1 Control

value: Rabbit anti-H3K4me1

value: Abcam


title: H1_WT_GT.ChIP-Seq.H3K4me1.replicate.1

description: Histone marker

value: Gut tube


title: Cyt49_PP2_shPDX1.ChIP-Seq.FOXA2.replicate.2

description: Transcription factor

source_name: Cyt49 shPDX1

value: Goat anti-FOXA2

value: Santa Cruz Biotechnology


title: Cyt49_HP.ChIP-Seq.Input.replicate.1

description: Input

source_name: Cyt49 Control

value: Hepatic progenitor


title: Cyt49_PP2_shPDX1.ChIP-Seq.Input.replicate.1

description: Transcription factor


title: iAEC2_AFG.ChIP-Seq.FOXA1.replicate.1

description: Transcription factor

source_name: iAEC2 Control

value: Anterior foregut

value: Goat anti-FOXA1


title: H1_FOXA1_2_Exon_Deletion_PP2.RNA-Seq.replicate.1

description: RNA

library_source: transcriptomic

molecule: total RNA

extract_protocol:
RNA was isolated from cell samples using the RNeasy® Micro Kit (Qiagen) according to the manufacturer instructions.
Libraries were prepared using the TruSeq® Stranded mRNA Library Prep Kit
Libraries were prepared using the TruSeq® Stranded mRNA Library Prep Kit (RNA-seq) and the KAPA DNA Library Preparation Kits for Illumina® KAPA Kit (ChIP-seq)


title: H1_FOXA1_2_Exon_Deletion_PP2.ChIP-Seq.H3K4me1.replicate.1

description: Histone marker


title: Cyt49_HP.ChIP-Seq.H3K27ac.replicate.2

description: Histone marker


title: Cyt49_GT.ChIP-Seq.FOXA2.replicate.2

description: Transcription factor


title: Cyt49_PP2_shSCRAM.ChIP-Seq.Input.replicate.1

description: Input

source_name: Cyt49 shSCRAM


title: Cyt49_GT.ChIP-Seq.FOXA1.replicate.2

description: Transcription factor


title: Cyt49_GT.ChIP-Seq.FOXA2.replicate.1

description: Transcription factor


title: Cyt49_PP2_shSCRAM.ChIP-Seq.FOXA1.replicate.1

description: Transcription factor


title: Cyt49_GT.ChIP-Seq.FOXA1.replicate.1

description: Transcription factor


title: H1_FOXA1_2_Exon_Deletion_GT.ChIP-Seq.H3K27ac.replicate.2

description: Histone marker


title: Cyt49_PP2_shSCRAM.ChIP-Seq.FOXA1.replicate.2

description: Transcription factor


title: G_ctrl_Late_3

city: Cambridge

first: Shreeharsha

last: Tarikere

state: Massachusetts

address: 16 Divinity Avenue, Biolabs

department: Organismic and Evolutionary Biology

institute: Harvard University

data_processing:
Multiplexed reads pooled in a lane were demultiplexed and trimmed (of adapters) using the bcl2fastq2 v2.2 pipeline to yield final fastq files.
The reads in the fastq files were aligned with RSEM (v1.3.3) using STAR aligner (v2.7.6a)
Differential Expression analysis: Gene counts in each dataset were normalized with the variance stabilizing transformation (vst) method implemented in the DESeq2 (v1.26.0)
Genome_build: Drosophila melanogaster FlyBase version dmel_r6.36_FB2020_05
Supplementary_files_format_and_content: Tab-delimited text files include the number of raw counts for each biological sample. Whole ovary and tissue-specific data are stored in different files. Additional files with long-format and metadata information are also provided.

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: Ovary: Germ line Tissue 120h AEL

growth_protocol: Drosophila larvae and adult were reared at 25°C at 60% humidity with food containing yeast.

extract_protocol:
Whole ovaries were crushed in Trizol, Somatic and germ line tissue-FACS samples were sorted directly into 100-200µl of Trizol. Samples in Trizol were processed through Zymo RNA Micro-Prep kit (Zymo Research R2060) for RNA extraction.
Poly A selection was done using Takara PrepX mRNA-8 (Takara 640098) protocol. cDNA libraries were prepared with Takara PrepX mRNA-8 (Takara 640096) protocol. Libraries were amplified for 15 cycles in PCR with sample specific PrepX Index primers and sequenced in 50bp single end runs on a Illumina HiSeq 2500.

treatment_protocol: Three replicates each of three stages (early, mid, late ) of Whole ovary, Somatic tissue and Germ line tissue. Ovaries were dissociated with a sequential lysis using 0.25% Trypsin (Thermo Fisher 25200056) and 2.5% Liberase (Sigma 5401119001) for ten minutes each. Somatic and germline tissue were separated using GFP expression in somatic and germ line tissues and using FACS to sort GFP positive cells into Trizol.

tag: strain

value: White Pupae 120h AEL

tag: tissue

value: Germ line tissue


title: H1_FOXA1_2_Exon_Deletion_GT.ChIP-Seq.Input.replicate.1

description: Input


title: G_ctrl_Late_2


title: Cyt49_HP.ChIP-Seq.HNF4A.replicate.2

description: Transcription factor

value: Mouse anti-HNF4A

value: Novus Biologicals


title: Cyt49_PP2_shPDX1.ChIP-Seq.FOXA1.replicate.2

description: Transcription factor


title: Cyt49_PP2_shSCRAM.ChIP-Seq.FOXA2.replicate.1

description: Transcription factor


title: G_ctrl_Early_3

source_name: Ovary: Germ line Tissue 72h AEL

value: III instar Larvae 72h AEL


title: Cyt49_HP.ChIP-Seq.H3K27ac.replicate.1

description: Histone marker

value: differentiated hESCs


title: Cyt49_PP2_shSCRAM.ChIP-Seq.FOXA2.replicate.2

description: Transcription factor

value: Late pancreatic progenitor


title: Cyt49_PP2_shPDX1.ChIP-Seq.FOXA2.replicate.1

description: Transcription factor


title: Cyt49_HP.ChIP-Seq.FOXA1.replicate.1

description: Transcription factor


title: S_ctrl_Late_3

source_name: Ovary: Somatic Tissue 120h AEL

value: Somatic tissue


title: Cyt49_HP.ChIP-Seq.FOXA2.replicate.2

description: Transcription factor


title: Cyt49_HP.ChIP-Seq.HNF4A.replicate.1

description: Transcription factor


title: S_ctrl_Late_1


title: S_ctrl_Mid_2

source_name: Ovary: Somatic Tissue 96h AEL

value: III instar Larvae 96h AEL


title: Cyt49_PP2_shPDX1.ChIP-Seq.FOXA1.replicate.1

description: Transcription factor


title: Cyt49_HP.ChIP-Seq.FOXA1.replicate.2

description: Transcription factor


title: G_ctrl_Mid_1

source_name: Ovary: Germ line Tissue 96h AEL


title: S_ctrl_Mid_1


title: G_ctrl_Late_4


title: G_ctrl_Early_2


title: G_ctrl_Mid_4


title: G_ctrl_Early_1


title: W_ctrl_Mid_2

source_name: WT Whole Ovary 96h AEL

value: Oregon R

value: Whole Ovary


title: G_ctrl_Mid_3


title: W_ctrl_Late_2

source_name: WT Whole Ovary 120h AEL


title: W_ctrl_Early_3

source_name: WT Whole Ovary 72h AEL


title: S_ctrl_Late_2


title: W_ctrl_Mid_1


title: W_ctrl_Early_2


title: Cyt49_HP.ChIP-Seq.FOXA2.replicate.1

description: Transcription factor


title: S_ctrl_Early_3

source_name: Ovary: Somatic Tissue 72h AEL


title: S_ctrl_Early_1


title: BL160138C

city: shanghai

first: sheng

last: zhang

address: 270 Dongan Road, Shanghai

country: China

institute: Shanghai Cancer Center, Fudan University

description: Y200810_C_YX20200513001_BL160138C_S66_L004

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh38 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene FPKM values for every gene and every sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: adjacent tissue

extract_protocol:
The control tissue is the adjacent non-cancerous bladder tissue in the same patient. After collection, all samples were washed with pre-cooled RNA-free PBS (Thermo, USA), then placed in RNAlater™ Stabilization Solution (Thermo, USA), and stored at -80°C.Use MagMAX™ mirVana™ Total RNA Isolation Kit (Thermo, USA) to extract total RNA from the sample. Subsequently, Ribo-Zero Magnetic kit (Epicentre, USA) and magnetic stand (Thermo, USA) were used to remove ribosomal RNA (rRNA) from the total RNA sample.
the library was constructed using the Illumina TruseqTM RNA sample prep Kit method (Illumina, USA). Finally, the library was sequenced on Novaseq 6000 SBS Kit v3-HS (200cycles) (Illumina, USA)

tag: tissue type

value: adjacent tissue


title: BL160124N

description: Y200810_C_YX20200720004_BL160124N_S64_L004


title: BL160138T

description: Y200810_C_YX20200513001_BL160138T_S65_L004

source_name: bladder cancer

value: bladder cancer


title: BL160124T

description: Y200810_C_YX20200720004_BL160124T_S63_L004


title: W_ctrl_Late_3


title: W_ctrl_Mid_3


title: invasive front area_1

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

description: invasive front area_1

data_processing:
Sequencing was performed on an Illumina HiSeq 2500 platform in 75-base single-end mode.
The sequenced reads were mapped to the human reference genome sequences (hg19) using TopHat version 2.0.13 in combination with Bowtie2 version 2.2.3 and SAMtools version 0.1.19.
The fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cufflinks version 2.2.1.
Genome_build: hg19
Supplementary_files_format_and_content: FPKMs

source_name: invasive front area_1

extract_protocol:
Total RNA was extracted from the cells using the miRNeasy FFPE Kit (Qiagen, Hilden, Germany), in accordance with the manufacturer’s protocol.
NGS library preparation was performed using the SMARTer® Stranded Total RNA Sample Prep Kit-Pico Input Mammalian (Clontech, TaKaRa) according to the manufacturer’s instructions.

treatment_protocol: We prepared 10‐µm‐thick formalin-fixed paraffin-embedded (FFPE) sections and mounted them on a DIRECTOR Laser Microdissection Slide (AMR, Tokyo, Japan). We microdissected tumor cells in the invasive front area and the surface area separately in each case and subjected to RNA sequencing analysis.

value: endometrioid carcinoma

tag: region

value: invasive front area


title: W_ctrl_Early_1

source_name: WT Whole Ovary 72hours After Egg Laying (h AEL)


title: W_ctrl_Late_1


title: S_ctrl_Early_2


title: S_ctrl_Mid_3


title: invasive front area_2

description: invasive front area_2

source_name: invasive front area_2


title: BL160082N

description: Y200810_C_YX20200720004_BL160082N_S62_L004


title: BL160082T

description: Y200810_C_YX20200720004_BL160082T_S61_L004


title: Planktonic cells, biological replicate 3

type: RNA

city: Bozeman

first: Kerry

middle: S

last: Williamson

state: Montana

address: 109 Lewis Hall

department: Microbiology and Immunology

institute: Montana State University

description: Gene expression data from exponential phase cells.

hyb_protocol: Samples hybridized to microarrays contained a minimum of 1500 picomoles Cy dye and 4 ug cDNA.  Custom microarrays were designed by MYcroarray (now Arbor Biosciences, Ann Arbor, MI) specifically for Acinetobacter baumannii AB5075, with 5 replicate probes for every transcript. Four independent biological replicates were performed for each of the three conditions, for a total of 12 microarrays. A hybridization mixture containing 6x SSPE, 20% formamide, 0.12 mg acetylated BSA, 0.02% Tween20, 1% MYcroarray control oligos, 10 ug salmon sperm, and 4 ug cDNA in a 130 ul final volume was prepared for each sample. This was mixed, incubated at 65°C for 5 minutes, and then kept on ice for 5 minutes. The hybridization chamber (Agilent G2534A), gasket slide (Agilent Technologies G2534-60011), and MYcroarray slide (custom slide array CAT-3x20k-Acinetobacter_baumannii_AB5075) were preheated to 65°C. Samples were hybridized to the microarray for 18 hours at 48°C secured to the front of a culture roller with constant vertical rotation at 1.7 rpm. Array slides were then liberated from the gasket slide in 1x SSPE and washed with gentle agitation on a rocker (Boekel Scientific, Feasterville, PA). The washes were performed as follows: 1X SSPE at room temperature for 3 minutes, 1X SSPE at room temperature for 3 minutes, 1X SSPE at 48°C for 3 minutes, and then 0.25x SSPE at room temperature for 30 seconds. The slides were spun for 1 min in a high speed microarray centrifuge (ArrayIt Corporation, Sunnyvale, CA).

