title: EA_3032__47_S7

city: Charleston

first: Gary

last: Hardiman

state: SC

address: 135 Cannon Street

department: Medicine

institute: Medical University of South Carolina

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads (fastq files) were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform (OnRamp Bioinformatics, San Diego, CA). OnRamp’s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data, including data validation and quality control and read alignment to the human genome (hg19) using blastx
The resulting SAM files were sorted and inputted into the Python package HTSeq to generate count data for gene-level differential expression analyses.
Transcript count data from DESeq2 analysis of the samples were sorted according to their adjusted p-value or q-value, which is the smallest false discovery rate (FDR) at which a transcript is called significant.
Genome_build: HG19
Supplementary_files_format_and_content: tab-delimited .txt files include DESEQ2 output for each Comparison ...

source_name: Prostate Core Biopsy

extract_protocol:
100–200 ng of total RNA was used to prepare RNA-Seq libraries using the TruSeq RNA Sample Prep Kit (Illumina, CA, USA), following the protocol described by the manufacturer. High-throughput sequencing (HTS) was performed using an Illumina HiSeq2500 with each sample sequenced to a minimum depth of ∼ 50 million reads.
To prepare RNA-Seq libraries using the SMART-Seq® v4 RNA-seq kit (Clontech Laboratories, Mountain View, CA), 10 pg–10 ng of total RNA was used following the protocol described by the manufacturer.

treatment_protocol: Patients underwent a medically indicated prostate biopsy procedure because of rising serum levels of the prostate-specific antigen (PSA), or to monitor a low-risk prostate cancer, as part of the standard of care for “active surveillance.” Deidentified subjects donated a biopsy core (per the IRB-approved informed consent document) which was processed in the MUSC Genomic Center for RNA sequencing (RNA-seq).

tag: race

value: EA


title: EA_2989__24

status: Public on Sep 02 2023

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens


title: NA_3195__114

value: Native American


title: HA_3046__68

value: Hispanic


title: AA_9169_58835_119-R

value: AA


title: AA_8859_58835_120


title: AA_8856__58835_117


title: AA_8862_58835_123


title: AA_8882_58835_116-R


title: EA_2984__18


title: HA_6795__107


title: AA_8858_58835_119


title: AA_3197__116


title: nchip_Z1_OMPgfp_tk79_r3

city: New York

first: Elizaveta

last: Bashkirova

state: NY

address: 3227 Broadway

department: Biochemistry

institute: Columbia University

library_source: genomic

data_processing:
Adapter sequences were trimmed with Cutadapt (--minimum-length 18, and --nextseq-trim=20 for samples sequenced on Nextseq 550).
Native ChIP-seq libraries were aligned with Bowtie2, with default setting except for maximum insert size set to 1000 (-X 1000). Unmapped reads and reads with a mapping quality below q30 were filtered out with Samtools.
BigWig files were generated using HOMER
genome_build/assembly: mm10
supplementary_files_format_and_content: BigWig files at base pair resolution normalized to a library size of 10,000,000 reads

molecule: genomic DNA

organism: Mus musculus

source_name: mature olfactory sensory neurons (mOSN)

growth_protocol: Used adult >8 weeks mice

extract_protocol:
Cells were lysed to extract nuclei , nuclei were digested with Micrococcal Nuclease (Sigma), digested chromain was used as input for native chromatin immunoprecipitation with H3K79me3 antibody.
nativeChIP-seq libraries were prepared using NuGEN Ovation Ultralow Ststem V2 (0344)

treatment_protocol: Mice were sacrificed using CO2 followed by cervical dislocation. The olfactory epithelium ("zone1" anatomical region) was dissected and transferred to ice-cold PBS, dissociated with a papain dissociation system (Worthington Biochemical), washed once with cold PBS and resuspended in cold sort media (2% FBS in PBS) with 500ng/mL DAPI (Invitrogen). Cells were passed through a 40um filter, then GFP + cells were isolated with FAC-sorting

tag: cell type

value: mature olfactory sensory neurons (mOSN)

tag: genotype


title: AA_3194__113


title: AA_3196__115


title: AA_3187__106


title: AA_3185__102


title: AA_3186__105


title: AA_3183__100


title: AA_3182__99


title: AA_3181__98


title: Myc+GFP-CPSF6 Gruop1-3

status: Public on Sep 03 2023

city: Guangzhou

first: Wu

last: Runze

address: SUN YAT-SEN UNIVERSITY

country: China

institute: SUN YAT-SEN UNIVERSITY

data_processing:
Sequencing data were analyzed with our in-house pipeline (Fu et al. 2011, 2015)
Sequencing reads were mapped to the human hg19 reference genomes, and internal priming was filtered.
poly(A) sites were defined for each sample by clustering the unique mapped reads, and then, the poly(A) sites were merged together across samples.
Assembly: hg19
Supplementary files format and content: Wiggle Track format files containing a graphical trace on a genome

growth_protocol: Cells were maintained in DMEM or 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Cells were harvested and total RNA was extracted with TRIzol
1 ug total RNA was used to prepare the IVT-SAPAS library according to the previous report (Fu et al., 2015). The quality of the library was evaluated with a Qsep400 Advance.

treatment_protocol: Cells cells were transiently transfected with plasmids carrying Myc tagged CLK2(Myc-CLK2) or carrying PEGFP tagged CPSF6/CPSF6_6SA or corresponding shRNA.In the drug treatment experiment, RKO cells were treated with corresponding concentrations of SM04690 (0nM(DMSO), 25nM, 50nM) for 6 hours and collected

tag: cell line

value: GFP-CPSF6 overexpression


title: AA_3178__95


title: AA_3179__96


title: AA_8879_58835_095-R


title: AA_3176__93


title: AA_3171__86


title: HS_2_KC

city: San Francisco

first: Margaret

last: Lowe

state: CA

address: 513 Parnassus Avenue, HSW1201B

institute: UCSF

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Fastq files were analyzed with Cell Ranger Version 3.0.2
Assembly: GRCh38
Supplementary files format and content: filtered feature bc matrices

molecule: polyA RNA

source_name: skin

extract_protocol:
Keratinocytes were purified by dispase separation of the epidermis (overnight at 4°C, 5U/mL), which was then chopped and digested with 0.25% trypsan-EDTA for 15 minutes at 37°C. Cells were then sort-purified as live CD45-
scRNASeq was performed using the 10x Single Cell 3' v3 Chemistry

tag: tissue

value: skin

value: keratinocyte

tag: disease

value: HS


title: RNA_Z5_wt_K5CreER_INP_r2

data_processing:
Adapter sequences were trimmed with Cutadapt (--minimum-length 18, and --nextseq-trim=20 for samples sequenced on Nextseq 550). Reads were trimmed to 50bp before aligning.
Alignment: All samples were aligned to mm10. RNA-seq samples were aligned with STAR with the following parameters: --outFilterIntronMotifs RemoveNoncanonical --outFilterType BySJout --outFilterMultimapNmax 20. Unmapped reads and reads with a mapping quality below q30 were filtered out with Samtools.
BigWig files were generated using HOMER
genome_build/assembly: mm10
supplementary_files_format_and_content: BigWig files at base pair resolution normalized to a library size of 10,000,000 reads

source_name: tdTomato +(dim) cells from the regenerating olfactory epithelium: immediate neuronal progenitors (INP)

growth_protocol: Adult mice were injected 3x IP with tamoxifen (24 hours apart), 10 days following the first injection olfactory epithelium was ablated with an IP injection of methimazole. Then olfactory epithelium was regenerated for 8 days.

extract_protocol:
Cells were lysed in Trizol (ThermoFisher) then RNA was extracted and treated with Turbo-DNase (ThermoFisher).
RNA-seq libraries were prepared using Ovation RNA-Seq System 1-16 for Model Organisms (Nugen 0348)

treatment_protocol: Mice were sacrificed using CO2 followed by cervical dislocation. The olfactory epithelium ("zone4-5" anatomical region) was dissected and transferred to ice-cold PBS, dissociated with a papain dissociation system (Worthington Biochemical), washed once with cold PBS and resuspended in cold sort media (2% FBS in PBS) with 500ng/mL DAPI (Invitrogen). Cells were passed through a 40um filter, then tdTomato + (dim) cells were isolated with FAC-sorting

value: tdTomato +(dim) cells from the regenerating olfactory epithelium:immediate neuronal progenitors (INP)

value: K5CreER*/+; Rosa-CAG-tdtomfl/fl


title: HS_1_KC

description: 10x Genomics

source_name: skjn

value: skjn


title: BMDM cells, Stat-1Klf6 without mannose, 24 h, biol rep 1

city: Livermore

first: Cody

middle: Scott

last: Madsen

state: California

address: 4000 East Avenue Bldg 411

department: Biosciences and Biotechnology Division

institute: Lawrence Livermore National Lab

data_processing:
Base calling was done by Illumina Real Time Analysis (RTA) v3.4.4 and output of RTA was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v2.20.0
RNA-seq data was analyzed using FastQC (v0.11.7), GNU parallel (20180422), Trimmomatic (0.39), STAR (2.6.0c) and featureCounts to generate the count table for all treatments and time points
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file for raw counts including all samples and time points

source_name: Bone marrow

growth_protocol: NA. Bone marrow derived macrophages were simply maintained in culture after extraction

extract_protocol:
Total RNA that was extracted by a Qiagen RNeasy kit (Qiagen, cat#74104) with RNase-free DNase Set (Qiagen, cat#79254) for NGS library preparation and sequencing
Libraries were prepared using the Illumina TruSeq Stranded mRNA Library Preparation Kit with IDT for Illumina TruSeq Unique Dual Index adapters following manufacturer’s recommendations. Completed libraries were QC’d and quantified using a combination of Qubit dsDNA HS and Agilent 4200 TapeStation HS DNA1000 assays

treatment_protocol: Bone marrow derived macrophages were maintained at 37°C and 5% CO2 in DMEM (ThermoFisher, MA, USA), supplemented with 10% fetal bovine serum (FBS), 1% penicillin-streptomycin and 100 U/mL recombinant macrophage colony-stimulating factor (M-CSF). BMDMs were maintained in these conditions for 7 days before being seeded at 5x104 into 96-well plates or 7x105-1x106 in 6-well plates and allowed to adhere overnight without penicillin-streptomycin

value: Bone marrow

value: Bone marrow derived macrophages

value: macrophage

value: WT

tag: treatment

value: Stat-1Klf6 strain without mannose

tag: time


title: AA_3170__85


title: AA_3169__84


title: Healthy_2_KC

description: 10x Genomics

value: Normal


title: Healthy_1_KC

description: 10x Genomics


title: HeLa cells, INPUT

city: Beijing

first: Xianhua

last: Wang

address: 5 Summer Palace Road, Haidian District, Beijing

department: Institute of Molecular Medicine, College of Future Technology

institute: Peking University

library_source: other

data_processing:
ChIP-seq reads were trimmed after a quality drop below a mean of Q15 in a window of 5   nucleotides, using Trimmomatic (Version: 0.39), discarding reads left with < 15 bp.
ChIP-seq reads were aligned to the UCSC hg38 genome using BWA-MEM (Version: 0.7.17-r1188) with the standard default settings. Only reads with mapping quality over 20 were retained. Duplicate reads were removed using picard tools (Version: 2.25.0).
To create ChIP-seq coverage plots along mitochondrial, the mapped ChIP-seq reads were normalized (to reads per million, rpm) and reformatted in the bedgraph file format for IP and input samples.
Mitochondrial coverage profiles were generated with samtools (Version: 1.3.1) and bedtools (Version: 2.30.0). Per base coverage was normalized to total reads mapped to genome and circular figures were generated with R library circlize (Version: 0.4.14).
Assembly: hg38
Supplementary files format and content: bedgraph

molecule: other

source_name: Cervical cancer

growth_protocol: DMEM, 10% fetal bovine serum, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were fixed with 4% formaldehyde for 15 minutes. After quenching, mitochondrial isolation and  lysis, chromatin was sonicated in a Bioruptor.
The DNA sequencing libraries for input and IP samples were built using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB) according to the manufacturer’s instructions.

treatment_protocol: The C17orf80-HA proteins were expressed using ADV.

value: Cervical cancer

value: HeLa

value: Cervical cancer cells

tag: chip antibody


title: AA_8877_58835_082-R

value: AA


title: HeLa cells, C17orf80 IP

value: HA(Abcam, #ab9110)


title: AA_3167__81


title: AA_3168__82


title: Jurkat T cells incubated with FLU, 4 hrs 1

city: Sydney

first: Susan

last: Corley

state: NSW

address: D26, Kensignton Campus

department: Biotechnology & Biomolecular Sciences

country: Australia

institute: UNSW

data_processing:
Subread (1.6.3) was used for aligning reads to the Ensembl human genome (GRCh38) .
The featureCounts function of Subread was used to quantify reads using the Homo_sapiens.GRCh38.84.gtf.
Assembly: GRCh38
Supplementary files format and content: featureCounts.txt is a tab-delimited text file which includes read counts for each sample

source_name: Jurkat T cells

growth_protocol: Jurkat T cells grown to confluence in 100 mm plates in complete medium .

