title: hippocampus, left, fasted, 7

tag: tissue

tag: "experiment duration"

tag: box id

tag: bodyweight start_acclimation

tag: bodyweight start_experiment

tag: food weight_end_experiment

tag: kcal intake


title: hypothalamus, both, fasted, 11

status: Public on Nov 21 2023

type: SRA

city: Copenhagen

first: Lars

middle: Roed

last: Ingerslev

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

country: Denmark

institute: Copenhagen University

library_source: transcriptomic

data_processing:
Basecalling was performed using Illumina's bcl2fastq (v2.20.0).
Sequenced reads were then mapped to the GRCm39 build of the Mus musculus genome using STAR (v2.7.3a) with an overhang length of 50.
The files for the reads, specified in the format of fastq, were processed individually.
The read files were provided as input to STAR, using a "zcat" command to read the compressed files.
Quantification mode was set to GeneCounts in the STAR alignment to obtain count data for each gene.
Following the alignment process, raw counts for each sample were combined using R (v4.1.3) and the tidyverse (v2.0.0) package to create a count matrix.
Assembly: The metadata for sample 142.3_SCL_chow and sample 145.4_SCL_fast were corrected to account for the fact that they were erroneously swapped during handling and sequencing.
Supplementary files format and content: GRCm39
Supplementary files format and content: csv file of raw read counts for each sample

molecule: total RNA

organism: Mus musculus

source_name: hypothalamus

extract_protocol:
RNA extraction was performed using the RNeasy Micro Kit
RNA libraries for RNA-seq were prepared using NEBNext Kits with rRNA depletion and Multiplex Oligos for Illumina

treatment_protocol: In the 24 hour study sample processing was randomized in blocks of 24

value: hypothalamus

tag: hemisphere

value: both

tag: diet

value: fasted

tag: diet kcal

tag: animal id

tag: rna concentration_qbit

tag: "experiment start"

tag: time of_euthanasia

tag: bodyweight before_euthanasia

tag: bodyweight change

tag: bodyweight change_percent

tag: bodyweight change_percent_per_hour

tag: food weight_start_experiment

tag: kcal per_hour

tag: notes

tag: qc

value: ok

tag: flowcell


title: inferior colliculus, right, fasted, 12

source_name: inferior colliculus

tag: tissue

value: inferior colliculus

value: right

tag: "experiment duration"

tag: box id

tag: bodyweight start_acclimation

tag: bodyweight start_experiment

tag: food weight_end_experiment

tag: kcal intake


title: prefrontal cortex, right, chow, 5

source_name: prefrontal cortex

value: prefrontal cortex

tag: hemisphere

tag: diet

value: chow

tag: diet kcal

tag: animal id

tag: rna concentration_qbit

tag: "experiment start"

tag: time of_euthanasia

value: fail PCA


title: hypothalamus, both, fasted, 8

tag: bodyweight before_euthanasia

tag: bodyweight change

tag: bodyweight change_percent

tag: bodyweight change_percent_per_hour

tag: food weight_start_experiment

tag: kcal per_hour

tag: notes


title: prefrontal cortex, left, chow, 3

tag: tissue

value: left

tag: "experiment duration"

tag: box id

tag: bodyweight start_acclimation

tag: bodyweight start_experiment

tag: qc

tag: flowcell


title: hypothalamus, both, fasted, 9

tag: hemisphere

tag: diet

tag: diet kcal

tag: animal id

tag: rna concentration_qbit

tag: food weight_end_experiment

tag: kcal intake


title: inferior colliculus, right, fasted, 10

tag: "experiment start"

tag: time of_euthanasia

tag: bodyweight before_euthanasia

tag: bodyweight change

tag: bodyweight change_percent

tag: bodyweight change_percent_per_hour

tag: food weight_start_experiment


title: prefrontal cortex, right, chow, 6

tag: tissue

tag: "experiment duration"

tag: box id

tag: bodyweight start_acclimation

tag: bodyweight start_experiment

tag: kcal per_hour

tag: notes


title: prefrontal cortex, right, chow, 4

tag: hemisphere

tag: diet

tag: diet kcal

tag: animal id

tag: rna concentration_qbit

tag: qc

tag: flowcell


title: inferior colliculus, right, chow, 5

tag: "experiment start"

tag: time of_euthanasia

tag: bodyweight before_euthanasia

tag: bodyweight change

tag: bodyweight change_percent

tag: food weight_end_experiment

tag: kcal intake


title: inferior colliculus, right, chow, 6

tag: tissue

tag: "experiment duration"

tag: box id

tag: bodyweight start_acclimation

tag: bodyweight start_experiment

tag: bodyweight change_percent_per_hour

tag: food weight_start_experiment


title: inferior colliculus, right, chow, 4

tag: hemisphere

tag: diet

tag: diet kcal

tag: animal id

tag: rna concentration_qbit

tag: kcal per_hour

tag: notes


title: superior colliculus, right, chow, 6

source_name: superior colliculus

value: superior colliculus

tag: "experiment start"

tag: time of_euthanasia

tag: bodyweight before_euthanasia

tag: bodyweight change

tag: bodyweight change_percent

tag: qc

tag: flowcell


title: inferior colliculus, left, chow, 3

tag: tissue

tag: "experiment duration"

tag: box id

tag: bodyweight start_acclimation

tag: bodyweight start_experiment

tag: food weight_end_experiment

tag: kcal intake


title: inferior colliculus, left, chow, 1

tag: hemisphere

tag: diet

tag: diet kcal

tag: animal id

tag: rna concentration_qbit

tag: bodyweight change_percent_per_hour

tag: food weight_start_experiment


title: inferior colliculus, left, chow, 2

tag: "experiment start"

tag: time of_euthanasia

tag: bodyweight before_euthanasia

tag: bodyweight change

tag: bodyweight change_percent

tag: kcal per_hour

tag: notes


title: superior colliculus, left, chow, 2

tag: tissue

tag: "experiment duration"

tag: box id

tag: bodyweight start_acclimation

tag: bodyweight start_experiment

tag: qc

tag: flowcell


title: superior colliculus, left, chow, 1

tag: hemisphere

tag: diet

tag: diet kcal

tag: animal id

tag: rna concentration_qbit

tag: food weight_end_experiment

tag: kcal intake


title: superior colliculus, left, chow, 3

tag: "experiment start"

tag: time of_euthanasia

tag: bodyweight before_euthanasia

tag: bodyweight change

tag: bodyweight change_percent

tag: bodyweight change_percent_per_hour

tag: food weight_start_experiment


title: hippocampus, right, chow, 5

source_name: hippocampus

tag: tissue

value: hippocampus

tag: "experiment duration"

tag: box id

tag: bodyweight start_acclimation

tag: bodyweight start_experiment

tag: kcal per_hour

tag: notes


title: hippocampus, right, chow, 4

tag: hemisphere

tag: diet

tag: diet kcal

tag: animal id

tag: rna concentration_qbit

tag: qc

value: fail STAR

tag: flowcell


title: prefrontal cortex, left, chow, 1

tag: "experiment start"

tag: time of_euthanasia

tag: bodyweight before_euthanasia

tag: bodyweight change

tag: bodyweight change_percent

tag: food weight_end_experiment

tag: kcal intake


title: hippocampus, right, chow, 6

tag: tissue

tag: "experiment duration"

tag: box id

tag: bodyweight start_acclimation

tag: bodyweight start_experiment

tag: bodyweight change_percent_per_hour

tag: food weight_start_experiment


title: hippocampus, left, chow, 2

tag: hemisphere

tag: diet

tag: diet kcal

tag: animal id

tag: rna concentration_qbit

tag: kcal per_hour

tag: notes


title: hypothalamus, both, fasted, 7

tag: "experiment start"

tag: time of_euthanasia

tag: bodyweight before_euthanasia

tag: bodyweight change

tag: bodyweight change_percent

tag: qc

tag: flowcell


title: superior colliculus, right, chow, 4

tag: tissue

tag: "experiment duration"