scan_protocol: Image acquisition was performed on the GenePix 4000B scanner (Molecular Devices, San Jose, CA) at 532 nm wavelength, a PMT gain of 600, 100% laser power, pixel size 5, with averaging 3 lines.

data_processing: Resulting Genepix images were saved as tiff files and converted to intensity values with GenePix Pro v 6.1 software. Gpr files of Acinetobacter baumannii array data were imported into Flexarray v 1.6.1, where local background correction and quantile normalization were performed. Resulting normalized median pixel intensity values for each probe were exported to Excel, where the trimmed mean was calculated and combined with annotation obtained from MYcroarray, PATRIC, NCBI, and the Manoil group (Ghallager, 2015). Trimmed means were reimported in to Flexarray 1.6.1, and ANOVA was performed to determine differentially expressed gene at p < 0.05 and fold change > 2.

label: Cy3 dye (GE Healthcare, Chicago, IL)

organism: Acinetobacter baumannii AB5075

source_name: Planktonic cells

label_protocol: Each cDNA sample was labeled with Cy 3 dye (GE Healthcare, Chicago, IL) for a minimum of 90 minutes at room temperature, protected from light, with mixing every 30 minutes. The reaction was quenched with 40 µl 0.1 M NaOAc, pH 5.2. Unincorporated dye molecules were removed with Clean and Concentrator-25 columns (Zymo Research, Irvine, CA). Quantities and incorporation rates were assessed with the Nanodrop 1000 (ThermoFisher Scientific, Waltham, MA).

growth_protocol: Acinetobacter baumannii AB5075 was cultured using a medium designed to mimic the exudate from a human chronic wound, referred to as artificial chronic wound exudate (ACWE) medium.  ACWE was composed of basal salts, amino acids, L-lactate, glucose, MgCl2, CaCl2, thiamine, nicotinic acid, and FeSO4, adjusted to pH 7.5, as described in Stewart, 2019. Planktonic cultures were prepared by inoculating 100 mL of ACWE medium with 1 mL of an overnight culture in 500 mL baffled Erlenmeyer flasks. Cultures were incubated to early exponential phase (OD 0.50, 3 x108 CFU x ml-1 ) at 33˚C (the approximate surface temperature of a dermal wound). Cells were harvested by centrifugation at 5,125 x g for 5 minutes at 4˚C in an Allegra® X-15R Centrifuge (Beckman Coulter, Brea, CA) and frozen at -80˚C for use in metabolomic and transcriptomic studies.Four independent biological replicates were performed. Biofilms were grown as described in Stewart, 2019. Briefly, biofilms were cultivated on hydroxyapatite-coated glass slides (Clarkson Chromatography, South Williamsport, PA) in a drip flow reactor (DFR) designed by Biosurface Technologies Corp., Bozeman, MT. 5 mls of exponential phase culture in ACWE was added to each channel of the DFR and incubated for one hour at 33˚C to allow for cell attachment. Following batch phase, a MasterFlex® L/S™ model 7519-20 peristaltic pump (Cole-Parmer, Vernon Hills, IL) was started at a flow rate of 10 mL/hour, and biofilms were cultivated at 33˚C for 72 hours. ACWE medium containing 20 mg/L tigecycline was then pumped through the treatment chambers, while ACWE without antibiotic continued to flow through the untreated control chambers for 24 h. After a total of 96 h of growth, biofilms were harvested by scraping into 10 mL phosphate buffered saline (PBS). The cell suspension was homogenized by vortexing and passage through an 18 gauge, 1.5-inch long Precisionglide® needle (Beckton Dickinson and Co., Franklin Lakes, NJ).  Cell pellets were collected by centrifugation and placed into a -80˚C freezer. Four independent biological replicates were performed.

extract_protocol: Frozen Acinetobacter baumannii cell pellets were resuspended in 100 µl TE/lysozyme, with lysozyme concentration at 5 mg ml-1. Following a 3 min room temperature incubation, tri-reagent (Zymo Research, Irvine, CA) was added and the samples were further incubated 5 minutes at room temperature. After the addition of an equal volume of 100% ethanol, the mixture was applied to a Zymo-Spin IIC column. RNA extraction was performed using the Direct-Zol Mini-Prep kit (Zymo Research, Irvine, CA) as per the manufacturer’s instructions, including an on-column DNase treatment. Samples were then treated with Turbo DNase (Thermo Fisher Scientific, Waltham, MA) following the rigorous treatment protocol in the presence of 1 µl of RnaseIn Plus (Promega, Madison, WI). Next, samples were applied to Clean and Concentrator-25 columns (Zymo Research, Irvine, CA) following the manufacturer’s procedure for recovery of total RNA greater than 200 nucleotides in size.

treatment_protocol: Planktonic cells were harvested by centrifugation at 5,125 x g for 5 minutes at 4˚C in an Allegra® X-15R Centrifuge (Beckman Coulter, Brea, CA) and frozen at -80˚C. After a total of 96 h of growth, biofilms were harvested by scraping into 10 mL phosphate buffered saline (PBS). The cell suspension was homogenized by vortexing and passage through an 18 gauge, 1.5-inch long Precisionglide® needle (Beckton Dickinson and Co., Franklin Lakes, NJ).  Cell pellets were collected by centrifugation and placed into a -80˚C freezer.

tag: antibiotic treatment

value: Untreated


title: Planktonic cells, biological replicate 2


title: Biofilm cells, biological replicate 3

description: Gene expression data from 96 hour old drip flow biofilms.

source_name: Biofilm cells


title: Biofilm cells, biological replicate 4


title: Biofilm cells, biological replicate 1


title: Antibiotic treated biofilm cells, biological replicate 2

description: Gene expression data from 96 hour old drip flow biofilms which were treated with tigecycline for the final 24 hours.

source_name: Antibiotic treated biofilm cells, replicate 2

value: 24 h of tigecycline treatment


title: Biofilm cells, biological replicate 2


title: Planktonic cells, biological replicate 1


title: Antibiotic treated biofilm cells, biological replicate 3

source_name: Antibiotic treated biofilm cells, replicate 3


title: Planktonic cells, biological replicate 4


title: Antibiotic treated biofilm cells, biological replicate 4

source_name: Antibiotic treated biofilm cells, replicate 4


title: Antibiotic treated biofilm cells, biological replicate 1

source_name: Antibiotic treated biofilm cells


title: Sample94.Naked mole rat.203203210035_R04C02

type: genomic

city: Los Angeles

first: Steve

last: Horvath

address: 695 Charles E. Young Drive South, Box 708822

department: Human Genetics

institute: University of California, Los Angeles

description: genomic DNA methylation from Naked mole rat Liver

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to the the Beadchip HorvathMammalMethylChip40 using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: SeSaMe normalization as described in W. Zhou et al 2018. PMID: 30085201