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen, cat. 74004) with minor modification.
RNA samples were submitted to the UNSW Ramaciotti Centre for Genomics for TruSeq Stranded mRNA-seq preparation and sequencing by NextSeq 6000 to produce 75 bp single end reads.

treatment_protocol: The Jurkat T cells were incubated with 10 µM FLU or vehicle for 4 h

value: Jurkat T cells

value: T cells

value: Flubendazole

value: 4 hrs


title: AA_8876_58835_073-R


title: HEK-293T cells, KO, rep2

data_processing:
Raw reads were pre-processed and quality controlled with FastQC (Version: 0.11.9).
Reads for each library were mapped using HISAT2 (Version: 2.2.1) against the human reference genome assembly GRCh38 with default parameters.
Uniquely mapped reads were extracted to calculate the read counts of each gene, using the matching gene Annotation from Ensembl with HTSeq (Version: 0.12.4).
Genes were further filtered, and those with low expression in all samples (FPKM < 0.5 in all samples) were removed from differential gene expression analysis. Differential analysis was conducted with DEseq2. Genes with an adjusted P-value<0.05 were taken as significantly differentially expressed genes.
Mitochondrial coverage profiles were generated with samtools (Version: 1.3.1) and bedtools (Version: 2.30.0). Per base coverage was normalized to total reads mapped to genome and circular figures were generated with R library circlize (Version: 0.4.14).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw gene counts for each Sample
Supplementary files format and content: tab-delimited text files include per base normalized coverages in mitochondrial for each Sample

source_name: Embryonic Kidney

growth_protocol: HEK-293T cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
RNA was harvested using TRIzol™ (Invitrogen).
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Sequencing libraries were built using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB).

treatment_protocol: The C17orf80 knockout HEK-293T cell line was generated using CRISPR/Cas9 system and 3 μg/ml puromycin was used for selecting monoclonal cells.

value: Embryonic Kidney

value: Human embryonic kidney

value: C17orf80 knockout

value: C17orf80 sgRNA


title: HEK-293T cells, KO, rep1


title: AA_8874_58835_066-R


title: AA_8880_58835_096-R


title: AA_8873_58835_065-R


title: HEK-293T cells, WT, rep2

value: non targeted sgRNA


title: AA_8872_58835_043-R


title: AA_8868_58835_038-R


title: AA_8871_58835_041-R


title: HEK-293T cells, WT, rep1

value: WT


title: 93-11 RNA-seq Rep1

city: Nanjing

first: Mengqi

last: Li

state: Jiangsu

address: No.1, Weigang Street, Xuanwu District, Nanjing

institute: NanJing Argricultural University

data_processing:
Quality filtering and adapter trimming were done using fastp.
MH-seq: Clean data from NIP and 93-11 were mapped to MSU7.0 and pseudo reference genome, respectively, by using Bowtie2.Only uniquely mapped reads were retained for the downstream analyses.
MH-seq: MHS peaks were identified using MACS2 software with the following parameters: macs2 callpeak -f BAMPE -g 3.8e+8 -q 0.01 --nomodel.
RNAseq: Clean data from NIP and 93-11 were mapped to MSU7.0 and pseudo reference genome, respectively, by using Hisat2.FPKM of each sample was calculated by using StringTie . The differentially expressed genes (DEGs) were compared by using DESeq2
Genome_build: MSU7.0
Supplementary_files_format_and_content: bigWig file were generated using deepTools
Supplementary_files_format_and_content: bed files were generated using MACS2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Oryza sativa Indica Group

source_name: seedlings

growth_protocol: Uniformly germinated seeds of Nipponbare (Oryza sativa ssp. japonica) and 93-11 (Oryza sativa ssp. indica) were grown in the nutrient soil in a greenhouse with 28-30 °C and a 14 h/10 h light-dark cycle. Two-week-old seedlings from each variety were collected

extract_protocol:
RNA-seq: Two-week-old seedlings were collected from each variety were round into a fine powder in liquid nitrogen and immediately kept at -80 ℃ for RNA sequencing.
RNA-seq: Total RNA was extracted from ground powder using TRIzol. Total RNA was treated with DNaseI for completely removing contamination of genomic DNA. mRNA was enriched from DNaseI-treated RNA for library preparation and sequenced.

tag: cultivar

value: seedlings

tag: replicate

value: biological replicate1

tag: age

value: two weeks

tag: growth temperature

value: 28-30 degrees C and a 14 h/10 h light-dark cycle


title: 93-11 RNA-seq Rep2

value: biological replicate2


title: AA_6806_58835_017-R

value: AA


title: AA_8864_58835_007-R


title: AA_9168_85140_026


title: EA_8861_58835_122

value: EA


title: 93-11 MH-seq Rep1

extract_protocol:
MH-seq: Two-week-old seedlings from each variety were collected for cross-linking using 1% formaldehyde in HEPES buffer pH=8.0 (20 mM HEPES, 1 mM EDTA, 100 mM NaCl and 1mM PMSF). The cross-linked samples were ground into a fine powder in liquid nitrogen for the preparation of nuclei and chromatin for the downstream experiments.
MH-seq: Nuclei isolation and purification was conducted as previously described (Zhang and Jiang 2018). The nuclei pellet was re-suspended using 1.0 ml of MNase digestion buffer, and equally divided into 200 μl each aliquot. The aliquoted nuclei were trimmed at 37 ℃ for 10 min using a series of MNase. After stopping enzymatic digestion using 0.5 M EDTA (pH 8.0), each MNase cleaved nuclei were reversely cross-linked at 65 ℃ overnight. After removal of RNA and protein contamination using sequential treatment with RNase A at 37 ℃ for 30 min and proteinase K at 55 ℃ for 2 h. DNA was precipitated using cold ethanol after phenol/chloroform purification. The DNA pellet was dissolved using 20 μl EB (10 mM Tris-HCl, pH 8.0). After running 12% PAGE in 1xTBE buffer, 40-100 bp small sized DNA fragments were recovered from the purified DNA for MNase hypersensitive sequencing (MH-seq) library preparation. MH-seq library was prepared using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (E7645S).


title: 93-11 MH-seq Rep2


title: HEK-293T cells, KO, rep3


title: EA_8857_58835_118


title: EA_3193__112


title: EA_8860_58835_121


title: EA_3192__111


title: AA84

type: RNA

city: Melbourne

first: Lynette

last: Chee

state: VIC

address: 305 Grattan Street

department: ACRF Laboratory

institute: The Royal Melbourne Hospital/ Peter MacCallum Cancer Centre

data_processing:
miRNA profiling:  Samples were analysed using the NanoString nCounter system with the Human miRNA expression assay v3 (Nanostring, Seattle, WA, USA) according to manufacturer’s instructions.  Raw data were analysed using NanoString nSolver software (Nanostring, Seattle, WA, USA).
There were 798 miRNAs (excluding quality control probes) in the NanoString nCounter Human v3 panel included for downstream analysis.  Quality control probes (ligation, mRNA housekeeping genes, positive and negative spike-ins) were used for assessing sample quality during preprocessing.  NormFinder and RUVIII methods were used to find unvarying miRNA to serve as “housekeeping” genes for normalization which showed high expression and low variation in samples: hsa-miR-302d-3p and hsa-miR-548ar-5p.  Batch normalisation was then performed using RUVIII method, using control replicate samples on each run.  After the data had been normalised, differential expression analysis was performed using Limma method and p-values were adjusted for multiple hypothesis testing using Benjamini-Hochberg procedure.

source_name: bone marrow

extract_protocol: RNA extraction:  Total RNA, including miRNA, was isolated from biobanked Trizol-treated bone marrow samples using the Direct-zol DNA/RNA mini Prepz kit (Zymo, Irvine, CA, USA) according to the manufacturer’s instructions. Quantification of the RNA was performed using an Agilent 2200 TapeStation System (Santa Clara, CA, USA).

tag: patientid

tag: type

value: aplastic anaemia

tag: Sex

value: M

tag: denovomds

value: N

tag: mds/ aml/ clonal progression

tag: diagnosis timepoint

tag: pnh at diagnosis

tag: posttreatment

value: Y

tag: best response achieved

value: partial response

tag: blastpct


title: EA_3191__110

tag: race


title: EA_8863_58835_124


title: AA86

value: N - No eventual progression

value: no response to eventual treatment


title: AA85

value: no response


title: AA83


title: AA81


title: EA_3190__109


title: EA_8881_58835_109-R


title: AA80

value: complete response to eventual treatment


title: EA_3189__108


title: AA79

value: Y - Eventual progression

value: partial response to eventual treatment


title: EA_3180__97


title: HEK-293T cells, WT, rep3

tag: tissue

value: Embryonic Kidney

tag: cell line

tag: cell type

value: Human embryonic kidney

tag: genotype

value: WT

tag: treatment

value: non targeted sgRNA


title: EA_3177__94


title: EA_3175__92


title: MDS21

value: myelodysplastic syndrome

tag: age


title: AA77

tag: patientid


title: MDS20

tag: type


title: EA_3174__91

value: EA


title: EA_8878_58835_090-R


title: AA75

value: aplastic anaemia

tag: Sex

value: F


title: EA_3172__87


title: EA_8867_58835_037-R


title: EA_8875_58835_067-R


title: EA_8870_58835_039-R2


title: AA72

tag: denovomds

value: N


title: AA71

tag: mds/ aml/ clonal progression

value: Y


title: AA.Ctrl.10

value: control


title: AA82

value: M

tag: diagnosis timepoint


title: AA78

value: N - No eventual progression

tag: pnh at diagnosis

value: no response to eventual treatment


title: EA_8869_58835_039-R


title: MDS18


title: EA_3198__15Repeat


title: AA70

tag: posttreatment

value: N/A (untreated)


title: AA69

tag: best response achieved


title: EA_3184__101


title: EA_9167_85140_25-R


title: AA74

value: no response

tag: blastpct

value: N/A (no differential available)


title: EA_3173__90

tag: race


title: EA_8865_58835_015-R2


title: AA76


title: SHS394Solar14DAFHeatSiliqueS20203

city: Valdivia

first: Javier

last: Canales

state: Los Ríos

address: Campus Isla Teja s/n

department: Instituto de Bioquimica y Microbiologia

country: Chile

institute: Universidad Austral de Chile

data_processing:
Sequenced reads were pseudo-aligned to the publicly available Brassica napus transcriptome obtained from Ensembl Plants using kallisto (v0.46). RNA-seq data was normalized using the R package sleuth
Assembly: AST_PRJEB5043_v1
Supplementary files format and content: tab-delimited text files include tpm values for each sample

organism: Brassica napus

source_name: Silique

growth_protocol: The field experiments and conditions were described in Verdejo and Calderini (…). Briefly, two ﬁeld experiments were set in 2019-20 and 2020-21 growing seasons at the Austral Farming Experimental Station (EEAA) of the Universidad Austral de Chile in Valdivia, Chile (39° 47’ S., 73° 14’ W.).

extract_protocol:
Total RNA extraction was performed using a method adapted for Brassica seeds (Graeber et al., 2011;doi:10.1105/tpc.111.084103) with 100 mg of each sample and using NucleoSpin® Gel and PCR columns
RNA quality analysis, libraries construction and sequencing were performed by Novogene (Beijing, China) using standard Illumina protocols

treatment_protocol: In each experiment, two adapted spring rapeseed hybrids (Lumen and Solar from NPZ-Lembke, Germany) were assessed under two heat stress treatments: a control without manipulation and a thermal increase treatment where plots were heated by 5°C above the environmental temperature from the beginning of flowering [BBCH 61] to 15 days after flowering. The hybrids Lumen and Solar were chosen for their similar phenology and confirmed adaptation to southern Chile. Experiment 1 was arranged in a split plot design with three replicates in which the heat stress treatments were assigned to the main plots and genotypes to sub-plots. In Experiment 2, plots were arranged in a randomized block design with three replicates in which, the heat stress treatments and genotypes were fully randomized in each block. In both experiments rapeseed plants were sown at a plant density of 55 plants m-2.