tag: box id

tag: bodyweight start_acclimation

tag: bodyweight start_experiment

tag: food weight_end_experiment

tag: kcal intake


title: hypothalamus, both, chow, 6

tag: hemisphere

tag: diet

tag: diet kcal

tag: animal id

tag: rna concentration_qbit

tag: bodyweight change_percent_per_hour

tag: food weight_start_experiment


title: hypothalamus, both, chow, 5

tag: "experiment start"

tag: time of_euthanasia

tag: bodyweight before_euthanasia

tag: bodyweight change

tag: bodyweight change_percent

tag: kcal per_hour

tag: notes


title: superior colliculus, right, chow, 5

tag: tissue

tag: "experiment duration"

tag: box id

tag: bodyweight start_acclimation

tag: bodyweight start_experiment

tag: qc

tag: flowcell


title: hypothalamus, both, chow, 2

tag: hemisphere

tag: diet

tag: diet kcal

tag: animal id

tag: rna concentration_qbit

tag: food weight_end_experiment

tag: kcal intake


title: hypothalamus, both, chow, 4

tag: "experiment start"

tag: time of_euthanasia

tag: bodyweight before_euthanasia

tag: bodyweight change

tag: bodyweight change_percent

tag: bodyweight change_percent_per_hour

tag: food weight_start_experiment


title: prefrontal cortex, left, chow, 2

tag: tissue

tag: "experiment duration"

tag: box id

tag: bodyweight start_acclimation

tag: bodyweight start_experiment

tag: kcal per_hour

tag: notes


title: hypothalamus, both, chow, 3

tag: hemisphere

tag: diet

tag: diet kcal

tag: animal id

tag: rna concentration_qbit

tag: qc

tag: flowcell


title: MES, Intact

city: Milano MI

first: Aurora

last: Maurizio

state: Italy

address: Via Olgettina, 60

department: Center for Omics Sciences (COSR)

country: Italy

institute: IRCCS Ospedale San Raffaele

description:
Sample 3
Pdgfrb-TdTomato+ cells from intact nerve

library_source: transcriptomic single cell

data_processing:
Raw sequencing data was demultiplexed with the mkfastq application (CellRanger v6.1.2) (10X).
A reference genome was prepared from mm10, GENCODE Mus musculus basic gene annotation (version M16), and TdTomato exogenous transgene following 10x Genomics' instructions for custom genome builds (cellranger mkref).
The libraries were then mapped to the custom reference genome using CellRanger (v3.0.2) (10× Genomics).
The raw gene expression matrices generated with CellRanger (cellranger count) were analysed with the Seurat R package (v4.0.1)
Assembly: mm10, GRCm38, GENCODE Mus musculus basic gene annotation (version M16)
Supplementary files format and content: Filtered feature-barcode matrices produced by CellRanger (cellranger count) and CellType metadata.

source_name: sciatic nerve

extract_protocol: Nerves were freshly harvested in F12 medium, pooled, finely chopped and incubated in dissociation buffer (Collegenase Type II 50ul/ml, Hyaluyronidase 1:50, DNAse 2.5μg/ml) in DMEM and incubated on rotor at 37C with intermittent mixing for 30 min. Enzymes were inactivated with 5% FBS+ 2mM EDTA in PBS w/o Ca2+, Mg2+. Myelin-removal beads were used for the intact nerve sample. Cell suspension was passed through cell strainer and resuspended in 2% BSA PBS w/o Ca2+, Mg2+ and TdTomato + cells were FACS purified.

value: sciatic nerve

tag: cell type

value: FACS-isolated peripheral nerve MES

tag: reporter

value: Pdgfrb-TdTomato

tag: condition

value: Intact


title: MES, Injury_D7

description:
Sample 2
Pdgfrb-TdTomato+ cells at 7dpi

tag: tissue


title: hypothalamus, both, chow, 1

value: hypothalamus

tag: "experiment start"

tag: time of_euthanasia

tag: "experiment duration"

tag: bodyweight before_euthanasia

tag: bodyweight change

tag: bodyweight change_percent

tag: bodyweight change_percent_per_hour

tag: food weight_start_experiment

tag: food weight_end_experiment

tag: kcal intake


title: hippocampus, left, chow, 3

tag: hemisphere

tag: diet

tag: diet kcal

tag: animal id

tag: rna concentration_qbit

tag: box id

tag: bodyweight start_acclimation

tag: bodyweight start_experiment

tag: kcal per_hour

tag: notes


title: MES, Injury_D21

description:
Sample 1
Pdgfrb-TdTomato+ cells at 21dpi

tag: tissue

tag: cell type

tag: reporter

tag: condition

value: 21 days post injury (dpi)


title: ECs, Injury_D7

description:
Sample 2
7 days after injury of sciatic nerve endothelial cells

data_processing:
Raw sequencing data was demultiplexed with the mkfastq application (CellRanger v6.1.2) (10X).
A reference genome was prepared from mm10, GENCODE Mus musculus basic gene annotation (version M16), and TdTomato exogenous transgene following 10x Genomics' instructions for custom genome builds (cellranger mkref).
The libraries were then mapped to the custom reference genome using CellRanger (v3.0.2) (10× Genomics).
The raw gene expression matrices generated with CellRanger (cellranger count) were analysed with the Seurat R package (v4.0.1).
Assembly: mm10, GRCm38, GENCODE Mus musculus basic gene annotation (version M16)
Supplementary files format and content: Filtered feature-barcode matrices produced by CellRanger (cellranger count) and CellType metadata.

extract_protocol: Sciaric nerves were freshly harvested in F12medium, pooled, finely chopped and incubated in dissociation buffer (Trypsin 0.2mg/ml, Collegenase Type II 50ul/ml, Hyaluyronidase 1:50, PronaseE 1:10, DNAse 2.5μg/ml) in DMEM and incubated on rotor at 37C with intermittent mixing for 30 min. Enzymes were inactivated with 5% FBS+ 2mM EDTA in PBS w/o Ca2+, Mg2+. Cell suspension was passed through cell strainer, stained (CD45-APC BD Pharm #559864) andresuspended in 2% BSA PBS w/o Ca2+, Mg2+. TdTomato+ cells (negative for CD45+ myeloid population) were purified by FACS.

value: FACS-isolated peripheral nerve ECs

value: 7 days post injury (dpi)


title: hippocampus, left, chow, 1

tag: "experiment start"

tag: time of_euthanasia

tag: "experiment duration"

tag: bodyweight before_euthanasia

tag: bodyweight change

tag: bodyweight change_percent

tag: bodyweight change_percent_per_hour

tag: food weight_start_experiment

tag: qc

value: ok

tag: flowcell


title: ECs, Intact

description:
Sample 1
Intact sciatic nerve endothelial cells


title: scRNA-Seq of skin, SBM

city: Nanjing

first: zhang

last: zhang chenyang

address: 163 Xianlin Avenue

country: China

institute: Nanjing University

description:
SBM
The SBM group was treated with Shi-Bi-Man and imiquimod.

data_processing:
Sample demultiplexing, barcode processing, and single cell 3’ gene counting were performed by the CeleScope pipelines (v1.11.0, singleron).
Assembly: mm10 (GRCm38)
Supplementary files format and content: barcodes.tsv, features.tsv, and matrix.mtx (filtered_feature_bc_matrix files).

source_name: Skin

extract_protocol:
The mice project from dorsal skin.
RNA: 3' transcriptome sequencing, cDNA fragmentation, end filling, adding A, connection connector, Index PCR.

tag: strain

tag: age

value: Postnatal 7 weeks

value: Skin

tag: treatment

value: Shi-Bi-Man + imiquimod


title: DDKO-4

city: Shanghai

first: Ma

last: Chunxiao

address: Huashan Road

institute: Ma Chunxiao

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 mapping to reference genome.
Count counting.
Assembly: mm10
Supplementary files format and content: All.counts.exp.txt: Tab-delimited text file contains counts for each sample.

source_name: colon

extract_protocol:
Total RNA was extracted from the samples by Trizol reagent (Invitrogen) separately.
mRNA libraries were prepared for sequencing using standard Illumina protocols.

tag: tissue

value: colon

value: intestinal epithelial cell

tag: genotype

value: AOM/DSS


title: scRNA-Seq of skin, IMQ

description:
IMQ
The IMQ group was treated with imiquimod.