label: Cy3 and Cy5

organism: Heterocephalus glaber

source_name: Liver

label_protocol: Standard Illumina Protocol

growth_protocol: DNA extracted from tissues

extract_protocol: genomic DNA was extracted

treatment_protocol: Standard Illumina Protocol

tag: species

value: Naked mole rat

value: Liver

tag: age

tag: confidenceinageestimate

tag: canbeusedforagingstudies

value: yes

tag: Sex

value: Male

tag: queen

value: no


title: Sample86.Naked mole rat.203203210035_R02C01


title: Sample91.Naked mole rat.203203210035_R01C02

description: genomic DNA methylation from Naked mole rat Skin

source_name: Skin

value: Skin

value: Female


title: Sample95.Cape mole rat.203203210035_R05C02

description: genomic DNA methylation from Cape mole rat Liver

organism: Georychus capensis

value: Cape mole rat


title: Sample96.Naked mole rat.203203210035_R06C02

description: genomic DNA methylation from Naked mole rat Kidney

source_name: Kidney

value: Kidney


title: Sample92.Naked mole rat.203203210035_R02C02


title: Sample89.Naked mole rat.203203210035_R05C01


title: Sample81.Naked mole rat.203203210043_R03C02


title: Sample85.Naked mole rat.203203210035_R01C01


title: Sample83.Naked mole rat.203203210043_R05C02


title: Sample82.Naked mole rat.203203210043_R04C02


title: Sample74.Naked mole rat.203203210043_R02C01


title: Sample78.Naked mole rat.203203210043_R06C01


title: Sample93.Naked mole rat.203203210035_R03C02


title: Sample90.Naked mole rat.203203210035_R06C01


title: Sample73.Naked mole rat.203203210043_R01C01


title: Sample87.Cape mole rat.203203210035_R03C01


title: Sample69.Naked mole rat.203203210170_R03C02


title: Sample70.Naked mole rat.203203210170_R04C02


title: Sample71.Damaraland mole rat.203203210170_R05C02

description: genomic DNA methylation from Damaraland mole rat Liver

organism: Fukomys damarensis

value: Damaraland mole rat


title: Sample75.Naked mole rat.203203210043_R03C01


title: Sample65.Naked mole rat.203203210170_R05C01


title: Sample79.Damaraland mole rat.203203210043_R01C02


title: Sample67.Naked mole rat.203203210170_R01C02


title: Sample88.Naked mole rat.203203210035_R04C01


title: Sample76.Naked mole rat.203203210043_R04C01


title: Sample64.Naked mole rat.203203210170_R04C01


title: Sample77.Naked mole rat.203203210043_R05C01


title: Sample84.Naked mole rat.203203210043_R06C02


title: Sample72.Naked mole rat.203203210170_R06C02


title: Sample66.Naked mole rat.203203210170_R06C01


title: Sample58.Naked mole rat.203203210218_R04C02


title: Sample68.Naked mole rat.203203210170_R02C02


title: Sample61.Naked mole rat.203203210170_R01C01


title: Sample62.Naked mole rat.203203210170_R02C01


title: Sample63.Damaraland mole rat.203203210170_R03C01


title: Sample53.Naked mole rat.203203210218_R05C01


title: Sample57.Naked mole rat.203203210218_R03C02


title: Sample56.Naked mole rat.203203210218_R02C02


title: Sample60.Naked mole rat.203203210218_R06C02


title: Sample59.Naked mole rat.203203210218_R05C02


title: Sample49.Naked mole rat.203203210218_R01C01


title: Sample52.Naked mole rat.203203210218_R04C01


title: Sample51.Naked mole rat.203203210218_R03C01


title: Sample41.Naked mole rat.203203210093_R05C01


title: Sample43.Naked mole rat.203203210093_R01C02


title: Sample47.Damaraland mole rat.203203210093_R05C02


title: Sample48.Naked mole rat.203203210093_R06C02


title: Sample50.Naked mole rat.203203210218_R02C01


title: Sample44.Naked mole rat.203203210093_R02C02


title: Sample45.Naked mole rat.203203210093_R03C02


title: Sample39.Damaraland mole rat.203203210093_R03C01


title: Sample42.Naked mole rat.203203210093_R06C01


title: Sample46.Naked mole rat.203203210093_R04C02


title: Sample55.Damaraland mole rat.203203210218_R01C02


title: Sample54.Naked mole rat.203203210218_R06C01


title: Sample38.Naked mole rat.203203210093_R02C01


title: Sample40.Naked mole rat.203203210093_R04C01


title: Sample31.Damaraland mole rat.203203210174_R01C02


title: Sample30.Naked mole rat.203203210174_R06C01


title: Sample34.Naked mole rat.203203210174_R04C02


title: Sample24.Cape mole rat.203203210147_R06C02


title: Sample35.Naked mole rat.203203210174_R05C02


title: Sample27.Naked mole rat.203203210174_R03C01


title: Sample36.Naked mole rat.203203210174_R06C02


title: Sample25.Naked mole rat.203203210174_R01C01


title: Sample20.Naked mole rat.203203210147_R02C02


title: Sample23.Damaraland mole rat.203203210147_R05C02


title: Sample33.Naked mole rat.203203210174_R03C02


title: Sample37.Naked mole rat.203203210093_R01C01


title: Sample26.Naked mole rat.203203210174_R02C01


title: Sample29.Naked mole rat.203203210174_R05C01


title: Sample32.Cape mole rat.203203210174_R02C02


title: Sample13.Naked mole rat.203203210147_R01C01


title: Sample22.Naked mole rat.203203210147_R04C02


title: Sample16.Cape mole rat.203203210147_R04C01


title: Sample18.Naked mole rat.203203210147_R06C01


title: Sample14.Naked mole rat.203203210147_R02C01


title: Sample28.Naked mole rat.203203210174_R04C01


title: Sample12.Naked mole rat.203203210214_R06C02


title: Sample17.Naked mole rat.203203210147_R05C01


title: Sample15.Damaraland mole rat.203203210147_R03C01


title: Sample8.Cape mole rat.203203210214_R02C02


title: Sample10.Naked mole rat.203203210214_R04C02


title: Sample7.Damaraland mole rat.203203210214_R01C02


title: Sample11.Naked mole rat.203203210214_R05C02


title: Sample21.Naked mole rat.203203210147_R03C02


title: Sample2.Naked mole rat.203203210214_R02C01


title: Sample5.Naked mole rat.203203210214_R05C01


title: Sample296.Naked mole rat.205307780006_R03C01

description: genomic DNA methylation from Naked mole rat iPSC

source_name: iPSC

tag: tissue/cell type

value: iPSC


title: Sample287.Naked mole rat.204854860019_R06C01

description: genomic DNA methylation from Naked mole rat Blood

source_name: Blood

value: Blood


title: Sample6.Naked mole rat.203203210214_R06C01


title: Sample299.Naked mole rat.205307780006_R06C01

description: genomic DNA methylation from Naked mole rat Fibroblast

source_name: Fibroblast

value: Fibroblast


title: Sample285.Naked mole rat.204854860019_R04C01


title: Sample295.Naked mole rat.205307780006_R02C01


title: Sample284.Naked mole rat.204854860013_R06C02


title: Sample290.Naked mole rat.204854860019_R03C02


title: Sample286.Naked mole rat.204854860019_R05C01


title: Sample289.Naked mole rat.204854860019_R02C02


title: Sample297.Naked mole rat.205307780006_R04C01


title: Sample1.Naked mole rat.203203210214_R01C01


title: Sample9.Naked mole rat.203203210214_R03C02


title: Sample281.Naked mole rat.204854860013_R03C02


title: Sample283.Naked mole rat.204854860013_R05C02


title: Sample278.Naked mole rat.204854860013_R06C01


title: Sample3.Naked mole rat.203203210214_R03C01


title: Sample275.Naked mole rat.204854860013_R03C01


title: Sample293.Naked mole rat.204854860019_R06C02


title: Sample269.Naked mole rat.204854860020_R03C02


title: Sample294.Naked mole rat.205307780006_R01C01


title: Sample262.Naked mole rat.204854860020_R02C01


title: Sample260.Naked mole rat.204854860035_R06C02


title: Sample259.Naked mole rat.204854860035_R05C02


title: Sample257.Naked mole rat.204854860035_R03C02


title: Sample291.Naked mole rat.204854860019_R04C02


title: Sample298.Naked mole rat.205307780006_R05C01


title: Sample4.Naked mole rat.203203210214_R04C01


title: Sample263.Naked mole rat.204854860020_R03C01


title: Sample264.Naked mole rat.204854860020_R04C01


title: Sample255.Naked mole rat.204854860035_R01C02


title: Sample258.Naked mole rat.204854860035_R04C02


title: Sample277.Naked mole rat.204854860013_R05C01


title: Sample288.Naked mole rat.204854860019_R01C02


title: Sample256.Naked mole rat.204854860035_R02C02


title: Sample280.Naked mole rat.204854860013_R02C02


title: Sample292.Naked mole rat.204854860019_R05C02


title: Sample268.Naked mole rat.204854860020_R02C02


title: Sample276.Naked mole rat.204854860013_R04C01


title: Sample282.Naked mole rat.204854860013_R04C02


title: Sample279.Naked mole rat.204854860013_R01C02


title: Sample252.Naked mole rat.204854860035_R04C01


title: Sample249.Naked mole rat.204854860035_R01C01


title: Sample270.Naked mole rat.204854860020_R04C02


title: Sample250.Naked mole rat.204854860035_R02C01


title: Sample266.Naked mole rat.204854860020_R06C01


title: Sample265.Naked mole rat.204854860020_R05C01


title: Sample243.Naked mole rat.204854860052_R01C02


title: Sample248.Naked mole rat.204854860052_R06C02


title: Sample244.Naked mole rat.204854860052_R02C02


title: Sample267.Naked mole rat.204854860020_R01C02


title: Sample242.Naked mole rat.204854860052_R06C01


title: Sample271.Naked mole rat.204854860020_R05C02


title: Sample240.Naked mole rat.204854860052_R04C01


title: Sample261.Naked mole rat.204854860020_R01C01


title: Sample246.Naked mole rat.204854860052_R04C02


title: Sample238.Naked mole rat.204854860052_R02C01


title: Sample235.Naked mole rat.204549720012_R05C02


title: Sample233.Naked mole rat.204549720012_R03C02

description: genomic DNA methylation from Naked mole rat Spleen

source_name: Spleen

value: Spleen


title: Sample254.Naked mole rat.204854860035_R06C01


title: Sample232.Naked mole rat.204549720012_R02C02


title: Sample253.Naked mole rat.204854860035_R05C01


title: Sample245.Naked mole rat.204854860052_R03C02


title: Sample239.Naked mole rat.204854860052_R03C01


title: Sample236.Naked mole rat.204549720012_R06C02

description: genomic DNA methylation from Naked mole rat Cortex

source_name: Cortex

value: Cortex


title: Sample225.Naked mole rat.204549720012_R01C01

description: genomic DNA methylation from Naked mole rat Lung

source_name: Lung

value: Lung


title: Sample227.Naked mole rat.204549720012_R03C01


title: Sample226.Naked mole rat.204549720012_R02C01


title: Sample231.Naked mole rat.204549720012_R01C02


title: Sample241.Naked mole rat.204854860052_R05C01


title: Sample230.Naked mole rat.204549720012_R06C01


title: Sample234.Naked mole rat.204549720012_R04C02


title: Sample251.Naked mole rat.204854860035_R03C01


title: Sample247.Naked mole rat.204854860052_R05C02


title: Sample220.Naked mole rat.204549720002_R02C02


title: Sample229.Naked mole rat.204549720012_R05C01

description: genomic DNA methylation from Naked mole rat Muscle

source_name: Muscle

value: Muscle


title: Sample237.Naked mole rat.204854860052_R01C01

value: Naked mole rat


title: Sample213.Naked mole rat.204549720002_R01C01


title: Sample228.Naked mole rat.204549720012_R04C01


title: Sample217.Naked mole rat.204549720002_R05C01


title: Sample215.Naked mole rat.204549720002_R03C01


title: Sample224.Naked mole rat.204549720002_R06C02


title: Sample211.Naked mole rat.204549720001_R05C02


title: Sample209.Naked mole rat.204549720001_R03C02


title: Sample207.Naked mole rat.204549720001_R01C02


title: Sample198.Naked mole rat.204549720003_R04C02


title: Sample212.Naked mole rat.204549720001_R06C02


title: Sample204.Naked mole rat.204549720001_R04C01


title: Sample221.Naked mole rat.204549720002_R03C02


title: Sample222.Naked mole rat.204549720002_R04C02

description: genomic DNA methylation from Naked mole rat Heart

source_name: Heart

value: Heart


title: Sample199.Naked mole rat.204549720003_R05C02

value: yes


title: Sample218.Naked mole rat.204549720002_R06C01


title: Sample216.Naked mole rat.204549720002_R04C01


title: Sample193.Naked mole rat.204549720003_R05C01


title: Sample196.Naked mole rat.204549720003_R02C02

value: Male


title: Sample219.Naked mole rat.204549720002_R01C02

value: no


title: Sample200.Naked mole rat.204549720003_R06C02


title: Sample205.Naked mole rat.204549720001_R05C01


title: Sample208.Naked mole rat.204549720001_R02C02


title: Sample203.Naked mole rat.204549720001_R03C01


title: Sample214.Naked mole rat.204549720002_R02C01


title: Sample201.Naked mole rat.204549720001_R01C01


title: Sample202.Naked mole rat.204549720001_R02C01


title: Sample206.Naked mole rat.204549720001_R06C01


title: Sample197.Naked mole rat.204549720003_R03C02


title: Sample185.Naked mole rat.204551090038_R03C02


title: Sample192.Naked mole rat.204549720003_R04C01


title: Sample191.Naked mole rat.204549720003_R03C01


title: Sample188.Naked mole rat.204551090038_R06C02


title: Sample180.Naked mole rat.204551090038_R04C01


title: Sample177.Naked mole rat.204551090038_R01C01


title: Sample175.Naked mole rat.204551090060_R05C02

description: genomic DNA methylation from Naked mole rat Cerebellum

source_name: Cerebellum

value: Cerebellum


title: Sample190.Naked mole rat.204549720003_R02C01

value: Female


title: Sample186.Naked mole rat.204551090038_R04C02


title: Sample189.Naked mole rat.204549720003_R01C01


title: Sample195.Naked mole rat.204549720003_R01C02


title: Sample181.Naked mole rat.204551090038_R05C01


title: Sample168.Naked mole rat.204551090060_R04C01


title: Sample182.Naked mole rat.204551090038_R06C01


title: Sample179.Naked mole rat.204551090038_R03C01


title: Sample210.Naked mole rat.204549720001_R04C02


title: Sample178.Naked mole rat.204551090038_R02C01


title: Sample174.Naked mole rat.204551090060_R04C02


title: Sample167.Naked mole rat.204551090060_R03C01


title: Sample173.Naked mole rat.204551090060_R03C02


title: Sample161.Naked mole rat.204551090007_R03C02

value: Liver


title: Sample160.Naked mole rat.204551090007_R02C02


title: Sample162.Naked mole rat.204551090007_R04C02


title: Sample163.Naked mole rat.204551090007_R05C02


title: Sample171.Naked mole rat.204551090060_R01C02


title: Sample159.Naked mole rat.204551090007_R01C02


title: Sample164.Naked mole rat.204551090007_R06C02


title: Sample176.Naked mole rat.204551090060_R06C02


title: Sample170.Naked mole rat.204551090060_R06C01


title: Sample172.Naked mole rat.204551090060_R02C02


title: Sample169.Naked mole rat.204551090060_R05C01


title: Sample157.Naked mole rat.204551090007_R05C01


title: Sample156.Naked mole rat.204551090007_R04C01


title: Sample154.Naked mole rat.204551090007_R02C01


title: Sample165.Naked mole rat.204551090060_R01C01


title: Sample151.Naked mole rat.204551090043_R05C02


title: Sample144.Naked mole rat.203877620028_R06C02


title: Sample158.Naked mole rat.204551090007_R06C01


title: Sample153.Naked mole rat.204551090007_R01C01


title: Sample155.Naked mole rat.204551090007_R03C01


title: Sample166.Naked mole rat.204551090060_R02C01


title: Sample147.Naked mole rat.204551090043_R01C02


title: Sample184.Naked mole rat.204551090038_R02C02


title: Sample150.Naked mole rat.204551090043_R04C02


title: Sample140.Naked mole rat.203877620028_R02C02


title: Sample139.Naked mole rat.203877620028_R01C02


title: Sample223.Naked mole rat.204549720002_R05C02


title: Sample148.Naked mole rat.204551090043_R02C02


title: Sample149.Naked mole rat.204551090043_R03C02


title: Sample146.Naked mole rat.204551090043_R06C01


title: Sample142.Naked mole rat.203877620028_R04C02


title: Sample152.Naked mole rat.204551090043_R06C02


title: Sample141.Naked mole rat.203877620028_R03C02


title: Sample136.Naked mole rat.203877620028_R04C01


title: Sample138.Naked mole rat.203877620028_R06C01


title: Sample143.Naked mole rat.203877620028_R05C02


title: Sample145.Naked mole rat.204551090043_R05C01


title: Sample194.Naked mole rat.204549720003_R06C01


title: Sample137.Naked mole rat.203877620028_R05C01


title: Sample128.Naked mole rat.203877620093_R02C02

value: Kidney


title: Sample118.Naked mole rat.203877620048_R04C02


title: Sample130.Naked mole rat.203877620093_R04C02


title: Sample131.Naked mole rat.203877620093_R05C02


title: Sample127.Naked mole rat.203877620093_R01C02


title: Sample135.Naked mole rat.203877620028_R03C01


title: Sample133.Naked mole rat.203877620028_R01C01


title: Sample183.Naked mole rat.204551090038_R01C02


title: Sample126.Naked mole rat.203877620093_R06C01


title: Sample187.Naked mole rat.204551090038_R05C02


title: Sample114.Naked mole rat.203877620048_R06C01


title: Sample119.Naked mole rat.203877620048_R05C02


title: Sample120.Naked mole rat.203877620048_R06C02


title: Sample121.Naked mole rat.203877620093_R01C01


title: Sample122.Naked mole rat.203877620093_R02C01


title: Sample117.Naked mole rat.203877620048_R03C02


title: Sample134.Naked mole rat.203877620028_R02C01


title: Sample123.Naked mole rat.203877620093_R03C01


title: Sample125.Naked mole rat.203877620093_R05C01


title: Sample113.Naked mole rat.203877620048_R05C01


title: Sample124.Naked mole rat.203877620093_R04C01


title: Sample115.Naked mole rat.203877620048_R01C02


title: Sample110.Naked mole rat.203877620048_R02C01

value: Skin


title: Sample116.Naked mole rat.203877620048_R02C02


title: Sample112.Naked mole rat.203877620048_R04C01


title: Sample132.Naked mole rat.203877620093_R06C02


title: ILC2_Id1-Tg3_HDM

city: Seattle

first: Elia

middle: D.

