title: STM815 wt terrestrial gravity replicate 3

city: Zürich

first: Gabriella

last: Pessi

address: Winterthurerstrasse 190

country: Switzerland

institute: University of Zürich

data_processing:
The sequences of the reads were quality trimmed using the program fastq_quality_trimmer
Sequencing reads were mapped to the Pp STM815 genome using CLC Genomics Workbench v7.0 (CLCbio) allowing up to 2 mismatches per read
RNA-Seq count data were subsequently analyzed with the DESeq software (Anders & Huber 2010)
Assembly: STM815 genome sequence (accession no. NC_010622.1, NC_010623.1, NC_010625.1 and NC_010627.1)
Supplementary files format and content: tab-delimited text files include RPKM and mean values for each sample
Supplementary files format and content: TPM     RPKM    Gene length     Unique gene reads       Total gene reads

organism: Paraburkholderia phymatum STM815

source_name: bacterial cell

extract_protocol:
Cells were flash frozen on dry ice, and RNA was harvested using hot phenol protocol (Pessi et al 2007) . The cDNA was produced and Tecan libraries obtained.
RNA libraries were prepared using Ovation® Complete Prokaryotic RNA-Seq DR Multiplex Systems

value: bacterial cell

value: wild-type

value: terrestrial gravity


title: PCB187_25_4 [CAGGCCAT-CCATAGGG-2]

status: Public on Apr 10 2024

type: SRA

city: Ann Arbor

first: Justin

last: Colacino

state: MI

address: 6651 SPH1, 1415 Washington Heights

department: Environmental Health Sciences

country: USA

institute: University of Michigan

library_source: transcriptomic

data_processing:
Sequencing read quality was assessed via FastQC and MultiQC.
Reads were aligned to a splice junction aware build of the human genome (GRCh38) using STAR.
Aligned reads were assigned to genes using featureCounts, where multimapping and multi-overlapping reads were not counted.
Assembly: GRCh38
Supplementary files format and content: Tab deliminted files containnig the read counts per sample

molecule: total RNA

organism: Homo sapiens

growth_protocol: MCF10A cells were cultured and expanded at passage 105 for all rounds of cell culture. Cells were plated in black, clear flat bottom 384 well plates (Corning, Corning, NY, USA) using a 2.5-125uL multi-channel pipette. First, 10uL of plain media was added to pre-warmed plates. 500 cells in 30 uL of media were added to each well at a slow speed to make up a final volume of 40 uL. The cells were left undisturbed to allow the cells to attach and distribute uniformly over the well. Each microplate was incubated at 37oC humidified incubator with 5% CO2 for 24 hours prior to dosing.

extract_protocol:
To conduct high throughput RNA-sequencing, we developed an adapted version of the plexWell (SeqWell, Beverly, MA, USA) plate-based sequencing method to make the method applicable for high throughput in vitro toxicological analysis. In the plexWell protocol, sequencing reactions are prepared in custom 96 well plates, where each well contains a unique oligo barcode. Plates are also assigned a unique oligo barcode. Cells are lysed and cDNA is directly prepared from the cellular lysate.
A tagmentation reaction adds the well specific barcode to the cDNA from each well. The tagmented cDNAs are then pooled prior to library preparation, where plate specific barcodes can also be incorporated for ultrahigh sample multiplexing prior to sequencing. For example, 384 wells of treated samples would be processed across 4 custom 96 well plates, where each of the samples receives a well specific barcode and each of the 4 plates receives a plate specific barcode. This leads to each of the 384 samples receiving a unique combination of well and plate barcodes, which can be bioinformatically deconvoluted following sequencing.
Libraries were sequenced at Illumina NovaSeq 6000 l at the Advanced Genomics Core.

treatment_protocol: Cells were then exposed to test chemicals for 48 hours with 4 biological replicates per dose. Doses are in micromolar in the "treatment" column

tag: cell line

tag: cell type

value: Nontumorigenic breast

tag: genotype

value: WT

tag: treatment

tag: time

value: 48 hrs

tag: control flags

value: DMSO

tag: plate id


title: STM815 wt terrestrial gravity replicate 2


title: m1_stimul_Ics_6h

city: Lübeck

first: Axel

last: Künstner

address: Ratzeburger Allee 160

department: LIED

country: Germany

institute: University of Lübeck

data_processing:
Data was mapped against a cDNA library using a pseudo-aligner approach (kallisto v0.46.1)
Assembly: GRCm38
Supplementary files format and content: Processed data contains length-scaled TPM values.

organism: Mus musculus

source_name: Ics

extract_protocol:
Total RNA from bone marrow derived murine neutrophils and monocytes, or whole blood, from control and treated mice was purified using the RNeasy Plus Mini kit (QIAGEN, Germany) following the manufacturer’s instructions.
Library was prepared using a 250-300 bp insert cDNA library (low-input). mRNA was enriched using oligo (dT) beads and randomly fragmented in fragmentation buffer followed by cDNA synthesis using random hexamers and reverse transcriptase. After first-strand synthesis, a custom second-strand synthesis buffer (Illumina) was added with dNTPs, RNase H and Escherichia coli polymerase I to generate the second strand by nick-translation. The final cDNA library was ready after a round of purification, terminal repair, A-tailing, ligation of sequencing adapters, size selection, and PCR enrichment.

tag: tissue

value: Ics

tag: condition


title: 40453, nonpregnant

city: Gainesville

first: Peter

last: Hansen

state: Florida

address: 2250 Shealy Drive

department: Department of Animal Sciences

institute: University of Florida

data_processing:
Trimming with cutadapt (v.3.4); phred-like score <20 and reads <65 bases
Mapped with STAR package (v2.7.9) to ARS-UCD1.3
Mapped reads processed with HTSeq, samtools, and scripts to remove PCR duplicates and to count uniquely mapped reads
Read counts normalized by library size
Assembly: Bos taurus (ARS-UCD1.3)
Supplementary files format and content: Txt data file includes Gene ID in first column. Expression data in reads per million

organism: Bos taurus

source_name: Endometrial cells from uterine body

extract_protocol:
Qiagen Rneasy Microkit with prior tissue homogenization using beads
NEBNext Ultra II Directional RNA Library Prep Kit and SPT Labtech mosquito LV liquid handling instrument

value: Endometrial cells from uterine body


title: Arsenic_25_1 [GTTCGTCT-ATAGAGAG-2]

value: Arsenic 25

value: Water


title: S3_blood_6_ivig

source_name: Blood

value: Blood

value: IVIG


title: 40306, nonpregnant


title: S3_blood_5

value: PBS


title: STM815 wt terrestrial gravity replicate 1


title: BPF_2.5_2 [GGTGTGAC-ATATGAGA-2]

value: BPF 2.5


title: STM815 wt microgravity replicate 3

value: microgravity


title: 39789, pregnant


title: S3_blood_2_ivig


title: 39997, nonpregnant


title: STM815 wt microgravity replicate 2


title: STM815 wt microgravity replicate 1


title: S5_Skin_13_ivig

source_name: Skin

value: Skin


title: PCB187_0.25_3 [CGATGGCA-CCATAGGG-2]


title: m3_stimul_Ics_3h


title: 37666, nonpregnant


title: 12788, nonpregnant


title: BPF_0.025_3 [ATTCGCAG-ATATGAGA-2]


title: KD_pd_Dep1

city: New York

first: Caryn

middle: R

last: Hale

state: New York

address: 1230 York Avenue

institute: Rockefeller University

description: ribosomal profiling of pulldown fraction of cytosol region in KCl-depolarized and eIF4G2 knockdown neuron, replicate 1

library_source: other

data_processing:
Tab-delimited text files include RPKM values and counts for each sample.
Remove ribosomal reads: The processed reads were aligned to mouse ribosomal sequences (mm10) by Rsubread. The aligned reads were removed, and the filtered reads were converted into fastq format for the following analysis.
Align to mouse genome: The filtered reads were aligned to BSgenome (mm10) with Rsubread. The alignment results were stored as BAM format.
Annotation and counting: After alignment, Plastid was applied to count expression level of each transcript in each sample. Before counting, the annotation files for U5/CDS/U3 were derived from TxDb.Mmusculus.mm10.knownGene. The annotations were based on Ensembl transcript ID. Then, the counts for U5/CDS/U3 in each sample was calculated by Plastid. The RPKM value of each transcript ID in each sample was gathered into single table for following analysis.
Assembly: Reference genome: Bsgenome.Mmusculus.UCSV.mm10; Annotation database: Txdb.Mmusculus.UCSC.mm10.knownGene.
Supplementary files format and content: Tab-delimited text files include RPKM values and counts for each sample.

molecule: other

source_name: primary neuronal culture (cortical)

growth_protocol: Primary cortical neurons were grown in Neurobasal media supplemented with B27 and Glutamax.

extract_protocol:
RNA from inputs and streptavidin pulldowns (from beads directly) was extracted using the TRIzol protocol.
RNA from inputs and streptavidin pulldowns was resolved by electrophoresis through a denaturing gel to isolate ribosome footprints. The expected size range fragments were extracted, and 3’ ends of these RNA fragments were treated with T4 polynucleotide ligase to ligate a pre-adenylated barcoded DNA linker to be able to pool samples. After treatment with deadenylase and RecJ, inputs and pulldowns were pooled, purified with Zymo columns, and were depleted of ribosome RNA (rRNA) using Ribo-Zero. Following rRNA removal, RNA was used as template for reverse transcription, using an oligo specifically designed to be able to sequence from the 5’end of the ribosome protected fragment. The single-stranded cDNA is then circularized using an optimized CircLigase after another gel purification step of full-length products. A double stranded DNA library is generated using the circularized cDNA fragments that are amplified with the Kapa enzyme and a fixed primer combined with an Illumina index encoding primer. The resulting products are gel purified from a non-denaturing gel and quantified on a bioanalyzer. Pooled libraries were then sequenced on the Illumina Novaseq 6000 sequencer.

treatment_protocol: Primary cortical neurons were treated with cycloheximide for 2 minutes before biotinylation for 30 minutes. For the samples labeled with "DHPG", activation by DHPG was performed by incubating the cells with tetrodotoxin and DL-AP5 for 2 hours before 100 µM DHPG addition for 10 minutes, followed by resting in biotin added media for 30 minutes before harvest. For the samples that are labeled as "KD", neurons were treated with 20 nM siRNA targeting eIF4G2 for 72 hours. In these neurons, depolarization was performed by incubating the cells with tetrodotoxin and DL-AP5 for 2 hours before 55 mM KCl addition for 1 hour, followed by resting in biotin supplemented media for 30 minutes before harvest.

value: primary neuronal culture (cortical)

tag: lentivirus

tag: fraction

value: streptavidin pulldown

value: eIF4G2 siRNAs + Chx + KCl depolarization


title: 12404, nonpregnant


title: Control_0_12 [TGGACAAC-ATAGAGAG-2]

value: Nontumorigenic breast

value: Control 0


title: KD_pd_Dep2

description: ribosomal profiling of pulldown fraction of cytosol region in KCl-depolarized and eIF4G2 knockdown neuron, replicate 2


title: m4_stimul_Ics_3h


title: m2_stimul_Ics_3h


title: BPF_2.5_4 [TCAGATAC-ATATGAGA-2]

value: WT

value: 48 hrs


title: KD_in_Dep2

description: ribosomal profiling of input fraction of cytosol region in KCl-depolarized and eIF4G2 knockdown neuron, replicate 2

value: input


title: 12381, pregnant

value: Endometrial cells from uterine body


title: m1_stimul_Ics_3h

value: Ics


title: 12266, nonpregnant


title: S5_Skin_10


title: Control_0_35 [ATAGATCC-CTATGATC-2]

value: DMSO


title: 12250, pregnant


title: KD_pd_Rest2

description: ribosomal profiling of pulldown fraction of cytosol region in resting and eIF4G2 knockdown neuron, replicate 2

value: eIF4G2 siRNAs + Chx


title: KD_in_Dep1

description: ribosomal profiling of input fraction of cytosol region in KCl-depolarized and eIF4G2 knockdown neuron, replicate 1


title: DCB_14_25_2 [CCAGGTAA-CCATAGGG-2]


title: S5_Skin_6_ivig

value: IVIG


title: 12148, nonpregnant


title: S5_Skin_5

value: PBS


title: 11898, nonpregnant


title: KD_pd_Rest1

description: ribosomal profiling of pulldown fraction of cytosol region in resting and eIF4G2 knockdown neuron, replicate 1


title: Phenanthrene_0.25_4 [CGACTAGC-CTATGATC-2]

value: Phenanthrene 0.25


title: KD_in_Rest2

description: ribosomal profiling of input fraction of cytosol region in resting and eIF4G2 knockdown neuron, replicate 2


title: S5_Skin_2_ivig


title: Lead_2.5_4 [CCTGTTAC-ATAGAGAG-2]

value: Lead 2.5

value: Water


title: 11784, nonpregnant


title: S5_Skin_1

value: Skin


title: DHPG_pd_rep3

description: ribosomal profiling of pulldown fraction of psd region in DHPG treated neuron, replicate 3