tag: tissue

value: Silique

value: Solar

tag: days after_flowering

value: Heat

tag: season

tag: replicate


title: SHS398Solar14DAFHeatSiliqueS20204

tag: genotype

tag: treatment


title: AA73

tag: patientid

tag: age

value: partial response


title: EA_9166_85140_125


title: SHS370Solar7DAFHeatSiliqueS20201


title: SHS238Solar14DAFHeatSiliqueS20193


title: SHS374Solar7DAFHeatSiliqueS20202


title: AA62

tag: type

tag: Sex

value: N/A (unknown)


title: AA67

tag: denovomds

tag: mds/ aml/ clonal progression


title: AA63

tag: diagnosis timepoint

tag: pnh at diagnosis

value: partial response to eventual treatment


title: AA65

value: aplastic anaemia

tag: posttreatment

tag: best response achieved


title: AA.Ctrl.9


title: AA64

value: F

tag: blastpct


title: MDS19

value: myelodysplastic syndrome


title: AA68

value: N

value: Y


title: AA60

value: M


title: AA61

value: N - No eventual progression


title: MDS17


title: SHS230Solar14DAFHeatSiliqueS20192

tag: tissue


title: AA59

value: no response to eventual treatment


title: SHS378Solar7DAFHeatSiliqueS20203

tag: days after_flowering


title: SHS214Solar7DAFHeatSiliqueS20193

tag: season


title: SHS222Solar14DAFHeatSiliqueS20191

tag: replicate


title: SHS382Solar7DAFHeatSiliqueS20204

tag: genotype


title: SHS390Solar14DAFHeatSiliqueS20202

tag: treatment


title: AA58

tag: patientid

value: N/A (untreated)


title: SHS386Solar14DAFHeatSiliqueS20201


title: SHS206BSolar7DAFHeatSiliqueS20192


title: SHS198Solar7DAFHeatSiliqueS20191


title: AA57

tag: age


title: AA55

tag: type


title: AA56

tag: Sex


title: MDS16

tag: denovomds


title: AA.Ctrl.8

value: control


title: SHG385Solar14DAFHeatSeedS20201

source_name: Seed

value: Seed


title: SHG389Solar14DAFHeatSeedS20202


title: SHG397Solar14DAFHeatSeedS20204


title: AA54

tag: mds/ aml/ clonal progression


title: SHG373Solar7DAFHeatSeedS20202


title: SHG377Solar7DAFHeatSeedS20203


title: SHG393Solar14DAFHeatSeedS20203


title: SHG381BSolar7DAFHeatSeedS20204


title: SHG369Solar7DAFHeatSeedS20201


title: AA52

tag: diagnosis timepoint

value: complete response to eventual treatment


title: AA51

tag: pnh at diagnosis


title: MDS15


title: SHG237Solar14DAFHeatSeedS20193

value: Solar


title: SHG229Solar14DAFHeatSeedS20192

value: Heat


title: AA50

tag: posttreatment

value: no response


title: AA.Ctrl.7


title: SHG205Solar7DAFHeatSeedS20192


title: SHG197Solar7DAFHeatSeedS20191


title: AA46

tag: best response achieved


title: SHG213Solar7DAFHeatSeedS20193


title: SHG221Solar14DAFHeatSeedS20191


title: AA48

tag: blastpct


title: AA47


title: AA49


title: SCS400Solar14DAFControlSiliqueS20204

tag: tissue

value: Silique

value: Control


title: AA45

value: aplastic anaemia


title: AA43

value: F


title: AA44

value: N/A (unknown)


title: AA53

value: N


title: SCS392Solar14DAFControlSiliqueS20202

tag: days after_flowering


title: MDS14

value: myelodysplastic syndrome

value: Y


title: SCS388Solar14DAFControlSiliqueS20201

tag: season


title: SCS380Solar7DAFControlSiliqueS20203

tag: replicate


title: SCS376Solar7DAFControlSiliqueS20202

tag: genotype


title: SCS384Solar7DAFControlSiliqueS20204

tag: treatment


title: MDS13

tag: patientid

value: M


title: MDS12

tag: age


title: SCS240Solar14DAFControlSiliqueS20193


title: AA.Ctrl.6

tag: type


title: MDS11

tag: Sex


title: SCS372Solar7DAFControlSiliqueS20201


title: AA42

tag: denovomds

value: N - No eventual progression

value: partial response to eventual treatment


title: AA.Ctrl.5

value: control


title: MDS9

tag: mds/ aml/ clonal progression


title: MDS10


title: SCS224Solar14DAFControlSiliqueS20191


title: SCS208Solar7DAFControlSiliqueS20192


title: SCS216BSolar7DAFControlSiliqueS20193


title: SCS200Solar7DAFControlSiliqueS20191


title: SCS396Solar14DAFControlSiliqueS20203


title: SCG395Solar14DAFControlSeedS20203

value: Seed


title: SCG399Solar14DAFControlSeedS20204


title: AA40

tag: diagnosis timepoint


title: AA38

tag: pnh at diagnosis


title: AA39


title: AA37

tag: posttreatment

value: partial response


title: AA36

tag: best response achieved


title: SCG391Solar14DAFControlSeedS20202

value: Solar


title: SCG375Solar7DAFControlSeedS20202


title: AA34

tag: blastpct


title: SCG371Solar7DAFControlSeedS20201

tag: tissue


title: AA35


title: SCS232Solar14DAFControlSiliqueS20192

tag: days after_flowering


title: AA33

value: N/A (untreated)


title: SCG239Solar14DAFControlSeedS20193

tag: season


title: SCG383Solar7DAFControlSeedS20204

tag: replicate


title: SCG231Solar14DAFControlSeedS20192

tag: genotype


title: SCG223Solar14DAFControlSeedS20191

tag: treatment


title: AA.Ctrl.3


title: AA29

tag: patientid


title: AA32

tag: age


title: AA31

tag: type

value: no response


title: AA30

tag: Sex


title: MDS7

tag: denovomds


title: AA41

tag: mds/ aml/ clonal progression


title: SCG215Solar7DAFControlSeedS20193


title: SCG387Solar14DAFControlSeedS20201


title: SCG199Solar7DAFControlSeedS20191


title: SCG379BSolar7DAFControlSeedS20203


title: SCG207BSolar7DAFControlSeedS20192


title: LHS366Lumen14DAFHeatSiliqueS20204

value: Silique

value: Lumen

value: Heat


title: AA28

value: aplastic anaemia

tag: diagnosis timepoint

value: N/A (no differential available)


title: MDS8

value: F


title: AA26


title: MDCKII_CGNL1-KO_22_N3

city: Geneva

first: Natacha

last: Civic

address: Rue Michel-Servet 1

department: iGE3 Genomics Platform

country: Switzerland

institute: University of Geneva

data_processing:
Sequenced reads were aligned to the NCBI canis lupus familiaris canFam3.1 genome with STAR v. 2.7.0f.
The reads counts were prepared with HTSeq count v.0.9.1
.
Assembly: canFam3.1

organism: Canis lupus familiaris

source_name: Kidney

extract_protocol: RNA libraries for RNA-seq were prepared using Illumina TruSeq HT kit following manufacturer's protocols.

value: Kidney

tag: cell line

value: MDCKII

tag: cell type

value: Epithelial

value: No


title: MDCKII_CGNL1-KO_22_N2


title: LHS362Lumen14DAFHeatSiliqueS20203


title: LHS350Lumen7DAFHeatSiliqueS20204


title: LHS354Lumen14DAFHeatSiliqueS20201


title: LHS346Lumen7DAFHeatSiliqueS20203


title: LHS358Lumen14DAFHeatSiliqueS20202


title: MDCKII_CGN_CGNL1-dKO_21D3_N3


title: AA25

value: N

value: N - No eventual progression

value: Y

tag: pnh at diagnosis

tag: posttreatment

tag: best response achieved

value: no response to eventual treatment


title: AA.Ctrl.4

value: control


title: LHS342Lumen7DAFHeatSiliqueS20202

tag: tissue

tag: days after_flowering


title: MDCKII_CGN_CGNL1-dKO_21D3_N2


title: MDS6

value: myelodysplastic syndrome

value: M

tag: blastpct


title: LHS190Lumen14DAFHeatSiliqueS20193

value: Silique

tag: genotype

tag: season

tag: replicate


title: AA27

tag: patientid

tag: age


title: MDCKII_CGN-KO_1G8_N3

value: CGN-KO

tag: treatment


title: MDCKII_CGN_CGNL1-dKO_21D3_N1


title: MDS5

tag: type

tag: Sex

tag: denovomds


title: LHS158Lumen7DAFHeatSiliqueS20192

value: Lumen

value: Heat


title: LHS174Lumen14DAFHeatSiliqueS20191


title: LHS166Lumen7DAFHeatSiliqueS20193


title: MDCKII_CGNL1-KO_22_N1

tag: cell line


title: AA24

value: aplastic anaemia


title: MDCKII_CGN-KO_1G8_N2

tag: cell type


title: MDCKII_CGN-KO_1G8_N1


title: LHG365Lumen14DAFHeatSeedS20204

value: Seed


title: AA23

value: F

tag: mds/ aml/ clonal progression

tag: diagnosis timepoint

tag: pnh at diagnosis

value: no response


title: LHS150Lumen7DAFHeatSiliqueS20191

tag: tissue


title: LHG353Lumen14DAFHeatSeedS20201

tag: days after_flowering


title: LHG361Lumen14DAFHeatSeedS20203


title: AA21

tag: posttreatment

tag: best response achieved

value: partial response

tag: blastpct


title: LHS338Lumen7DAFHeatSiliqueS20201

tag: genotype

tag: season

tag: replicate


title: LHG345Lumen7DAFHeatSeedS20203

tag: treatment


title: LHG349Lumen7DAFHeatSeedS20204


title: LHG357Lumen14DAFHeatSeedS20202


title: pulpitisD

city: Wuhan

first: Pei

last: Huang

state: Hubei

address: 237 Luoyu Road

department: School and Hospital of Stomatology

institute: Wuhan University

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads  containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base  quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown  base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored  in FASTQ format.
The clean reads were mapped to the reference genome using HISAT2 (v2.0.4). Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set, then expression level of gene was calculated by RSEM (v1.2.12).
Assembly: GCF_000001405.37_GRCh38.p11
Supplementary files format and content: tab-delimited text files include FPKM values for each gene in each sample.

source_name: human dental pulp tissue

extract_protocol:
Total RNA was isolated from the dental pulp tissues of normal, deep caries and pulpitis teeth using Trizol reagent (Invitrogen, USA). A total of 12 RNA samples (4 samples each group, 3 groups in total) were subjected to RNA sequencing.
RNA libraries were prepared for sequencing using the following protocols: Briefly, the total RNA samples were processed by mRNA enrichment or rRNA removal to gain mRNA fragments. Random N6 primers were used for reverse transcription (RT) to form double-stranded DNA. Polymerase chain reaction (PCR) amplification was performed after the double-stranded DNA ends were processed. PCR products were thermally degenerated into single strands, and a single-stranded DNA was cycled to obtain a single-stranded cyclic DNA library with a single bridge primer.