value: Imiquimod


title: DDKO-2

tag: cell type


title: DDKO-3


title: DDKO-1


title: S-2


title: S-1


title: S-4


title: S-3


title: Control Liver cells, Chow Diet 52w, rep E

city: Odense M

first: Kim

last: Ravnskjaer

address: Campusvej 55

department: Biochemistry and Molecular Biology

institute: University of Southern Denmark

description: Cell isolation performed on day 2

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)   To perform the abovementioned steps the features mkfastq and count were run.  Supplementary_files_format_and_content: The raw count matrix is provided as an mtx.gz file along with gene and barcode names as tsv.gz files
Assembly: mm10

source_name: Liver

extract_protocol:
Cells were isolated based on enzymatic digestion followed by fluorescent antibody labeling for partial immunodepletion of ASGR1 and CD31 positive cells. Non-fluorescent singlets, negative for SyTOX live-dead stain were purified by FACS.   10x Genomics Chromium Single Cell 3' V2 solution
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics)

treatment_protocol: Mice were treated as indicated above. Cell isolation was peformed on two separate days.

value: Liver

tag: Sex

value: Male

value: Chow Diet

tag: time

value: 52 weeks

tag: disease state

value: Control

tag: fasting time_prior_to_sacrifice


title: Smad4-KO,Input

library_source: genomic

data_processing:
ChIP-seq reads were aligned to the mm10 reference genome using Bowtie2 (2.4.1).
Sam files were converted to Bam format using Samtools and used for peak calling.
MACS2 (2.2.7.1) was used to call peaks with the sonicated input as a control and an initial threshold p-value of 0.01 as cutoff.
Assembly: GRCm38
Supplementary files format and content: bigwig files were generated using Deeptools (3.5.0).

molecule: genomic DNA

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: chip antibody


title: Control Liver cells, Chow Diet 52w, rep F

description: Cell isolation performed on day 2


title: Control Liver cells, Chow Diet 52w, rep D

description: Cell isolation performed on day 1


title: Control Liver cells, Chow Diet 52w, rep C

description: Cell isolation performed on day 1


title: Control Liver cells, Chow Diet 52w, rep B

description: Cell isolation performed on day 1


title: NASH Liver cells, Western Diet 52w, rep D

description: Cell isolation performed on day 1

value: Western Diet + fructose (42g/L) in drinking water

value: Advanced NASH


title: NASH Liver cells, Western Diet 52w, rep C

description: Cell isolation performed on day 1


title: NASH Liver cells, Western Diet 52w, rep F

description: Cell isolation performed on day 2


title: NASH Liver cells, Western Diet 52w, rep A

description: Cell isolation performed on day 1


title: Hepatic stellate cells, Ctrl, 24h, rep C

data_processing:
STAR was utilized for alignment of reads to the mm10 genome. DESeq216 was used through the Next-Generation Sequencing HOMER pipeline17 with default settings to identify differentially expressed genes
Assembly: mm10

molecule: polyA RNA

source_name: Hepatic Stellate cell

growth_protocol: Primary hepatic stellate cells (HSCs) were isolated from female C57BL/6JBomTac mice essentially as described described in Mederacke et al., 2015 (DOI: https://doi.org/10.1038/nprot.2015.017).

extract_protocol:
Medium was removed and cells lyzed in Trizol directly in plates and snap-frozen. After addition of chloroform and separation of phases, RNA was purified from the aquous phase using RNeasy micro columns.
libraries were constructed using the NEBNext Ultra RNA Library Prep Kit for Illumina (according to manufacturer)

treatment_protocol: Two days post isolation, cells were treated with either 5 uM Forskolin or same volume vehicle (DMSO, 1:1000) added to existing medium. After three hours, medium was changed and cells incubated for additional 21 hours.

value: Hepatic Stellate cell

value: wt

value: DMSO

value: 24 hours


title: NASH Liver cells, Western Diet 52w, rep B

description: Cell isolation performed on day 1


title: Hepatic stellate cells, Ctrl, 24h, rep B


title: Control Liver cells, Chow Diet 52w, rep A

description: Cell isolation performed on day 1


title: DDKO-5


title: Hepatic stellate cells, Ctrl, 24h, rep A


title: Smad4-KO,H3K36me3,ChIP


title: Hepatic stellate cells, Fsk, 24h, rep B

value: Fsk

value: Stimulated


title: Hepatic stellate cells, Fsk, 24h, rep C


title: mCherry+ cells, Control, rep A

data_processing:
Fastq-files were quality trimmed to Q10. Sequences were aligned to the mm10 mouse genome using STAR v2.7.0 [88], producing a single alignment file in .sam format. This was sorted by chromosome coordinate and converted to the binary .bam file format using SAMtools [89] for easier processing. All mitochondrial reads were removed using SAMtools, and all duplicates were removed using the Picard MarkDuplicates tool. All filtered fragments below 100 bp in length were extracted using SAMtools to be used for further analysis, and BedTools  was used to shift the positive strand 4 bases forward and the negative strand 5 bases backwards to counteract the 9 bp displacement caused by Tn5 sequence insertion.
Peaks were called from the shifted files using Model-based Analysis of ChIP-Seq 2 (MACS2)
To visualize fragment distributions across the mouse genome, the Hypergeometric Optimization of Motif EnRichment (HOMER) suite
Assembly: mm10
Supplementary files format and content: NarrowPeak files from MACS2

extract_protocol:
Nuclei were isolated by dounce homogenization and purified by density gradient centrifugation followed by selective sorting based on transgenic expression of mCherry-RPL10A  10x Genomics Chromium Single Cell 3' V2 solution
DNA library preparation was done using Tn5/TDE1 transposase [Illumina, 15028212], and Nextera index primers

tag: diet

value: Chow

value: Healthy


title: Hepatic stellate cells, Fsk, 24h, rep A


title: Hepatic stellate cells, OCA+VIP, 3h, rep C

data_processing:
STAR was utilized for alignment of reads to the mm10 genome. DESeq2 was used through the Next-Generation Sequencing HOMER pipeline with default settings to identify differentially expressed genes
Assembly: mm10

extract_protocol:
Medium was removed and cells lyzed in Trizol directly in plates and snap-frozen. After addition of chloroform and separation of phases, RNA was purified from the aquous phase using RNeasy micro columns.
Libraries were constructed using the NEBNext Ultra RNA Library Prep Kit for Illumina (according to manufacturer)

treatment_protocol: Two days post isolation, cells were treated with either 10 uM obeticholic acid or same volume vehicle (DMSO, 1:1000) added to the medium. After three hours, vasoactive intestinal peptide (500nM) was added to the medium and cells incubated for additional 3 hours.

value: OCA + VIP

value: 3+3 hours


title: Hepatic stellate cells, OCA+VIP, 3h, rep B


title: mCherry+ cells, Control, rep B


title: Hepatic stellate cells, OCA+VIP, 3h, rep A


title: Hepatic stellate cells, DMSO+VIP, 3h, rep C

value: DMSO+ VIP


title: Hepatic stellate cells, DMSO+VIP, 3h, rep B


title: Hepatic stellate cells, Ctrl, 6h, rep C

treatment_protocol: Two days post isolation, cells were treated with either 10 uM obeticholic acid or same volume vehicle (DMSO, 1:1000) added to existing medium. Cells were incubated for six hours before harvest.

value: Female

value: 6 Hours


title: Hepatic stellate cells, DMSO+VIP, 3h, rep A


title: Hepatic stellate cells, Ctrl, 6h, rep B


title: Hepatic stellate cells, OCA, 6h, rep C

value: OCA


title: Hepatic stellate cells, Ctrl, 6h, rep A

value: Control


title: Hepatic stellate cells, OCA, 6h, rep B


title: Hepatic stellate cells, OCA, 6h, rep A


title: Hepatic stellate cells, Ctrl, 3h, rep C

data_processing:
STAR was utilized for alignment of reads to the mm10 genome. DESeq216 was used through the Next-Generation Sequencing HOMER pipeline with default settings to identify differentially expressed genes
Assembly: mm10

treatment_protocol: Two days post isolation, cells were treated with either 5 uM Forskolin or same volume vehicle (DMSO, 1:1000) added to existing medium. Cells were incubated for three hours before harvest.