value: primary neuronal culture (cortical)

value: streptavidin pulldown

value: Chx + DHPG treatment


title: S3_blood_1

value: Blood


title: 11670, pregnant


title: Arsenic_25_2 [CCAGGTAA-ATAGAGAG-2]

value: Nontumorigenic breast

value: WT

value: Arsenic 25


title: 11375, nonpregnant

value: Endometrial cells from uterine body


title: DHPG_pd_rep2

description: ribosomal profiling of pulldown fraction of psd region in DHPG treated neuron, replicate 2


title: BPF_25_4 [TCCTATCT-ATATGAGA-2]

value: BPF 25

value: 48 hrs


title: S3_Monocytes_1

source_name: Monocyte

value: Monocyte


title: 11321, nonpregnant


title: S3_Monocytes_14_ivig

value: IVIG


title: BPF_0.25_1 [TACAGAGT-ATATGAGA-2]

value: DMSO


title: DHPG_pd_rep1

description: ribosomal profiling of pulldown fraction of psd region in DHPG treated neuron, replicate 1


title: 11142, nonpregnant


title: Lead_0.025_3 [TCTATTGG-ATAGAGAG-2]


title: DHPG_in_rep3

description: ribosomal profiling of input fraction of cytosol region in DHPG treated neuron, replicate 3

value: input


title: 11135, nonpregnant


title: KD_in_Rest1

description: ribosomal profiling of input fraction of cytosol region in resting and eIF4G2 knockdown neuron, replicate 1

value: eIF4G2 siRNAs + Chx


title: S3_Monocytes_13

value: PBS


title: 10991, nonpregnant


title: PCB153_25_3 [GATGAGAA-CCATAGGG-2]


title: DHPG_in_rep2

description: ribosomal profiling of input fraction of cytosol region in DHPG treated neuron, replicate 2


title: Cadmium_0.25_2 [ACGCTGCA-ATAGAGAG-2]

value: Cadmium 0.25

value: Water


title: Cadmium_0.25_4 [CAACCGTG-ATAGAGAG-2]


title: DHPG_in_rep1

description: ribosomal profiling of input fraction of cytosol region in DHPG treated neuron, replicate 1

value: primary neuronal culture (cortical)


title: S5_Monocytes_13_ivig


title: DCB_14_0.025_3 [TCAAGGAT-CCATAGGG-2]


title: Liver Day14-2

city: Chongqing

first: Qihuan

last: Fu

state: Chongqing

address: 181 Hanyu Road, Shapingba District

department: Chongqing University Cancer Hospital

country: China

institute: Chongqing University

data_processing:
Illumina bcl2fastq 2.0 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using HISAT2
Transcript abundance values were obtained from gene-level count matrices were generated by StringTie
Gene counts were normalized using geometric mean (GEO) in DESeq2 package and log2 transformed. Removal of unwanted variation (RUV) was used to remove batch effects and genes with no counts in over 50% of the samples were removed.
Differential gene expression by limma voom was performed on normalized gene counts, using batch effects and the first two PCAs of aligning and sequencing as covariates.
Assembly: Genome_build: mm10
Supplementary files format and content: Supplementary_files_format_and_content: tab-delimited text file includes gene abundance for each sample
Supplementary files format and content: Supplementary_files_format_and_content: tab-delimited text file includes gene counts for each sample

source_name: Liver

growth_protocol: The mice were housed at 25°C and fed standard rodent chow and tap water.

extract_protocol:
Total RNA was extracted from sample using the Trizol method.
RNA libraries were prepared for sequencing using TruePrepTM DNA Library Prep Kit V2 for Illumina following manufactory's protocols.

treatment_protocol: Logarithmic phase L. monocytogenes (1X104 CFU) was injected intravenously into eight-week-old female C57BL/6 mice (Beijing Charles River). Liver and spleen were harvested from infected mice 5,7 and 14 days after infection. Single-cell suspensions isolated from the liver and spleen were first stained with T-Select H-2Kb OVA Tetramer-SIINFEKL-APC (TS-5001-2C, MBL) at room temperature for 30 minutes, followed by stained with FITC anti-mouse CD8a (KT15, MBL), PerCP-Cy™5.5 anti-mouse CD3e (145-2c11, BD) at 4℃ for 15 min. To exclude dead cells, cells were washed in PBS and then treated with LIVE/DEAD-Fixable-Aqua (Invitrogen). We used BD FACS Aria III flow cytometers to sort the cells as desired.

value: Liver

value: T cells

value: CD3+CD8+OVATetramer+ T cells

value: Listeria-OVA infection 14 day


title: Liver Day14-3

value: WT


title: S5_Monocytes_5


title: 10366, nonpregnant

value: Endometrial cells from uterine body


title: S5_Monocytes_2_ivig


title: Liver Day14-1


title: 10913, nonpregnant


title: CellID Library

city: Hangzhou

first: Lijia

last: Ma

state: Zhejiang

address: Shilongshan Road No.18, Cloud Town, Xihu District

department: School of Life Sciences

institute: Westlake university

description:
oligonucleotides
CellID library
FB4.xlsx

data_processing:
SMART-seq: The SMART-seq NGS data was firstly removed adapters and aligned to the pre-designed oligonucleotide sequence using bowtie2. The nucleotides with the range of the 12-nt random sequences were further visualized using WebLogo
10x Genomics: The sequencing data of the scRNA-seq libraries were processed by Cell Ranger (provided by 10x Genomics Inc.). Each transcript was first assigned with a 10x Cell Barcode. Transcripts with the same Cell Barcode were considered to originate from the same cell and were used to determine the cell type identity of that cell. For each cell, we further counted the sequencing reads aligned to the CellIDs, which were further normalized as z-scores. And the most dominant CellID, which exhibited the highest z-score, determines the representative CellID of that cell. Thus, for each cell in our analysis, the classification performance of CellID can be evaluated by the cell type identity.
Screening: The CRISPR screening NGS libraries were sequenced as 150-bp paired-end. The sequencing reads were firstly undergone adapter removal by ‘cutadapter’ with parameters ‘-n 1 -e 0.11 -O 15 -m 16’. The sequences were then aligned to the designed CRISPR library sequences using bowtie2 with ‘–np 0 –n-ceil L,0,0.2 –very-sensitive’. We counted the reads number of each gRNA from the Brunello CRISPR library in both the mgSrtA labeled sample and the control sample (starting reference). The reads numbers were then normalized according to the sequencing depth of each NGS library, and an enrichment score was calculated for each gRNA (thus the targeted gene) using MAGeCK.

organism:
Homo sapiens
Mus musculus

growth_protocol: K562 and Jurkat cells  were cultured in RPMI1640 medium supplemented with 10% FBS and 1% penicillin/streptomycin. 293T, HeLa, A549, MC-38, Hepa1-6 and C2C12 cells were cultured in DMEM supplemented with 10% FBS and 1% penicillin/streptomycin. Cells were incubated at 37°C with 5% CO2.

extract_protocol:
OligoFITC.noSrtA and OligoFITC.SrtA library: Oligonucleoides were captured using SMART-seq and enriched with 2X beads selection, followed by two round PCR amplification.
scFB4 library: Library was prepared using Chromium Single Cell3' v3 (10x Genomics)
FB4.PA library: CellID-derived cDNA were enriched after cDNA amplification with 2X beads selection and amplified by one round PCR amplification.
Screening library: Genomic DNA (gDNA) was extracted from the sorted cells.The gRNA cassette was amplified  from the gDNA.

value: Different cell lines were labeled with different CellIDs and mixed together.


title: Liver Day7-3

value: Listeria-OVA infection 7 day


title: S5_Monocytes_1

value: Monocyte


title: 3'cDNA Library

description:
3' mRNA library
FB4.xlsx

molecule: polyA RNA


title: PFDA_2.5_2 [ATTCCGTA-CTATGATC-2]

value: Nontumorigenic breast

value: PFDA 2.5

value: 48 hrs


title: S3_neutrophils_14_ivig

source_name: Neutrophil

value: Neutrophil

value: IVIG


title: S2_Monocytes_9

value: PBS


title: Liver Day7-2


title: BPS_0.25_3 [CACCGCAA-ATATGAGA-2]

value: DMSO


title: DCP_25_0.25_1 [TACAGAGT-CCATAGGG-2]


title: S5_blood_14_ivig

value: Blood


title: Canine cutaneous histiocytoma, group 3 according to Cockerell & Slauson 1979, lymphocyte enriched, FFPE, 5

city: Berlin

first: Alina

middle: Katharina

last: Loriani Fard

address: Robert-von-Ostertag Straße 15

department: Department of Veterinary Medicine

institute: Freie Universität Berlin

description:
male
AL57_3
3_vs_2b.diffexp.tsv

data_processing:
The FASTQ sequencing files were first preprocessed (adapter trimmed, filtered) using Cutadapt and subsequently aligned to the NCBI Reference Sequence (RefSeq) assembly for the dog (Canis lupus familiaris) ROS_Cfam_1.0 (NCBI RefSeq assembly GCF_014441545.1) with the STAR aligner. Read counts per gene were generated with 2 rounds of featureCounts to mitigate the effect of too short 3' UTR annotations. Reads that remained unassigned in the first round were subjected to the second round of featureCounts on an adjusted annotation with a 3' extension by 2 kilobases. Differential gene expression (DGE) analysis for the comparisons of group 2a versus group 1 and group 3 versus group 2b was performed with R using DESeq2. Significance thresholds were drawn at a log2 (fold change) (log2FC) of ≤ -1 or ≥ 1 and an adjusted p-value (padj) of ≤ 0.05.
Assembly: ROS_Cfam_1.0 (NCBI RefSeq assembly GCF_014441545.1)
Supplementary files format and content: tab-delimited text file includes normalized counts and differential expression data for each sample

organism: Canis lupus familiaris

source_name: FFPE

extract_protocol:
Total RNA was extracted utilizing the PureLink FFPE Total RNA Isolation Kit (Thermo Fisher Scientific Inc.). After DNase I treatment 375 ng total RNA was used for library construction.
QuantSeq 3' mRNA-Seq FWD Library Preparation Kit (Lexogen) was used according to the manufacturer's guidelines (user guide 015UG009V0251) at Lexogen Services (Lexogen GmbH, Vienna) using the low-quality RNA protocol.

value: FFPE

tag: breed

value: Jack Russell Terrier

tag: age (years)


title: Liver Day7-1

value: Liver

value: T cells

value: CD3+CD8+OVATetramer+ T cells


title: S3_neutrophils_13


title: Canine cutaneous histiocytoma, group 3 according to Cockerell & Slauson 1979, lymphocyte enriched, FFPE, 4

description:
male
AL54_3
3_vs_2b.diffexp.tsv

value: Bullterrier


title: Liver Day5-3

value: WT

value: Listeria-OVA infection 5 day


title: Cadmium_0.25_3 [CGATGGCA-ATAGAGAG-2]

value: Cadmium 0.25

value: Water


title: S3_neutrophils_10_ivig


title: Control_0_7 [TGGTGGAA-ATAGAGAG-2]

value: Nontumorigenic breast

value: Control 0


title: Thiram_25_3 [CAGGAAGG-CCATAGGG-2]

value: Thiram 25

value: 48 hrs


title: S3_neutrophils_9

value: Neutrophil

value: PBS

value: IVIG


title: Liver Day5-2


title: Canine cutaneous histiocytoma, group 3 according to Cockerell & Slauson 1979, lymphocyte enriched, FFPE, 2

description:
female
AL51_3
3_vs_2b.diffexp.tsv

value: FFPE

value: Beagle


title: Liver Day5-1

value: Liver


title: Canine cutaneous histiocytoma, group 3 according to Cockerell & Slauson 1979, lymphocyte enriched, FFPE, 1

description:
male neutered
AL48_3
3_vs_2b.diffexp.tsv

value: Rottweiler


title: Copper_2.5_4 [TCAGATAC-ATAGAGAG-2]

value: Copper 2.5


title: S3_neutrophils_5_ivig


title: PFNA_0.025_4 [CGCGTGAT-CTATGATC-2]

value: DMSO


title: S3_neutrophils_2


title: Arsenic_2.5_4 [TGAACTCT-ATAGAGAG-2]

value: WT

value: Arsenic 2.5


title: Canine cutaneous histiocytoma, group 2 according to Cockerell & Slauson 1979, lymphocyte enriched, FFPE, 5

description:
female, male, male neutered, female
AL40_2b
3_vs_2b.diffexp.tsv

source_name: FFPE, pooled sample

value: FFPE, pooled sample

value: Flat Coated Retriever, n/s, Boxer, Bernese Mountain Dog


title: Spleen Day14-2

source_name: Spleen

value: Spleen

value: T cells

value: CD3+CD8+OVATetramer+ T cells

value: Listeria-OVA infection 14 day


title: Spleen Day14-1


title: Canine cutaneous histiocytoma, group 2 according to Cockerell & Slauson 1979, lymphocyte enriched, FFPE, 4