value: human dental pulp from third molars

tag: age

value: 18-25 years old

tag: disease state

value: pulpitis


title: AA20

tag: patientid

tag: type

tag: Sex

tag: denovomds

value: N

value: Y


title: AA22

tag: mds/ aml/ clonal progression

tag: diagnosis timepoint


title: LHS182Lumen14DAFHeatSiliqueS20192

tag: tissue


title: pulpitisC


title: LHG341Lumen7DAFHeatSeedS20202

tag: days after_flowering


title: pulpitisB


title: pulpitisA


title: AA19

tag: pnh at diagnosis

tag: posttreatment


title: LHG337Lumen7DAFHeatSeedS20201


title: CariesD

value: deep caries


title: LHG173Lumen14DAFHeatSeedS20191


title: LHG189Lumen14DAFHeatSeedS20193


title: LHG165Lumen7DAFHeatSeedS20193


title: AA17

value: Y - Eventual progression

tag: best response achieved

value: partial response to eventual treatment

tag: blastpct


title: CariesC


title: AA18


title: CariesB


title: LCS368Lumen14DAFControlSiliqueS20204

value: Silique

tag: genotype

value: Control

tag: season


title: AA.Ctrl.2

value: control


title: LCS360Lumen14DAFControlSiliqueS20202

value: Lumen

tag: treatment

tag: replicate


title: LHG157Lumen7DAFHeatSeedS20192

value: Heat


title: LCS356Lumen14DAFControlSiliqueS20201


title: CariesA

tag: age

tag: disease state


title: normalD

value: normal


title: LCS352Lumen7DAFControlSiliqueS20204


title: LCS364Lumen14DAFControlSiliqueS20203


title: LCS348Lumen7DAFControlSiliqueS20203


title: LCS344Lumen7DAFControlSiliqueS20202


title: LHG181Lumen14DAFHeatSeedS20192

value: Seed


title: MDS3

tag: patientid

tag: type

value: myelodysplastic syndrome

value: M


title: MDS4

tag: Sex

tag: denovomds


title: LHG149Lumen7DAFHeatSeedS20191


title: normalC

value: human dental pulp from third molars


title: LCS340Lumen7DAFControlSiliqueS20201


title: LCS192Lumen14DAFControlSiliqueS20193


title: normalB

value: 18-25 years old


title: AA16

value: aplastic anaemia

tag: mds/ aml/ clonal progression

tag: diagnosis timepoint

value: no response


title: LCS184Lumen14DAFControlSiliqueS20192

tag: tissue

tag: days after_flowering


title: AA15

value: N

value: Y

tag: pnh at diagnosis

tag: posttreatment

value: no response to eventual treatment


title: LCS176Lumen14DAFControlSiliqueS20191


title: AA14

value: F

tag: best response achieved

value: N/A (unknown)

tag: blastpct


title: normalA


title: LCS168Lumen7DAFControlSiliqueS20193

value: Silique

tag: genotype

value: Control

tag: season


title: AA13

value: N/A (untreated)


title: LCS160Lumen7DAFControlSiliqueS20192

value: Lumen

tag: treatment

tag: replicate


title: AA12

tag: age


title: 4T1, ShTAZ 3

city: Rehovot

first: Ori

last: Hassin

address: Hertzel 234

department: MCB

country: Israel

institute: Weizmann Institute

description:
FY5_2946
deseq in vitro ShC vs ShTAZ.xlsx

data_processing:
Reads were trimmed using cutadapt. After trimming the reads were mapped to the mm10 genome. Deduplication was carried out by flagging all reads that were mapped to the same gene and had the same UMI (read 2 had the UMI). Counting proceeded over genes (1000 bases of the 3’ UTR) using htseq-count. Normalization and differential expression was performed using DESeq2.
Assembly: mm10
Supplementary files format and content: Excel file includes DESeq2 analysis using umi counts

growth_protocol: 4T1 cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin (P/S).

extract_protocol:
Nucleospin RNA, MACHEREY-NAGEL
A bulk adaptation of the MARS-Seq protocol was used to generate RNA-seq libraries. Briefly, 30ng of input RNA from each sample was barcoded during reverse transcription and pooled. Following Agencourt AMPure XP beads cleanup (Beckman Coulter), the pooled samples underwent second strand synthesis and were linearly amplified by T7 in vitro transcription. The resulting RNA was fragmented and converted into a sequencing-ready library by tagging the samples with Illumina sequences during ligation, RT and PCR. Libraries were quantified by Qubit (Thermo Fisher Scientific) and TapeStation (Agilent).
MARS-seq

tag: infection

value: lentivirus expression of ShTAZ

tag: cell line

tag: cell type

value: Breast cancer cell line

value: WT

value: No treatment


title: LCS152Lumen7DAFControlSiliqueS20191


title: LCG367Lumen14DAFControlSeedS20204

value: Seed


title: 4T1, ShC 3

description:
FY5_2941
deseq in vitro ShC vs ShTAZ.xlsx

value: lentivirus expression of ShC


title: 4T1, ShTAZ 2

description:
FY3_2946
deseq in vitro ShC vs ShTAZ.xlsx


title: 4T1, ShC 2

description:
FY3_2941
deseq in vitro ShC vs ShTAZ.xlsx


title: 4T1, TAZ WT 3

description:
AL2WT
deseq TAZ WT vs TAZ KO.xlsx

data_processing:
UTAP transcriptome analysis pipeline
Assembly: mm10
Supplementary files format and content: Excel file includes DESeq2 analysis using umi counts

extract_protocol:
Nucleospin RNA, MACHEREY-NAGEL
INCPM Mrna-seq


title: AA11

tag: patientid

tag: type

value: aplastic anaemia


title: 4T1, TAZ KO 2

description:
GGYAP
deseq TAZ WT vs TAZ KO.xlsx

value: TAZ KO


title: LCG363Lumen14DAFControlSeedS20203


title: 4T1, TAZ WT 2

description:
ATWT
deseq TAZ WT vs TAZ KO.xlsx


title: AA10

tag: Sex

tag: denovomds

value: N

tag: mds/ aml/ clonal progression

tag: diagnosis timepoint

value: no response


title: LCG359Lumen14DAFControlSeedS20202

tag: tissue

tag: days after_flowering


title: LCG351Lumen7DAFControlSeedS20204


title: 4T1, ShTAZ 1

description:
FY1_2946
deseq in vitro ShC vs ShTAZ.xlsx


title: LCG355Lumen14DAFControlSeedS20201


title: 4T1, ShC 1

description:
FY1_2941
deseq in vitro ShC vs ShTAZ.xlsx


title: AA9

value: Y

tag: pnh at diagnosis

tag: posttreatment

tag: best response achieved

tag: blastpct


title: LCG347Lumen7DAFControlSeedS20203

tag: genotype

tag: treatment

tag: season

tag: replicate


title: 4T1, TAZ WT 1

description:
ASWT
deseq TAZ WT vs TAZ KO.xlsx

tag: cell line

tag: cell type


title: 4T1, TAZ KO 1

description:
GDYAP
deseq TAZ WT vs TAZ KO.xlsx


title: AA.Ctrl.1

tag: type

value: control


title: Mammary fat pad, 4T1, ShTAZ 4

description:
FM12-shTAZ
Deseq in-vivo ShC vs ShTAZ.xlsx

source_name: Mammary fat pad

tag: infection

value: Mammary fat pad


title: LCG343BLumen7DAFControlSeedS20202


title: nchip_Z5_Ngn1GFPbright_tk79_r1

data_processing:
Adapter sequences were trimmed with Cutadapt (--minimum-length 18, and --nextseq-trim=20 for samples sequenced on Nextseq 550). Reads were trimmed to 50bp before aligning.
Native ChIP-seq libraries were aligned with Bowtie2, with default setting except for maximum insert size set to 1000 (-X 1000). Libraries were aligned single end with read 1 only. Unmapped reads and reads with a mapping quality below q30 were filtered out with Samtools.
BigWig files were generated using HOMER
genome_build/assembly: mm10
supplementary_files_format_and_content: BigWig files at base pair resolution normalized to a library size of 10,000,000 reads

source_name: immature olfactory sensory neurons (iOSN)

growth_protocol: used young pups < P6

treatment_protocol: Mice were sacrificed using CO2 followed by cervical dislocation. The olfactory epithelium ("zone4-5" anatomical region) was dissected and transferred to ice-cold PBS, dissociated with a papain dissociation system (Worthington Biochemical), washed once with cold PBS and resuspended in cold sort media (2% FBS in PBS) with 500ng/mL DAPI (Invitrogen). Cells were passed through a 40um filter, then GFP + (bright) cells were isolated with FAC-sorting


title: LCG339Lumen7DAFControlSeedS20201


title: AA8

tag: patientid

tag: Sex

value: M

tag: age

tag: denovomds


title: EN

city: Shanghai

first: Ronhua

last: Liu

address: No.138, Yi Xue Yuan Rd.

institute: Department of Immunology, Fudan University

description: All.counts.txt

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
Hisat2 2.0.4 mapping to reference genome
count counting
Genome_build: hg19_GRCh38
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: esophageal squamous normal tissue

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Patients  underwent  esophagectomy  without  preoperative  chemotherapy   or  radiotherapy  at  our  institution

tag: sample type

value: patient with esophageal squamous cell carcinoma

tag: tissue

value: adjacent normal tissues


title: Mammary fat pad, 4T1, ShTAZ 3

description:
FM8-shTAZ
Deseq in-vivo ShC vs ShTAZ.xlsx


title: MDS1

value: myelodysplastic syndrome

value: F

tag: mds/ aml/ clonal progression


title: Mammary fat pad, 4T1, ShC 4

description:
FM5-shC
Deseq in-vivo ShC vs ShTAZ.xlsx

value: Breast cancer cell line


title: MDS2


title: LCG191Lumen14DAFControlSeedS20193

value: Lumen

tag: days after_flowering

value: Control


title: JDH-N

description: All.counts.txt


title: Mammary fat pad, 4T1, ShC 3

description:
FM4-shC
Deseq in-vivo ShC vs ShTAZ.xlsx

value: WT

value: No treatment


title: LCG183Lumen14DAFControlSeedS20192

value: Seed


title: LCG175Lumen14DAFControlSeedS20191


title: AA6

value: aplastic anaemia

tag: diagnosis timepoint

tag: pnh at diagnosis

tag: posttreatment

tag: best response achieved

value: partial response

tag: blastpct


title: AA7

value: N


title: Mammary fat pad, 4T1, ShC 1

description:
FG11-shC
Deseq in-vivo ShC vs ShTAZ.xlsx

value: lentivirus expression of ShC

tag: cell line

tag: genotype

tag: treatment


title: Mammary fat pad, 4T1, ShC 2

description:
FG12-shC
Deseq in-vivo ShC vs ShTAZ.xlsx

tag: infection

tag: cell type


title: JDH-T

description: All.counts.txt

source_name: esophageal squamous tumor tissue

value: esophageal squamous cell carcinoma tissue


title: LCG167Lumen7DAFControlSeedS20193

tag: season

tag: replicate


title: LCG159Lumen7DAFControlSeedS20192


title: AA4

tag: patientid

tag: type

tag: Sex

tag: age

tag: denovomds

value: Y


title: XJY-T

description: All.counts.txt

tag: sample type

tag: tissue


title: Mammary fat pad, 4T1, ShTAZ 1

description:
FG7-shTAZ
Deseq in-vivo ShC vs ShTAZ.xlsx

value: lentivirus expression of ShTAZ

value: Mammary fat pad


title: Mammary fat pad, 4T1, ShTAZ 2

description:
FG8-shTAZ
Deseq in-vivo ShC vs ShTAZ.xlsx


title: AA3


title: AA2

value: M

tag: mds/ aml/ clonal progression

tag: diagnosis timepoint

tag: pnh at diagnosis

tag: posttreatment

value: N/A (unknown)


title: LCG151Lumen7DAFControlSeedS20191

tag: genotype

tag: days after_flowering


title: rgl2_7dL_Rep3

status: Public on Sep 01 2023

city: Wien

first: Zsuzsanna

last: Mérai

address: 1030 Wien Dr. Bohr-Gasse 3.

country: Austria

institute: Gregor Mendel Institute

data_processing:
Basecalling was done by using RTA software version 1.18.54.0
Files were generated by bcl2fastq tool version 2.17.1 and bam files were generated by fastq2bam tool version 0.7.
The sequence libraries were processed using Trimmomatic with options “ILLUMINACLIP:adaptors:2:20:8, SLIDINGWINDOW:4:15, TRAILING:15, HEADCROP:12, MINLENGTH:20”
Trimmed and filtered reads were mapped against the Aethionema arabicum genome version 3.0, using Bowtie2 version 2.3.5.1 with the options "--no-unal and --very-sensitive-local" and uniquely mapped reads were kept.
Mapped reads per feature were counted using HTSeq-count version 0.11.2 with the options “-f bam -s no -t gene -i ID -m intersection-nonempty”.
Assembly: Aethionema arabicum genome version 3.0 (id59426) https://genomevolution.org/coge/OrganismView.pl?gid=36061
Supplementary files format and content: Processed excel (xls) matrix table contains the gene ID of Aethionema gene model v3.1, gene length, Arabidopsis orthologue TAIR10 identifier,  raw counts and RPKM values of each sample, short and long gene description.

organism: Aethionema arabicum

source_name: imbibed seeds

extract_protocol:
Intact, non-germinating seeds were collected into liquid nitrogen. RNA was extracted as described at Chang et. al. 1993 (http://dx.doi.org/10.1007/BF02670468) followed by additional purification using columns (QIAGEN RNeasy Kit, Cat. No. 74104).
Libraries were constructed from 500 ng RNA using NEB mRNA seq library preparation Kit including  Poly(A) RNA Selection Kit.