value: 3 hours


title: Hepatic stellate cells, Ctrl, 3h, rep B


title: Hepatic stellate cells, Fsk, 3h, rep C


title: Hepatic stellate cells, Fsk, 3h, rep A


title: PBLI 1

city: Tianjin

first: QIanying

last: Lu

address: No. 92, Weijin Road, Nankai District

institute: Tianjin University

data_processing:
Basecalls performed using CASAVA version 1.8
High quality reads were aligned to the reference genome/transcriptome with STAR software (v2.5.1b).
CircRNAs were detected and identified with DCC software (v0.4.4)
Genome_build: mm10

source_name: Lung

extract_protocol:
RNA was isolated from the lung of the control group and PBLI group using TRizol reagent (Invitrogen) according to the manufacturer’s instructions.
Total RNA was used for removing the rRNAs with NEBNext® rRNA Depletion Kit (New England Biolabs, Inc., Massachusetts, USA) following the manufacturer's instructions. RNA libraries were constructed by using rRNA-depleted RNAs with TruSeq Stranded Total RNA Library Prep Kit (Illumina, USA) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using the BioAnalyzer 2100 system (Agilent Technologies, USA).
Library sequencing was performed on an illumina Novaseq 6000 instrument with 150bp paired end reads

value: Lung

value: The chest of the mice was exposed to blast waves with an overpressure of 0.5 bar


title: Hepatic stellate cells, Ctrl, 3h, rep A

value: Hepatic Stellate cell

value: wt


title: PBLI 3


title: PBLI 2


title: Hepatic stellate cells, Fsk, 3h, rep B


title: NASH Liver cells, Western Diet 52w, rep E

description: Cell isolation performed on day 2

value: Liver

value: Male

value: Western Diet + fructose (42g/L) in drinking water

value: 52 weeks

value: Advanced NASH


title: Control 3

value: untreated


title: Control 1


title: Control 2


title: Draining brachial lymph node, day 8 p.i. (experiment 1)  scRNA

city: Parkville

first: Jan

last: Schroeder

state: Victoria

address: Peter Doherty Institute Melbourne

department: DMI

country: Australia

institute: University of Melbourne

data_processing:
Sequencing reads were aligned to the reference genome using cellranger (v 7.0.0)
We used the count subcommand to align samples from the EB203 library to the transcriptome and TCR references
We used the multi subcommand to demultiplex hashtags (see EB210_hashtags.csv) and align samples from the EB210 library to the transcriptome.
We used the count command to align TCR sequences for the EB210 library to the VDJ reference.
Assembly: GRCm38-alts-ensembl-5.0.0 (TCR reference)
Assembly: Cellranger 10x genome mm10-2020-A (transcriptome)
Supplementary files format and content: Tar files of VDJ-seq contains CSV files from the cellranger count command
Supplementary files format and content: Tar files of filtered feature barcode matrices from the cellranger count/multi command.

source_name: lymph node

extract_protocol:
To generate single-cell suspensions, tumour and skin samples were digested in collagenase for 90 minutes, manually digested and filtered through a 70-micron mesh. Lymph nodes were pressed through a wire sieve and filtered through a 70-micron mesh.
Library was performed according to the manufacter’s instructions (Chromium Next GEM Single Cell 5' Reagent Kits v2 (Dual Index), 10x Genomics)

value: lymph node

value: CD4+ CD44+ CD62L low

tag: gender

value: female

value: Melanoma inoculation (B16.gD)


title: Draining brachial lymph node, day 8 p.i. (experiment 1) scTCR

data_processing:
Sequencing reads were aligned to the reference genome using cellranger (v 7.0.0)
We used the count subcommand to align samples from the EB203 library to the transcriptome and TCR references
We used the multi subcommand to demultiplex hashtags (see EB210_hashtags.csv) and align samples from the EB210 library to the transcriptome.
We used the count command to align TCR sequences for the EB210 library to the VDJ reference.
Assembly: GRCm38-alts-ensembl-5.0.0 (TCR reference)
Assembly: Cellranger 10x genome mm10-2020-A (transcriptome)
Supplementary files format and content: Tar files of VDJ-seq contains CSV files from the cellranger count command
Supplementary files format and content: Tar files of filtered feature barcode matrices from the cellranger count/multi command.
Library strategy: scTCR-seq


title: Naive brachial lymph node (experiment 1) scTCR

value: CD4+ CD44negative


title: Skin, day 8 p.i., (experiment 1) scTCR

source_name: skin

value: skin


title: Skin, day 8 p.i., (experiment 1)  scRNA


title: wt2

first: Liu

last: Xinnan

address: South Chongqing Road

institute: Shanghai institute of immunology

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.6).
Bowtie2(v2.3.4.3) was applied to align the clean reads to the reference  gene set.
Expression level of gene was calculated by RSEM (v1.3.1).
Differential expression analysis was performed using the DESeq2(v1.4.5)
Assembly: GRCm38
Supplementary files format and content: csv file includes raw counts for each sample

source_name: Tumor

extract_protocol:
Total RNA was extracted using TRIzol reagent (Ambion)
RNA libraries for RNA-seq were prepared using SMARTER mRNA-seq Library Prep Kit following manufacture’s protocols.

value: Tumor

value: Tumor infiltrating Treg cells

value: WT

value: MC38 tumor model


title: ko1

value: Ifitm3 conditonal knockout


title: V7

city: Shijiazhuang

first: Xin

last: Li

address: No.215 West Heping Street

institute: The Second Hospital of Hebei Medical University

data_processing:
Total RNA was isolatTotal RNA was isolated using TRIzol reagent from samples. RNA-sequencing was performed based on DNBseq platform (PE100 strategy).ed using TRIzol reagent from samples.
To obtain the clean reads from RNA-sequencing results, sequence with low quality including adapter sequences, sequences with quality score < 20, sequences with N base rate of raw reads > 10% and sequence less than 25bp were removed.
HISAT2 (version 2.1.0) was used to align the clean reads with the human reference genome GRCh38.
DEseq2 was applied to obtain DEmRNAs and DElncRNAs with p <0.05 and |log2foldchange| >1.
Assembly: hg18
Supplementary files format and content: explevel_analysis_lnc_salmon_fpkm.csv
Supplementary files format and content: explevel_analysis_mRNA_salmon_fpkm.csv

organism: Homo sapiens

source_name: whole blood

extract_protocol:
Five patients with bacterial meningitis and five patients with viral meningitis were included in the study. Control group comprised five children. Peripheral whole blood drawn from each individual was used for RNA extraction.
RNA sequencing and identification of DEmRNAs and DElncRNAs Total RNA was isolated using TRIzol reagent from samples. RNA-sequencing was performed based on DNBseq platform (PE100 strategy).

value: whole blood

value: viral meningitis

value: male


title: V5


title: ko2


title: V4


title: V1


title: wt1


title: N5

value: control


title: N4


title: N3


title: V8


title: N2


title: N1


title: B5

value: bacterial meningitis

value: 53 days


title: B4

value: 99 days


title: B1


title: B3


title: FB98

city: Guangzhou

first: Wenhao

last: Ouyang

state: GuangDong

address: Department of Medical Oncology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University

data_processing:
Total RNA was extracted from FFPE samples using the QIAGEN FFPE RNeasy kit (QIAGEN GmbH, Hilden, Germany)
RNA was analyzed using an Agilent RNA 6000 Nano Kit (Aglient Technologies, Santa Clara, CA, USA), and RNA integrity numbers were determined to evaluate RNA integration using an Agilent Bioanalyzer 2100 (Aglient Technologies, Santa Clara, CA, USA)
An input of 500 ng of total RNA was amplified using an Ovation FFPE WTA System (NuGEN, San Carlos, CA, USA)
NEBNext® Ultra™ II DNA Library Prep Kit (Illumina) was used for fragmentation and labelling
The quality and quantity of amplified libraries were evaluated using Qubit (Invitrogen, Carlsbad, CA, USA) and Agilent Bioanalyzer 2100 (Aglient Technologies, Santa Clara, CA, USA).
All libraries were sequenced using an DNBSEQ-T7RS (MGI) with 100 bp paired end reads
Base call files were converted to fastq format using cal2Fastq. Raw data were normalized using the fastp (version 0.20.1) for data processing
Supplementary_files_format_and_content: tab-delimited text files include read counts values for each Sample