description:
male, male neutered, female, n/s
AL39_2b
3_vs_2b.diffexp.tsv

value: Doberman, French Bulldog, Jack Russel Mix, n/s


title: S3_neutrophils_1_ivig

value: Neutrophil

value: PBS


title: S2_neutrophils_10


title: Canine cutaneous histiocytoma, group 2 according to Cockerell & Slauson 1979, lymphocyte enriched, FFPE, 2

description:
female neutered
AL34_2b
3_vs_2b.diffexp.tsv

value: FFPE

value: Pug


title: Spleen Day7-2

value: Listeria-OVA infection 7 day


title: PFNA_2.5_3 [CGCAACAG-CTATGATC-2]

value: Nontumorigenic breast

value: PFNA 2.5

value: 48 hrs


title: S5_neutrophils_5


title: Spleen Day7-1

value: WT


title: Canine cutaneous histiocytoma, group 3 according to Cockerell & Slauson 1979, lymphocyte enriched, FFPE, 3

description:
male
AL52_3
3_vs_2b.diffexp.tsv


title: Copper_0.025_1 [CTCGTACA-ATAGAGAG-2]

value: Copper 0.025

value: Water


title: DCP_25_0.25_2 [CTTGTTGG-CCATAGGG-2]

value: DMSO


title: Canine cutaneous histiocytoma, group 2 according to Cockerell & Slauson 1979, lymphocyte enriched, FFPE, 3

description:
female, female, male, male
AL35_2b
3_vs_2b.diffexp.tsv

value: FFPE, pooled sample

value: Rhodesian Ridgeback, French Bulldog, French Bulldog, Dachshund


title: Control_0_30 [CTGCGAAC-ATATGAGA-2]

value: Control 0


title: Control_0_63 [GCCAGTGT-CCATAGGG-2]


title: Spleen Day7-3

value: Spleen

value: T cells

value: CD3+CD8+OVATetramer+ T cells


title: Spleen Day14-3

value: Listeria-OVA infection 14 day


title: Canine cutaneous histiocytoma, group 2 according to Cockerell & Slauson 1979, lymphocyte enriched, FFPE, 6

description:
male, female, male
AL45_2b
3_vs_2b.diffexp.tsv

value: Bordeaux Mastiff, French Bulldog, Labradoodle


title: S3_blood_14_ivig

value: Blood

value: IVIG

value: PBS


title: Canine cutaneous histiocytoma, group 2 according to Cockerell & Slauson 1979, tumor cell enriched, FFPE, 5

description:
male
AL28_2a
2a_vs_1.diffexp.tsv

value: FFPE

value: Mix


title: PFOA_25_2 [TTCACACT-CTATGATC-2]

value: Nontumorigenic breast

value: WT

value: PFOA 25

value: 48 hrs


title: S5_neutrophils_14_ivig

value: Neutrophil


title: Canine cutaneous histiocytoma, group 2 according to Cockerell & Slauson 1979, lymphocyte enriched, FFPE, 1

description:
female
AL33_2b
3_vs_2b.diffexp.tsv

value: Akita


title: Spleen Day5-3

value: Listeria-OVA infection 5 day


title: PFDA_25_4 [TGGTACAG-CTATGATC-2]

value: PFDA 25

value: DMSO


title: Copper_25_2 [TTCACACT-ATAGAGAG-2]

value: Copper 25

value: Water


title: Spleen Day5-1

value: Spleen

value: T cells

value: CD3+CD8+OVATetramer+ T cells


title: Canine cutaneous histiocytoma, group 2 according to Cockerell & Slauson 1979, tumor cell enriched, FFPE, 4

description:
female neutered
AL25_2a
2a_vs_1.diffexp.tsv

value: Doberman


title: m4_unstimulated

value: Ics

value: IVIG


title: Spleen Day5-2


title: Canine cutaneous histiocytoma, group 2 according to Cockerell & Slauson 1979, tumor cell enriched, FFPE, 3

description:
female
AL24_2a
2a_vs_1.diffexp.tsv

value: FFPE

value: Hovawart


title: Thiram_0.025_4 [TGAATGTG-CCATAGGG-2]

value: Nontumorigenic breast

value: WT

value: Thiram 0.025


title: m3_unstimulated


title: m2_unstimulated


title: Canine cutaneous histiocytoma, group 2 according to Cockerell & Slauson 1979, tumor cell enriched, FFPE, 2

description:
male neutered
AL22_2a
2a_vs_1.diffexp.tsv

value: English Bulldog


title: Canine cutaneous histiocytoma, group 2 according to Cockerell & Slauson 1979, tumor cell enriched, FFPE, 1

description:
male
AL17_2a
2a_vs_1.diffexp.tsv

value: Bavarian Mountain Hound


title: Copper_2.5_3 [CCACAATG-ATAGAGAG-2]

value: Copper 2.5

value: 48 hrs


title: m1_unstimulated


title: Canine cutaneous histiocytoma, group 1 according to Cockerell & Slauson 1979, FFPE, 5

description:
female
AL8_1
2a_vs_1.diffexp.tsv

value: French Bulldog


title: S5_blood_5

value: Blood

value: PBS


title: Lead_0.25_4 [CGACTAGC-ATAGAGAG-2]

value: Lead 0.25

value: Water


title: Thiram_2.5_4 [CCTGTTAC-CCATAGGG-2]

value: Thiram 2.5

value: DMSO


title: Canine cutaneous histiocytoma, group 1 according to Cockerell & Slauson 1979, FFPE, 4

description:
male neutered
AL7_1
2a_vs_1.diffexp.tsv

value: Boxer


title: 24 hours post injury (HPI), old, batch 3, 10X chip channel A

city: Berkeley

first: John

last: Ngai

state: CA

address: Department of Molecular & Cell Biology

institute: University of California, Berkeley

description: propidium iodide sorted cells (alive)

data_processing:
Read are aligned using cellranger version 3.0 on mouse mm10, cellranger reference 3.0.0, Ensembl v93 gene annotation
Gene-barcode matrix is generated using cellranger version 3.0
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include cell barcode names and gene names
Supplementary_files_format_and_content: Matrix table with gene-barcode matrix

source_name: Olfactory Epithelium, YFP+

growth_protocol: olfactory epithelium anatomical dissections were extracted from mice

extract_protocol:
lysates were clarified from alive cells from the sorter
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: in the FACS facility only cells that were alive (PI sorting rule) were taken

tag: mouse strain

tag: mouse age

value: 18 months

tag: animal sex

value: Female (1) / Male (1)

value: olfactory epithelium

tag: mouse treatment

value: 24 hous post injury of methimazole injection


title: 24 hours post injury (HPI), old, batch 3, 10X chip channel B

description: propidium iodide sorted cells (alive)


title: DCB_14_2.5_4 [TGAACTCT-CCATAGGG-2]

tag: cell line

value: Nontumorigenic breast

value: WT


title: PCB187_0.025_2 [CAAGTAGT-CCATAGGG-2]

tag: cell type


title: Canine cutaneous histiocytoma, group 1 according to Cockerell & Slauson 1979 , FFPE, 1

description:
male neutered
AL3_1
2a_vs_1.diffexp.tsv

value: FFPE


title: 24 hours post injury (HPI), young, batch 3, 10X chip channel B

description: propidium iodide sorted cells (alive)

value: 2 months


title: Canine cutaneous histiocytoma, group 1 according to Cockerell & Slauson 1979, FFPE, 3

description:
n/s
AL6_1
2a_vs_1.diffexp.tsv

value: Terrier

value: n/s


title: 24 hours post injury (HPI), old, batch 2, 10X chip channel A

description: propidium iodide sorted cells (alive)


title: PFNA_25_3 [GATGAGAA-CTATGATC-2]

tag: genotype

value: PFNA 25

value: 48 hrs


title: Canine cutaneous histiocytoma, group 1 according to Cockerell & Slauson 1979, FFPE, 2

description:
male
AL4_1
2a_vs_1.diffexp.tsv

value: Goldendoodle


title: 24 hours post injury (HPI), young, batch 2, 10X chip channel B

description: propidium iodide sorted cells (alive)


title: cartilage_rrbs_male_ACa08

city: Tokyo

first: Makii

last: Fukami

address: 2-10-1 Okura, Setagaya

department: Department of Molecular Endocrinology

country: Japan

institute: National Research

library_source: genomic

data_processing:
Sequence reads were mapped to the human reference genome for bisulfite sequencing (CT-converted hs37d5) using the Bismark program.
The depth of reads harboring C and T at each CpG site was calculated using the methylKit package (v.1.10.0) in R.
Genome_build: hs37d5
Supplementary_files_format_and_content: rrbs_adult_knee_cartilage.txt (Text file describing the depth of the total coverage and reads harboring C and T at each CpG site in the X chromosome.)

molecule: genomic DNA

source_name: articular cartilage of the knee

extract_protocol:
Cartilage tissues were stored in RNAlater. Genomic DNA was extracted using the Gentra Puregene kit (QIAGEN).
Genome DNA samples were sonicated and treated with proteinase K (Thermo Fisher Scientific) and RNase A (Nacalai Tesque). Purified samples were digested with MspI (New England BioLabs), subjected to gap filling and A-tailing with the Klenow fragment (Thermo Fisher Scientific), and ligated with the NEBNext methylated adaptor (New England BioLabs). The adaptor-ligated DNA samples were subjected to bisulfite conversion by the EZ DNA Methylation-Gold kit (Zymo Research) and amplified by PCR with the KAPA HiFi HotStart Uracil+ ReadyMix kit (Roche).

tag: gender

value: male

value: articular cartilage of the knee


title: cartilage_rrbs_male_ACa07


title: PFOS_2.5_4 [ATGCCGCT-CTATGATC-2]

tag: treatment

value: PFOS 2.5

tag: time

value: DMSO


title: 24 hours post injury (HPI), young, batch 2, 10X chip channel A

description: propidium iodide sorted cells (alive)


title: Phenanthrene_25_1 [GGCTCCTA-CTATGATC-2]

value: Phenanthrene 25

tag: control flags

tag: plate id


title: PPB_0.025_3 [GTGTCCAT-ATATGAGA-2]


title: PCB187_2.5_3 [GTGCGAGT-CCATAGGG-2]


title: cartilage_rrbs_female_ACa01

value: female

tag: tissue


title: cartilage_rrbs_female_ACa02


title: un-injured (UI), old, batch 3, 10X chip channel A

description: propidium iodide sorted cells (alive)

value: 18 months

value: Female (1) / Male (1)

value: olfactory epithelium


title: Control_0_42 [CTAAGGCG-CTATGATC-2]

value: Nontumorigenic breast

value: WT

value: Control 0


title: PCB187_0.25_4 [CAACCGTG-CCATAGGG-2]


title: un-injured (UI), young, batch 3, 10X chip channel B

description: propidium iodide sorted cells (alive)

value: 2 months


title: 24 hours post injury (HPI), old, batch 2, 10X chip channel B

description: propidium iodide sorted cells (alive)

value: 24 hous post injury of methimazole injection


title: PCB187_0.025_3 [GTGTCCAT-CCATAGGG-2]


title: Mouse primary neuron (DIV14), MICAL1-FL, ATRX, ChIP

city: shanghai

first: Dong

last: Jian

address: 393 Middle Huaxia  Road

institute: shanghaitech university

data_processing:
The ChIP-seq data of ATRX were aligned to the mouse genome (release 109) using the Bowtie (1.3.0). SAM files were sorted and filtered using samtools (1.9)
Peak-calling performed with MACS (1.4.2) was run independently for each BAM files to detect genomic regions enriched for multiple overlapping DNA fragments (peaks) that were considered to be putative binding sites.
Peaks for further analyses were filtered using the same p value cutoff (5 ⅹ 10-2) by comparing the peaks obtained from the samples with those from the control samples.
Target genes were considered by at least one peak within 3 kb from the transcription start site (TSS)
Heat maps for showing the peaks within 3 kb from the TSS were visualized using the CHIPseeker package (1.26.2), GO terms analysis was generated using the clusterProfiler package (3.18.1).
Assembly: release 109
Supplementary files format and content: narrowPeak (except for Input group)

source_name: Mouse primary neuron

growth_protocol: Mouse primary neurons were isolated from C57BL6/J mice at E15.5-17.5. The cultured neurons were maintained in Neurobasal A media (Gibco), supplemented with B27, 2 mM glutamine, and 2% fetal bovine serum (Gibco).

extract_protocol:
The samples for ChIP analysis were extracted using SimpleChIP Enzymatic Chromatin IP Kit (Cell Signaling Technology, 91820s) with antibodies against ATRX (Abcam ab97508). Input DNA was used to control for background.
DNA samples in input and IP groups were pair-end sequenced on Illumina Hi-Seq2500 platform.

treatment_protocol: Mouse primary neurons were infected by lentivirus at DVI5.