treatment_protocol: All samples are seed material, treated on wet filter paper at 14°C. The light conditions are indicated separately.

value: imbibed seeds

tag: cultivar

value: Cyprus

tag: treatment

value: 7 days kept under 100µmol m-2s-1 white light


title: WT_7dL_Rep3

value: wild-type


title: rgl2_7dL_Rep1


title: rgl2_7dL_Rep2


title: rgl2_1dL_Rep1

value: 23 hours kept under 100µmol m-2s-1 white light


title: rgl2_1dL_Rep3


title: WT_7dL_Rep2


title: XJY-N

description: All.counts.txt

value: patient with esophageal squamous cell carcinoma

value: adjacent normal tissues


title: ET

description: All.counts.txt


title: rgl2_1dL_Rep2


title: WT_1dL_Rep2


title: AA1

value: aplastic anaemia

value: N - No eventual progression

tag: best response achieved

value: complete response to eventual treatment

tag: blastpct


title: WT_1dL_Rep3


title: WT_7dL_Rep1


title: AA5

tag: patientid

value: F

value: N

value: no response


title: WT_1dL_Rep1


title: NFD_2

city: wuxi

first: Yi-Fan

last: Tao

state: jiangsu

address: 9 Shanshui East Road

institute: Freshwater Fisheries Research Center

data_processing:
The raw reads was filtered using Cutadapt v1.10  to remove low quality reads and adaptor sequences. Sequence quality was checked by FastQC v0.10.1
HISAT2 v2.0.4 was used to map reads to Nile tilapia genome
The mapped reads were then assembled to transcripts using StringTie v1.3.0  and classified with Gffcompare v.0.11.2
The lncRNAs were screened based on the following criterion: (1) the transcript, which length shorter than 200 bp or contained less than one exon was filtered; (2) transcript, which reads coverage less than three was filtered; (3) transcript with known non-lncRNA annotation was filtered; (4) Two different software, coding potential calculator (CPC) v0.9-r2  and coding-non-coding index (CNCI) v2.0 were used to estimate coding potential of each transcript. Transcripts with CPC score < 0 and CNCI score <0 were considered as the lncRNAs.
StringTie v1.3.0  was used to standardized the expression of lncRNA and mRNA in each sample by calculating FPKM (fragments per kilobase per million mapped reads). Then, edgeR v3.22.3 was performed to determine the differentially expressed (DE)-mRNAs and DE-lncRNAs between HFD and NFD group . |log2 fold change | > 1 and P < 0.05 were considered significant.
Assembly: 8126
Supplementary files format and content: standardized the expression of lncRNA and mRNA in each sample by calculating FPKM

organism: Oreochromis niloticus

source_name: liver

growth_protocol: fish were stocked in 600L circulating water tanks (DO > 5.0 mg L−1, 27-29 °C, and pH 7.4-7.6) for 56 days

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
The sequencing was performed with three bio-replicates per group (RNA from three samples per group was mixed), so that six cDNA libraries was constructed (HFD_1, HFD_2, HFD_3, NFD_1, NFD_2, NFD_3) using the mRNA-Seq sample preparation kit (Illumina, USA) after removal of rRNA by Epicentre Ribo-Zero Gold Kit (Illumina, USA), following standard procedure.

treatment_protocol: fed with the NFD (8% lipid) or HFD (18.5% lipid) to apparent satiation two times per day

value: liver

value: juvenile fish

value: male

value: WT

value: fed with 8% diet


title: NFD_3


title: HFD_3

value: fed with 18.5% diet


title: NFD_1


title: HFD_2


title: HFD_1


title: panc_nanopore, II-B, 64, 7

city: Santa Cruz

first: Daniel

last: Kim

address: McLaughlin Dr

department: Biomolecular Engineering

institute: UC Santa Cruz

data_processing:
RNA sequencing reads (FASTQ) were trimmed with Trimmomatic (v0.39), quality assessed using FASTQC (v0.11.9) and visualized using MultiQC (v1.11). Quantification was performed using Salmon (v1.9.0).
Assembly: Hg38
Supplementary files format and content: csv, normalized gene counts
Supplementary files format and content: tsv, normalized gene counts

source_name: Blood Plasma

extract_protocol:
The ExoRNeasy kit (Qiagen) was used to isolate cell-free RNA from blood plasma of de-identified healthy controls (Discovery Life Sciences, blood collected in K2EDTA tubes) and pancreatic cancer patients (BioIVT, blood collected in K2EDTA tubes). Samples were initially filtered through a 0.8 um filter to remove any contaminants such as buffy coat. Filtered plasma was then processed using the ExoRNeasy kit to isolate cell-free RNA according to manufacturer instructions.
Full-length cDNA was synthesized from cell-free RNA from pancreatic cancer and healthy control samples (Takara SMART-Seq HT kit). Size distribution of cell-free RNA and resulting cDNA were evaluated using an Agilent bioanalyzer. Final libraries were made using the Illumina Nextera XT DNA Prep kit. These libraries were then sequenced (PE150) on an Illumina NextSeq 500.  Nanopore full-length cDNA libraries were prepared as described above, followed by manufacturer instructions for the Oxford Nanopore ligation kit LSK109. Sequencing for each library was performed on an Oxford Nanopore MinION device with R9.4 flowcells.

value: Blood Plasma

tag: subject status

value: pancreatic cancer patient

tag: Stage

value: II-B

tag: subject id


title: panc_nanopore, III, 64, 6

value: III

tag: age


title: HCT116 long-read RNA-seq

city: Hong Kong

first: Sojung

last: LEE

address: 21 Sassoon Rd, Pok Fu Lam

department: Faculty of Medicine

country: Hong Kong

institute: The Hong Kong University

data_processing:
Basecalling for raw fast5 files was performed using Guppy(v.4.2.2) with minimum mean base quality of 7.0. Pychopper was then used for adapter trimming and read orientation. The resulting fastq file contains pass reads and rescued reads.
Raw reads were mapped to the human genome (hg38) using Minimap2. Read counts were computed by featureCounts based on transposable elements defined in RepeatMasker.
Assembly: hg38
Supplementary files format and content: RNA-Seq expression matrix(txt)

extract_protocol:
HCT116 cells were cultured in McCoy’s 5A media supplemented with 10% FBS and seeded into 35 cm dishes.
For long read RNA-seq, 50 ng was used for library preparation using Oxford Nanopore cDNA-PCR barcoding kit (Oxford Nanopore, SQK-PCB109)

tag: cell line

tag: cell type

value: Human colorectal carcinoma cell line

value: DMSO


title: R. porcellionis strain ZGO, 8 dpi (late phase), rep3

city: Vienna

first: Matthias

last: Horn

address: Djerassiplatz 1

department: Division of Microbial Ecology

institute: University of Vienna, Center of Microbiology and Environmental Systems Science

data_processing:
The quality of the sequencing reads was checked using fastqc (v.0.11.8)
Sequencing adapters were clipped and sequences shorter than 30 bp were removed with cutadapt (v3.5; “-m 30”)
Reads were mapped to the R. porcellionis genome with bowtie2 (v.2.3.5.1; “-N 1 --very-sensitive-local --reorder --no-unal”) and only unambiguously mapped reads were kept using SAMtools (v1.15.1)
Strand-specific reads were counted for each coding sequence using featureCounts (v.2.0.0; “-p -t CDS -s 2”)
Assembly: Assemblies and genome sequencing data are registered under the NCBI sample accessions: SAMN10089613 (15C), SAMN30436884 (ZGO)
Supplementary files format and content: tab-delimited text files include count values for each sample

organism: Candidatus Rhabdochlamydia porcellionis

source_name: ZGO

extract_protocol:
RNA was extracted with the All-In-One DNA/RNA/Protein Mini_Prep Kit (Bio Basic) according to the manufacturer's recommendation. Remaining DNA was removed using the GeneJET RNA Cleanup and Concentration Micro Kit (Thermo Scientific) as recommended by the manufacturer.
Chlamydial and host (Spodoptera frugiperda) rRNAs were removed using custom rRNA primers and RNase H and afterwards polyadenylated host mRNAs were depleted using oligo (dT) beads.  For strand-specific cDNA library preparation, the NEBNext Ultra directional RNA library prep kit for Illumina (New England Biolabs) and the NEBNext multiplex oligonucleotides (New England Biolabs) were used.

tag: strain

value: ZGO

tag: host

value: Spodoptera frugiperda

tag: phase

value: 8 dpi (late phase)


title: R. porcellionis strain ZGO, 8 dpi (late phase), rep2


title: R. porcellionis strain ZGO, 2 dpi (mid phase), rep3

value: 2 dpi (mid phase)


title: R. porcellionis strain ZGO, 2 dpi (mid phase), rep1


title: R. porcellionis strain ZGO, 2 dpi (mid phase), rep2


title: R. porcellionis strain ZGO, 8 dpi (late phase), rep1


title: R. porcellionis strain ZGO, extracellular phase, rep3

value: extracellular phase


title: R. porcellionis strain 15C, 5 dpi (late phase), rep2

value: 5 dpi (late phase)


title: R. porcellionis strain ZGO, extracellular phase, rep1


title: R. porcellionis strain 15C, 5 dpi (late phase), rep3


title: R. porcellionis strain ZGO, extracellular phase, rep2


title: R. porcellionis strain 15C, 5 dpi (late phase), rep1


title: NZBWF_28_nine_(Clariom_S_Mouse)

city: beijng

first: shipeng

address: Nan Li Shi Road No. 56,Beijing

institute: Beijing children's hospital

description: Gene expression data from 28-week-old NZBWF1

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Transcriptome Array 2.0 were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000 7G.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100

label: total RNA

source_name: 28-week-old NZBWF1 kidney

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA

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

tag: tissue

value: kidney


title: NZBWF_28_seven_(Clariom_S_Mouse)


title: NZBWF_8_two_(Clariom_S_Mouse)

description: Gene expression data from 8-week-old NZBWF1

source_name: 8-week-old NZBWF1 kidney


title: NZBWF_8_three_(Clariom_S_Mouse)


title: NZBWF_8_four_(Clariom_S_Mouse)


title: NZBWF_8_one_(Clariom_S_Mouse)


title: R. porcellionis strain 15C, 2 dpi (mid phase), rep3


title: NZBWF_28_eight_(Clariom_S_Mouse)


title: R. porcellionis strain 15C, 2 dpi (mid phase), rep1


title: NZBWF_28_six_(Clariom_S_Mouse)


title: R. porcellionis strain 15C, extracellular phase, rep2


title: R. porcellionis strain 15C, extracellular phase, rep3


title: B728a_N1

city: Tucson

first: David

last: Baltrus

state: AZ

address: 1140 E. South Campus Drive

institute: University of Arizona

data_processing:
Alignment: HISAT2 v2.2.1 (plant) or bowtie2 v (bacterial)
Quantification: StringTie v2.2.0 (plant) or featureCounts (bacterial)
Expression Analysis: DESeq2
Assembly: N. benthamianaGenome v1.0.1 with NbD transcriptome, P. syringae B728a (Genbank: CP000075.1), and P. amygdali pv. tabaci (Genbank: CP042804.1)
Supplementary files format and content: Output from StringTie (plant) or featureCounts (bacterial)

organism: Pseudomonas syringae pv. syringae

source_name: bacterial cells (not pelleted)

extract_protocol:
Frozen samples were homogenized in 2mL homogenization tubes with high-density zirconium beads (Glen Mills) using a Geno/Grinder (SPEX SamplePrep) for 1 min at 1,750 Hz with a LN2 chilled sample holder. RNA was extracted using the DirectZol RNA miniprep kit (Zymo Research). RNA samples were DNAse treated with the Turbo DNAse (Thermo-Fisher) followed by cleanup with the Monarch RNA Cleanup Kit (NEB). Reagents were used according to the manufacturer’s recommendations.
Plant mRNA sequencing libraries were prepared with the Illumina-compatible KAPA Stranded mRNA-seq Kit (Roche) by the Georgia Genomics and Bioinformatics Core (GGBC). The Psy RNA samples were rRNA depleted using the RiboMinus Bacterial kit (Thermo Fisher) and libraries were prepared with the Illumina-compatible KAPA Stranded RNA-seq Kit (Roche) by the GGBC. The Pta RNA samples were rRNA depleted using both RiboZero Plant and RiboZero Bacteria (Illumina) in combination and RNA sequencing libraries were prepared in-house using the TruSeq Stranded Total RNA kit (Illumina). Library prep kits were used according to the manufacturer’s recommendations.