last: Tait Wojno

state: WA

address: 750 Republican St.

department: Department of Immunology

institute: University of Washington

data_processing:
ATAC raw data was mapped to the Mus musculus 10 (mm10) genome using the Burrows-Wheeler Alignment (BWA)-mem algorithm (PMID: 19451168) and peaks were called using MACS2 (PMID: 18798982).
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated based on MACS2 pileup bedgraphs
Supplementary_files_format_and_content: narrowPeak files were generated by MACS2

organism: Mus musculus

source_name: Lung ILC2

growth_protocol: Id1tg/tg and Id1tg/WT mice were as described (PMID: 10567549). For Id1tg/WT mice, Id1tg/tg mice were crossed with C57BL/6 WT mice (Jackson Laboratories, Bar Harbor, ME) and bred in-house. Co-housed experimental controls were Id1WT/WT male or female littermates, in specific pathogen-free conditions at Cornell University or the University of Washington, in accordance with protocols approved by the respective Institutional Animal Care and Use Committees.

extract_protocol:
For flow sorting, the entire lung was collected for tissue digestion. Lungs were digested with 20 µg/mL DNAase (Roche) and 2 mg/mL collagenase D (Roche) or 1 U/mL Liberase TL (Roche) at 37°C. Single cell suspensions were mashed through a 40 μm strainer. Lungs were RBC lysed with ACK lysis buffer (Lonza). For ILC2s and CD4+ T cells, single cell suspensions were sorted using a 4-laser FACS Fusion (BD Biosciences) (WT ILC2 and CD4+ T cell ATAC-seq), or a 4-laser and 3-laser Aria (BD Biosciences) (Id1WT/WT versus Id1tg/WT ILC2 ATAC-seq ) with an 85 μm nozzle. All leukocyte populations were gated as singlet, live (Live/Dead Aqua-) CD45+ leukocytes (by FSC-A/SSC-A), ILC2s were gated as lineage (lin) (CD3/CD5orTCRβ/CD11b/CD11c/CD19/NK1.1/TCRγδ)-CD90.2+/-CD127+Klrg1+/-ST2+/-, and CD4+ T cells were gated as TCRβ+, lineage (lin) (CD11b/CD11c/CD19/NK1.1/TCRγδ)-CD4+, further subdivided as Foxp3+ Tregs, Foxp3- CD44hiCD62Llo activated, and Foxp3-Gata3+, or ST2+ Th2 cells.
Following flow sorting, ILC2s or CD4+ T cells were resuspended in cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40 Lysis Buffer (IGEPAL) in H2O) with 1x protease and 2 U/mL SuperaseIN RNase (ThermoFisher) inhibitors. Permeabilized cells were resuspended in storage buffer (50 mM Tris-HCl, pH 8.3, 5 mM MgCl2, 40% glycerol, 0.1 mM EDTA, pH 8.0, plus 40 U RNase inhibitor in H2O) and stored at -80 °C. Permeabilized cells were washed in PBS, then incubated in Transposition Mix (Nextera DNA Sample Preparation kit, Illumina), as previously described (PMID: 25559105). Following transposition, WT CD4+ T cells and ILC2 samples from PBS- or HDM-treated mice were purified using the Monarch Gel Extraction kit (NEB). Libraries were amplified using Nextera PCR oligos (Illumina) and Next High-Fidelity PCR Master Mix (NEB) for 12-14 cycles, cleaned up using the Monarch Gel Extraction kit and AMPure beads (Beckman Coulter), and sequenced with 2x 41 nucleotide paired-end reads on the NextSeq500 (Illumina). For Id1WT/WT and Id1tg/WT ILC2 analysis from HDM-treated mice, following transposition, samples were purified using the Qiagen MinElute PCR Purification kit. All libraries were amplified using PCR oligos as described previously (PMID: 24097267) and NEB Next High-Fidelity PCR Master Mix (NEB) for 11 cycles. Libraries were purified using the Qiagen MinElute PCR Purification kit and treated with the Free Adapter Blocking Reagent (Illumina) with 1.8x Agencourt AMPure XP bead size selection (Beckman Coulter).  Sequencing was performed with a target of 50M reads per library using 59 base paired-end reads on a P2 flowcell on the NextSeq2000 (Illumina).

treatment_protocol: Mice were administered 80 mg of HDM (Greer) in 40 mL PBS or PBS alone intranasally (IN), every 7 days for 3 weeks. Tissues were collected 3 days after the final treatment.

tag: genotype/variation


title: Sample129.Naked mole rat.203877620093_R03C02


title: Sample93.Naked mole rat.203877620033_R03C02


title: Sample99.Naked mole rat.203877620041_R03C01


title: ILC2_Id1-Tg2_HDM


title: Sample92.Naked mole rat.203877620033_R02C02


title: Sample108.Naked mole rat.203877620041_R06C02


title: Sample100.Naked mole rat.203877620041_R04C01


title: Sample104.Naked mole rat.203877620041_R02C02


title: Sample89.Naked mole rat.203877620033_R05C01


title: Sample96.Naked mole rat.203877620033_R06C02


title: Sample109.Naked mole rat.203877620048_R01C01


title: Sample111.Naked mole rat.203877620048_R03C01


title: Sample94.Naked mole rat.203877620033_R04C02


title: Sample102.Naked mole rat.203877620041_R06C01


title: Sample101.Naked mole rat.203877620041_R05C01


title: ILC2_Id1-Tg1_HDM


title: Sample98.Naked mole rat.203877620041_R02C01


title: Sample105.Naked mole rat.203877620041_R03C02


title: ILC2_WT2_HDM


title: ILC2_WT1_HDM


title: VM294-total

city: New York

first: Stuart

middle: Aidan

last: Quinn

state: NY

address: 1130 St Nicholas Ave

department: Institute for Cancer Genetics

institute: Columbia University

data_processing:
Reads were mapped to mm10 mouse reference genome using HISAT2 (v 2.1.0) with default parameters.
Count matrix were generated with Htseq (v 0.5.4) with genecode mouse transcript reference annotation vM24.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.counts.txt: Tab-delimited text files include counts.

source_name: Whole spleen

extract_protocol:
RNA was extracted with RNeasy Micro Kit (Qiagen) following manufacturer's guidelines.
We performed RNA library preparations and next-generation sequencing using the SMART-Seq v4 Ultra Low Input Kit for Sequencing for full-length cDNA synthesis and amplification at Genewiz.
Illumina Nextera XT Library Preparation Kit was used for library preparation. Sequencing was performed on an Illumina HiSeq platform (Illumina).

value: Whole spleen

tag: status

value: tumor

tag: genotype

value: CD4-CreERT2Vav1Myo1f fl/wt


title: Sample106.Naked mole rat.203877620041_R04C02


title: Sample88.Naked mole rat.203877620033_R04C01


title: Sample86.Naked mole rat.203877620033_R02C01


title: Sample85.Naked mole rat.203877620033_R01C01


title: Sample87.Naked mole rat.203877620033_R03C01


title: Sample90.Naked mole rat.203877620033_R06C01


title: VM231-CD4

source_name: CD4+ T Cells

value: CD4+ T Cells


title: A3-ERT2-total

value: normal

value: CD4-CreERT2 (WT)


title: Sample103.Naked mole rat.203877620041_R01C02


title: Sample107.Naked mole rat.203877620041_R05C02


title: ILC2_WT3_HDM

value: Lung


title: Sample97.Naked mole rat.203877620041_R01C01

value: Naked mole rat


title: VM236-total


title: Sample79.Naked mole rat.203877620054_R01C02


title: A1-ERT2-CD4


title: VM236-CD4


title: Sample76.Naked mole rat.203877620054_R04C01


title: Sample83.Naked mole rat.203877620054_R05C02


title: Sample74.Naked mole rat.203877620054_R02C01


title: F1619_L_V1C

city: New Haven

first: Nenad

last: Sestan

address: 333 Cedar Street, SHM C-316C

department: Neuroscience

institute: Yale University School of Medicine

description:
marmoset.injured.V1.UMIs.txt
marmoset.injured.V1.meta.txt

data_processing:
The cellranger version 3.1.0 commercial software was utilized to conduct the initial data processes.
Seurat and some in-house customized scripts were used to manage the single nuclei transcriptomic datasets.
For detailed snRNAseq analysis methods see Supplementary Information.
Genome_build: calJac3
Supplementary_files_format_and_content: Tab-delimited text file includes UMI values for every gene in each cell
Matrix table with meta information for every cell

organism: Callithrix jacchus

source_name: primary visual cortex (V1)

extract_protocol:
Adult marmosets in both injured (one-week post-ET-1-induced ischemic stroke, n=3) and uninjured cohorts (control, n=3) were administered an overdose of sodium pentobarbitone (100mg/ kg; IM). Following the loss of corneal and muscular reflexes, the animals were decapitated, and the brain removed under aseptic conditions. Cerebral tissues were rinsed in chilled PBS to remove excess blood, before microdissection of regions of interest within V1, including operculum V1 but excluding calcarine V1 and associated white matter. In stroke animals, this also included the core and penumbra. Dissected tissues were placed in sterile tubes and dropped into liquid nitrogen before storage at -80˚C. The procedures/ dissections were performed in chilled RNAase-free PBS with RNase-free sterilized instruments under RNase-free conditions. Approximate time from apnea to snap-freezing ranged from 20-30m. Nuclei from injured and control frozen cerebral tissues were isolated by Dounce homogenization and centrifugation. For more detail see Supplementary Methods.
RNA libraries were prepared for sequencing using standard manufacturer (Illumina/ MGITech) protocols

value: Adult

tag: treatment

value: Injured


title: A2-ERT2-total


title: Sample82.Naked mole rat.203877620054_R04C02

value: yes

value: Male


title: Hbo1fl/fl;Mx1Cre progenitor cells with both alleles of Hbo1 deleted - prog Mx1Cre HBO1 knokout replicate 2

city: Parkville

first: Waruni

last: Abeysekera

state: Victoria

address: 1G Royal Parade

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
FASTQ files were output using standard Illumina protocols and software.
Reads were aligned to the mouse genome by Rsubread version 1.29.6
Read counts were summarized by Entrez Gene ID using the Rsubread featureCounts function and NCBI annotation
Genome_build: mm10 (NCBI build 38.1)
Supplementary_files_format_and_content: Tab-delimited text files; columns represent Entrez Gene ID, total gene length (total base count of all exons) and the number of reads mapping to that gene

source_name: Progenitor cells

growth_protocol: adult samples

extract_protocol:
RNA (50 ng) isolated from FACS-sorted LSK or progenitor cells was used to generate barcoded sequencing libraries
libraries were constructed using the Illumina TrueSeq library construction kit
Paired-end 80 bp RNA-sequencing short reads were generated using NextSeq500 (Illumina), between 20 and 48 million read pairs for each sample

treatment_protocol: Stem cells (LSK) and progenitors were isolated by FACS from mice in which HBO1 deletion was induced either by the MX1-Cre recombinase after treatement with PolyIC (induceing interferon) or the RosaCreERT2 recombinase after treatment with tamoxifen and their respective wild type Cre expressing controls

value: HBO1 knokout

tag: mouse

tag: gender

tag: cell type

value: Progenitor cells


title: A1-ERT2-total

tag: strain

tag: tissue


title: Hbo1fl/fl;Mx1Cre progenitor cells with both alleles of Hbo1 deleted - prog Mx1Cre HBO1 knokout replicate 1

value: Female


title: Sample80.Naked mole rat.203877620054_R02C02


title: Sample78.Naked mole rat.203877620054_R06C01

value: no


title: Sample72.Naked mole rat.203877620044_R06C02

value: Skin


title: Sample70.Naked mole rat.203877620044_R04C02


title: Sample77.Naked mole rat.203877620054_R05C01


title: Hbo1fl/fl;CreER progenitor cells with both alleles of Hbo1 deleted - prog CreER HBO1 knokout replicate 3


title: VM231-total

value: Whole spleen


title: Sample84.Naked mole rat.203877620054_R06C02


title: Hbo1fl/fl;CreER progenitor cells with both alleles of Hbo1 deleted - prog CreER HBO1 knokout replicate 2


title: 6m5_DMSO_S4

first: Yijiang

last: Shi

address: 11301 wilshire blvd

institute: UCLA

data_processing:
Reads were obtained by Illumina HiSeq 3000 sequencer for Single End 50bp.
Partek Flow Genomic Analysis Software was used for bioinformatics analysis including reads alignment, gene feature annotation, and differential gene expression analysis.
The differential gene expressions were examined using DESeq2 algorithm.
QIAGEN Ingenuity Pathway Analysis (IPA) software was used for pathway enrichment analysis of differentially expressed genes.
Genome_build: MM10
Supplementary_files_format_and_content: comparison of RNA abundance in the DMSO and J007 treated MM lines; raw counts

source_name: Cultured MM line from IL6myc transgenic mouse

extract_protocol:
Total RNA were extracted using RNeasy kit (Qiagen)
the cDNA library were prepared using KAPA Stranded mRNA-Seq Kit(Roche).