value: Mouse primary neuron

tag: antibody

value: ATRX


title: Mouse primary neuron (DIV14), mcherry,  ATRX, ChIP


title: un-injured (UI), old, batch 2, 10X chip channel B

description: propidium iodide sorted cells (alive)


title: un-injured (UI), young, batch 3, 10X chip channel A

description: propidium iodide sorted cells (alive)


title: Mouse primary neuron, input of Control neurons


title: Tumor bearing KPC with Metastasis A

city: Charleston

first: Stefano

last: Berto

state: SC

address: 68 President Street

department: Neuroscience

institute: Medical University of South Carolina

data_processing:
Bulk RNA-seq reads were aligned with STAR 2.7.1a to the reference sequence (mm10 from UCSC). Mouse reference was used for gene annotation and counting (gencode M27). Uniquely mapped reads were quantified using featureCounts using protein coding genes by gene.
Assembly: Mouse mm10
Supplementary files format and content: tab-delimited text files raw counts for each sample

source_name: Skeletal Muscle

extract_protocol:
Cells were  homogenized in 1mL of Trizol and RNA extracted as per manufacters protocol
Libraries were prepared by MUSC Translational Core using the New England Biolabs NEBNext Poly(A) mRNA Magnetic Isolation Module (Cat# 7490L) and Ultra II Directional RNA Library Prep Kit from Illumina (Cat# 7760L). Dual indexed libraries were pooled and sequenced at VANTAGE (Vanderbilt University Medical Center) on an Illumina NovaSeq 6000 to a depth of approximately 25 million paired-end 150 bp reads per library.

value: Skeletal Muscle

value: tumor bearing


title: Tumor bearing KPC with Metastasis B


title: un-injured (UI), old, batch 2, 10X chip channel A

description: propidium iodide sorted cells (alive)


title: Arsenic_25_3 [CACAGTCT-ATAGAGAG-2]

value: Arsenic 25

value: 48 hrs

value: Water


title: PFOA_0.025_3 [ATTCGCAG-CTATGATC-2]


title: Tumor bearing KPC with no Metastasis B


title: un-injured (UI), young, batch 2, 10X chip channel A

description: propidium iodide sorted cells (alive)


title: PFNA_25_1 [CAGAGTGG-CTATGATC-2]

value: PFNA 25

value: DMSO


title: un-injured (UI), young, batch 2, 10X chip channel B

description: propidium iodide sorted cells (alive)


title: Control_0_23 [TGGTGGAA-ATATGAGA-2]


title: Tumor bearing KPC with no Metastasis A


title: DCP_25_25_3 [ATGGTCCG-CCATAGGG-2]


title: un-injured (UI), old, batch 1, 10X chip channel B

description: propidium iodide sorted cells (alive)

value: 18 months


title: Ctrl KPC_B

value: Control


title: un-injured (UI), old, batch 3, 10X chip channel B

description: propidium iodide sorted cells (alive)

value: Female (1) / Male (1)

value: olfactory epithelium


title: un-injured (UI), old, batch 1, 10X chip channel A

description: propidium iodide sorted cells (alive)


title: BPA_2.5_4 [CCTGTTAC-ATATGAGA-2]

value: Nontumorigenic breast

value: WT

value: BPA 2.5


title: un-injured (UI), young, batch 1, 10X chip channel B

description: propidium iodide sorted cells (alive)

value: 2 months


title: Arsenic_0.25_4 [TGCTCCGT-ATAGAGAG-2]

value: Arsenic 0.25


title: BPF_2.5_3 [CCACAATG-ATATGAGA-2]

value: BPF 2.5


title: Lead_2.5_1 [ACTCGAAT-ATAGAGAG-2]

value: Lead 2.5


title: un-injured (UI), young, batch 1, 10X chip channel A

description: propidium iodide sorted cells (alive)


title: Phenanthrene_0.025_2 [AACCAATC-CTATGATC-2]

value: Phenanthrene 0.025


title: Tumor bearing KPP B

value: Skeletal Muscle

value: tumor bearing


title: Control for KPP B


title: Tumor bearing C26 B


title: Clone11_Minus [RNA-Seq]

city: Boston

first: David

middle: T

last: Scadden

state: MA

address: 185 Cambridge St

department: Center for Regenerative Medicine

institute: MGH

description: Gene expression data in ER-Hoxb8 cells

data_processing:
Illumina software used for basecalling.
Raw sequences of RNA-seq were mapped to the mouse transcript (mm10) using a Salmon mapper (v.1.1.0). The count of mapped reads was normalized as transcripts per million (TPM) using an R package of tximport.
Genome_build: mm10
Supplementary_files_format_and_content: TPM

source_name: Mouse Bone Marrow ER-Hoxb8 monocytic cells

growth_protocol: ER-HoxB8 cells were maintained in RPMI medium supplemented with 10% FBS, penicillin/streptomycin, and SCF.

extract_protocol:
For RNA-seq, total RNAs were extracted using RNeasy mini kit (Qiagen).
RNA-sequencing libraries were generated using library prep kits (NEB) according to the manufacturer’s instructions.

value: ER-Hoxb8 cells


title: Control_0_16 [GTGCGTTC-ATAGAGAG-2]

value: Control 0

value: 48 hrs

value: Water


title: Thiram_2.5_1 [ACTCGAAT-CCATAGGG-2]

value: Thiram 2.5

value: DMSO


title: Clone10_Minus [RNA-Seq]

description: Gene expression data in ER-Hoxb8 cells


title: Tumor bearing C26 A


title: PCB153_0.025_2 [CAGGCTTC-CCATAGGG-2]


title: Control_0_38 [CCGAGTTA-CTATGATC-2]


title: Clone9_Minus [RNA-Seq]

description: Gene expression data in ER-Hoxb8 cells


title: Clone12_Minus [RNA-Seq]

description: Gene expression data in ER-Hoxb8 cells


title: Control for C26 B

value: Control


title: Tumor Bearing KPP A


title: Mercury_25_3 [GATGAGAA-ATAGAGAG-2]

value: Nontumorigenic breast

value: Mercury 25


title: PFOS_0.25_3 [CGATGGCA-CTATGATC-2]

value: WT

value: PFOS 0.25


title: Control for C26 A


title: Control for KPP A


title: Ctrl KPC_A


title: Clone7_Minus [RNA-Seq]

description: Gene expression data in ER-Hoxb8 cells


title: Thiram_25_2 [CAGAAGAA-CCATAGGG-2]

value: Thiram 25


title: Clone6_Minus [RNA-Seq]

description: Gene expression data in ER-Hoxb8 cells


title: Tumor bearing LLC A


title: M2-IL7

city: Philadelphia

first: Caitlin

last: Tilsed

state: Pennsylvania

address: 407F 4312 Chestnut St

institute: The University of Pennsylvania

data_processing:
Fastq files were aligned using Kalisto.
Assembly: GRCm39
Supplementary files format and content: Raw counts were log2CPM normalized

source_name: CD8 t cells

extract_protocol:
RNA was extracted by Azenta life sciences
2x150bl, 350M paired end reads.

value: CD8 t cells

tag: strain


title: Clone5_Minus [RNA-Seq]

description: Gene expression data in ER-Hoxb8 cells


title: PFOS_25_3 [ACACAACA-CTATGATC-2]

value: PFOS 25


title: Clone13_Minus [RNA-Seq]

description: Gene expression data in ER-Hoxb8 cells


title: BPA_25_4 [CGTCTGAA-ATATGAGA-2]

value: BPA 25


title: Clone4_Minus [RNA-Seq]

description: Gene expression data in ER-Hoxb8 cells


title: M5-R

value: MEDIA


title: Control for LLC A

value: Skeletal Muscle


title: Clone8_Minus [RNA-Seq]

description: Gene expression data in ER-Hoxb8 cells

value: ER-Hoxb8 cells


title: BPA_2.5_1 [ACTCGAAT-ATATGAGA-2]

value: BPA 2.5


title: Clone3_Minus [RNA-Seq]

description: Gene expression data in ER-Hoxb8 cells


title: M5-IL15


title: Cadmium_2.5_3 [GTGCGAGT-ATAGAGAG-2]

value: Cadmium 2.5

value: 48 hrs


title: Clone2_Minus [RNA-Seq]

description: Gene expression data in ER-Hoxb8 cells


title: M5-IL7


title: KPCML1 A

source_name: Pancreatic Tumor Derived Cells

value: Pancreatic Tumor Derived Cells

value: KPC

value: Pancreatic Cancer Cell Line

value: metastatic line


title: Tumor bearing LLC B

value: tumor bearing


title: Mercury_0.25_2 [CTAACAAC-ATAGAGAG-2]

value: Nontumorigenic breast

value: WT

value: Mercury 0.25

value: Water


title: Phenanthrene_0.025_1 [GTTAAGCA-CTATGATC-2]

value: Phenanthrene 0.025

value: DMSO


title: Clone1_Minus [RNA-Seq]

description: Gene expression data in ER-Hoxb8 cells


title: M4-R

value: CD8 t cells

value: MEDIA


title: KPC B

value: parental cell line


title: KPC A


title: DCB_14_25_4 [TGGTACAG-CCATAGGG-2]


title: Clone12_Plus [RNA-Seq]

description: Gene expression data in ER-Hoxb8 cells

source_name: Mouse Bone Marrow ER-Hoxb8 GMP cells

value: ER-Hoxb8 cells


title: M4-IL15


title: Control_0_19 [ATAGATCC-ATATGAGA-2]

value: Control 0


title: Clone26_Minus [RNA-Seq]

description: Gene expression data in ER-Hoxb8 cells


title: Control for LLC B

value: Skeletal Muscle

value: Control


title: M4-IL7


title: Clone24_Minus [RNA-Seq]

description: Gene expression data in ER-Hoxb8 cells


title: KPCML1 B

value: Pancreatic Tumor Derived Cells

value: KPC


title: M4-IL2


title: M5-IL2


title: Clone23_Minus [RNA-Seq]

description: Gene expression data in ER-Hoxb8 cells


title: Clone11_Plus [RNA-Seq]

description: Gene expression data in ER-Hoxb8 cells


title: BPA_0.025_2 [AACCAATC-ATATGAGA-2]

value: 48 hrs


title: Clone9_Plus [RNA-Seq]

description: Gene expression data in ER-Hoxb8 cells


title: Clone8_Plus [RNA-Seq]

description: Gene expression data in ER-Hoxb8 cells


title: Clone13_Plus [RNA-Seq]

description: Gene expression data in ER-Hoxb8 cells


title: PCB153_0.25_2 [CTAACAAC-CCATAGGG-2]


title: Clone21_Minus [RNA-Seq]

description: Gene expression data in ER-Hoxb8 cells


title: Clone7_Plus [RNA-Seq]

description: Gene expression data in ER-Hoxb8 cells


title: M1-R


title: Clone20_Minus [RNA-Seq]

description: Gene expression data in ER-Hoxb8 cells


title: Cadmium_2.5_1 [CAACTCCG-ATAGAGAG-2]

value: Cadmium 2.5


title: Clone19_Minus [RNA-Seq]

description: Gene expression data in ER-Hoxb8 cells


title: Clone18_Minus [RNA-Seq]

description: Gene expression data in ER-Hoxb8 cells


title: Clone6_Plus [RNA-Seq]

description: Gene expression data in ER-Hoxb8 cells


title: M1-IL7


title: Clone5_Plus [RNA-Seq]

description: Gene expression data in ER-Hoxb8 cells


title: BPA_0.25_1 [GTTGACAG-ATATGAGA-2]

value: Nontumorigenic breast


title: PFOA_25_4 [TCCTATCT-CTATGATC-2]

value: WT

value: PFOA 25


title: Clone10_Plus [RNA-Seq]

description: Gene expression data in ER-Hoxb8 cells


title: Clone4_Plus [RNA-Seq]

description: Gene expression data in ER-Hoxb8 cells


title: Clone22_Minus [RNA-Seq]

description: Gene expression data in ER-Hoxb8 cells


title: PCB187_25_3 [ACACAACA-CCATAGGG-2]


title: Clone17_Minus [RNA-Seq]

description: Gene expression data in ER-Hoxb8 cells


title: M1-IL2


title: M3-IL2


title: Clone3_Plus [RNA-Seq]

description: Gene expression data in ER-Hoxb8 cells


title: PCB153_0.25_3 [CCATACTC-CCATAGGG-2]


title: Clone16_Minus [RNA-Seq]

description: Gene expression data in ER-Hoxb8 cells


title: Clone26_Plus [RNA-Seq]

description: Gene expression data in ER-Hoxb8 cells


title: Clone15_Minus [RNA-Seq]

description: Gene expression data in ER-Hoxb8 cells


title: BPS_2.5_4 [TGAACTCT-ATATGAGA-2]

value: BPS 2.5


title: PCB153_25_1 [CAGAGTGG-CCATAGGG-2]


title: Clone1_Plus [RNA-Seq]

description: Gene expression data in ER-Hoxb8 cells


title: MIN6 stable cells with miR-146a-5p inhibited, treated with proinflammatory cytokines - replicate4 [P68-ZIP-Cy]

city: Indianapolis

first: Carmella

last: Evans-Molina

state: Indiana

address: 16 Tech Innovation Bldg 1; 1210 Waterway Blvd Ste 4100

department: Pediatrics

institute: Indiana University School of Medicine

data_processing:
The quality of sequencing data was first assessed using FastQC (Babraham Bioinformatics).Further analysis using Fastq files was performed using Partek Flow 11.0.24.0204.
Sequencing files were aligned to mm10 mouse reference genome using STAR aligner 2.7.8a and mapped to mRNA using RefSeq Transcripts 96 annotation database.
Genes with less than 10 read counts in total were removed
Differential expression analysis was performed using DESeq2, and genes with fold-change ≥ 1.5 and p-value < 0.05 were considered as differentially expressed
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes normalized counts (median ratio values) for each sample

growth_protocol: MIN6 cells were grown in DMEM (11965-092; GIBCO) containing 4.5 g/L D-glucose, 4 mM L-glutamine, 10% fetal bovine serum (FBS, 35-015-CV; Corning), 100 units/mL penicillin, 100 µg/mL streptomycin (30-002-CI; Corning), and 50 µM β-mercaptoethanol (034461-100; ThermoFisher Scientific). Cells were cultured at 37 °C in a humidified atmosphere containing 5% CO2. The medium was changed every other day, and cells were passaged weekly and regularly tested for mycoplasma contamination by PCR-based assay (G238; ABM).