source_name: Primary breast cancer

extract_protocol: RNA libraries were prepared for sequencing using standard DNBSEQ-T7RS(MGI) protocols

tag: status

value: non-relapse


title: Naive brachial lymph node (experiment 1)  scRNA

value: lymph node

value: female


title: FB96

institute: Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University


title: FB89


title: FB84


title: FB76

value: relapse


title: FB47


title: FB331


title: FB325


title: FB327


title: FB303


title: FB302


title: FB320


title: FB319


title: FB296


title: FB297


title: FB99


title: FB245


title: FB295


title: FB290


title: FB257


title: B2


title: FB79


title: FB234


title: FB235


title: FB233


title: FB244


title: FB88


title: FB230


title: FB226


title: FB222


title: FB156


title: FB139


title: FB138


title: FB260


title: FB128


title: FB124


title: FB247


title: FB121


title: FB112


title: FB119


title: FB107


title: FB241


title: FB101


title: FB109


title: FB104


title: BR401


title: FB100


title: BR385


title: BR364


title: BR366


title: BR384


title: BR389


title: BR354


title: BR343


title: BR347


title: FB219


title: FB220


title: BR335


title: BR333


title: BR5


title: BR328


title: FB108


title: BR316


title: BR313


title: BR327


title: BR329


title: BR332


title: BR305


title: BR309


title: BR314


title: BR303


title: BR304


title: BR299


title: BR298


title: BR271


title: BR272


title: BR290


title: BR284


title: BR263


title: BR270


title: BR341


title: BR257


title: BR282


title: BR254


title: BR252


title: BR247


title: BR246


title: BR219


title: BR225


title: BR223


title: BR231


title: BR220


title: BR399


title: BR193


title: BR218


title: BR198


title: BR285


title: CAL-27SPHERE, CON, rep2

city: Wuhan

first: Yuantong

last: Liu

state: Hubei

address: Luoyu road

institute: Wuhan University

data_processing:
BGISEQ-500 sequencer.
Clean reads were mapped to the reference genome using HISAT/Bowtie2 tools.
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: xls file includes TPM values for each sample

extract_protocol:
Total RNA was extracted from the cells using Trizol (Invitrogen, Carlsbad, CA, USA) according to manual instruction.
The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29(Thermo Fisher Scientific, MA, USA) to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on BGISEQ500 platform (BGI-Shenzhen, China)

tag: cell line

value: Normal control


title: CAL-27, CON, rep3


title: CAL-27SPHERE, CON, rep1


title: CAL-27, CON, rep2


title: CAL-27, ESCU, rep2

value: Cal27 treated with elesclomol-Cu for 24h.


title: CAL-27SPHERE, CON, rep3


title: CAL-27SPHERE, LF3, rep3

value: Cal-27 sphere cells treated with elesclomol-Cu for 24h.


title: CAL-27, ESCU, rep3


title: CAL-27SPHERE, LF3, rep1


title: CAL-27SPHERE, LF3, rep2


title: CAL-27, ESCU, rep1


title: TNNT1 KO-Huh7.5.1 cells_1

first: Haoran

last: Qu

address: Wuhan University School of Basic Medical Sciences, Donghu Road 185#, Wuhan 430071, Hubei Province, P. R. China

data_processing:
The sequencing data was filtered with SOAPnuke by (1)  Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) 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 subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com).
RNA identification: Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Gene Quantification Differential Expression Analysis: Expression level of gene was calculated by RSEM (v1.3.1) . The heatmap was drawn by pheatmap (v1.0.8)  according to the gene expression difference in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5) (or DEGseq or PoissonDis)with Q value ≤ 0.05 (or FDR ≤ 0.001).
Gene Annotation: To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expression gene was performed by Phyper (https://en.wikipedia.org/wiki/Hypergeometric_distribution) based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05).
Assembly: hg19
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: Huh7.5.1 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidifed atmosphere wit 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing ibraries
Single-stranded circle DNA molecules are replicated via rolling cycle amplification, and a DNA nanoball (DNB) which contain multiple copies of DNA is generated. Sufficient quality DNBs are then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS).

treatment_protocol: TNNT1 knock out by crispr-cas9.

value: Liver

value: HCC cell line

value: TNNT1 KO


title: Huh7.5.1 cells_2

value: WT


title: TNNT1 KO-Huh7.5.1 cells_3


title: TNNT1 KO-Huh7.5.1 cells_2


title: RNA_batch_2_GIMEN_ASCL1_Pos_4TF_Pos_Rep2

city: Singapore

first: Tze King

last: Tan

address: 14 Medical Drive

department: Cancer Science Institute

country: Singapore

institute: National University of Singapore

data_processing:
RNA-seq datasets of ASCL1 overexpressed GIMEN cells were aligned to the hg19 human genome using STAR 2.5.2a with the parameter outFilterMultimapNmax set to 1.
featureCount was used for the mapped reads in .bam files to generate count tables based on the Ensembl gene annotation
Bioconductor package DESeq2 v1.12.4 was used to analyze differential gene expression using 2 control vs 2 ASCL1 overexpression samples (2 overexpression vs control with 2 replicates).
Assembly: hg19

source_name: GI-MEN cells

growth_protocol: All cells cells were cultured in RPMI-1640 medium supplemented with 10% tetracycline-free FBS and Pen/Strep.

extract_protocol:
Total RNA was harvested using the miRNeasy Mini Kit (Qiagen).
Strand-specific library construction and sequencing of paired-end, 100-bp-long reads by the BGISeq500 were performed at the BGI Biotech Solutions (Hong Kong) Co Ltd (Hong Kong).

treatment_protocol: GI-MEN cells were infected with ASCL1-expressing lentiviruses or TFs expressing retroviruses. At 48 hours post infection, drug selection or fluorescent sorting was carried out for 36 hours, after which cells were treated with doxycycline and total RNA were harvested.

value: GI-MEN cells

value: Neuroblastoma

value: 4TF+ASCL1 overexpression


title: Huh7.5.1 cells_1


title: CAL-27, CON, rep1


title: RNA_batch_2_GIMEN_ASCL1_Pos_Rep2

value: ASCL1 overexpression


title: RNA_batch_2_GIMEN_ASCL1_Neg_Rep1

value: control


title: RNA_batch_2_GIMEN_ASCL1_Neg_Rep2


title: RNA_batch_1_GIMEN_ASCL1_Pos_Rep2

growth_protocol: GI-MEN DOX-ASCL1/ GI-MEN DOX-ASCL1 cells cells were cultured in RPMI-1640 medium supplemented with 10% tetracycline-free FBS and Pen/Strep.

treatment_protocol: GI-MEN cells were infected with ASCL1-expressing lentiviruses. At 48 hours post infection, drug selection was carried out for 36 hours, after which cells were treated with doxycycline and total RNA were harvested.

tag: timepoint


title: RNA_batch_2_GIMEN_ASCL1_Pos_Rep1


title: RNA_batch_1_GIMEN_ASCL1_Pos_Rep1


title: RNA_batch_1_GIMEN_ASCL1_Neg_Rep2


title: RNA_batch_1_GIMEN_ASCL1_Neg_Rep1


title: Huh7.5.1 cells_3


title: snRNA-seq, D. melanogaster central brain, biol rep2

city: Suwon

first: Daehan

last: Lee

state: Gyeonggi

address: 2066 Seobu-ro

country: South Korea

institute: Sungkyunkwan University

description: 10x Genomics

data_processing:
Raw snRNA-seq data was first processed through Cell Ranger (v6.0.1, default parameters except --include-introns)
Assembly: D. melanogaster reference genome and transcriptome from FlyBase (release 6.34)
Supplementary files format and content: TSV files and matrix files

organism: Drosophila melanogaster

source_name: central brain

growth_protocol: Standard fly growth medium

extract_protocol:
Newly-eclosed 30-50 male and female adult flies were collected and placed together for mating, followed by sorting by sex on day 5. The central brains of 20 mated female flies were dissected and collected in 100 μl Schneider’s medium, flash-frozen in liquid nitrogen, and stored at -80ºC for nuclear extraction. Sample homogenization, single-nucleus suspension, and nuclear sorting were performed using the standard protocol described in the Fly Cell Atlas (Li et al. 2022)
To obtain sequencing data from 10,000 nuclei, 15-20,000 nuclei were collected and loaded onto the Chromium Next GEM Chip (10x Genomics). Sequencing libraries were prepared with the Chromium Single Cell 3ʹ reagent kit v3.1 dual index, strictly following the manufacturer’s recommendations.