value: IL6myc transgenic

value: myc-driven murine myeloma cells

value: DMSO


title: F1711_L_V1C


title: Sample75.Naked mole rat.203877620054_R03C01

source_name: Skin


title: F1565_L_V1C


title: Antibiotic treated biofilm cells, biological replicate 3

first: Michael

middle: J

last: Franklin

state: MT

department: Microbiology and Cell Biology

description: Gene expression data from 96 hour old drip flow biofilms which were treated with daptomycin for the final 24 hours.

hyb_protocol: Labeled cDNA was then hybridized to GeneChip™ S. aureus genome arrays (Applied Biosystems, ThermoFisher Scientific, Waltham, MA, part 9003514) for 16 h at 45˚C with constant rotation.

scan_protocol: Microarrays were stained using a GCOS Fluidics Station 450 and scanned with an Affymetrix 7G scanner.

data_processing: Affymetrix GCOS v1.4 was used to generate CEL files, which were imported into FlexArray v1.6.1 for quality control and data analysis. Staphylococcus aureus microarray data from three independent biological replicates from each condition (planktonic, biofilm, and treated biofilm) was background corrected and normalized using the GC-RMA algorithm in Flexarray 1.6.1 as published in Stewart, 2019. ANOVA was performed to determine genes with statistically significantly changes in expression (2-fold change at p < 0.05). Strain USA300_FPR3757 was hybridized to Affymetrix S. aureus microarrays which contain probes designed for the following four strains: N315, Mu50, NCTC 8325, and COL. Affymetrix identifiers from the four strains were converted to USA300 gene IDs based on PanGenome identifiers from AureoWiki, the repository of the Staphylococcus aureus research and annotation community.

label: Biotin

organism: Staphylococcus aureus

source_name: Antibiotic treated biofilm cells, replicate 3

label_protocol: Staphylococcus aureus RNA samples (10 µg) were reverse transcribed, fragmented, and labeled according to the Affymetrix prokaryotic target labeling protocol (GeneChip expression analysis technical manual, November 2004).

growth_protocol: Staphylococcus aureus USA300 FPR3757 was cultured using a medium designed to mimic the exudate from a human chronic wound, referred to as artificial chronic wound exudate (ACWE) medium.  ACWE was composed of basal salts, amino acids, L-lactate, glucose, MgCl2, CaCl2, thiamine, nicotinic acid, and FeSO4, adjusted to pH 7.5, as described in Stewart, 2019. Planktonic cultures were prepared by inoculating 100 mL of ACWE medium with 1 mL of an overnight culture in 500 mL baffled Erlenmeyer flasks. Cultures were incubated to early exponential phase (OD 0.10, 1. 3 x10^8 CFU ml-1) at 33˚C (the approximate surface temperature of a dermal wound). Cells were harvested by centrifugation at 5,125 x g for 5 minutes at 4˚C in an Allegra® X-15R Centrifuge (Beckman Coulter, Brea, CA) and frozen at -80˚C for use in metabolomic and transcriptomic studies. Three independent biological replicates were performed. Biofilms were grown as described in Stewart, 2019. Briefly, biofilms were cultivated on hydroxyapatite-coated glass slides (Clarkson Chromatography, South Williamsport, PA) in a drip flow reactor (DFR) designed by Biosurface Technologies Corp., Bozeman, MT. 5 mls of exponential phase culture in ACWE was added to each channel of the DFR and incubated for one hour at 33˚C to allow for cell attachment. Following batch phase, a MasterFlex® L/S™ model 7519-20 peristaltic pump (Cole-Parmer, Vernon Hills, IL) was started at a flow rate of 10 mL/hour, and biofilms were cultivated at 33˚C for 72 hours. ACWE medium containing 10 mg/L daptomycin was then pumped through the treatment chambers, while ACWE without antibiotic continued to flow through the untreated control chambers for 24 h. After a total of 96 h of growth, biofilms were harvested by scraping into 10 mL phosphate buffered saline (PBS). The cell suspension was homogenized by vortexing and passage through an 18 gauge, 1.5-inch long Precisionglide® needle (Beckton Dickinson and Co., Franklin Lakes, NJ).  Cell pellets were collected by centrifugation and placed into a -80˚C freezer. Three independent biological replicates were performed.

extract_protocol: Cell pellets from planktonic cultures, biofilms, and treated biofilms were incubated for 2 min at 37C in TE pH 8.0 containing 0.5 mg/ml lysostaphin and 3.0 mg/ml lysozyme with frequent vortexing. Following the addition of 1 mL of tri-reagent (Zymo Research, Irvine, CA), samples were incubated 5 min at room temperature, and then 5 min at 65C with vortexing. After the addition of an equal volume of 100% ethanol, the mixture was applied to a Zymo-Spin IIICG column. RNA extraction was performed using the Direct-Zol Mini-Prep kit (Zymo Research, Irvine, CA) as per the manufacturer’s instructions, including on-column DNase treatment. Samples were then treated with Turbo DNase (Thermo Fisher Scientific, Waltham, MA) following the rigorous treatment protocol in the presence of 1 µl of RnaseIn Plus (Promega, Madison, WI). Next, samples were applied to Clean and Concentrator-25 columns (Zymo Research, Irvine, CA) following the manufacturer’s procedure for recovery of total RNA greater than 200 nucleotides in size.  For all samples, RNA quality was assessed on the BioAnalyzer 2100 (Agilent, Santa Clara, CA) RNA6000 nano assay.

tag: antibiotic treatment

value: 24 h of daptomycin treatment


title: Biofilm cells, biological replicate 2

description: Gene expression data from 96 hour old drip flow biofilms.

source_name: Biofilm cells, replicate 2

value: Untreated


title: Biofilm cells, biological replicate 1

source_name: Biofilm cells, replicate 1


title: Sample67.Naked mole rat.203877620044_R01C02

tag: species


title: Planktonic cells, biological replicate 3

description: Gene expression data from exponential phase cells.

source_name: Planktonic cells, replicate 3


title: Hbo1fl/fl;Mx1Cre progenitor cells with both alleles of Hbo1 deleted - prog Mx1Cre HBO1 knokout replicate 3


title: Antibiotic treated biofilm cells, biological replicate 1

source_name: Antibiotic treated biofilm cells, replicate 1


title: Sample66.Naked mole rat.203877620044_R06C01

description: genomic DNA methylation from Naked mole rat Adipose

source_name: Adipose

value: Adipose

tag: age


title: Hbo1fl/+;Mx1Cre progenitor cells with one allele of Hbo1 deleted - prog Mx1Cre control replicate 4

value: Control


title: Sample73.Naked mole rat.203877620054_R01C01

description: genomic DNA methylation from Naked mole rat Skin

value: Naked mole rat

tag: confidenceinageestimate


title: Hbo1fl/fl;CreER progenitor cells with both alleles of Hbo1 deleted - prog CreER HBO1 knokout replicate 4


title: Sample69.Naked mole rat.203877620044_R03C02

tag: canbeusedforagingstudies


title: Hbo1fl/+;Mx1Cre progenitor cells with one allele of Hbo1 deleted - prog Mx1Cre control replicate 2


title: A3-ERT2-CD4

value: CD4+ T Cells

value: normal

value: CD4-CreERT2 (WT)


title: Sample62.Naked mole rat.203877620044_R02C01

value: yes

tag: Sex

value: Male


title: Hbo1fl/+;Mx1Cre progenitor cells with one allele of Hbo1 deleted - prog Mx1Cre control replicate 3

value: Progenitor cells


title: Foxp3_1 [bulk RNA-seq]

city: Montreal

first: Judith

last: Mandl

state: Quebec

address: 3649 Promenade Sir William Osler

country: Canada

institute: McGill University

data_processing:
FASTQ files from L003, L004, L005, L006, L007, and L008 were merged for each R1 and R2 per sample.
Reads were then mapped to the mouse UCSC mm9 reference assembly using TopHat v2.0.11 (Kim et al., 2013).
Reads overlapping exons were counted using featureCounts v1.4.5 from the SubRead package (Liao et al., 2014) with a minimum mapping quality of 10.
Normalized read counts differential gene expression analysis was performed with EdgeR (Robinson et al., 2010). We retained genes that had an expression level of minimum 5 counts per million reads (CPM) in at least 3 of the 4 biological replicates.
Pairwise comparisons were perfomed. The p-values were corrected using the Benjamini-Hochberg method and a FDR threshold of <0.01 was considered significant. No fold change threshold was set.
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with CPM values
Supplementary_files_format_and_content: Tab-delimited text with raw gene counts for every gene in each sample

source_name: Lymphocytes

growth_protocol: Both males and females were used.

extract_protocol:
Mouse spleen and lymph nodes were processed to single-cell suspension and T cells were enriched prior to FACS staining. CD5lo and CD5hi naïve CD4+ T cells were sorted by Live, singlets, Dump-, TCRb+, CD4+, CD8-, Foxp3-GFP-, CD44-, 15% CD5lo or 15% CD5hi. Tregs were sorted by Live, singlets, Dump-, TCRb+, CD4+, CD8-, Foxp3-GFP+. Dump channel included B220, CD11c, F4/80, NK1.1, CD11b, CD69, and Ly6G. Cells were placed in 500uL TRIzol (ThermoFisher Scientific). RNA was isolated using RNA miniprep kit (Zymo Research).
Library preparation were performed using the TruSeq mRNA library preparation kit v2 (Illumina).The libraries were sequenced on an Illumina HiSeq 2000 sequencer using v3 chemistry and 50 cycle paired end reads.

treatment_protocol: Freshly sorted CD5lo and CD5hi naïve CD4+ T cells were either directly processed for sequencing or rested in culture with IL-7 (10ng/mL) for 22 hours at which point cells were processed for sequencing. Tregs were directly processed for sequencing.

value: 8-12 weeks of age

value: pooled male and female

value: Spleen and lymph node

value: CD5lo naive CD4+ T cells (sorted by TCRb+,CD4+,CD8-,Foxp3-GFP+)

value: Freshly sorted


title: Foxp3_2 [bulk RNA-seq]


title: Sample71.Naked mole rat.203877620044_R05C02

value: Skin

tag: queen


title: Antibiotic treated biofilm cells, biological replicate 2

source_name: Antibiotic treated biofilm cells, replicate 2

value: 24 h of daptomycin treatment


title: rCD5hi_3 [bulk RNA-seq]

value: CD5lo naive CD4+ T cells (sorted by TCRb+,CD4+,CD8-,Foxp3-GFP-,CD44lo,15% CD5hi)

value: Rested in dissociated culture for 22hr with IL-7


title: Sample68.Naked mole rat.203877620044_R02C02

tag: tissue/cell type

value: Female


title: Foxp3_4 [bulk RNA-seq]


title: Foxp3_3 [bulk RNA-seq]


title: 6m5_J007_S5

tag: genotype/variation

value: IL6myc transgenic

value: myc-driven murine myeloma cells


title: Hbo1fl/fl;CreER progenitor cells with both alleles of Hbo1 deleted - prog CreER HBO1 knokout replicate 1

value: HBO1 knokout


title: rCD5hi_4 [bulk RNA-seq]


title: rCD5lo_2 [bulk RNA-seq]

value: CD5lo naive CD4+ T cells (sorted by TCRb+,CD4+,CD8-,Foxp3-GFP-,CD44lo,15% CD5lo)


title: rCD5hi_2 [bulk RNA-seq]


title: Biofilm cells, biological replicate 3

source_name: Biofilm cells, replicate 3

value: Untreated


title: Sample60.Naked mole rat.203877620092_R06C02

value: Naked mole rat

value: yes

value: no


title: Sample59.Naked mole rat.203877620092_R05C02


title: Hbo1fl/+;CreER progenitor cells with one allele of Hbo1 deleted - prog CreER control replicate 3

value: Control

value: Progenitor cells


title: Sample58.Naked mole rat.203877620092_R04C02

value: Male


title: Hbo1fl/+;CreER progenitor cells with one allele of Hbo1 deleted - prog CreER control replicate 2


title: Hbo1fl/+;CreER progenitor cells with one allele of Hbo1 deleted - prog CreER control replicate 4