extract_protocol:
Total RNA was isolated using miRNeasy mini kit (217004; Qiagen). RNA concentration was measured using a NanoDrop 2000 (ThermoFisher Scientific).
One hundred nanograms of total RNA was used for library preparation.Library amplification was performed following the KAPA mRNA Hyper Prep Kit Technical Data Sheet, KR1352 – v4.17 (Roche Corporate)

treatment_protocol:
MIN6 stable cells were generated by transducing MIN6 cells with lentiviral vectors overexpressing miR-146a-5p, inhibting miR-146a-5p and scrambled sequence.For clonal selection, transduced cells were cultured with 1 µg/mL of puromycin for 7 days. Single clones were picked, seeded in 96-well plates, and cultured with puromycin-containing complete media. The clones were expanded and screened for miR-146a-5p using qRT-PCR, and the clones showing expression patterns of inhibition and overexpression were picked and used for further experiments
MIN6 cells were cultured in the presence or absence of a combination of three pro-inflammatory cytokines: 5 ng/mL IL1β (Cyt-273; Prospec Protein Specialists), 100 ng/mL IFNγ (Cyt-358; Prospec Protein Specialists), and 10 ng/mL TNFα (Cyt-252; Prospec Protein Specialists) for 24 hours.

value: Cells transduced with lentiviral vector inhibiting miR-146a-5p

value: miR-146a-5p inhibition

value: Treatment with proinflammatory cytokines


title: M1-IL15

value: CD8 t cells


title: Control MIN6 stable cells transduced with scrambled without proinflammatory cytokines - replicate4 [P68-SCR]

value: Cells transduced with scrambled sequence

value: No treatment


title: Control_0_39 [TGGTGGAA-CTATGATC-2]

value: Control 0

value: Water


title: Clone24_Plus [RNA-Seq]

description: Gene expression data in ER-Hoxb8 cells

value: ER-Hoxb8 cells


title: DCB_14_2.5_2 [ATTCCGTA-CCATAGGG-2]

value: DMSO


title: Tnm+union-3

city: HeFei

first: He

last: Kan

state: AnHui

address: No. 111 Jiulong Road, Furong community, Shushan District, Hefei City, Anhui province

institute: Anhui University

data_processing:
In this project, mRNA with polyA structure in total RNA was enriched by Oligo(dT) magnetic beads, and a gene library was constructed using RNA as a template, and the library fragments were enriched by PCR amplification. The library was inspected by Agilent 2100 Bioanalyzer, and then the total concentration and effective concentration of the library were detected. Then, according to the effective concentration of the library and the amount of data required by the library, the libraries containing different Index sequences are mixed proportionally to form a single strand library.
After RNA extraction, purification, and library construction, the libraries were Paired-end (PE) sequenced using Next-Generation Sequencing (NGS) based on the Illumina HiSeq sequencing platform.
Data analysis: First, the original data were filtered, and the high-quality sequences obtained after filtering were compared to the reference genome of the species. According to the comparison results, the expression level of each gene was calculated. On this basis, the expression difference analysis, enrichment analysis and cluster analysis of the samples were further conducted.
Appropriate reference genomes were selected, and the sequences with 3' end-band junction were removed by Cutadapt through data filtering, while Reads with average mass scores lower than Q20 were removed. The data were analyzed by expression level, the gene structure annotation information (GTF file) was read, and then the comparison results were compared with the gene structure and the results were counted. Meanwhile, the filtered Reads were compared to the reference genome using an updated version of TopHat2's HISAT2 software.
We use the HTSeq(0.9.1) statistic to compare the Read Count value of each gene as the original expression of that gene, and then normalize the expression using FPKM. DESeq(1.30.0) was used to analyze the differential expression of genes, and the screening criteria were as follows: llog2FoldChange>1, the significant P value <0.05. The R language Pheatmap(1.0.8) software package was used for directional cluster analysis of all the different genes in the sample.
Assembly: Mus_musculus.GRCm39.dna.toplevel.fa
Supplementary files format and content: tab-delimited text files include the expression values of this transcript for each Sample .

source_name: tumor stage

extract_protocol:
Mouse 4T1 breast cancer cells were cultured in complete medium containing 90%DMEM, 10% fetal bovine serum (high quality) and 1% penicillin streptomycin at 37℃ in a 5% C02 incubator, and cell suspension with cell concentration of 1×10^7/ml was prepared for use. Thirty healthy BALB/c mice, aged 4 to 6 weeks and weighing 18 to 20 g, were randomly divided into 5 groups, 5 in each group. The ck group was injected with the same amount of normal saline, and the BALB/c mice in the other 4 groups were subcutly inoculated with 0.2ml cell suspension of corresponding concentration (the number of cells was about 200W) on the chest wall of 5-6 intercostocal and lateral abdominal walls. The four groups were named Tnm, Tnm+swim, Tnm+cur and Tnm+union. Each afternoon, the Tnm group and Tnm+swim group received 200ul solution intragastric administration, and the Tnm+cur and Tnm+union group received 200ul curcumin solution dissolved in corn oil (100mg/Kg) intragastric administration. Half an hour after gavage, Tnm+swim and Tnm+union groups were subjected to swimming exercise intervention for 30 minutes, and weight and tumor volume were weighed every two days.
PE150 platform used forbasecalling. sequenced reads were trimmed for adaptorsequence,and masked forlow-complexity or low-qualitysequence,then mapped tomm9 whole genome using HISAT2 v2.0.5. We used HTSeq(0.9.1) statistics to compare the ReadCount values on each gene asthe original expression of thegene, and then used FPKM tostandardize the expression.Difference expression of genes was analyzed by DESeq(1.30.0) with screened

value: tumor stage

value: Breast cancer cell

tag: host strain

value: BALB/c

value: Mice were given curcumin solution (100mg/Kg)


title: Tnm+union-2


title: Control MIN6 stable cells transduced with scrambled treated with proinflammatory cytokines - replicate4 [P68-SCR-Cy]

value: Control


title: MIN6 stable cells overexpressing miR-146a-5p without proinflammatory cytokines - replicate4 [P68-OE]

value: Cells transduced with lentiviral vector overexpressing miR-146a-5p

value: miR-146a-5p overexpression


title: BPA_0.25_2 [AATGTGCC-ATATGAGA-2]

value: Nontumorigenic breast

value: WT

value: 48 hrs


title: Clone23_Plus [RNA-Seq]

description: Gene expression data in ER-Hoxb8 cells


title: MIN6 stable cells overexpressing miR-146a-5p treated with proinflammatory cytokines - replicate4 [P68-OE-Cy]

value: Treatment with proinflammatory cytokines


title: MIN6 stable cells with miR-146a-5p inhibited, without proinflammatory cytokines - replicate4 [P68-ZIP]

value: Cells transduced with lentiviral vector inhibiting miR-146a-5p

value: miR-146a-5p inhibition


title: Clone22_Plus [RNA-Seq]

description: Gene expression data in ER-Hoxb8 cells


title: PPB_0.25_2 [ACGCTGCA-ATATGAGA-2]


title: Clone2_Plus [RNA-Seq]

description: Gene expression data in ER-Hoxb8 cells


title: Tnm-swim-3

value: The mice were given corn oil


title: Tnm+union-1


title: PPB_0.025_2 [CAAGTAGT-ATATGAGA-2]


title: Clone21_Plus [RNA-Seq]

description: Gene expression data in ER-Hoxb8 cells


title: Mercury_0.25_1 [ATGGAACA-ATAGAGAG-2]

value: Mercury 0.25

value: Water


title: MIN6 stable cells with miR-146a-5p inhibited, without proinflammatory cytokines - replicate3 [P67-ZIP]

value: No treatment


title: Tnm-swim-2

value: tumor stage


title: Clone20_Plus [RNA-Seq]

description: Gene expression data in ER-Hoxb8 cells

value: ER-Hoxb8 cells


title: MIN6 stable cells with miR-146a-5p inhibited, treated with proinflammatory cytokines - replicate3 [P67-ZIP-Cy]


title: Clone19_Plus [RNA-Seq]

description: Gene expression data in ER-Hoxb8 cells


title: Tnm-swim-1

value: Breast cancer cell

value: BALB/c


title: Mercury_25_1 [CAGAGTGG-ATAGAGAG-2]

value: Mercury 25


title: Control MIN6 stable cells transduced with scrambled without proinflammatory cytokines - replicate3 [P67-SCR]

value: Cells transduced with scrambled sequence

value: Control


title: BPA_0.25_4 [CGACTAGC-ATATGAGA-2]

value: Nontumorigenic breast

value: DMSO


title: Control MIN6 stable cells transduced with scrambled treated with proinflammatory cytokines - replicate3 [P67-SCR-Cy]


title: Clone18_Plus [RNA-Seq]

description: Gene expression data in ER-Hoxb8 cells


title: MIN6 stable cells overexpressing miR-146a-5p without proinflammatory cytokines - replicate3 [P67-OE]

value: Cells transduced with lentiviral vector overexpressing miR-146a-5p

value: miR-146a-5p overexpression


title: DCP_25_25_1 [CCATTGCG-CCATAGGG-2]

value: WT

value: 48 hrs


title: Tnm-cur-2

value: Mice were given curcumin solution (100mg/Kg)


title: Control_0_5 [TGGTGACT-ATAGAGAG-2]

value: Control 0


title: Clone17_Plus [RNA-Seq]

description: Gene expression data in ER-Hoxb8 cells


title: Tnm-cur-1


title: Tnm-cur-3


title: PFNA_0.25_3 [CCATACTC-CTATGATC-2]

value: PFNA 0.25


title: Tnm-3

value: The mice were given corn oil


title: PFOS_0.25_2 [ACGCTGCA-CTATGATC-2]

value: PFOS 0.25


title: MIN6 stable cells with miR-146a-5p inhibited, without proinflammatory cytokines - replicate2 [P66-ZIP]

value: Cells transduced with lentiviral vector inhibiting miR-146a-5p

value: miR-146a-5p inhibition

value: No treatment


title: Clone15_Plus [RNA-Seq]

description: Gene expression data in ER-Hoxb8 cells

value: ER-Hoxb8 cells


title: Tnm-2

value: tumor stage

value: Breast cancer cell

value: BALB/c


title: MIN6 stable cells with miR-146a-5p inhibited, treated with proinflammatory cytokines - replicate2 [P66-ZIP-Cy]

value: Treatment with proinflammatory cytokines


title: MIN6 stable cells overexpressing miR-146a-5p treated with proinflammatory cytokines - replicate3 [P67-OE-Cy]

value: Cells transduced with lentiviral vector overexpressing miR-146a-5p


title: Control_0_47 [GCCAGTGT-CTATGATC-2]

value: Nontumorigenic breast

value: Water


title: Clone26_Minus [ATAC-seq]

description: ATAC-Seqdata in ER-Hoxb8 cells

data_processing:
Illumina software used for basecalling.
Raw sequences of ATAC-seq data were mapped with a Bowtie2 mapper with a default setting to the mouse genome (mm10).
Genome_build: mm10
Supplementary_files_format_and_content: peaks

extract_protocol: ATAC-seq samples were performed as previously described (Buenrostro et al., 2015)


title: Tnm-1


title: Clone16_Plus [RNA-Seq]

description: Gene expression data in ER-Hoxb8 cells


title: Control MIN6 stable cells transduced with scrambled without proinflammatory cytokines - replicate2 [P66-SCR]

value: Cells transduced with scrambled sequence

value: Control


title: Clone24_Minus [ATAC-seq]

description: ATAC-Seqdata in ER-Hoxb8 cells


title: Control_0_24 [CTGTACGC-ATATGAGA-2]

value: WT

value: Control 0

value: 48 hrs

value: DMSO


title: SR21,WCO,72h,rep3

city: Luleå

first: ALOK

middle: KUMAR

last: PATEL

address: Department of Civil, Environmental and Natural Resources Engineering  Luleå University of Technology,  Luleå, Sweden SE-97187

country: Sweden

institute: LULEA UNIVERSITY OF TECHNOLOGY

data_processing:
Sequencing reads were filtered using BGI-SOAPnuke.
We used HISAT2 (Hierarchical Indexing for Spliced Alignment of Transcripts) to do the mapping step to the reference genome (Schizochytrium_limacinum_SR21_CNCB).
We use StringTie to reconstruct transcripts, and use Cuffcompare to compare reconstructed transcripts to reference annotation.
clean reads were mapped using Bowtie2, and gene expression level was calculated with RSEM
We detect DEGs with DEseq2
Assembly: Schizochytrium_limacinum_SR21_CNCB (accession no. GWHABLD00000000)
Supplementary files format and content: Excel file with FPKM for each sample
Supplementary files format and content: Excel file with FPKM for all sample

organism: Aurantiochytrium limacinum

source_name: whole cell

growth_protocol: SR21 cells were cultivated in artificial sea water (18 g/L salinity) with a C/N ratio of 10 maintained by yeast extract in the presence of glucose, WCO, mCOs, acetate and butyrate. pH was mainatined at 6.8 for all the media compositions. Cell were innoculated with 10% v/v. Cells were harvested at 72 hr for glucose, WCO and mCO and at 96 h for acetate and butyrate.