value: central brain

value: Canton S


title: snRNA-seq, D. melanogaster central brain, biol rep1

description: 10x Genomics


title: snRNA-seq, D. melanogaster central brain, biol rep4

description: 10x Genomics


title: snRNA-seq, D. melanogaster central brain, biol rep6

description: 10x Genomics


title: YPS606 TF yap1 mutant NaCl stress Rep1

city: Fayetteville

first: Jeffrey

middle: A.

last: Lewis

state: AR

address: 850 W. Dickson St.

department: Biological Sciences

country: USA

institute: University of Arkansas

data_processing:
Reads were trimmed of adapter and low quality reads using Trimmomatic with the following paramaters: ILLUMINACLIP:Kapa_indices.fa:2:30:10 LEADING:3 TRAILING:3 MAXINFO:40:0.4 MINLEN:40
Trimmed reads were mapped to the S288c genome (Ensembl sacCer3; Saccharomyces_cerevisiae.R64-1-1.84.gtf) using Bowtie2 (version 2.3.4.1), variants were called using bcftools (version 1.9), and then variant calls were used to generate new reference genomes using GATK3 (Version 3.8-1-0).
Trimmed reads were were then mapped to their new corresponding reference genomes using STAR (version 2.6.1).
Expected counts for each transcript were generated using RSEM (version 1.3.1).
Differential expression was performed in EdgeR using TMM normalization on all genes with at least one count per million (CPM) in at least one strain-condition, and the quasi-likelihood (QL) model, using sample type (e.g., S288c unstressed, S288c ethanol stressed, S288c NaCl stressed…) and biological replicate as factors. Benjamini-Hochberg was applied for FDR correction.
Assembly: sacCer3
Supplementary files format and content: Excel files containing edgeR ouput (logFC and BH-adjusted p-values for each gene)

organism: Saccharomyces cerevisiae

growth_protocol: Cells were grown at 30°C in 80 ml YPD (2% peptone, 2% dextrose, 1% yeast extract) for >8 generations to an OD600 of 0.3-0.6.

extract_protocol:
RNA was extracted by the hot phenol method from Gasch, Methods in Enzymology, 2002, followed by DNase I (Ambion) digestion followed by cleanup with a Quick-RNA MiniPrep Plus Kit (Zymo Research) including optional on-column DNase digestion.
RNA-seq libraries were prepared using the KAPA mRNA HyperPrep Kit (Roche) and KAPA Single-Indexed Adapter Set A + B, according to manufacturer specifications. 500 ng of total RNA was used as starting material for each sample, polyA-enrichment was performed, mRNA was fragmented to an average size of 200–300 nucleotides, and the cDNA libraries were amplified for 9 PCR cycles.

treatment_protocol: Fifteen ml of an unstressed control sample was collected, and then the culture was split, with 20 ml being added to 20 ml media containing 10% EtOH (5% final concentration) or 0.8M NaCl (0.4 M final concentration). Cells were incubated in EtOH for 30 minutes and NaCl for 45 minutes.

value: yap1 deletion

value: 0.4 M NaCL for 45 min


title: YPS606 TF yap1 mutant NaCl stress Rep3


title: YPS606 TF yap1 mutant ethanol stress Rep4

value: 5% (v/v) ethanol for 30 min


title: YPS606 TF yap1 mutant ethanol stress Rep2


title: YPS606 TF yap1 mutant unstressed Rep2

value: unstressed control


title: YPS606 TF yap1 mutant NaCl stress Rep4


title: YPS606 TF yap1 mutant NaCl stress Rep2


title: YPS606 TF yap1 mutant ethanol stress Rep3


title: snRNA-seq, D. melanogaster central brain, biol rep5

description: 10x Genomics


title: YPS606 TF yap1 mutant unstressed Rep3


title: YPS606 TF yap1 mutant unstressed Rep4


title: snRNA-seq, D. melanogaster central brain, biol rep3

description: 10x Genomics


title: RNA_batch_2_GIMEN_ASCL1_Pos_4TF_Pos_Rep1


title: RNA_batch_2_GIMEN_ASCL1_Neg_4TF_Pos_Rep1

value: 4TF overexpression


title: RNA_batch_2_GIMEN_ASCL1_Neg_4TF_Pos_Rep2


title: YPS606 TF yap1 mutant unstressed Rep1


title: YPS606 TF yap1 mutant ethanol stress Rep1


title: YPS606 TF WT NaCl stress Rep3

value: wild type


title: YPS606 TF WT NaCl stress Rep4


title: YPS606 TF WT NaCl stress Rep1


title: YPS606 TF WT unstressed Rep4


title: YPS606 TF WT NaCl stress Rep2


title: Segestria senoculata adult 1

city: Berlin

first: Lauren

last: Sumner-Rooney

address: Museum für Naturkunde, FB1, Invalidenstrasse 43

country: Germany

institute: Museum für Naturkunde

data_processing:
NovaSeq platform (100 bp PE, Edinburgh Genomics)
Erroneous k-mers were removed using rCorrector v.1.0.4 (default settings)
uncorrectable read pairs were were discarded using a custom Python script (available at https://github.com/harvardinformatics/TranscriptomeAssemblyTools/blob/master/FilterUncorrectabledPEfastq.py courtesy of Adam Freeman
Adapter sequences were identified and removed, and low-quality ends trimmed using TrimGalore! v.0.6.5 (phred score cutoff =5).
Assembly: De novo transcriptome assembly with Trinity v.2.11.0 (default settings)
Supplementary files format and content: tab-delimited text file: kallisto.gene.counts.matrix
Supplementary files format and content: tab-delimited text file: kallisto.gene.TPM.not_cross_norm
Supplementary files format and content: Trinity assembly, Segestria_sp_adult_Trinity.fasta

organism: Segestria senoculata

source_name: Whole adult female organism

growth_protocol: Wild collected animal

extract_protocol:
QIAzol lysis reagent following the standard protocol (Qiagen)
TruSeq RNA kit (including polyA selection)