title: B728a_P1

source_name: bacterial cells (pelleted)


title: B728a_P3


title: B728a5_1

data_processing:
Alignment: HISAT2 v2.2.1 (plant) or bowtie2 v (bacterial)
Quantification: StringTie v2.2.0 (plant) or featureCounts (bacterial)
Expression Analysis: DESeq2
Assembly: N. benthamiana Genome v1.0.1 with NbD transcriptome, P. syringae B728a (Genbank: CP000075.1), and P. amygdali pv. tabaci (Genbank: NZ_CP042804.1 and NZ_CP042805.1).
Supplementary files format and content: Output from StringTie (plant) or featureCounts (bacterial)

source_name: leaf intercellular wash fluid

extract_protocol:
Frozen samples were homogenized in 2mL homogenization tubes with high-density zirconium beads (Glen Mills) using a Geno/Grinder (SPEX SamplePrep) for 1 min at 1,750 Hz with a LN2 chilled sample holder. RNA was extracted using the DirectZol RNA miniprep kit (Zymo Research). RNA samples were DNAse treated with the Turbo DNAse (Thermo-Fisher) followed by cleanup with the Monarch RNA Cleanup Kit (NEB). Reagents were used according to the manufacturer’s recommendations.
Plant mRNA sequencing libraries were prepared with the Illumina-compatible KAPA Stranded mRNA-seq Kit (Roche) by the Georgia Genomics and Bioinformatics Core (GGBC). The Psy RNA samples were rRNA depleted using the RiboMinus Bacterial kit (Thermo Fisher) and  libraries were prepared with the Illumina-compatible KAPA Stranded RNA-seq Kit (Roche) by the GGBC. The Pta RNA samples were rRNA depleted using both RiboZero Plant and RiboZero Bacteria (Illumina)  in combination and RNA sequencing libraries were prepared in-house using the TruSeq Stranded Total RNA kit (Illumina). Library prep kits were used according to the manufacturer’s recommendations.

tag: tissue/sample type

value: leaf intercellular wash fluid


title: B728a5_2


title: B728a5_3


title: Donor 3, R848 + Dex + MSC 15nm

city: Billerica

first: Andrew

last: Bender

state: MA

address: 45 Middlesex Turnpike

department: Research Unit - Neuroscience & Immunology

institute: EMD Serono

description:
10X Genomics Chromium Next GEM Single Cell 3ʹ Kit v3.1
steroid.synergy.post-bc.v3.RDS
steroid.synergy.post-bc.v3.h5ad

data_processing:
FASTQ files were used as input to the scRNA-seq workflow of the Python-based snakePipes pipeline (v2.6.1). STARsolo methods were used for read mapping and quantification. The Single Cell 3' v3 whitelist (10x Genomics) was provided for barcode identification.
Read counts were used as input to the Seurat 4.0 package in R (version 4.2) to perform quality control and quantitative analyses. Cells were filtered out when the number of unique features (genes) were <200 or >5000. Additionally, cells were also excluded if >5% of their identified genes were mitochondrial.
Cellular identification was performed using the SingleR (version 1.10.0) in R, with PBMC datasets derived from Celldex version 1.6.0 as references. Differential expression and sub-clustering analyses were also performed using Seurat.
Assembly: hg38
Supplementary files format and content: A R readable Seurat class object file (.RDS) with all processed data and metadata annotations, steroid.synergy.post-bc.FINALforpublication.RDS
Supplementary files format and content: A AnnData class object file (.h5ad) with all processed data and metadata annotations,steroid.synergy.post-bc.FINALforpublication.h5ad

source_name: Peripheral blood

extract_protocol:
Blood was obtained from healthy donor leukopaks (New York Blood Center, New York, USA) and peripheral blood mononuclear cells (PBMCs) were isolated using ACCUPSIN Tubes according to the manufacturer’s protocol (Sigma-Aldrich, Missouri, USA). Cell viability was assessed with Trypan Blue Stain (BioRad, California, USA). Cells were cultured in RPMI 1640 Medium (Gibco, ThermoFisher Scientific, Massachusetts, USA) with 10% Fetal Bovine Serum (Corning, Arizona, USA) and 1x Penicillin-Streptomycin (Gibco).
Single-cell RNA sequencing (scRNA-seq) was performed using the 10x Genomics platform (California, USA). Chromium Next GEM Single Cell 3ʹ Kit v3.1 was used for sample processing and library construction. The cells were loaded into the Chromium Controller with a target of 10,000 cells collected per sample and were captured and processed according to the manufacturer’s instructions. Library QC was performed using the Agilent Bioanalzyer and High Sensitivity DNA kit (California, USA) and DNA concentrations were measured using a Qubit fluorometer (ThermoFisher Scientific). Sequencing was performed using the Illumina NextSeq 2000 (California, USA). Libraries were loaded at a concentration of 650 pM and were sequenced using a P3 200 cycle sequencing kit.

treatment_protocol: PBMCs were pre-treated for 15 minutes with Dex (Sigma-Aldrich) starting at 10 µM with a 3-fold serial dilution and 1 µM CMPD2 with a 2-fold serial dilution. Cells were then stimulated with 3–5 µM of the TLR7/8 agonist R848 (InvivoGen, Toulouse, France), 3 µM of a TLR7 agonist (synthesized in-house; same as CL-087), or 1 µM of the TLR8 agonist motolimod (Selleckchem, Texas, USA). Plates were incubated overnight at 37°C and 5% CO2. Cell viability was assessed using CellTiter-Glo Luminescent Cell Viability Assay (Promega, Wisconsin, USA).

value: Peripheral blood

value: PBMC


title: B728a_P2


title: Donor 3, R848 + MSC 5nm


title: Donor 3, R848 + MSC 15nm


title: Donor 3, R848 only


title: R. porcellionis strain 15C, 2 dpi (mid phase), rep2


title: Donor 3, R848 + Dex

value: R848 (3 uM) + Dexamethasone (200 nM)


title: Donor 2, R848 + Dex + MSC 15nm


title: Donor 2, R848 + Dex + MSC 5nm

value: R848 (3 uM) + Dexamethasone (200 nM) + MSC2581131 (5 nM)


title: Donor 2, Dex only

value: Dexamethasone (200 nM)


title: Donor 2, No Treatment


title: Donor 2, R848 only


title: Donor 3, No Treatment


title: Donor 3, Dex only


title: Donor 2, R848 + MSC 5nm


title: Donor 2, R848 + MSC 15nm


title: B728a_N3


title: R. porcellionis strain 15C, extracellular phase, rep1


title: Donor 1, R848 + MSC 5nm


title: Donor 1, R848 only


title: Donor 1, R848 + MSC 15nm


title: Donor 1, Dex only


title: Donor 1, No Treatment


title: Donor 2, R848 + Dex


title: B728a_N2


title: Donor 3, R848 + Dex + MSC 5nm


title: Donor 1, R848 + Dex


title: Lineage 13 in Isolation Rep3

city: Milano

first: Kristina

last: Havas

address: Via Adamello 16

country: Italy

institute: IFOM-ETS AIRC Institute of Molecular Oncology

description:
13CR_A_R3
gene_counts_length_scaled_RPMI24h.tsv

data_processing:
Read alignment and quality check was performed with the nf-core rnaseq pipeline (Ref: Ewels et al., The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. (2020)). In particular, reads were aligned to the GRCh38/hg38 assembly human reference genome using the STAR aligner (v 2.6.1d; Ref: Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15-21 (2013)) and quantified using Salmon (v1.4.0; Ref: Patro, et al. Salmon provides fast and bias-aware quantification of transcript expression. Nature Methods (2017)).
Assembly: GRCh38/hg38 assembly
Supplementary files format and content: gene length normalized counts of sequencing reads

source_name: breast cancer

growth_protocol: For the “”_A samples, cells were culture at 37C, 5% CO2 in RPMI-1640 supplemented with 10% dialyzed Fetal bovine serum and 2mM L-glutamine for approximately 24 hours. For “”_C samples 22CR, 35CR and 45CR were kept for 15 days as part of a 6-member co-culture. The co-culture was maintained in RPMI-1640 supplemented with 10% dialyzed Fetal Bovine Serum and 2mM L-Glutamine at 37C, 5% CO2, and was passaged through a bottel neck every three days for the course of the co-culture.

extract_protocol:
For ""_A samples: culture media was removed and the monolayer washed once with DPBS thenTRIzol was added directly to the cells. The cells were detached into the TRIzol by scrapping. The samples were then frozen at -80C until processing. RNA was phase separated by adding chloroform, followed by centrifugation and collection of the entire aqueous phase. The RNA was then precipitated using Isopropanol and pelleted by centrifugation. The pellet was washed with 75% ethanol/water solution before being dried and resuspended in RNase free water. Following the first extraction, RNA was processed using a RNeasy MiniKit (Qiagen) and optional DNase treatment.  For ""_C samples: After fifteen days in culture the three lineages (22CR, 35CR and 45CR) were isolated from the combination culture via FACS sort using a Moflo Astrios and their RNA extracted using an RNeasy Plus Mini Kit (Qiagen).
A Stranded mRNA Preparation Ligation Kit (Illumina) was used for library preparation, starting from 500ng of RNA. Libraries were quality checked using Qubit HS DNA kit prior to sequencing. Paired-End sequencing, 2x75nt was preformed using a NextSeq550Dx (Illumina). An average of 40 million pair end reads were generated per library.

treatment_protocol: Cells were not exposed to a specific treatment, however cells from the “”_C sample series were subjected to a 6-way co-culture for 15 days prior to separation via FACS and collection of RNA.

value: breast cancer

value: MDA-MB-231 Derived Lineage

tag: genotype

value: wt - distinct lineage

tag: growth condition

value: RPMI 24 hours


title: Lineage 13 in Isolation Rep1

description:
13CR_A_R1
gene_counts_length_scaled_RPMI24h.tsv


title: Lineage Pop in Isolation Rep2

description:
Pop_A_R2
gene_counts_length_scaled_RPMI24h.tsv


title: Lineage 10 in Isolation Rep3

description:
10CR_A_R3
gene_counts_length_scaled_RPMI24h.tsv


title: Lineage 13 in Isolation Rep2

description:
13CR_A_R2
gene_counts_length_scaled_RPMI24h.tsv


title: Donor 1, R848 + Dex + MSC 15nm

tag: treatment


title: Donor 1, R848 + Dex + MSC 5nm


title: Lineage 10 in Isolation Rep2

description:
10CR_A_R2
gene_counts_length_scaled_RPMI24h.tsv


title: Lineage 03 in Isolation Rep3

description:
03CR_A_R3
gene_counts_length_scaled_RPMI24h.tsv


title: Lineage 45 from co-culture Rep1

description:
45CR_C_R1
gene_counts_length_scaled_223545.tsv

value: Co-culture for 15 days before separation by FACS


title: Lineage 45 from co-culture Rep2

description:
45CR_C_R2
gene_counts_length_scaled_223545.tsv


title: Lineage 03 in Isolation Rep1

description:
03CR_A_R1
gene_counts_length_scaled_RPMI24h.tsv


title: Lineage 45 from co-culture Rep3

description:
45CR_C_R3
gene_counts_length_scaled_223545.tsv


title: Lineage Pop in Isolation Rep1

description:
Pop_A_R1
gene_counts_length_scaled_RPMI24h.tsv


title: Lineage Pop in Isolation Rep3

description:
Pop_A_R3
gene_counts_length_scaled_RPMI24h.tsv


title: Lineage 35 from co-culture Rep3

description:
35CR_C_R3
gene_counts_length_scaled_223545.tsv


title: Lineage 45 in Isolation Rep3

description:
45CR_A_R3
gene_counts_length_scaled_223545.tsv


title: Lineage 35 in Isolation Rep3

description:
35CR_A_R3
gene_counts_length_scaled_223545.tsv


title: Lineage 10 in Isolation Rep1

description:
10CR_A_R1
gene_counts_length_scaled_RPMI24h.tsv


title: Lineage 22 from co-culture Rep2

description:
22CR_C_R2
gene_counts_length_scaled_223545.tsv


title: Lineage 35 in Isolation Rep1

description:
35CR_A_R1
gene_counts_length_scaled_223545.tsv


title: Lineage 45 in Isolation Rep1

description:
45CR_A_R1
gene_counts_length_scaled_223545.tsv


title: Lineage 35 in Isolation Rep2

description:
35CR_A_R2
gene_counts_length_scaled_223545.tsv


title: Lineage 22 from co-culture Rep3

description:
22CR_C_R3
gene_counts_length_scaled_223545.tsv


title: Lineage 45 in Isolation Rep2

description:
45CR_A_R2
gene_counts_length_scaled_223545.tsv


title: Lineage 35 from co-culture Rep1

description:
35CR_C_R1
gene_counts_length_scaled_223545.tsv


title: Nb_B728a5_3

organism: Nicotiana benthamiana

source_name: leaf tissue

value: leaf tissue

tag: infection

value: P. syringae pv. syringae B728a (Psy)