extract_protocol:
RNA was extracted using TRIzol reagent.
oligo dT beads to enrich mRNA with poly A tail. RNA fragmentation and first_x0002_strand cDNAs were generated using random N6-primed reverse transcription, followed by the second_x0002_strand cDNA synthesis. The synthesized cDNA was subjected to end-repair and then was 3’ adenylated. Adaptors were ligated to the ends of these 3’ adenylated cDNA fragments. Many rounds of PCR amplification were performed to enrich the purified cDNA template using PCR primer. Denature the PCR product by  heat and the DNA is cyclized by splint oligo and DNA ligase. DNA nanoball was synthesised.

value: whole cell

value: whole microbial cell

value: waste cooking oil


title: PFOA_2.5_3 [CCACAATG-CTATGATC-2]

data_processing:
Sequencing read quality was assessed via FastQC and MultiQC.
Reads were aligned to a splice junction aware build of the human genome (GRCh38) using STAR.
Aligned reads were assigned to genes using featureCounts, where multimapping and multi-overlapping reads were not counted.
Assembly: GRCh38
Supplementary files format and content: Tab deliminted files containnig the read counts per sample

extract_protocol:
To conduct high throughput RNA-sequencing, we developed an adapted version of the plexWell (SeqWell, Beverly, MA, USA) plate-based sequencing method to make the method applicable for high throughput in vitro toxicological analysis. In the plexWell protocol, sequencing reactions are prepared in custom 96 well plates, where each well contains a unique oligo barcode. Plates are also assigned a unique oligo barcode. Cells are lysed and cDNA is directly prepared from the cellular lysate.
A tagmentation reaction adds the well specific barcode to the cDNA from each well. The tagmented cDNAs are then pooled prior to library preparation, where plate specific barcodes can also be incorporated for ultrahigh sample multiplexing prior to sequencing. For example, 384 wells of treated samples would be processed across 4 custom 96 well plates, where each of the samples receives a well specific barcode and each of the 4 plates receives a plate specific barcode. This leads to each of the 384 samples receiving a unique combination of well and plate barcodes, which can be bioinformatically deconvoluted following sequencing.
Libraries were sequenced at Illumina NovaSeq 6000 l at the Advanced Genomics Core.

value: PFOA 2.5


title: Clone23_Minus [ATAC-seq]

description: ATAC-Seqdata in ER-Hoxb8 cells

value: ER-Hoxb8 cells


title: Copper_0.25_2 [CTTGTTGG-ATAGAGAG-2]

value: Copper 0.25


title: Clone21_Minus [ATAC-seq]

description: ATAC-Seqdata in ER-Hoxb8 cells


title: MIN6 stable cells overexpressing miR-146a-5p treated with proinflammatory cytokines - replicate2 [P66-OE-Cy]

value: miR-146a-5p overexpression


title: Control MIN6 stable cells transduced with scrambled treated with proinflammatory cytokines - replicate2 [P66-SCR-Cy]

value: Treatment with proinflammatory cytokines


title: Clone20_Minus [ATAC-seq]

description: ATAC-Seqdata in ER-Hoxb8 cells


title: Clone22_Minus [ATAC-seq]

description: ATAC-Seqdata in ER-Hoxb8 cells


title: SR21,WCO,72h,rep1


title: MIN6 stable cells with miR-146a-5p inhibited, without proinflammatory cytokines - replicate1 [P65-ZIP]

value: Cells transduced with lentiviral vector inhibiting miR-146a-5p

value: miR-146a-5p inhibition

value: No treatment


title: SR21,WCO,72h,rep2


title: SR21,MO,72h,rep3

value: mixture of commercial oils (mCOs)


title: MIN6 stable cells overexpressing miR-146a-5p without proinflammatory cytokines - replicate2 [P66-OE]

value: Cells transduced with lentiviral vector overexpressing miR-146a-5p


title: SR21,MO,72h,rep1


title: Phenanthrene_2.5_1 [ACTCGAAT-CTATGATC-2]

value: Nontumorigenic breast

value: WT

value: Phenanthrene 2.5


title: Clone19_Minus [ATAC-seq]

description: ATAC-Seqdata in ER-Hoxb8 cells


title: Phenanthrene_0.25_1 [GTTGACAG-CTATGATC-2]

value: Phenanthrene 0.25

value: 48 hrs

value: DMSO


title: SR21,MO,72h,rep2

value: whole cell

value: whole microbial cell


title: MIN6 stable cells with miR-146a-5p inhibited, treated with proinflammatory cytokines - replicate1 [P65-ZIP-Cy]


title: DCP_25_0.25_3 [TGTAAGAC-CCATAGGG-2]


title: Control MIN6 stable cells transduced with scrambled without proinflammatory cytokines - replicate1 [P65-SCR]

value: Cells transduced with scrambled sequence

value: Control


title: SR21,Glucose,72h,rep3

value: glucose


title: Control MIN6 stable cells transduced with scrambled treated with proinflammatory cytokines - replicate1 [P65-SCR-Cy]

value: Treatment with proinflammatory cytokines


title: Control_0_4 [GGAGCTAT-ATAGAGAG-2]

value: Control 0

value: Water


title: Clone17_Minus [ATAC-seq]

description: ATAC-Seqdata in ER-Hoxb8 cells

value: ER-Hoxb8 cells


title: Clone18_Minus [ATAC-seq]

description: ATAC-Seqdata in ER-Hoxb8 cells


title: SR21,Glucose,72h,rep2


title: MIN6 stable cells overexpressing miR-146a-5p without proinflammatory cytokines - replicate1 [P65-OE]

value: miR-146a-5p overexpression

value: No treatment


title: Clone16_Minus [ATAC-seq]

description: ATAC-Seqdata in ER-Hoxb8 cells


title: 7940B_ESK250nM_8hr_2

first: Brian

last: Magnuson

address: 1500 East Medical Center Drive

data_processing:
Basecalling was performed using bcl2fastq 2 (Illumina).
Trimming was performed using BBDuk (BBtools) and parameters minlength=25 k=31 qskip=3 rieb=t tbo=t tpe=t.
Transcripts were quantified from trimmed reads using Kallisto 0.46.0 (Bray et al. 2016) with parameter --rf-stranded. The Kallisto index was generated from the mouse reference genome mm10/GRCm38 and the annotation was from Ensembl 99.
Gene-level counts were obtained by summing transcript counts.
Assembly: mm10
Supplementary files format and content: Transcript abundance TSV files contain the Ensembl transcript ID (target_id), transcript length(length), transcript effective length (eff_length), estimated pseudocounts (est_counts), and TPM normalized counts (tpm).
Supplementary files format and content: Gene abundance TSV files contain Ensembl gene ID (gen_id), gene symbol (gene_name), estimated pseudocounts (est_counts), and TPM normalized counts (tpm).

growth_protocol: 7940B cells (murine PDAC) were grown in Gibco DMEM (Thermo) + 10%FBS.

extract_protocol:
Total RNA was isolated using the miRNeasy kit (Qiagen).
RNA-seq libraries were prepared using 800 ng of total RNA. Ribosomal RNA were removed by enzymatic digestion of the specific probe-bound duplex rRNA, and then fragmented to around 200-300bp with heat in fragmentation buffer (KAPA RNA Hyper+RiboErase HMR, Roche). Double-stranded cDNA was then synthesized by reverse transcription and underwent end-repair and ligation using New England Biolabs (NEB) adapters. Final library preparation was then prepared by amplification with 2x KAPA HiFI HotStart mix and NEB dual barcode. Library quality was measured on an Agilent 2100 Bioanalyzer (DNA 1000 chip) for concentration and product size. Paired-end libraries were sequenced with the Illumina NovaSeq, (2 × 151 nucleotide read length) with sequence coverage to 30-40 million paired reads.

treatment_protocol: After overnight seeding, cells were treated with DMSO, apilimod (25nM), or ESK981 (250nM) for 8 hours.

value: pancreatic ductal adenoarcinoma cells


title: Clone26_Plus [ATAC-seq]

description: ATAC-Seqdata in ER-Hoxb8 cells


title: SR21,Butyrate,96h,rep3

value: butyrate


title: Control_0_36 [GGAGCTAT-CTATGATC-2]

first: Justin

last: Colacino

address: 6651 SPH1, 1415 Washington Heights

value: Nontumorigenic breast

value: WT


title: SR21,Glucose,72h,rep1


title: MIN6 stable cells overexpressing miR-146a-5p treated with proinflammatory cytokines - replicate1 [P65-OE-Cy]

value: Cells transduced with lentiviral vector overexpressing miR-146a-5p


title: Clone23_Plus [ATAC-seq]

description: ATAC-Seqdata in ER-Hoxb8 cells


title: 7940B_AP25nM_8hr_2

value: apilimod 25nM


title: Clone22_Plus [ATAC-seq]

description: ATAC-Seqdata in ER-Hoxb8 cells


title: SR21,Butyrate,96h,rep2

value: whole cell


title: Control_0_27 [GTTATCGA-ATATGAGA-2]

value: 48 hrs

value: DMSO


title: SR21,Acetate,96h,rep3

value: whole microbial cell

value: acetate


title: Mercury_0.25_3 [CCATACTC-ATAGAGAG-2]

value: Mercury 0.25


title: MPB_0.25_4 [TCCTTGGC-ATATGAGA-2]


title: 7940B_DMSO_8hr_2


title: Clone15_Minus [ATAC-seq]

description: ATAC-Seqdata in ER-Hoxb8 cells


title: SR21,Acetate,96h,rep2


title: Clone21_Plus [ATAC-seq]

description: ATAC-Seqdata in ER-Hoxb8 cells


title: 7940B_ESK250nM_8hr_1


title: Clone24_Plus [ATAC-seq]

description: ATAC-Seqdata in ER-Hoxb8 cells


title: SR21,Butyrate,96h,rep1


title: Arsenic_0.025_1 [CGAGCATT-ATAGAGAG-2]

value: Arsenic 0.025


title: SR21,Acetate,96h,rep1


title: DDE_0.25_11 [CCATACTC-CTATGATC-1]


title: Control_0_12 [CAACCGTG-CTATGATC-1]

value: Control 0

value: Water


title: 7940B_AP25nM_8hr_1


title: 7940B_DMSO_8hr_1


title: PFNA_25_2 [TTGGCTGC-CTATGATC-2]

value: PFNA 25


title: Clone20_Plus [ATAC-seq]

description: ATAC-Seqdata in ER-Hoxb8 cells

value: ER-Hoxb8 cells


title: mock_4

city: Fontenay aux roses

first: federica

last: ferri

address: 18 route du panorama

country: France

institute: cea

data_processing:
Sequence reads were converted into FASTQ files. Reads under 300 bp or with a quality score under 9 were discarded. The remaining reads were mapped on the human GRCh38.p13 and SARS-coV2 ASM985889v3 transcriptome of reference using minimap2 version 2.17. To quantify transcripts, the resulting alignments were given to Salmon version 1.6.0
Assembly: human GRCh38.p13 and SARS-CoV2 ASM985889v3
Supplementary files format and content: tab-delimited file includes raw counts for each sample

source_name: Calu-3 cells

growth_protocol: Calu-3 cells were cultured in EMEM supplemented with 15% FCS.