treatment_protocol: No treatment

value: Whole adult female organism

value: Wild collected


title: YPS606 TF WT unstressed Rep1


title: YPS606 TF WT unstressed Rep2


title: YPS606 TF WT ethanol stress Rep1


title: YPS606 TF skn7 mutant NaCl stress Rep4

value: skn7 deletion


title: YPS606 TF skn7 mutant NaCl stress Rep2


title: YPS606 TF skn7 mutant unstressed Rep2


title: YPS606 TF WT ethanol stress Rep3


title: YPS606 TF WT ethanol stress Rep2


title: YPS606 TF skn7 mutant unstressed Rep4


title: YPS606 TF skn7 mutant NaCl stress Rep1


title: YPS606 TF skn7 mutant unstressed Rep3


title: YPS606 TF skn7 mutant ethanol stress Rep2


title: YPS606 TF skn7 mutant ethanol stress Rep3


title: YPS606 TF skn7 mutant unstressed Rep1


title: YPS606 TF WT unstressed Rep3


title: YPS606 TF msn2/4 mutant NaCl stress Rep1

value: msn2/4 deletion


title: YPS606 TF msn2/4 mutant NaCl stress Rep4


title: YPS606 TF msn2/4 mutant NaCl stress Rep3


title: YPS606 TF skn7 mutant ethanol stress Rep1


title: YPS606 TF msn2/4 mutant NaCl stress Rep2


title: YPS606 TF msn2/4 mutant unstressed Rep4


title: YPS606 TF msn2/4 mutant unstressed Rep2


title: YPS606 TF msn2/4 mutant unstressed Rep1


title: YPS606 TF msn2/4 mutant ethanol stress Rep4


title: YPS606 TF WT ethanol stress Rep4


title: YPS606 TF msn2/4 mutant ethanol stress Rep3


title: YPS606 TF msn2/4 mutant unstressed Rep3


title: YPS606 TF msn2/4 mutant ethanol stress Rep2


title: YPS606 TF msn2/4 mutant ethanol stress Rep1


title: YPS606 TF skn7 mutant ethanol stress Rep4


title: YPS606 NaCl stress Rep3


title: YPS606 TF skn7 mutant NaCl stress Rep3


title: YPS606 NaCl stress Rep1


title: YPS606 unstressed Rep3


title: YPS606 ethanol stress Rep1


title: YPS163 NaCl stress Rep2


title: YPS606 ethanol stress Rep3


title: YPS606 unstressed Rep2


title: YPS606 unstressed Rep1


title: YPS163 ethanol stress Rep2


title: YPS163 unstressed Rep1


title: YPS606 ethanol stress Rep2


title: YPS163 unstressed Rep3


title: YPS163 unstressed Rep2


title: YJM308 NaCl stress Rep3


title: YPS163 ethanol stress Rep3


title: YJM308 NaCl stress Rep2


title: YJM308 NaCl stress Rep1


title: YJM308 unstressed Rep3


title: YJM308 unstressed Rep2


title: YJM308 unstressed Rep1


title: YJM308 ethanol stress Rep3


title: YJM308 ethanol stress Rep1


title: YJM1129 NaCl stress Rep2


title: YPS163 NaCl stress Rep3


title: YJM1129 NaCl stress Rep1


title: YPS606 NaCl stress Rep2


title: YJM1129 unstressed Rep3


title: YPS163 ethanol stress Rep1


title: YJM1129 ethanol stress Rep3


title: YJM1129 unstressed Rep2


title: YJM1129 ethanol stress Rep2


title: YJM1129 ethanol stress Rep1


title: Y10 NaCl stress Rep1


title: Y10 ethanol stress Rep3


title: Y10 NaCl stress Rep2


title: Y10 unstressed Rep2


title: Y10 unstressed Rep3


title: Y10 unstressed Rep1


title: Y10 ethanol stress Rep2


title: Y10 ethanol stress Rep1


title: YJM308 ethanol stress Rep2


title: M22 unstressed Rep3


title: M22 unstressed Rep1


title: M22 unstressed Rep2


title: M22 NaCl stress Rep3


title: M22 NaCl stress Rep2


title: M22 ethanol stress Rep1


title: M1 NaCl stress Rep3


title: M22 ethanol stress Rep2


title: M1 NaCl stress Rep1


title: M22 ethanol stress Rep3


title: M1 unstressed Rep3


title: M1 NaCl stress Rep2


title: YJM1129 unstressed Rep1


title: M1 unstressed Rep2


title: M22 NaCl stress Rep1


title: DBY8268 NaCl stress Rep2


title: M1 ethanol stress Rep1


title: DBY8268 unstressed Rep3


title: DBY8268 NaCl stress Rep3


title: DBY8268 NaCl stress Rep1


title: DBY8268 unstressed Rep2


title: DBY8268 unstressed Rep1


title: DBY8268 ethanol stress Rep1


title: DBY8268 ethanol stress Rep2


title: DBY8268 ethanol stress Rep3


title: RNA-seq C.elegans xpc-1

city: College Station

first: Yuchao

last: Jiang

state: TX

address: 3143 TAMU

institute: Texas A&M University

data_processing:
For XR-seq, cutadapt was used to trim reads with adaptor sequence TGGAATTCTCGGGTGCCAAGGAACTCCAGTNNNNNNACGATCTCGTATGCCGTCTTCTGCTTG at the 3′-end and to discard untrimmed reads. Bowtie 2 was used for read alignment to the ce11 reference genome, followed by filtering, sorting, deduplication, and indexing. Post-alignment filtering steps were adopted using Rsamtools. We only keep reads that: (i) have mapping quality greater than 20; (ii) are from chromosome I, II, III, IV, V, and X; and (iii) are of length 19-24 bp. For plotting strand-based average repair profiles of the genes, we selected 7061 genes longer than 1 kilobase pair, situated at least 500 base pairs away from neighboring genes. Each gene was evenly divided into 100 bins from the Transcription Start Site (TSS) to the Transcription End Site (TES), and 25 bins (2 kbp) upstream of TSS, 25 bins (2 kbp) downstream of TES. Bed files of the reads were intersected to the 150 bin-divided-gene list by Bedtools intersect with the following commands -d -wa -F 0.5 -S or -s for TS and NTS, respectively22. We present the descriptive properties of our data in Supplementary Table 1. For RNA-seq, reads were aligned using STAR, followed by a filtering step to remove unmapped reads, reads with unmapped mates, reads that do not pass quality controls, reads that are unpaired, and reads that are not properly paired. We only kept the first read from the mate pair to ensure independent measures. Read counts for each gene were obtained using FeatureCounts.
Assembly: ce11
Supplementary files format and content: bigwig

organism: Caenorhabditis elegans

source_name: L1 larvae

growth_protocol: The C. elegans wild-type (N2 ancestral) and xpc-1 (tm3886) strains were obtained from the Caenorhabditis Genetics Center and were cultured under standard conditions at room temperature on nematode growth media plates with E. coli strain OP50.

extract_protocol:
For XR-seq, supernatants were incubated with 5μL RNase A and then 5μL Proteinase K, purified, and then immunoprecipitated with either anti-CPD or anti-(6-4)PP antibodies. For RNA-seq, L1 stage wild-type (WT) and xpc-1 C. elegans were collected in M9 and washed until the supernatant was clear, followed by incubation with TRizol and chloroform. After centrifugation at 14,000g for 15min at 4°C, the aqueous phase was mixed with an equal volume of isopropanol. Following centrifugation, the RNA pellet was washed several times and then resuspended in RNase-free water.
For XR-seq, immunoprecipitations were ligated to the adaptors, purified with the antibody used in the first purification, and DNA damage was reversed by either CPD or (6-4)PP photolyase. After PCR amplification, the library was sequenced. For RNA-seq, quality control, followed by stranded and poly(A) enriched library preparation and sequencing, was performed by Novogene.
Single-end for XR-seq, paired-end for poly(A) RNA-seq.

treatment_protocol: To obtain L1 larvae, eggs were collected from adult animals by hypochlorite treatment, and kept in M9 buffer at 22℃ for 16 hours with gentle rotation. L1 larvae were exposed to 4,000 J/m2 of UVB radiation (313 nm). The animals were collected in M9 buffer at 5 minutes, 1 hour, 8 hours, 16 hours, 24 hours, and 48 hours after irradiation, and washed until the supernatant became clear. The pelleted C. elegans (~50 μl for each) were then incubated for 2 hours at 62°C with 450 μl of Worm Hirt Lysis Buffer (0.15M Tris pH 8.5, 0.1M NaCl, 5mM EDTA, 1% SDS) and 20 μl of Proteinase K (NEB, cat. no. P8107S). Subsequently, 120 μl of 5M NaCl was added, and the mixture was inverted to ensure proper mixing, followed by an overnight incubation and one hour centrifugation at 4°C.

value: L1 larvae


title: RNA-seq C.elegans WT


title: SHR_PD_rep3

type: RNA

city: Araçatuba

first: Victor Gustavo Balera

last: Brito

email: vgb.brito@unesp.br, brito@wustl.edu

state: SP

address: Marechal Rondon, km 527/8

department: Basic sciences

country: Brazil

institute: São Paulo State University

description: MicroRNA expression in the mandibles of SHR rats with periodontal disease

hyb_protocol: Sample hybridization was conducted for 20 hours at 48°C, followed by washes and staining steps using the GeneAtlas™ Hybridization, Wash, and Stain Kit (Thermo Fisher Scientific), following the manufacturer's instructions.

scan_protocol: Microarray strips were scanned using the Gene Atlas Imaging Station (Thermo Fisher Scientific).