title: Lineage 35 from co-culture Rep2

description:
35CR_C_R2
gene_counts_length_scaled_223545.tsv


title: Lineage 03 in Isolation Rep2

description:
03CR_A_R2
gene_counts_length_scaled_RPMI24h.tsv


title: Lineage 22 in Isolation Rep1

description:
22CR_A_R1
gene_counts_length_scaled_223545.tsv


title: Nb_B728a5_1


title: Lineage 22 in Isolation Rep3

description:
22CR_A_R3
gene_counts_length_scaled_223545.tsv


title: Nb_B728a5_2


title: Nb_Ptab5_3

value: P. amygdali pv. tabaci 11528 (Pta)


title: Nb_Ptab5_2


title: Lineage 22 from co-culture Rep1

description:
22CR_C_R1
gene_counts_length_scaled_223545.tsv


title: Nb_Ptab5_1


title: Nb_Ptab0_2


title: Nb_B728a0_1


title: Nb_B728a0_2


title: Nb_Ptab0_3


title: Nb_B728a0_3


title: Nb_Ptab0_1


title: Lineage 22 in Isolation Rep2

description:
22CR_A_R2
gene_counts_length_scaled_223545.tsv


title: Salt_48h3

city: Beltsville

first: Sunchung

last: Park

state: MD

address: 10300 Baltimore ave, Bldg001

department: ARS-NEA

institute: USDA -ARS

data_processing:
Sequenced reads were trimmed for adaptor sequence, and those with N (based underterminded) > 10% or low quality bases (Qscore <=5) >50% were removed.
The filtered reads were mapped to lettuce (v8) whole genome using STAR v2.5.2  with default parameters; the resulting BAM files were used to count reads at the gene-level using featureCounts.
Counts per million (CPM) mapped reads for each of biological samples were calculated using edgeR based on raw counts of STAR.
Assembly: version8; id 37106
Supplementary files format and content: A comma-delimited text files includes CPM values for each of samples

organism: Lactuca sativa

source_name: aerial tissue

growth_protocol: Plants were grown on soil in pots in a growth chamber at 20°C under a 16-h photoperiod with a light intensity of 350-400 μmol m−2 sec−1.

extract_protocol:
Total RNA was isolated for each experimental replicate using Plant RNeasy kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Abiotic stress treatments were conducted on eighteen-day-old plants. For cold treatment, plants were exposed to low temperature (4°C) for 4 h, 24 h, or 7 days. For high salt stress conditions, plants were treated with 250 mM NaCl. For heat stress conditions, plants were exposed to 34 °C. For drought stress conditions, watering was withheld after ensuring all excess water was drained and absorbed by paper towels from the pots. Following exposure to these stress conditions, leaf samples were collected at 0 h, 5 h, 24 h, and 48 h for each treatment, with the 0 h samples serving as controls.

tag: cultivar

value: Salinas

value: 18 days

value: aerial tissue

value: 250mM for 48h


title: Salt_24h1

value: 250mM for 24h


title: Salt_24h3


title: Salt_48h2


title: Salt_5h2

value: 250mM for 5h


title: Salt_24h2


title: Salt_5h3


title: Heat_48h3

value: 34 °C for 48h


title: Salt_5h1


title: Heat_48h1


title: Heat_24h1

value: 34 °C for 24h


title: Heat_24h3


title: Heat_5h3

value: 34 °C for 5h


title: Drought_48h2

value: water with held after excess water removed for 48h


title: Heat_48h2


title: Drought_48h1


title: Drought_24h3

value: water with held after excess water removed for 24h


title: Heat_24h2


title: Drought_24h2


title: Heat_5h1


title: Drought_48h3


title: Drought_5h1

value: water with held after excess water removed for 5h


title: Control_0h2

value: warm-grown


title: Control_0h3


title: Drought_5h2


title: Salt_48h1


title: UC_7d3

value: 4°C for 7 days


title: Control_0h1


title: UC_7d1


title: UC_4h3

value: 4°C for 4h


title: UC_0h1


title: UC_7d2


title: UC_0h3


title: UC_24h3

value: 4°C for 24h


title: Heat_5h2


title: UC_0h2


title: UC_4h2


title: UC_24h2


title: UC_4h1


title: UC_24h1


title: PI284_7d1


title: PI284_24h2


title: PI284_7d2


title: Drought_24h1


title: PI284_24h1


title: PI284_24h3


title: Drought_5h3


title: PI284_4h2


title: PI284_4h3


title: PI284_4h1


title: PI284_0h1


title: last_day_TS543_DMSO_derived_xenograft_GEX

city: New York

first: Peter

middle: A.

last: Sims

address: 3960 Broadway

institute: Columbia University Medical Center

description:
GEX (3' mRNA library): fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains transcripts, matrix file contains the count matrix
PY053-701

data_processing:
GEX: Raw data obtained from NovaSeq was corrected for index swapping according to Griffiths et al. Nat Commun (2018). Raw reads were processed as described in Yuan et al. Genome Med (2018), with a brief description follows.  Raw reads were trimmed of polyA tail and aligned with STAR. We constructed an address comprised of cell-barcode, UMI, and gene identifier for each read with a unique, strand-specific alignment to exonic sequence. Reads with same address were collapsed and sequencing errors in cell-barcodes and UMI were corrected. Cell-barcodes of empty microwell or poor quality cells were removed. Empty cell-barcodes were identified with EmptyDrops algorithm (Lun et al Genome Biol (2019)). Cells are poor quality if they meet any of the following criteria: 1) fractional alignment to the mitochondrial genome per cell-barcode is greater than 10%; 2) a ratio of molecules aligning to whole gene bodies (including introns) to molecules aligning exclusively to exons is greater than 1.96 standard deviations above the mean; 3) average number of reads per molecule or average number of molecules per gene is greater than 2.5 standard deviations above the mean; or 4) more than 40% of UMI bases are T or where the average number of T-bases per UMI is at least 4. .
CellTag: CellTag binary count matrices were generated with the CellTagWorkflow algorithm (https://github.com/morris-lab/CellTagWorkflow), with an additional preprocessing step of removing UMI with less than three raw reads.
Assembly: GRCh38 GRCm38
Supplementary files format and content: GEX counts matrix file is a tab-delimited text file with rows being genes, columns being cell-barcodes and values being counts, with the first two columns being the gene IDs and gene symbols.   CellTag binary matrix file is a tab-delimited text file with rows being cell-barcode_sampleIDs, columns being celltags, and values being 0 or 1 for the absence and presence of the celltag in a given cell-barcode respectively.

organism:
Homo sapiens
Mus musculus

source_name: brain (xenograft)

growth_protocol: TS543 were cultured with NeuroCultTM NS-A Proliferation Kit Human from STEMCELL Technologies.

extract_protocol:
TS543 neurospheres were dissociated to single cells by mechanical pipetting. Mouse brain tumor resections were dissociated to single cells using Adult Brain Dissociation kit on gentleMACSTM Octo Dissociator with Heater (Miltenyi Biotec).
Microwell 3' scRNA-seq were performed as described in Yuan et al. Sci Rep (2016). Briefly, individual single cell was compartmentalized with a barcoded-mRNA-capture-bead (MACOSKO-2011-10, ChemGenes) and lysed in microwell-based platform, mRNA were captured and reverse transcribed on the bead, and cDNA-beads were pooled for PCR amplification and illumina Nextera library construction for each sample.   To sequence the CellTag library separately from the GEX library at greater sequencing depth, CellTag libraries were constructed with custom P5_TSO_hybrid primer and custom P7_TruSeq-Unique-Index_EGFP primer.
3' single-cell RNA-seq

treatment_protocol: TS543 were treated with 75 nM ispinesib or with vehicle DMSO.

value: brain (xenograft)

value: DMSO


title: PI284_7d3

value: 18 days


title: Met_s1

city: Irvine

first: Devon

last: Lawson

address: 839 Health Science Road, Sprague Hall 140

institute: University of California, Irvine

description:
Single-cell RNA-Seq [10X Genomics]
PolyA RNA

data_processing:
Sequencing reads were aligned utilizing 10x Genomics Cell Ranger Count 3.1.0 to the dual indexed mm10/GRCh38 genome provided by Cell Ranger.
All libraries were aggregated using 10x Genomics Cell Ranger Aggr 3.1.0, to normalize the number of mean reads per cells. MULTI-seq reads were processed according to McGinnis et al. 2019 MULTI-seq protocol (https://github.com/chris-mcginnis-ucsf/MULTI-seq).
Cells in dataset were subsequently trimmed and analyzed in Seurat v3, with assigned cell type labels and quality control metrics for each cell passing initial quality filtering included in the metadata sheets.
Genome_build: mm10/GRCh38
Supplementary_files_format_and_content: Space-delimited text files contain a matrix of counts; rows are genes and columns are samples.
Supplementary_files_format_and_content: Metadata sheets include quality control and cell type label information for the cells analyzed in the associated study.

source_name: Metastatic brain with MDA-MB-231BR2

extract_protocol:
At 10 weeks old, MITRG mice were injected intracardially with 500,000 mCherry labeled 231BR cells as previously described. 25 days after intracardiac injection and following perfusion with ice cold PBS containing 5μg/ml actinomycin D (act D), whole metastatic brains were briefly imaged on a dissection microscope (Leica Biosystems, DMC 2900) for mCherry and GFP intensity. Half brains were then dissected, fixing the left hemisphere in 4% PFA for histology and the right hemisphere was prepped for dissociation as described in Hasselmann and Coburn et al. (2019) with modifications. The cerebellum was removed and the whole right hemisphere was stored briefly in RPMI 1640 containing 5μg/mL act D, 10μM triptolide, and 27.1ug/mL anisomycin. Tissue dissociation was then performed using the Tumor Dissociation kit, human (Miltenyi Biotec) and the gentleMACS OctoDissociator with heaters (Miltenyi Biotec) according to manufacturer guidelines with modifications. Briefly, tissue was cut into ~1mm pieces and placed into the C-tubes with the kit’s enzymes, 5μg/mL act D, 10μM triptolide, and 27.1ug/mL anisomycin and samples were dissociated using the preprogrammed soft tumor protocol. Following enzymatic digestion, samples were strained through a 70μm filter and pelleted by centrifugation. Myelin and debris were removed by resuspending the pellet in 8mL 23% Percoll, overlaid with 2mL of 1X DPBS, spinning at 400xg for 25 minutes at 4°C, with acceleration and brake set to 0, and discarding the myelin band and supernatant.
For barcoding of cells from each individual mouse the MULTI-seq lipid-tagged indices for sample multiplexing for scRNAseq protocol was followed (McGinnis et al., 2019). Lipid anchor and co-anchor reagents were a generous gift from Zev Gartner, and barcode index oligos were purchased from Integrated DNA Technologies, Inc. Cells were resuspended and washed with 15 mL cold DPBS and pelleted by centrifugation (10 minutes, 400xg). The supernatant was discarded, and cells were resuspended in 180μL of DPBS. 20μL of 20μM Anchor:Barcode solution was added to a final concentration of 2μM, and incubated on ice for 5 minutes. Next 20μL of 20μM Co-Anchor solution was added, gently mixed and incubated for 5 minutes. After incubation 1mL 1% BSA in DPBS was added and cells were pelleted by centrifugation (5 minutes, 400xg). Finally, the supernatant was removed and washed a second time with 1mL 1% BSA in PBS and pelleted by centrifugation (5 minutes, 400xg). Next, mouse cell removal was performed by resuspending cell pellets in 160μL FACS buffer (0.5% BSA in 1X DPBS) + 40μL Mouse cell removal beads (Miltenyi Biotec) and incubated at 4°C for 15 minutes. Mouse and human cells were then separated using LS columns and the MidiMACs separator (Miltenyi Biotec) and the human cells were collected in the flow through. Human cells were pelleted via centrifugation (10 minutes, 400xg) and control samples and metastatic samples were then pooled separately. Cells were resuspended to ~1,000 cells per microliter in FACS buffer, according to counts performed on a hemocytometer.
MULTI-seq tagged isolated human cells were pelleted via centrifugation for 10 minutes at 400xg and resuspended to approximately 1,000 cells per microliter in FACS buffer. Replicate cell pools were counted by hemocytometer and pooled for further single cell sequencing. Final cell suspensions were counted on the Countess II automated cell counter to determine actual concentration for droplet generation. Cells were loaded onto the 10x Genomics Chromium Single Cell Gene Expression 3’ v3 Chemistry kits for GEMs generation. Following the Chromium Single Cell 3′ Reagents Kits version 3 user guide (CG000183 Rev C), cells were loaded to achieve approximately 10,000 cells for capture. MULTI-seq barcode libraries were prepared according to McGinnis et al. 2019 MULTI-seq protocol. Libraries were sequenced on the Illumina NovaSeq 6000 platform to achieve an average read depth of 50,000 mean reads per cell for 3’ gene expression libraries. MULTI-seq barcode libraries were sequenced to achieve at least 5,000 reads per cell.