extract_protocol:
Total RNA was extracted with the nucleospin RNA plus XS (Macherey-Nagel)
A total of 100 ng of RNA per sample was retrotranscribed by a strand-switching technique using Maxima H Minus Reverse Transcriptase (ThermoFisher) to synthesize a doublestranded cDNA. PCR, barcode and adapter attachment were performed according to PCR-cDNA Barcoding kit (Oxford Nanopore Technologies)

treatment_protocol: Calu-3 cells were infected with SARS-CoV-2 and treated or not with Sulfodyne at 12hpi. Cells were harvested at 0hpi (mock), 12hpi, 18hpi and 36hpi for RNA-seq

value: Calu-3 cells

value: lung epithelial cell

tag: time (hours_post_infection)

value: uninfected

value: untreated


title: Control_0_10 [ACGCTGCA-CTATGATC-1]

city: Ann Arbor

institute: University of Michigan

value: Nontumorigenic breast

value: WT


title: mock_3


title: Clone19_Plus [ATAC-seq]

description: ATAC-Seqdata in ER-Hoxb8 cells


title: DDE_0.025_15 [CCTACACA-CTATGATC-1]


title: cxC26 IL6KOs1-3

first: Kwon

last: Young-Yon

state: Massachusetts

address: 655 Huntington Ave

department: Molecular metabolism

institute: Harvard University School of Public Health

data_processing:
Raw sequence data (.bcl files) generated the sequencer were converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification.
Sequence reads were trimmed using Trimmomatric package with default option in Galaxy project (23.2.rc1)
Trimmed sequence reads were mapped to Grcm38/mm10 using HISAT2 package with defalut option in Galaxy project  (23.2.rc1)
Read count extraction and normilazation were performed limma-voom package in Galaxy project  (23.2.rc1)
Assembly: mm10
Supplementary files format and content: tab-deliminated csv file includes normalized CPM value for each samples

source_name: Tumor

growth_protocol: cxC26 scr (wild-type) and cxC26 IL6KOs1 (IL-6 knockout subclone 1) cells were subcutaneously implanted into CD2F1 male mice and maintained until the mice developed cachexia phenotype.

extract_protocol:
RNA extraction, library preparation, sequencing and analysis was conducted at Azenta Life Sciences (South Plainfield, NJ, USA). Total RNA was extracted from fresh frozen tissue samples using Qiagen RNeasy Plus Universal mini kit following manufacturer’s instructions (Qiagen, Hilden, Germany). Total RNA was RNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked using Agilent TapeStation 4200 (Agilent Technologies, Palo Alto, CA, USA).
RNA sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina using manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were initially enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing library was validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).

value: Tumor


title: cxC26 IL6KOs1-4


title: DDE_25_3 [GATGAGAA-CTATGATC-1]

value: DDE 25

value: 48 hrs


title: mock_2


title: Clone18_Plus [ATAC-seq]

description: ATAC-Seqdata in ER-Hoxb8 cells


title: Clone17_Plus [ATAC-seq]

description: ATAC-Seqdata in ER-Hoxb8 cells


title: cxC26 IL6KOs1-1


title: Control_0_9 [TCCTCAGA-CTATGATC-1]


title: cxC26 scr-4


title: Control_0_11 [CGATGGCA-CTATGATC-1]


title: DDE_2.5_5 [TGTTGCAC-CTATGATC-1]

value: DDE 2.5

value: DMSO


title: COV2_sulfodyne_36hpi_3

value: Sulfodyne


title: Clone15_Plus [ATAC-seq]

description: ATAC-Seqdata in ER-Hoxb8 cells


title: COV2_sulfodyne_36hpi_2


title: cxC26 scr-2


title: R228, Wolfram, rep 1

city: Leiden

first: Françoise

last: Carlotti

address: Albinusdreef 2

country: Netherlands

institute: Leiden University Medical Center

library_source: transcriptomic single cell

data_processing:
For sort seq samples Paired-end reads from automated CEL-seq2 (SORTseq) were aligned to the transcriptome using bwa with default parameters. The transcriptome contained all RefSeq gene models based on the human genome release hg38. All isoforms of the same gene were merged to a single gene locus. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first eight bases correspond to a sample specific barcode followed by a 4bp unique molecular identifier (UMI). The remainder of the left read contains a polyT stretch followed by a number (<40) of transcript derived bases. For 10X, BCL files resulting from sequencing were transformed to FASTQ files with 10x Genomics Cell Ranger mkfastq.FASTQ files were mapped with Cell Ranger count. During sequencing, 28 bp read 1 were used for identification of the Illumina library barcode, cell barcode and UMI. Read 2 was used to map to the reference transcriptome. Filtering of empty barcodes was done in Cell Ranger. HTO quantification was done using Cellranger by supplying the HTO barcodes.
Assembly: hg38
Supplementary files format and content: Tab-separated values files containing cell barcodes, read counts and transcript counts

source_name: Pancreatic islets

extract_protocol:
Pancreatic islets and islet-depleted tissue were dispersed into single-cells by dynamic incubation with 0.025% trypsin (Gibco) supplemented with 10 mg/mL DNase (Pulmozyme, Genentech) for 6–7 min and filtered through a 40 μm cell-strainer to remove undigested material.
For automated CEL-seq2, cells were FACS sorted into 384-well cell capture plates. Cells were lysed by heat (65 Celsius degrees) followed by a second-strand cDNA synthesis. For each plate, all barcoded material was amplified by in vitro transcription. Cel-Seq2 workflow was followed to generate the cDNA library using TruSeq small RNA primers (Illumina). The DNA library was paired-end sequenced using Illumina Nextseq 500, high output, with a 1x75 bp Illumina kit (read 1: 26 cycles, index read: 6 cycles, read 2: 60 cycles). For 10X, cells were loaded, and the sequencing libraries were prepared following the standard 10x Genomics 3' V3 chemistry protocol

value: Pancreatic islets

tag: donor

tag: disease state

value: Wolfram syndrome


title: DDE_2.5_8 [CTTCTGGC-CTATGATC-1]


title: cxC26 scr-3


title: M3-R

value: CD8 t cells

value: MEDIA


title: R154, T1D, rep 2

value: diabetic


title: cxC26 IL6KOs1-2


title: COV2_sulfodyne_36hpi_4

value: Calu-3 cells


title: R154, T1D, rep 1


title: COV2_sulfodyne_18hpi_4

value: lung epithelial cell


title: cxC26 scr-1


title: DDE_2.5_6 [ATTCTCCA-CTATGATC-1]


title: mock_1

value: uninfected


title: COV2_sulfodyne_36hpi_1


title: DDE_0.25_9 [ATGGAACA-CTATGATC-1]


title: Clone16_Plus [ATAC-seq]

description: ATAC-Seqdata in ER-Hoxb8 cells

value: ER-Hoxb8 cells


title: COV2_sulfodyne_18hpi_3


title: R141, T1D, rep 2


title: LXB4

first: Shubham

last: Maurya

address: Rm 596, Minor Hall

institute: University of California Berkeley

description: 10x Genomics

data_processing:
Barcode processing and cell counting was done using cell ranger v3.1.1(https://www.10xgenomics.com/support/software/cell-ranger)
Assembly: Mm10
Supplementary files format and content: tab-delimited values file and matrix files

source_name: Retina

extract_protocol:
Retina was dissociated to single-cell suspension using a papain dissociation kit (Worthington, Columbus, OH). Briefly, dissected retinas were placed in papain solution for 30 mins at 37 oC with exposure to 5% CO2 in the incubator. Retinas were gently tapped and incubated for 15 more mins for complete dissociation. The reaction was quenched by adding ovomucoid inhibitor solution, and cells were collected after centrifugation and dissolved in resuspension buffer containing PBS+5%BSA+ DNASE to form a single-cell solution of cells. Cells were passed from a 40mM cell strainer (Sigma) to remove debris and clumps. Before processing the cells for single-cell transcriptomics, rod cells were depleted to enrich the rest of the population. Cells were incubated with Biotin-CD133 antibody for rod-specific labeling and were depleted in the magnetic column after anti-biotin-magnetic bead labeling (Miltenyi Biotech, Bergisch Gladbach, Germany).
Barcoding and library preparation were done using a 10X Chromium Single Cell 3' reagent (v3.1 chemistry, 10x Genomics, Pleasanton, CA) per the manufacturer’s instructions. Briefly, Cells were loaded on the chromium chip to create gel beads containing unique oligo barcodes with single cells, creating cell-gel droplets. RNA from each cell was captured within the droplets, and cell-specific barcodes were linked to their respective transcripts. Reverse transcription and amplification of captured RNA were performed to generate cDNA libraries. Quality of cDNA preparation was checked using Bioanalyzer (Applied Bioscience)

value: Retina


title: Control

description: 10x Genomics


title: COV2_sulfodyne_18hpi_2


title: R141, T1D, rep 1


title: R141, T1D, rep 3


title: KGSMIOPLX3ON

data_processing:
Quality check of FASTQ files was done with FastQC v.0.11.9.
Adapters sequences were trimmed using Trim Galore! v.0.6.6.
Trimmed reads were mapped on macaque genome version Mmu10 (University of California Santa Cruz) with STAR alignment tool v.2.7.1a using RefGene annotation
The total number of read counts mapped for each gene was extracted from BAM files using FeatureCount v.1.5.3.
Count matrix was imported into Rstudio v.4.2.0. It was normalized using DeSEQ2.
Assembly: Mm39
Supplementary files format and content: tab-delimited text file include read count values for each Sample …

source_name: Optic nerve

extract_protocol:
RNA was isolated using the Trizol method
Sequencing libraries were prepared using SMARTer v4 Ultra Low Input RNA Kit

value: Optic nerve


title: COV2_36hpi_4

value: untreated


title: DDE_0.025_16 [CGCGTGAT-CTATGATC-1]

value: Nontumorigenic breast

value: WT


title: COV2_sulfodyne_18hpi_1


title: KGSMIOPLX1ON


title: R124, T1D, rep 2


title: DDE_25_2 [TTGGCTGC-CTATGATC-1]

value: DDE 25

value: 48 hrs


title: DDE_0.25_12 [TCCTTGGC-CTATGATC-1]

value: DMSO


title: KGSMIOPLX2ON


title: DDE_25_4 [ATGACACC-CTATGATC-1]


title: Control_0_14 [CAAGTAGT-CTATGATC-1]

value: Control 0

value: Water


title: COV2_36hpi_3


title: KGSMIOP3ON

value: OHT


title: COV2_36hpi_2


title: R124, T1D, rep 1

value: Pancreatic islets


title: Control_0_16 [CTAGCCGA-CTATGATC-1]


title: DDE_0.025_14 [CAGGCTTC-CTATGATC-1]


title: KGSMIOP2ON


title: KGSMIOP1ON


title: E2+MPA, RNA-seq

city: Ube

first: Yuichiro

last: Shirafuta

state: Yamaguchi

address: 1-1-1, minami-kogushi

institute: Yamaguchi university

data_processing:
To produce the raq bcl, or base call files, quality assessment and image analyses were performed using Next-seq packaging software Real Time Analysis
bcl2fastaq Conversion Software v2.19 was used for de-multiplexing of the samples
Reads with more than two ambiguous nucleotides and reads with quality scores less than 20 as calculated by the Phred program were removed using CLC Genomics Workbench software (ver.8.01, Qiagen)
Gene expression values were calculated as “trasncripts per million” (TPM).  1 was added to the TPM value before the following calculation.
Assembly: hg19
Supplementary files format and content: Comma Separated Values files include TPM values for each Sample ...

source_name: uterus

growth_protocol: Cells were seeded at 10*5 cells/cm2 in 75 cm2 tissue culture flasks and incubated in Phenol Red-free DMEM containing glutamine, antibiotics, and 10% dextran-coated charcoal-stripped FBS at 37°C, 95% air and 5% CO2.

extract_protocol:
Total RNA was isolated from the cultured cells with an RNeasy® Mini Kit.  (Qiagen, Valencia, CA, USA).
Complementary DNA (cDNA) libraries for Illumina sequencing were generated with NEBNext Ultra II RNA library Prep kit (NEB) and NEBNextplex Oligos for Illumina.

treatment_protocol: To induce decidualization, ESCs were incubated with treatment medium (Phenol Red-free DMEM supplemented with glutamine, antibiotics and 2% dextran-coated charcoal-stripped FBS) containing cAMP (0.5 mM) or cAMP(0.5mM)+MPA(1e-6M)for 4 days, or MPA or E2(1e-8)+MPA for 14 days.