data_processing: Transcriptome Analysis Console Software version 4.0.2 (Thermo Fisher Scientific) was used for data normalization and detection of expression signals, using the robust multichip analysis (RMA) and detection above background (DABG) algorithms. The same software was used for conducting differential expression analysis, employing the limma package with eBayes statistics (criteria: p<0.05 and fold change ≥ 1.5 or ≤ -1.5).

label: biotin

organism: Rattus norvegicus

source_name: Mandible body (molar region)

label_protocol: Total RNA samples (250 ng) underwent poly(A) tailing and biotin-based tagging using the FlashTag™ Biotin HSR RNA Labeling Kit (Thermo Fisher), following the manufacturer's instructions.

growth_protocol: Periodontal disease was induced in 10-week-old male Wistar and SHR rats by the bilateral placement of ligatures around the mandibular first molars, maintained for 15 days.

extract_protocol: Total RNA extraction was carried out using the mirVana™ miRNA Isolation Kit (Thermo Fisher), following the manufacturer's instructions.

value: shr

tag: condition

value: periodontal disease


title: SHR_PD_rep2

tag: strain


title: SHR_control_rep2

description: MicroRNA expression in the mandibles of SHR rats (control group)


title: SHR_PD_rep1


title: Wistar_PD_rep3

description: MicroRNA expression in the mandibles of Wistar rats with periodontal disease

value: wistar


title: M1 unstressed Rep1


title: SHR_control_rep1

value: control


title: M1 ethanol stress Rep3


title: M1 ethanol stress Rep2


title: Wistar_PD_rep2


title: Wistar_control_rep3

description: MicroRNA expression in the mandibles of Wistar rats (control group)


title: Wistar_PD_rep1


title: SHR_control_rep3


title: Wistar_control_rep2


title: H6-SF18101210-16h

city: Nashville

first: Taha

last: Jan

state: TN

address: 2220 Pierce Ave, PRB 752

department: Otolaryngology

institute: VUMC

data_processing:
Illumina NextGen Sequencing
demultiplexing
STAR alignment v2.5.3a
read quantification: RSEM v1.3.0
Assembly: galGal6
Supplementary files format and content: RDS file with metadata, counts, normcounts, and logcounts in SingleCellExperiment object format for R

organism: Gallus gallus

source_name: basilar papilla

extract_protocol:
FACS sorted into 96-well plates containing RNA lysis buffer
smartseq2

treatment_protocol: in vivo administration of sisomicin with harvesting of cells at indicated timepoints

value: basilar papilla


title: Wistar_control_rep1


title: G9-SF18101208-16h


title: H1-SF18101207-16h


title: G8-SF18101207-16h


title: G8-SF18101210-16h


title: G9-SF18101209-16h


title: G9-SF18101207-16h


title: G8-SF18101208-16h


title: G8-SF18101209-16h


title: G9-SF18101210-16h


title: G7-SF18101208-16h


title: G7-SF18101207-16h


title: G7-SF18101210-16h


title: G6-SF18101208-16h


title: G6-SF18101209-16h


title: G5-SF18101210-16h


title: G5-SF18101207-16h


title: G5-SF18101209-16h


title: G6-SF18101207-16h


title: G5-SF18101208-16h


title: G4-SF18101207-16h


title: G4-SF18101209-16h


title: G4-SF18101210-16h


title: G3-SF18101209-16h


title: YPS163 NaCl stress Rep1


title: G3-SF18101208-16h


title: G2-SF18101207-16h


title: G12-SF18101209-16h


title: G2-SF18101209-16h


title: G11-SF18101207-16h


title: G11-SF18101209-16h


title: G11-SF18101208-16h


title: G12-SF18101210-16h


title: G1-SF18101208-16h


title: G10-SF18101208-16h


title: G1-SF18101201-16h


title: G10-SF18101207-16h


title: G1-SF18101210-16h


title: G11-SF18101210-16h


title: G1-SF18101207-16h


title: F9-SF18101209-16h


title: F9-SF18101201-16h


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title: F9-SF18101208-16h


title: F9-SF18101210-16h


title: F8-SF18101208-16h


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title: F8-SF18101209-16h


title: F8-SF18101207-16h


title: G12-SF18101207-16h


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title: F7-SF18101207-16h


title: F7-SF18101208-16h


title: F7-SF18101201-16h


title: F8-SF18101210-16h


title: F7-SF18101202-16h


title: F6-SF18101209-16h


title: F6-SF18101207-16h


title: F6-SF18101201-16h


title: F5-SF18101202-16h


title: F6-SF18101210-16h


title: F5-SF18101210-16h


title: F5-SF18101201-16h


title: F5-SF18101208-16h


title: F4-SF18101209-16h


title: F4-SF18101208-16h


title: F4-SF18101202-16h


title: F4-SF18101201-16h


title: F3-SF18101209-16h


title: F4-SF18101207-16h


title: F3-SF18101207-16h


title: F3-SF18101208-16h


title: G6-SF18101210-16h


title: F3-SF18101210-16h


title: F2-SF18101209-16h


title: F6-SF18101208-16h


title: F2-SF18101202-16h


title: F2-SF18101210-16h


title: F12-SF18101209-16h


title: F2-SF18101201-16h


title: F12-SF18101201-16h


title: F12-SF18101208-16h


title: F5-SF18101209-16h


title: F11-SF18101209-16h


title: F11-SF18101201-16h


title: F4-SF18101210-16h


title: F11-SF18101210-16h


title: F12-SF18101210-16h


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title: E9-SF18101209-16h


title: E9-SF18101207-16h


title: F1-SF18101210-16h


title: E9-SF18101208-16h


title: YJM1129 NaCl stress Rep3


title: E9-SF18101201-16h


title: E8-SF18101209-16h


title: E8-SF18101201-16h


title: E8-SF18101202-16h


title: E8-SF18101208-16h


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title: E3-SF18101202-16h


title: E4-SF18101210-16h


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title: E12-SF18101207-16h


title: E2-SF18101207-16h


title: E2-SF18101201-16h


title: E2-SF18101209-16h


title: E2-SF18101202-16h


title: E2-SF18101210-16h


title: E6-SF18101201-16h


title: E11-SF18101209-16h


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title: D7-SF18101201-16h


title: D9-SF18101201-16h


title: D7-SF18101209-16h


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title: D6-SF18101202-16h


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title: D5-SF18101209-16h


title: D6-SF18101201-16h


title: D5-SF18101208-16h


title: D4-SF18101209-16h


title: D6-SF18101210-16h


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title: D8-SF18101209-16h


title: D5-SF18101210-16h


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title: C8-SF18101208-16h


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title: A4-SF18101210-16h


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title: G3-SF18100501-p7control


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title: G5-SF18100501-p7control


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title: F7-SF18100502-p7control


title: F7-SF18100504-p7control


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title: F6-SF18100503-p7control


title: F6-SF18100504-p7control


title: F5-SF18100502-p7control


title: F5-SF18100503-p7control


title: F5-SF18100505-p7control


title: F6-SF18100501-p7control


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title: F6-SF18100502-p7control


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title: F4-SF18100502-p7control


title: F3-SF18100503-p7control


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title: F3-SF18100502-p7control


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title: F2-SF18100503-p7control


title: F2-SF18100504-p7control


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title: F2-SF18100501-p7control


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title: F3-SF18100506-p7control


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title: F10-SF18100504-p7control


title: F1-SF18100505-p7control


title: E9-SF18100505-p7control


title: E9-SF18100506-p7control


title: F1-SF18100503-p7control


title: E9-SF18100503-p7control


title: E9-SF18100504-p7control


title: E9-SF18100502-p7control


title: E9-SF18100501-p7control


title: E8-SF18100505-p7control


title: E8-SF18100506-p7control


title: F12-SF18100501-p7control


title: E8-SF18100501-p7control


title: E8-SF18100504-p7control


title: E7-SF18100506-p7control


title: E7-SF18100504-p7control


title: E7-SF18100505-p7control


title: E7-SF18100503-p7control


title: E7-SF18100502-p7control


title: F1-SF18100502-p7control


title: E7-SF18100501-p7control


title: E6-SF18100504-p7control


title: F1-SF18100501-p7control


title: E6-SF18100506-p7control


title: E6-SF18100503-p7control


title: E5-SF18100506-p7control


title: E6-SF18100502-p7control


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