tag: mouse host strain common name

value: MITRG

tag: mouse host strain genotype

value: C:129S2- Rag2tm1.1Flv Csf1tm1(CSF1)Flv CSF2/IL3tm1.1(CSF2,IL3)Flv Thpotm1.1(TPO)Flv Il2rgtm1.1Flv/J

tag: mouse diagnosis

value: Breast cancer brain metastasis

value: Brain

value: Myeloid cells and 231BR cells

tag: pooled mouse barcodes

tag: batch

value: group 2


title: Control

source_name: Control brain

value: Control

value: Myeloid cells

value: group 1


title: Met_s2


title: last_day_TS543_ispinesib_derived_xenograft_GEX

description:
GEX (3' mRNA library): fastq R1 file contains cell barcodes and UMIs, fastq R2 file contains transcripts, matrix file contains the count matrix
PY053-702

tag: cell line

value: ispinesib


title: PI284_0h2

tag: age

value: aerial tissue

value: warm-grown


title: Liver - CHOW_VEH - Rep1

city: Toulouse

first: Hervé

last: Guillou

address: 180 Chemin de Tournefeuille

department: ToxAlim

country: France

institute: INRAE

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 10x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturer's instructions (Agilent Technologies, Santa Clara, CA). On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE v2 microarray (8X60K, Design 074809  enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min) and Wash buffer 2 (Agilent Technologies, 37°C, 1 min).

scan_protocol: Slides were scanned immediately after washing on a Agilent G2505C Microarray Scanner with Agilent Scan Control A.8.5.1 software

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent Technologies, Santa Clara, CA) using default parameters (protocol GE1_1010_Sep10 and Grid: 074809_D_F_20150624). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);} We selected the spots with a minimal weight of 1 for 20 out of 24 microarrays or with a minimal weight of 4 per group from at least one experimental group. At this step, 39375 spots out of 62976 were selected. Data were then stored in an ExpressionSet object and normalized by the qsmooth method using the qsmooth function from the qsmooth R library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 36711 rows each corresponding to a unique ProbeName (provided as data Matrix).

source_name: Liver

label_protocol: For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng of total RNA using the One-Color Quick Amp Labeling kit (Agilent Technologies, Santa Clara, CA) according to the manufacturer's instructions, followed by Agencourt RNAClean XP (Agencourt Bioscience Corporation, Beverly, Massachusetts) purification. Dye incorporation and cRNA yield were checked using Dropsense™ 96 UV/VIS droplet reader (Trinean, Belgium).

growth_protocol: C57BL/6J male mice (6 weeks old) were purchased from Charles Rivers Laboratories (L’Arbresle, France). Mice were allowed two weeks of acclimatization with free access and ad libitum water and food, with a standard rodent diet (safe 04 U8220G10R) from SAFE (Augy, France). Then, the mice were randomly divided into four groups of 12 mice each. Two groups (n=24, 4 cages of 6 mice) were fed a chow diet with 10 kcal% fat (CHOW, D12450J, Research Diets) and the other two groups (n=24, 4 cages of 6  130 mice) were fed a high-fat diet with 60 kcal% fat (HFD, D12492, Research Diets) for 15 weeks.

extract_protocol: Total cellular RNA was extracted with Trizol reagent (Invitrogen). Transcriptome profiles were performed with the Agilent Whole Mouse Genome microarray (4×44K), according to manufacturer instructions.

treatment_protocol: After 12 weeks of feeding, half of the CHOW (n=12, 2 cages of 6 mice) and HFD (n=12, 2 cages of 6 mice) groups were exposed to FB1 (10 mg/kg bw/day) by adjusting every two days the amount of consumed FB1 in the drinking water during 3 weeks in order to maintain a constant level of exposure. Every week, mice were weighed, and water consumption was measured to adjust the quantity of FB1 in the water. Food intake was also monitored.

tag: diet

value: CHOW

value: VEH

tag: Sex

value: Male

value: 25 weeks


title: Liver - HFD_FB1 - Rep5

value: HFD


title: Liver - CHOW_FB1 - Rep4


title: Liver - CHOW_VEH - Rep5


title: Liver - HFD_FB1 - Rep1


title: Liver - HFD_FB1 - Rep3


title: Liver - HFD_VEH - Rep3


title: Liver - CHOW_VEH - Rep2


title: Liver - CHOW_FB1 - Rep2


title: Liver - HFD_VEH - Rep4


title: Liver - CHOW_FB1 - Rep3


title: Liver - HFD_FB1 - Rep4


title: Liver - CHOW_FB1 - Rep6


title: Liver - CHOW_FB1 - Rep5


title: Liver - HFD_FB1 - Rep6


title: Liver - HFD_FB1 - Rep2


title: Liver - HFD_VEH - Rep5


title: Liver - CHOW_FB1 - Rep1


title: Liver - HFD_VEH - Rep6


title: Liver - HFD_VEH - Rep1


title: Liver - CHOW_VEH - Rep6


title: Liver - HFD_VEH - Rep2


title: roxd10

city: Baltimore

first: Ines

last: Godet

address: 1650 Orleans Street, CRB1, room 128

department: Oncology

institute: Johns Hopkins University

data_processing:
The reads were mapped to the latest UCSC transcript set using Bowtie2 version 2.1.0(40) and the gene expression level was estimated using RSEM v1.2.15(39).
TMM (Trimmed Mean of M-values) was used to normalize gene expression. Differentially expressed genes were identified using the edgeR program.
Assembly: hg38

growth_protocol: MDA-MB-231 cells were cultured for 1 or 10 days under 20% or 1% O2. To investigate the effect of reoxygenation, cells cultured for 10 days under 1% O2 were then subjected to 10 days under 20% O2.

extract_protocol:
RNA was extracted using the Direct-zol miniRNA kit (Zymo) and samples with RIN>9 were submitted to Quick Biology for library preparation, RNA sequencing and preliminary analysis.
Total RNA integrity was checked by Agilent Bioanalyzer 2100 and samples with clean rRNA peaks (RIN>6.5) were used for library preparation. RNA-Seq library was prepared according to the KAPA mRNA HyperPrep kit with 200-300 bp insert size using 500 ng of total RNAs as input. Final library quality and quantity were analyzed by Agilent Bioanalyzer 2100 and Life Technologies Qubit 3.0 Fluorometer.

tag: cell type

value: breast cancer


title: 1%d1

treatment_protocol: MDA-MB-231 cells were cultured for 1 or 10 days under 20% or 1% O2. To investigate the effect of reoxygenation, cells cultured for 10 days under 1% O2 were then subjected to 10 days under 20% O2.


title: 20%d10


title: 20%d1


title: 1%d10


title: HeLa cells,mitoEcSTH, 24h dox 2

city: San Diego

first: Xingxiu

last: Pan

address: 6868 Nancy Ridge Dr

institute: Scintillon institute

data_processing:
Illumina HiSeq X reads were trimmed and clipped for quality control inTrimmomatic v.0.36.
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality。
Using the STAR aligner v.2.5.2b., the trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL.
Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2.
Counts were then processed in R using the DESeq2 package
Assembly: GRCh38
Supplementary files format and content: unique hit counts for each sample:sample.counts.txt
Supplementary files format and content: hit count for all the gene

source_name: Uterus; Cervix

growth_protocol: Hela cells were cultured in DMEM+FBS [Dulbecco's Modified Eagle Medium without pyruvate and glucose supplemented with 25 mM glucose, 10% non-dialyzed FBS and 1% penicillin/streptomycin  at 37C in an atmosphere of 5% CO2

extract_protocol:
Twenty-four hours after addition of doxycycline, cells were harvested, and cell pellets were snapfrozen.Samples were submitted to GENEWIZ for NGS RNA sequencing.
RNA libraries for RNA-seq were prepared using polyA selection.

treatment_protocol: Twenty-four hours later, media was exchanged with 10 mL of DMEM+dFBS ± 300 ng/mL Dox.

tag: tissue

value: Uterus; Cervix

value: HeLa

value: epithelial cell

value: mitoEcSTH

value: 24h doxycycline


title: Liver - CHOW_VEH - Rep3


title: HeLa cells,EcSTH, 24h dox 3

value: EcSTH


title: Liver - CHOW_VEH - Rep4


title: C1

city: Hefei

first: mingming

last: wu

address: University of Science and Technology of China, No.96, JinZhai Road Baohe District

data_processing:
Quality control of the sequenced raw FASTQ-files was performed with Trimmomatic
Clean FASTQ-files was mapped to Ensembl human genome reference version GRCh38  using Hisat2.
Read counts of each gene were obtained by htseq-count. DEGs were identified using the DESeq R package functions estimateSizeFactors and nbinomTest. P-value < 0.05 and abs( foldChange )>1.5  was set as the threshold for significantly differential expression
Assembly: GRCh38
Supplementary files format and content: tab- -delimited text files include raw counts  for each Sample

source_name: HSPCs

extract_protocol:
Total RNA was extracted using mirVana™ miRNA ISOlation Kit and 4 μg total RNA was used for following library preparation.
The library generated with the TruSeq Stranded mRNA LTSample Prep Kit according to manufacturer’s instructions.

treatment_protocol: Purifiedhuman haematopoietic stem and progenitor cells derived from umbilical cord blood were treated with 50nM CRH for 16 hours in vitro

value: HSPCs


title: H4

institute: University of Science and Technology of China

value: CRH treat


title: H2


title: C2


title: C3


title: H1


title: H3


title: C4


title: HeLa cells,EcSTH, 24h dox 1


title: HeLa cells,EcSTH, 24h dox 2


title: HeLa cells,LbNOX, 24h dox 3

value: LbNOX


title: HeLa cells,LbNOX, 24h dox 2


title: HeLa cells,Luciferase, 24h dox 3

value: Luciferase


title: HeLa cells,Luciferase, 24h dox 2


title: CD45+ cells, Apoe/Cd36 double-null chow, scRNA-seq

city: Wauwatosa

first: Yiliang

last: Chen

address: 8727 W Watertown Plank

institute: Versiti

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v4.0
Assembly: mm10
Supplementary files format and content: Tab-seperated files and matrix files

source_name: adipose tissue

extract_protocol:
Mice were sacrificed and perfused with 10 ml PBS to remove peripheral blood from the adipose tissues. Then epididymal visceral white adipose tissue (eWAT) was isolated and washed with ice-cold PBS. eWAT was minced into 2-3 mm pieces by scissors and transferred to gentleMACS C-tubes (Miltenyi Biotec) with 1.5 ml enzymatic digestion mixture (Liberase, 0.77 mg/ml; Hyaluronidase, 0.3 mg/ml; Deoxyribonuclease, 0.3 mg/ml; BSA, 1mg/ml; CaCl2, in PBS). Tissues were digested in a gentle MACSTM Octo Dissociator with Heaters (Miltenyi Biotec) at 37°C for 30 min. Suspensions were immediately filtered with a 70 mm cell strainer (Fisher Scientific) and washed once with FACS buffer (5% FBS and 0.1% sodium azide in PBS). Then, CD45+ cells were selected by the EasySep Mouse CD45 Positive Selection Kit (STEMCELL Technologies). The CD45+ cells were then suspended in the FACS buffer, counted, and immediately loaded onto a 10X Genomics Chromium instrument according to the instructions from the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (10X Genomics, Pleasanton, CA, USA). 5,000 live cells per condition were loaded onto each GEM.
library construction was perfrmed according to the instruction from the Chromium Next GEM Single Cell 3' Reagent Kits v3.1

value: adipose tissue

value: Apoe/Cd36 double-null

value: chow diet 10 weeks


title: HeLa cells,mitoEcSTH, 24h dox 3


title: CD45+ cells, Apoe-null chow, scRNA-seq

value: Apoe-null