value: uterus

value: ESC

value: endometrial stromal cells

value: E2+MPA treatment


title: DDE_2.5_7 [CGCAACAG-CTATGATC-1]

value: DDE 2.5


title: COV2_18hpi_4

value: Calu-3 cells

value: lung epithelial cell


title: MPA, RNA-seq

value: MPA treatment


title: R124, T1D,rep 3

value: diabetic


title: Control_14 days, RNA-seq

value: no treatment


title: skinCCR5-3

city: Beijing

first: Yunxiong

last: Wei

address: 8 Gongren Tiyuchang Nanlu, Chaoyang District, Beijing, 100020

institute: Capital medical university

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using 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.
Assembly: GRCm38.99
Supplementary files format and content: tab-delimited text files include raw conts for each Sample
Supplementary files format and content: tab-delimited text files includes RPKM values for each Sample

source_name: skin

extract_protocol:
Obtain skin tissue of mice of the same volume from different groups of mice.And then RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: skin

value: Adoptive CCR5-/- DNT cells before IMQ treatment for 6 days


title: DDE_0.025_13 [TCACTCAC-CTATGATC-1]

value: Nontumorigenic breast

value: WT

value: 48 hrs

value: DMSO


title: skinCCR5-2


title: COV2_18hpi_2

value: untreated


title: COV2_18hpi_3


title: Control_0_13 [TCAACTGA-CTATGATC-1]

value: Control 0

value: Water


title: skinCCR5-1


title: DDE_25_1 [CAGAGTGG-CTATGATC-1]

value: DDE 25


title: cAMP, RNA-seq

value: uterus

value: ESC

value: endometrial stromal cells

value: cAMP treatment


title: Control_4 days, RNA-seq


title: Control_0_15 [GTGTCCAT-CTATGATC-1]


title: COV2_18hpi_1

value: Calu-3 cells

value: lung epithelial cell


title: COV2_12hpi_4


title: skinDNT-5

value: Adoptive WT DNT cells before IMQ treatment for 6 days


title: skinDNT-3

value: skin


title: COV2_36hpi_1


title: EE

city: Hefei

first: Jinghe

last: Zhang

state: Anhui

address: Huangshan Road 443

institute: University of Science and Technology of China

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: endometrium

extract_protocol:
The edometrial tissue  is digested with collagenase IV and filtered to produce single cells. CD45 positive cells were obtained by flow sorting
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: endometrium

value: endometriosis


title: COV2_12hpi_3


title: COV2_12hpi_2


title: skinDNT-1

value: WT


title: NE

description: 10x Genomics

value: uterine leiomyoma


title: plasma-NA-Normal healthy donor-5

city: Dallas

first: Nicole

last: Baldwin

address: 3434 Live Oak St

institute: Baylor Research Institute

data_processing:
RNAseq reads were trimmed and aligned to human genome using hisat2 and counted using featurecounts
Normalization and differential gene  expression (DGE) analysis was performed using DESeq2
Assembly: GRCh38
Supplementary files format and content: csv file includes counts or deseq2 data; file name includes either 'counts' for count data or 'deseq2' for deseq2 data

source_name: Normal healthy donor

extract_protocol:
patient samples collected at admission (before TPIAT) and healthy donor samples collected at various time points. miRNEasy serum/plasma advanced kit was used to extract small RNA from plasma samples.
Library construction as per Illumina TruSeq Small RNA Library Prep Kit

value: plasma

tag: aetiology

value: Normal healthy donor

tag: age

tag: race

value: Caucasian


title: plasma-NA-Normal healthy donor-6


title: siTNIK TERT rep5-72 hours

city: Saint Louis

first: Shayna

middle: T. J.

last: Bradford

state: MO

address: MCDONNELL MEDICAL SCIENCES BUILDING, 4565 Mckinley Ave ST 852

department: Department of Medicine, Division of Nephrology

institute: Washington University in Saint Louis

description: hTERT-RPTEC bulk RNA-seq

data_processing:
Fastq processing step: Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a maximum of one mismatch in the indexing read for sample demultiplexing.  RNA-seq reads were then aligned to the GRCh38 (for human) with STAR version 2.7.9a.  Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 2.0.3. Raw counts  were the output for downstream analysis.
Assembly: GRCh38
Supplementary files format and content: The processed files are the raw read counts for each gene/sample in txt format.

source_name: hTERT-immortalized renal proximal tubule epithelial cells

growth_protocol: cell culture protocol: primary and hTERT-immortalized RPTECs were cultured in 6-well plates according to the manufacturer's protocol and then subjected to siRNA treatment for either 48- or 72- hours

extract_protocol:
Total mRNA were isolated from mouse kidney and human RPTECs using a RNA kit from Qiagen (RNEASY Mini prep kit, Cat# 74104).
Total RNA integrity was determined using Agilent 4200 Tapestation. Library preparation was performed with 500ng to 1ug of total RNA. Ribosomal RNA was removed by an RNase-H method using RiboErase kits (Kapa Biosystems). mRNA was then fragmented in reverse transcriptase buffer and heating to 94 degrees for 8 minutes. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer’s instructions) and random hexamers. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt ended, had an A base added to the 3’ ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases.

treatment_protocol: siRNA Experimental Design for bulk RNA-seq  Experiment 1 performed in primary-hRPTECs (12 samples total):  50nM non-targeting siRNA, 72 hours, 6 replicates  50nM pooled siRNA targeting human TNIK, 72 hours, 6 replicates    Experiment 2 performed in primary-hRPTECs (12 samples total):  50nM non-targeting siRNA , 48 hours, 6 replicates  50nM pooled siRNA targeting human TNIK, 48 hours, 6 replicates    Experiment 3 performed in hTERT-hRPTECs (12 samples total):  50nM non-targeting siRNA, 72 hours, 6 replicates  50nM pooled siRNA targeting human TNIK, 72 hours, 6 replicates     Catalog number of siRNA used in each study:   non-targeting siRNA (Horizon Discovery; D-001210-05-05)   pooled siRNA targeting human TNIK (Horizon Discovery; M-004542-03-0020)

tag: cell line

value: ATCC (CRL-4031)

tag: Sex

value: Male

value: pooled siRNA targeting human TNIK rep5

tag: treatment timepoint

value: 3 days


title: skinIMQ-3

tag: genotype

tag: treatment

value: IMQ treatment for 6 days


title: COV2_12hpi_1

tag: cell type

value: untreated


title: cAMP+MPA, RNA-seq

value: uterus

value: ESC

value: endometrial stromal cells

value: cAMP+MPA treatment


title: skinIMQ-5

value: skin


title: skinIMQ-1


title: siTNIK TERT rep4-72 hours

description: hTERT-RPTEC bulk RNA-seq

value: pooled siRNA targeting human TNIK rep4


title: skinC-5

value: WT

value: No treatment


title: plasma-NA-Normal healthy donor-4

description:
outlier
cDNA6850

value: plasma


title: siTNIK TERT rep3-72 hours

description: hTERT-RPTEC bulk RNA-seq

value: pooled siRNA targeting human TNIK rep3


title: siTNIK TERT rep2-72 hours

description: hTERT-RPTEC bulk RNA-seq

value: pooled siRNA targeting human TNIK rep2


title: plasma-NA-Normal healthy donor-2

value: Normal healthy donor

value: Caucasian


title: DB1-1

city: Shang Hai

first: Yan

last: Wang

address: Yue yang Road 320

institute: Chinese Academy of Science

data_processing:
Transcriptomic reads from the RNA-Seq experiments were mapped to a reference genome (mm10) using Bowtie.
Gene expression levels were quantified using the RSEM software package.
Differentially expressed genes were subsequently analyzed using the DAVID bioinformatics platformand IPA.
Assembly: mm10
Supplementary files format and content: Processed data were xls format and all samples gene expression FPKM  were contained in the xls file.

source_name: intratumoural CD8+ T cells

growth_protocol: The intratumoural CD8+ T cells were sorted from B16 melanoma-bearing mice after treatment with PBS or DB1

extract_protocol:
Sorted cells was harvested using Invitrogen ™ TRIzol Reagent followed by total RNA isolation.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: When the tumour volume reached about 100 mm3, mice were randomly divided into groups of PBS or bacteria treatment. PBS or 107 bacterial cells at a volume of 125 μl were injected into the tail-vein of each mouse.

value: B16 melanoma-bearing mice

value: intratumoural CD8+ T cells

value: wild type


title: DB1-2


title: PBS-2

value: PBS


title: siTNIK TERT rep1-72 hours

description: hTERT-RPTEC bulk RNA-seq

value: ATCC (CRL-4031)

value: Male

value: pooled siRNA targeting human TNIK rep1

value: 3 days


title: PBS-1


title: DDE_0.25_10 [CTAACAAC-CTATGATC-1]

value: Nontumorigenic breast

tag: time

value: 48 hrs

tag: control flags

value: DMSO

tag: plate id


title: skinC-2

tag: tissue

value: skin

value: WT

value: No treatment


title: siTNIK TERT rep6-72 hours

description: hTERT-RPTEC bulk RNA-seq

value: pooled siRNA targeting human TNIK rep6


title: plasma-NA-Normal healthy donor-1

description:
outlier
cDNA6846

value: plasma

value: Normal healthy donor


title: sinc TERT rep6-72 hours

description: hTERT-RPTEC bulk RNA-seq

value: non-targeting siRNA rep6


title: VM3

city: qingdao

first: yuxi

address: Laoshan District Songling Road

institute: ocean university of china

data_processing:
A cDNA library constructed by technology from the pooled RNA from < sample description > samples of < research species > was sequenced run with Illumina Novaseq TM 6000 sequence platform.
Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads. Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis
Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9). The parameters were as follows:1) removing reads containing adapters;2) removing reads containing polyA and polyG;3) removing reads containing more than 5% of unknown nucleotides (N);4) removing low quality reads containing more than 20% of low quality (Q-value≤20) bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9). including the Q20, Q30 and GC-content of the clean data.
Assembly: NCBI_ASM378908v1
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Penaeus vannamei

source_name: hemolymph

growth_protocol: Use cotton balls soaked in 75% ethanol to wipe the haemocyte collection site of shrimp, aspirate an equal volume of Haemolymph using a 1ml syringe containing 400 µl pre-cooled anticoagulant

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) according to the manufacturer's procedure. Then 10 ug of total RNA was extracted according to the RNA-Seq sample preparation kit for constructing sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: transfer the mixture to a 1.5mL centrifuge tube and mix well, centrifuged at 1000 g 4℃ for 5 min, he precipitate was added to 1 mL Trizol reagent, lysed on ice for 5 min, frozen in liquid nitrogen and stored at -80℃

value: hemolymph

value: Haemocyte

value: male

tag: agent

value: Vibrio parahaemolyticus

value: immune


title: plasma-chronic pancreatitis-Pancreatioc divisum-3

source_name: Pancreatioc divisum

value: Pancreatioc divisum

value: chronic pancreatitis

value: Caucasian


title: sinc TERT rep5-72 hours

description: hTERT-RPTEC bulk RNA-seq

value: ATCC (CRL-4031)

value: Male

value: non-targeting siRNA rep5

value: 3 days


title: VM2


title: plasma-chronic pancreatitis-Pancreatioc divisum-2

value: White, not hispanic


title: sinc TERT rep4-72 hours

description: hTERT-RPTEC bulk RNA-seq

value: non-targeting siRNA rep4


title: VM1


title: 18720X8 shMcam-B

city: Salt Lake City

first: Benjamin

last: Spike

state: Utah

address: 1950 Circle of Hope Dr,

institute: Huntsman Cancer Institute, University of Utah

description: 10X Genomics

data_processing:
The Fastq files were aligned to the refdata-gex-mm10-2020-A.tar mouse reference from 10X genomics using cellranger count version 5.0.1 with 6000 expected cells.
Assembly: mm10
Supplementary files format and content: Filtered feature barcode matrices in h5 format

extract_protocol:
Py230 single cell suspension was isolated by trypsinization and resuspended in phosphate buffered saline with 0.04% bovine serum albumin. The cell suspension was filtered through 40-micron cell strainer. Viability and cell count were assessed on Countess 2 (Invitrogen, Carlsbad, CA). Equilibrium to targeted cell recovery of 6,000 cells along with 10x Gel Beads and reverse transcription reagents were loaded to Chromium Single Cell Chip G (PN-1000120) to form Gel-Bead-In EMulsions (GEMs), the nano-droplets. Within individual GEMs, barcoded cDNA generated from captured mRNA was synthesized by reverse transcription at the setting of 53°C for 45 min followed by 85°C for 5 min. Subsequent fragmentation, end repair and A-tailing, adaptor ligation and sample indexing with dual index (PN-1000215) were performed in bulk according to the user guide.  The resulting barcoded libraries were qualified using Agilent D1000 ScreenTape on Agilent Technology 2200 TapeStation system and quantified by quantification PCR using KAPA Biosystems Library Quantification Kit for Illumine Platforms (KK4842).
10X Genomics Next GEM Single Cell 3' Gene Expression Library prep v3.1 with UDI

value: Multipotent murine epithelial-like cell line

value: shMcam-B


title: 18720X7 shCon-B

description: 10X Genomics

value: shCon-B


title: plasma-NA-Normal healthy donor-3

description:
outlier
cDNA6849

value: plasma

value: Normal healthy donor


title: sinc TERT rep3-72 hours

description: hTERT-RPTEC bulk RNA-seq

value: non-targeting siRNA rep3


title: skinC-3

value: skin

value: WT

value: No treatment