title: rCD5lo_4 [bulk RNA-seq]

value: 8-12 weeks of age

value: pooled male and female

value: Spleen and lymph node


title: Sample61.Naked mole rat.203877620044_R01C01

value: Skin


title: Planktonic cells, biological replicate 2

source_name: Planktonic cells, replicate 2


title: Sample65.Naked mole rat.203877620044_R05C01


title: Hbo1fl/+;Mx1Cre progenitor cells with one allele of Hbo1 deleted - prog Mx1Cre control replicate 1


title: Hbo1fl/+;CreER progenitor cells with one allele of Hbo1 deleted - prog CreER control replicate 1


title: fCD5hi_4 [bulk RNA-seq]

value: CD5lo naive CD4+ T cells (sorted by TCRb+,CD4+,CD8-,Foxp3-GFP-,CD44lo,15% CD5hi)

value: Freshly sorted


title: rCD5hi_1 [bulk RNA-seq]

value: Rested in dissociated culture for 22hr with IL-7


title: Planktonic cells, biological replicate 1

source_name: Planktonic cells, replicate 1


title: rCD5lo_1 [bulk RNA-seq]


title: fCD5hi_3 [bulk RNA-seq]


title: rCD5lo_3 [bulk RNA-seq]


title: fCD5hi_1 [bulk RNA-seq]


title: fCD5lo_4 [bulk RNA-seq]


title: Sample57.Naked mole rat.203877620092_R03C02


title: fCD5lo_1 [bulk RNA-seq]


title: fCD5hi_2 [bulk RNA-seq]


title: fCD5lo_3 [bulk RNA-seq]


title: Hbo1fl/fl;Mx1Cre LSK cells with both alleles of Hbo1 deleted - LSK Mx1Cre HBO1 knokout replicate 2

source_name: LSK cells

value: Female

value: LSK cells


title: Hbo1fl/fl;Mx1Cre LSK cells with both alleles of Hbo1 deleted - LSK Mx1Cre HBO1 knokout replicate 3

value: HBO1 knokout


title: fCD5lo_2 [bulk RNA-seq]

value: CD5lo naive CD4+ T cells (sorted by TCRb+,CD4+,CD8-,Foxp3-GFP-,CD44lo,15% CD5lo)


title: Hbo1fl/fl;Mx1Cre LSK cells with both alleles of Hbo1 deleted - LSK Mx1Cre HBO1 knokout replicate 4


title: Hbo1fl/fl;Mx1Cre progenitor cells with both alleles of Hbo1 deleted - prog Mx1Cre HBO1 knokout replicate 4


title: Hbo1fl/fl;Mx1Cre LSK cells with both alleles of Hbo1 deleted - LSK Mx1Cre HBO1 knokout replicate 1


title: MRSA1679a-2

city: Shenzhen

first: ZAHID

last: IQBAL

address: Shenzhen University, Xili campus, A1-108

institute: Shenzhen University

data_processing:
Sequencing Reads Filtering
de novo assembly by Trinity
Unigene Functional Annotation with NR, NT, GO, COG, KEGG, Swissprot and Interpro
Unigene CDS Prediction with ESTScan
DEG Detection
Genome_build: de novo assembly
Supplementary_files_format_and_content: txt, unigenes with annotations

source_name: Poultry

growth_protocol: MRSA strain was cultured on Mueller-Hinton (MH) agar supplemented with 5% sheep blood (Ruite Bio-Technology Co. Ltd., Guangzhou, China) for 24-48 hours at 37°C under microaerobic conditions (5% O2, 10% CO2, and 85% N2).

extract_protocol:
Total RNA was extracted with TRIzol (Invitrogen, California, USA) from the bacterial samples, according to the manufacturer's instructions. Genomic DNA contamination was removed by using RNase-free DNase I (Ambion, Inc., Texas, USA) following  the manufacturer’s instructions. Ribosomal RNA was removed from the total RNA using the Ribozero Kit following the manufacturer’s protocol.
Purified mRNA from the bacterial samples was used for transcriptome sequencing, and the library was constructed by using Illumina HiSeq 4000 at the Beijing Genomics Institute. After filtering, the remaining clean reads were stored in FASTQ (Cock et al., 2010) format and Trinity was used to perform de novo assembly with clean reads. Then, gene family clustering was performed with Tgicl to get the final unigenes.
Differentially expressed genes (DEGs) were detected with NOIseq, which is based on a noisy distribution model, as described in a previous study (Tarazona et al., 2011). Hierarchical clustering was carried out for DEGs using a heatmap, which is a function of R. For clustering more than two groups, the intersection and union DEGs between them were shown on the heatmap.

treatment_protocol: A fresh overnight culture of MRSA1679a with an initial OD600 of 0.05 was added to two flasks containing 100 mL MHB and incubated to an OD600 of 0.3. Then, 1 mL of a stock solution of 128 μg/mL cefquinome was added to the experimental group to reach a final concentration of ½×MIC (0.50 μg/mL). The same volume of distilled water was added to the control culture. The experimental and control cultures were incubated further for 45 minutes before RNA extraction.

tag: strain background

tag: phenotype

value: methicillin resistant

value: untreated

tag: resistance

value: highly resistant against many kind of antibiotics


title: Hbo1fl/fl;CreER LSK cells with both alleles of Hbo1 deleted - LSK CreER HBO1 knokout replicate 4

tag: genotype

tag: mouse


title: CEQ-MRSA1679a-1

tag: treatment

value: treated


title: Hbo1fl/fl;CreER LSK cells with both alleles of Hbo1 deleted - LSK CreER HBO1 knokout replicate 2

tag: strain

tag: gender

tag: cell type


title: Hbo1fl/fl;CreER LSK cells with both alleles of Hbo1 deleted - LSK CreER HBO1 knokout replicate 3


title: MRSA1679a-1


title: Sample55.Naked mole rat.203877620092_R01C02

tag: species

value: Naked mole rat

value: yes

value: no


title: Sample53.Naked mole rat.203877620092_R05C01

tag: age


title: Uninfected hepatocytes [8.3]

city: Athens

first: Samarchith

last: Kurup

state: GA

address: 500 DW Brooks Dr, 330c Coverdell Center

department: CTEGD - Cellular Biology

institute: University of Georgia

description: Gene expression in uninfected hepatocytes

hyb_protocol: Biotin-labeled ss-cDNA was then mixed with Affymetrix eukaryotic hybridization buffer, placed onto the Affymetrix GeneChip Mouse Transcriptome  Array 1.0 (Part No. 902511), and incubated at 45º C for 18 h with 60 rpm rotation

scan_protocol: GeneChips were scanned using the Affymetrix Model 3000 scanner (with 7G upgrade).

data_processing:
The data were collected using Affymetrix Comand Console operating software v4.1.2 and  Affymetrix Expression Console Software Build 1.4.4.46 using Affymetrix default analysis settings and global scaling as normalization method.
affymetrix-algorithm-name = sst-rma-gene-full
affymetrix-algorithm-version = 1.0
affymetrix-array-type = MTA-1_0
program-name = Expression Console
program-version = 1.4.1.46

source_name: Primary hepatocyte culture, uninfected

label_protocol: 100 ng of total RNA was converted to amplified ss-cDNA using the GeneChip WT Plus Reagent Kit (Affymetrix,Cat. #902513). Following fragmentation (fragment size ~40-70nt ), the samples were labeled with biotin.

growth_protocol: Primary hepatocyte cultures maintained in 6 well-plates

extract_protocol: The hepatocytes were detached by trypsinization (0.25% Trypsin-EDTA), FACS sorted directly into fetal calf serum. The hepatocytes were pelleted and immediately used for RNA extraction. Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Co-incubated with freshly isolated Pb-GFP sporozoites from mosquitoes

tag: primary cell culture

value: Hepatocytes

value: uninfected


title: Sample54.Naked mole rat.203877620092_R06C01

value: Skin

tag: confidenceinageestimate

tag: canbeusedforagingstudies

value: Male


title: Sample52.Naked mole rat.203877620092_R04C01

tag: Sex

tag: queen


title: Sample56.Naked mole rat.203877620092_R02C02

tag: tissue/cell type


title: CEQ-MRSA1679a-2

tag: strain background


title: Sample50.Naked mole rat.203877620092_R02C01


title: Uninfected hepatocytes [8.2]


title: Uninfected hepatocytes [8.1]


title: Sample49.Naked mole rat.203877620092_R01C01


title: Sample51.Naked mole rat.203877620092_R03C01


title: P. berghei infected hepatocytes [4.2]

description: Gene expression in P. berghei infected hepatocytes

source_name: Primary hepatocyte culture, 36h post infection

value: P. berghei infected


title: P. berghei infected hepatocytes [4.1]


title: P. berghei infected hepatocytes [4.3]


title: Hbo1fl/+;Mx1Cre LSK cells with one allele of Hbo1 deleted - LSK Mx1Cre control replicate 4

value: Control


title: 786-OTR-Ctrl-Rep2

city: South Bend

first: XUECHUN

last: WANG

state: Indiana

address: university of notre dame

institute: University of Notre Dame

data_processing:
Illumina Casava  used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using STAR
counts per million reads mapped (CPM) were calculate
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Renal cell Carcinoma Cell lines

growth_protocol: Cell culture in RPMI1640 supplemented with 10% FBS and 1% penicillin/streptomycin

extract_protocol:
RNA was harvested using Quick-RNA Miniprep Kit (Zymo Research #R1054) . Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Wild type(VHL-null)

tag: cell line


title: 786-OTR-VHL-Rep2

value: VHL restoration


title: Hbo1fl/fl;CreER LSK cells with both alleles of Hbo1 deleted - LSK CreER HBO1 knokout replicate 1

value: HBO1 knokout

value: Female

value: LSK cells


title: 786-OTR-VHL-Rep1


title: Hbo1fl/+;Mx1Cre LSK cells with one allele of Hbo1 deleted - LSK Mx1Cre control replicate 3


title: Hbo1fl/+;Mx1Cre LSK cells with one allele of Hbo1 deleted - LSK Mx1Cre control replicate 1


title: Hbo1fl/+;Mx1Cre LSK cells with one allele of Hbo1 deleted - LSK Mx1Cre control replicate 2


title: H1_Motif_Optimized_PP2_scRNA

data_processing:
Sequencing reads were processed using CellRanger version 6.0.0.
Genome_build: Genome_build: hg19
Supplementary_files_format_and_content: Supplementary_files_format_and_content: barcodes, features, and matrix files were generated using CellRanger version 6.0.0.

source_name: H1 Motif Optimized

extract_protocol:
Pancreatic progenitor cells at day 11 of differentiation were allowed to settle in microcentrifuge tubes and washed with PBS. Cell aggregates were incubated with Accutase® at 37°C until a single-cell suspension was obtained. Cells were then resuspended in 1 mL ice-cold flow buffer comprised of 0.2% BSA in PBS and stained with propidium iodide (Sigma) to distinguish live cells. 500,000 live cells were collected using a FACSAriaTM Fusion Flow Sorter, and 10,000 cells per sample were then loaded onto a 10X Chromium Controller and run using Next GEM Single Cell 3’ v3.1 reagents.
Library preparation was performed using 10X Next GEM Single Cell 3’ v3.1 reagents according to manufacturer’s instructions.
Library preparation was performed using 10X Next GEM Single Cell 3’ v3.1 reagents according to manufacturer’s instructions.

value: differentiated hESCs

tag: developmental stage

value: Late pancreatic progenitor


title: Sample46.Naked mole rat.203203210156_R04C02

description: genomic DNA methylation from Naked mole rat Kidney

source_name: Kidney

value: Kidney


title: Sample48.Naked mole rat.203203210156_R06C02

value: Naked mole rat


title: 786-OTR-Ctrl-Rep1

tag: genotype


title: Hbo1fl/+;CreER LSK cells with one allele of Hbo1 deleted - LSK CreER control replicate 3

tag: mouse


title: Hbo1fl/+;CreER LSK cells with one allele of Hbo1 deleted - LSK CreER control replicate 4


title: Hbo1fl/+;CreER LSK cells with one allele of Hbo1 deleted - LSK CreER control replicate 1


title: Hbo1fl/+;CreER LSK cells with one allele of Hbo1 deleted - LSK CreER control replicate 2


title: Sample43.Naked mole rat.203203210156_R01C02

value: yes


title: Sample47.Naked mole rat.203203210156_R05C02


title: Sample45.Naked mole rat.203203210156_R03C02


title: Sample44.Naked mole rat.203203210156_R02C02


title: Plate_2 [scRNA-seq]

data_processing:
Paired-end reads from Illumina sequencing were aligned to the mouse transcriptome genome by BWA (Li and Durbin, 2010). Read 1 contained the barcode information and was used for assigning reads to correct cells and libraries, while read 2 was mapped to gene models. Reads that mapped equally well to multiple locations were discarded. Read counts were first corrected for UMI barcode by removing duplicate reads that had identical combinations of library, cell-specific, and molecular barcodes and were mapped to the same gene. For each cell barcode the number of UMIs for every transcript was counted, and transcript counts were then adjusted to the expected number of molecules based on counts, 256 possible UMI’s and poissonian counting statistics (Grün et al., 2014).
Raw read counts were first subjected to quality control. We identified two blocks of wells with fewer than 500 non-spike-in reads. To exclude these and similar low-content wells, we applied a UMAP clustering on all wells (including the spike-in reads) and excluded the cluster of cells that was mainly composed by the low-read wells. After quality control, 697 wells out of 1152 were kept in the analysis.
R packages ‘scater’ (McCarthy et al., 2017) and ‘scran’ (Lun et al., 2016) were used for further processing, the spike-in reads were removed and expression values were normalized to library size and normalized log expression values and gene variance were determined as described previously described (Lun et al., 2016). Mitochondrial genes were excluded before modeling gene variance.
The processed data was then plotted or subjected to UMAP clustering (McInnes et al., 2020), performed with the R package 'uwot' (Melville, 2019) using the cosine distance and a neighbourhood size of 30.
For defining CD5 low, mid, and high cells the CD5 mean fluorescent intensity was logged by the flow cytometer when we sorted the cells into individual wells.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for each cell
Supplementary_files_format_and_content: CD5 MFI determined by FACS for each cell
Supplementary_files_format_and_content: CD5 group classification (Low, Middle, or High) for each cell

growth_protocol: Mice were 8-12 weeks of age.

extract_protocol:
Mouse spleen and lymph nodes were processed to single-cell suspension and naïve CD4+ T cells were sorted by sorted by singlets, live, TCRb+, CD4+, CD8-, CD25-, CD44-, CD62L+, CD5+. Individual naïve CD4+ T cells across the full spectrum of CD5 expression were sorted into 384-well plates containing CEL-Seq2 primers covered by mineral oil. Primers consisted of a 24bp polyT stretch, a 6bp random molecular barcode (UMI), a cell-specific barcode, the 5’ Illumina TruSeq small RNA kit adaptor and a T7 promoter.
Libraries were prepared following the SORT-seq protocol (Muraro et al., 2016). Cells were lysed for 5 minutes at 65oC, and reverse transcription and second strand mixes were dispensed by the Nanodrop II liquid handling platform (GC Biotech). Single cell double stranded cDNAs were pooled together and in vitro transcribed for linear amplification. Illumina sequencing libraries were prepared using the TruSeq small RNA primers (Illumina) and sequenced paired-end at 75bp read length on the Illumina NextSeq 550.

value: 8-12 weeks of age

value: pooled male and female

tag: tissue

value: Spleen and lymph node

value: naive CD4+ T cells (sorted by singlets, live, TCRb+, CD4+, CD8-, CD25-, CD44-, CD62L+, CD5+)

tag: treatment

value: Freshly sorted


title: ILC2_HDM

source_name: Lung ILC2

value: Lung

tag: genotype/variation


title: ILC2_PBS


title: marmosetv1

description:
n=3 pooled
marmoset.control.V1.UMIs.txt
marmoset.control.V1.meta.txt

source_name: primary visual cortex (V1)

value: Adult

value: Control


title: H1_WT_PP2_scRNA

source_name: H1 Control

tag: cell type


title: CD4+T-cells_PBS

source_name: Lung CD4+ T-cells


title: Plate_1 [scRNA-seq]

tag: strain

tag: gender


title: evoA1-seBE4max-T2A-NoRapamycin_Rep3

city: Philadelphia

first: Rahul

middle: M.

last: Kohli

state: Pennsylvania

address: 3610 Hamilton Walk, 502B Johnson Pavilion

department: Department of Medicine

institute: University of Pennsylvania

data_processing:
Reads were analyzed using the RADAR pipeline (RNA-editing Analysis-pipeline to Decode All twelve-types of RNA-editing events).
For each sgRNA-only sample respectively (n = 2), RNA edits that were present in other samples were removed and unique editing events present in the sgRNA-only sample were used for comparison against editing events present in other samples but not in the sgRNA-only sample.
For the base editing samples, the average percentage of C to U edits from analyzing against each sgRNA-only sample are plotted.
The analysis of distribution of editing events was performed by removing any edits found in either of the sgRNA-only samples.
Genome_build: hg38
Supplementary_files_format_and_content: read count table recording the number of different base edits in each sample after subtracting the gRNA-only controls

growth_protocol: HEK293T d2GFP cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) media (Gibco) supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin at 37°C with 5% CO2 and cells were periodically tested to be mycoplasma negative. Cells were seeded on 24-well plates, and transfected at approximately 60% confluency. 660 ng of intact BE4max or seBE4max constructs and 330 ng of LRcherry2.1 sgRNA expression plasmids were transfected using 1.5 µL of Lipofectamine 2000 CD (Invitrogen) per well according to manufacturer’s protocol. The d2gfp-targeting sgRNA exposes a window where base editing can result in the introduction of a Q158X nonsense mutation in d2gfp. Transfected cells were harvested at day 3 after transfection. For RNA-seq analysis, negative control transfections included d2gfp-targeting LRcherry2.1 plasmid without any base editor construct.

extract_protocol:
Total RNA was isolated using Direct-zolTM RNA Miniprep Plus kit (Zymo Research #R2072) following the manufacturer’s protocol. Total RNA was analyzed for quality using the RNA 6000 Nano Bioanalyzer kit (Agilent). Only RNA with an RNA integrity number (RIN) ≥ 8 was used for subsequent library construction.
RNA-seq was performed on 0.5-1.0 μg of total RNA according to the Genewiz Illumina Hi-seq protocol for poly(A)-selected samples (2 × 150 bp pair-end sequencing, 350M raw reads per lane).

treatment_protocol: For seBE experiments, 24 hours after transfection, rapamycin (Research Products International) was added to select wells at a final concentration of 200 nM. This concentration was continuously maintained until the end of the experiment.

value: Human Embryonic Kidney cell line

value: split-engineered base editor construct

value: No Rapamycin


title: evoA1-seBE4max-T2A-NoRapamycin_Rep2


title: Plate_3 [scRNA-seq]

tag: age


title: Sample38.Naked mole rat.203203210156_R02C01

source_name: Skin

tag: species

value: Skin

tag: confidenceinageestimate

value: Male


title: Sample40.Naked mole rat.203203210156_R04C01

tag: canbeusedforagingstudies

tag: Sex


title: NNMT-knockout AN3CA cells_KO2

data_processing:
Sequencing was performed on an Illumina HiSeq 3000 platforms in 101-base single-end mode.
The sequenced reads were mapped to the human reference genome sequences (hg19) using TopHat version 2.0.13 in combination with Bowtie2 version 2.2.3 and SAMtools version 0.1.19.
The fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cufflinks version 2.2.1.
Genome_build: hg19
Supplementary_files_format_and_content: FPKMs

source_name: NNMT-knockout AN3CA cells

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

value: AN3CA cells

value: NNMT-knockout


title: evoA1-seBE4max-T2A-NoRapamycin_Rep1


title: Sample36.Naked mole rat.203203210166_R06C02

source_name: Muscle

value: Naked mole rat

tag: tissue/cell type

value: Muscle

tag: queen


title: Sample37.Naked mole rat.203203210156_R01C01

value: yes

value: Female


title: Sample39.Naked mole rat.203203210156_R03C01


title: evoA1-seBE4max-T2A-Rapamycin_Rep2

tag: cell line

value: treated with 200 nM Rapamycin for 48 hrs


title: control AN3CA cells_EV

source_name: control AN3CA cells

value: control


title: evoA1-seBE4max-T2A-Rapamycin_Rep3


title: Sample34.Naked mole rat.203203210166_R04C02


title: Sample42.Naked mole rat.203203210156_R06C01

description: genomic DNA methylation from Naked mole rat Blood

source_name: Blood

value: Blood


title: Sample35.Naked mole rat.203203210166_R05C02


title: Sample41.Naked mole rat.203203210156_R05C01


title: evoA1-seBE4max-T2A-Rapamycin_Rep1


title: Sample33.Naked mole rat.203203210166_R03C02


title: Sample29.Naked mole rat.203203210166_R05C01

source_name: Lung

value: Lung


title: Sample31.Naked mole rat.203203210166_R01C02


title: Sample30.Naked mole rat.203203210166_R06C01


title: evoA1-BE4max_Rep3

value: base editor constrict


title: Sample32.Naked mole rat.203203210166_R02C02


title: NNMT-knockout AN3CA cells_KO1


title: CD5lo_2_d5 [ATAC-seq]

data_processing:
FASTQ files from L1 and L2 were merged for each R1 and R2 per sample.
Sequence read quality was confirmed using FastQC tool v0.10.1 (Babraham Bioinformatics), and low-quality bases removed using Trimmomatic v.0.33 (Bolger et al., 2014).
Reads were then mapped to the mouse UCSC mm9 reference assembly using TopHat v2.1.0 in conjunction with Bowtie 1.0.0 (Langmead et al., 2009) algorithms.
Peak calling was performed using MACS1.4.1 (Zhang et al., 2008).
Genome_build: mm9
Supplementary_files_format_and_content: BW files for each sample

source_name: Lymphocytes

extract_protocol:
Mouse spleen and lymph nodes were processed to single-cell suspension and T cells were enriched prior to FACS staining. CD5lo and CD5hi naïve CD4+ T cells were sorted by Singlets, live, Dump-, CD4+, CD8-, CD44-, CD62L+, 15% CD5lo or 15% CD5hi. Dump channels included CD25, B220, CD11c, NK1.1, CD19, CD11b, and Ly6G.
Nuclei were isolated and immediately prepared for library preparation. Paired-end sequencing of 42bp length reads was performed on an Illumina NovaSeq6000.

treatment_protocol: Freshly sorted CD5lo and CD5hi naïve CD4+ T cells were either directly processed for sequencing or rested in culture with IL-7 (10ng/mL) for 1 or 5 days at which point cells were processed for sequencing.

value: 8-12 weeks of age

value: pooled male and female

value: Spleen and lymph node

value: CD5lo naive CD4+ T cells (sorted by singlets, live, dump-, CD4+, CD8-, CD44-, CD62L+, 15% CD5lo)

value: Rested in vitro for 5 days


title: CD5lo_2_d1 [ATAC-seq]

value: Freshly sorted


title: Sample27.Naked mole rat.203203210166_R03C01


title: Th2_HDM

source_name: Lung Th2 cells


title: evoA1-BE4max_Rep1

value: Human Embryonic Kidney cell line

value: No Rapamycin


title: Sample28.Naked mole rat.203203210166_R04C01

value: Naked mole rat

value: Male


title: CD5lo_1_d5 [ATAC-seq]


title: evoA1-BE4max_Rep2


title: CD5lo_2_d0 [ATAC-seq]


title: gRNA-only_Rep2

source_name: gRNA-only

value: No base editor construct


title: Sample25.Naked mole rat.203203210166_R01C01

value: yes

value: Female

value: unknwon


title: Sample26.Naked mole rat.203203210166_R02C01


title: CD5lo_1_d0 [ATAC-seq]


title: CD5lo_1_d1 [ATAC-seq]

value: Rested in vitro for 1 day


title: gRNA-only_Rep1


title: CD5hi_2_d5 [ATAC-seq]

value: CD5hi naive CD4+ T cells (sorted by singlets, live, dump-, CD4+, CD8-, CD44-, CD62L+, 15% CD5hi)


title: KD4, rep3

city: Nedlands

first: Danielle

middle: Louise

last: Rudler

address: 6 Verdun Street

department: Mitochondrial Medicine and Biology

institute: The Kids Research Institute

description:
KD4.3_FASTKD
72_H2G73DSXY_GTCTACAC-GCCAAGGT

data_processing:
Sequencing reads were trimmed of adapter sequences using cutadapt v1.18.
Sequencing reads were aligned against the NuMTs masked human genome sequence (Hg38) using STAR  v2.7.3a and GENCODE v34 gene annotation witha customized mitochondrial annotation. Salmon was also used v1.2.1 (-l ISR --seqBias --gcBias) in alignment based mode to quantify gene expression from the transcriptome alignments produced by STAR, and the subsequent alignments filtered with SAMtools v.1.10 (-q 2 -f 2 -F 256) to retain primary alignments of properly paired, full-length mitochondrial RNA fragments.
Mitochondrial alignments were extracted, split by template strand and converted to full-length RNA fragment BED files, before coverage was calculated with BEDtools genomecov v2.26.0 normalised to library size.
Total RNA alignments produced by Salmon were analysed in R for differential expression performed by DESeq2 by counts summarised with tximport.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited files containing raw counts, normalised counts, bedgraph giles of normalised coverage across chrM, and differential expression results.

growth_protocol: HAP1 human cells were grown in DMEM with 10% FCS in the presence of pryuvate.

extract_protocol:
RNA was isolated from human cells using the miRNeasy mini kit (QIAGEN).
RNA sequencing libraries were constructed with the Illumina TruSeq Sample Prep Kit. Paired end deep sequencing of the mitochondrial RNAs was performed on an Illumina HiSeq according to the manufacturer's instructions.


title: KD4, rep2

description:
KD4.2_FASTKD
71_H2G73DSXY_ACTCGTGT-ATTGGAAC


title: Sample24.Naked mole rat.203203210128_R06C02

description: genomic DNA methylation from Naked mole rat Liver

data_processing: SeSaMe normalization as described in W. Zhou et al 2018. PMID: 30085201

source_name: Liver

extract_protocol: genomic DNA was extracted

value: Liver


title: Sample23.Naked mole rat.203203210128_R05C02


title: KD4, rep1

description:
KD4.1_FASTKD
70_H2G73DSXY_ATTGTGAA-TGCATTGC


title: CD5hi_2_d0 [ATAC-seq]

value: 8-12 weeks of age


title: CD5hi_1_d1 [ATAC-seq]

value: pooled male and female


title: Sample20.Naked mole rat.203203210128_R02C02


title: Sample21.Naked mole rat.203203210128_R03C02


title: CD5hi_1_d5 [ATAC-seq]

value: Spleen and lymph node


title: KD34, rep3

description:
KD34.3_FASTKD
69_H2G73DSXY_GCCACAGG-CATGCCAT


title: KD34, rep1

description:
KD34.1_FASTKD
67_H2G73DSXY_TTCCTGTT-AGTATCTT


title: KD34, rep2

description:
KD34.2_FASTKD
68_H2G73DSXY_CCTTCACC-GACGCTCC


title: CD5hi_2_d1 [ATAC-seq]


title: KD5, rep3

description:
KD5.3_FASTKD
66_H2G73DSXY_GTGTCGGA-GCTTGCGC


title: CD5hi_1_d0 [ATAC-seq]


title: Sample22.Naked mole rat.203203210128_R04C02


title: KD5, rep2

description:
KD5.2_FASTKD
65_H2G73DSXY_ACACTAAG-ATCCATAT


title: Sample17.Naked mole rat.203203210128_R05C01

description: genomic DNA methylation from Naked mole rat Heart

source_name: Heart

value: Heart


title: Sample16.Naked mole rat.203203210128_R04C01


title: RAS-vaccinated + sporozoites 1

city: Iowa City

first: Isaac

last: Jensen

state: IA

institute: University of Iowa

data_processing:
The sequencing quality of RNA-Seq libraries were assessed by Agilent Bioanalyzer and  TapeStation Analysis Software 3.2 (https://www.agilent.com/en/product/automated-electrophoresis/tapestation-systems/tapestation-software).
Reads were trimmed with trim_galore (v0.6.4)
Trimmed reads were mapped to the mouse genome mm10 (downloaded from Ensembl: https://useast.ensembl.org/Mus_musculus/Info/Index) using Kallisto (v0.46.2).
Mapped reads were then processed using DESEq2 (1.26.0) to estimate expression levels of all genes.
Genome_build: GRCm38
Supplementary_files_format_and_content: Lefebvre_Gene Expression_Raw Read Counts.xlsx

source_name: whole liver tissue

extract_protocol:
Whole liver tissue was isolated from mice and total RNA was extracted using standard Qiagen RNease columns
RNA libraries were prepared for sequencing using Illumina's TruSeq RNA Sample Preparation Kit (Cat# RS-122-2001) and standard Illumina protocol

value: RAS-vaccinated + sporozoites

value: whole liver

tag: group

value: D


title: Sample15.Naked mole rat.203203210128_R03C01


title: Sample19.Naked mole rat.203203210128_R01C02


title: KD5, rep1

description:
KD5.1_FASTKD
64_H2G73DSXY_CCATTCGA-GTTGTCCG

tag: genotype


title: RAS-vaccinated + sporozoites 3


title: Sample18.Naked mole rat.203203210128_R06C01


title: KD45, rep1

description:
KD45.1_FASTKD
61_H2G73DSXY_CGGAACTG-CACTACGA


title: RAS-vaccinated control 3

value: RAS-vaccinated control

value: C


title: desmoplastic malignant pleural mesothelioma1

city: Tokyo

first: Rei

last: Noguchi

state: Tokyo

department: Division of Rare Cancer Research

institute: National Cancer Center Research Institute

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol for BeadChip Arrays

data_processing:
The scanned data files were processed by GenomeStudio Genotyping using the file InfiniumOmniExpress Exome-8_v1.4  provided by Illumina.  Genotype: AA,AB,BB,or NC (no call)
copy number <1 : deletion, copy number >3 : amplification

label: C-Bio and A-DNP

label_protocol: Standard Illumina labelling protocol

extract_protocol: gDNA extracted from cells of an established patient-derived desmoplastic malignant mesothelioma cell line by DNeasy Blood & Tissue Kit Qiagen

value: Male

tag: cell line source

value: patient-derived cell line


title: RAS-vaccinated + sporozoites 2

tag: tissue


title: KD45, rep3

description:
KD45.3_FASTKD
63_H2G73DSXY_TTGCCTAG-ACCACTTA


title: KD45, rep2

description:
KD45.2_FASTKD
62_H2G73DSXY_TAAGGTCA-TGTCGTAG


title: RAS-vaccinated control 2

tag: treatment


title: RAS-vaccinated control 1


title: Sample14.Naked mole rat.203203210128_R02C01

value: Naked mole rat

value: yes


title: Sample12.Naked mole rat.203203210200_R06C02

description: genomic DNA methylation from Naked mole rat Adipose

source_name: Adipose

value: Adipose


title: KD3, rep1

description:
KD3.1_FASTKD
58_H2G73DSXY_CATAATAC-TTCTAACG


title: Sample8.Naked mole rat.203203210200_R02C02

description: genomic DNA methylation from Naked mole rat Cortex

source_name: Cortex

value: Cortex


title: Sample9.Naked mole rat.203203210200_R03C02

value: Female


title: Sample13.Naked mole rat.203203210128_R01C01


title: WT, rep2

description:
WT2_FASTKD
56_H2G73DSXY_GAATGAGA-GAGGCATT

source_name: HAP1_WT +/+


title: Naïve + sporozoites 3

value: Naïve + sporozoites

value: B


title: KD3, rep3

description:
KD3.3_FASTKD
60_H2G73DSXY_AGCTCGCT-GCAGAATC


title: KD3, rep2

description:
KD3.2_FASTKD
59_H2G73DSXY_GATCTATC-ATGAGGCT


title: Naïve + sporozoites 2


title: Naïve + sporozoites 1


title: Sample7.Naked mole rat.203203210200_R01C02


title: Naïve control 3

value: Naïve control

value: A


title: TUS_3

status: Public on Oct 17 2021

city: Changsha

first: Touming

last: Liu

address: NO.348, western road of xianjia lake

department: Institute of Bast Fiber Crops

institute: Chinese Academy of Agricultural Sciences

data_processing:
cDNA library was carried out a paired-end sequencing using a HiSeq PE Cluster Kit v4 cBot (Illumina, San Diego, CA, USA) on the Illumina sequencing platform, following the manufacturer’s instructions.
After filtering the low-quality reads, the clean reads were aligned with the garlic genome (GenBank accession: GCA_014155895.2) using hisat2 software
Then, gene expression level was quantified by estimating fragments per kilobase per million reads (FPKM)
Differentially expressed genes between the bulbs of virus-free and viruses-accumulated garlic were determined using the DEseq program (version: 1.18.0)
Genome_build: GCA_014155895.2
Supplementary_files_format_and_content: the excel file contain the gene name and FPKM value,

organism: Allium sativum

source_name: Chalingzipisuan

growth_protocol: the virus-free and viruses-accumulated garlic，“Chalingzipisuan,” were planted in the insect-free greenhouse in Oct., 2019, and in April. of the next year, the enlarging-growth bulbs of each accessions were sampled

extract_protocol:
Total RNAs of each sample were extracted using an E.Z.N.A. Plant RNA Kit (OMEGA Bio-Tek, Norcross, GA, USA) according to the protocol of manufacturer.
these RNAs were individually used for performing the construction of cDNA libraries, with a fragment length of 300 bp (± 150 bp), using a NEBNext UltraTM RNA Library Prep Kit for Illumina (New England BioLabs, Ipswich, MA, USA) according to the manufacturer’s instructions.

treatment_protocol: Three biological replicates of each treatment were performed

value: bulb

tag: developmental stage

value: enlarging growth of bulb

value: virus-free


title: Sample6.Naked mole rat.203203210200_R06C01


title: WT, rep3

description:
WT3_FASTKD
57_H2G73DSXY_TGCGGCGT-CCTCGGTA

tag: cell type


title: Cba_1

value: virus-infection


title: Sample4.Naked mole rat.203203210200_R04C01


title: Sample1.Naked mole rat.203203210200_R01C01

description: genomic DNA methylation from Naked mole rat Cerebellum

source_name: Cerebellum

value: Cerebellum


title: GerSB3

data_processing:
cDNA library was carried out a paired-end sequencing using a HiSeq PE Cluster Kit v4 cBot (Illumina, San Diego, CA, USA) on the Illumina sequencing platform, following the manufacturer’s instructions.
After filtering the low-quality reads, the clean reads were aligned with the garlic genome (GenBank accession: GCA_014155895.2) using hisat2 software
Then, gene expression level was quantified by estimating fragments per kilobase per million reads (FPKM)
Genome_build: GCA_014155895.2
Supplementary_files_format_and_content: the excel file contain the gene name and FPKM value,

growth_protocol: When the flower stems sprout out with one week, the bulbs are generally enlarging, and we collected the bulbs. Then, the enlarging-growth bulbs, together the germinant bulbs (with < 5 cm shoot), and the dormant bulbs were used for sampling.

treatment_protocol: The basal and storage clove were separated manually, and then stored immediately at －80 °C until use.

value: storage clove

value: germination of bulb


title: TUS_2


title: GerLJ3

value: basal clove


title: GerSB2


title: Naïve control 2

value: whole liver


title: WT, rep1

description:
WT1_FASTKD
55_H2G73DSXY_AGGCAGAG-AGAATGCC


title: Cba_3


title: GerLJ2


title: DorSB2

value: dormancy of bulb


title: SKMES1_RNA_CRISPRa_sg_NC2

city: Salt Lake City

first: Xiaoyang

last: Zhang

address: 1950 CIrcle of Hope

institute: University of Utah

data_processing:
Bowtie2 to align sequencing reads
RSEM to quantify expression for each GENCODE gene
Genome_build: hg19
Supplementary_files_format_and_content: RSEM text file

source_name: Lung squamous cancer cell line

extract_protocol:
mRNA isolated using NEBNext Poly-A mRNA Magnetic Isolation Module (NEB E7490L)
NEBNext Ultra Directional RNA library prep kit (NEB  E7760S)

value: Lung squamous cancer cell line

value: CRISPRa sg-NC#2


title: SKMES1_RNA_CRISPRa_sg_e1_3

value: CRISPRa sg-e1#3


title: Cba_2


title: GerLJ1


title: GerSB1


title: DorSB1


title: DorSB3


title: TUS_1


title: Sample3.Naked mole rat.203203210200_R03C01

first: Steve

last: Horvath

value: Naked mole rat

value: yes

value: Female


title: Naïve control 1

value: Naïve control

value: A


title: SKMES1_RNA_CRISPRa_sg_NC1

value: CRISPRa sg-NC#1


title: KYSE140_RNA_ARV6hrs_B

source_name: Esophageal squamous cancer cell line

value: Esophageal squamous cancer cell line

value: 0.5uM ARV771 6hrs


title: DorLJ3


title: DorLJ2


title: KYSE140_RNA_ARV6hrs_A


title: KYSE140_RNA_DMSO6hrs_B

value: DMSO 6hrs


title: DorLJ1


title: SKMES1_RNA_CRISPRa_sg_e1_1

value: CRISPRa sg-e1#1


title: ADorSB3

value: storage clove

value: enlarging growth of bulb


title: Sample2.Naked mole rat.203203210200_R02C01

value: Cerebellum

value: Male


title: ADorSB2


title: Sample5.Naked mole rat.203203210200_R05C01

value: Cortex


title: ADorLJ3

value: basal clove


title: KYSE140_RNA_sgSOX2_2

value: CRISPR sg-SOX2#2