title: muscle, SMIR, 2 days, rep 4

value: SMIR

value: replicated 4


title: S010, chemo-naive, Tumor

status: Public on Oct 08 2024

type: SRA

city: Helsinki

first: Matías

last: M. Falco

address: Biomedicum Helsinki 1, Haartmaninkatu 8

department: Faculty of Medicine

country: Finland

institute: University of Helsinki

description: 10x Genomics, v2 chemistry

library_source: transcriptomic single cell

data_processing:
The Cell Ranger v.6.0.1 pipeline (10x Genomics) was used for demultiplexing, alignment, barcode processing, and unique molecular identifier (UMI) quantification.
Assembly: GRCh38.d1.vd1
Supplementary files format and content: Txt file with data frame with raw counts and additional txt file with metadata information for each cell

molecule: total RNA

organism: Homo sapiens

source_name: Tumor

extract_protocol:
Tumor specimens were incubated overnight in a mixture of collagenase and hyaluronidase (Department of Pathology, University of Turku) to obtain single-cell suspensions.
Library construction was performed according to the manufacturer's (10x Genomics) protocols for indicated assay chemistries (v2, v3, and v3.1).

tag: tissue

value: Tumor

tag: treatment

value: Chemo-naive


title: muscle, SMIR, 10 days, rep 3

city: Shanghai

first: xiaoyan

last: Meng

address: Changhai road 225. Shanghai, China

country: China

institute: eastern hepatobililary surgical hospital

library_source: transcriptomic

data_processing:
sequencing was carried out using the Illumina Novaseq 6000 instrument.
The raw data was handled by Skewer and data quality was checked by FastQC v0.11.2.
Clean reads were aligned to the Human genome hg38 using STAR. StringTie.
The expression of the transcript was calculated by FPKM using Perl.
Assembly: rn6
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample.
Supplementary files format and content: Tab-delimited text file includes FPKM values for each sample.

organism: Rattus

source_name: muscle

extract_protocol:
Rats were deeply anesthetized with isoflurane, transcardially perfused with nuclease-free saline (pH 7.4). The incised skin and muscle tissue were rapidly dissected, the C3-C6 DRGs of LPI and C2-C5 DRGs of SMIR were then extracted. All samples were immediately transferred to ice-cold RNAlater solution and refrigerated at 4°C for 48 hours. Then samples were removed from RNAlater solution, placed into fresh 1.5 mL conical tubes and stored at -80℃. Total RNA was isolated, then Gel electrophoresis and Qubit were used to exam the RNA quality and RNA integrity number (RIN). For RNA sequencing, RNA samples from seven to nine biological replicates at each time point were separated into three independent pools. Strand-specific libraries were constructed using the TruSeq RNA sample preparation kit, and sequencing was carried out using the Illumina Novaseq 6000 instrument.
Strand-specific libraries were constructed using the TruSeq RNA sample preparation kit (RS-122-2001, Illumina, San Diego, CA, USA)

value: muscle

tag: time

value: 10 day

tag: replicated animal_number

value: replicated 3


title: S009, chemo-naive, Omentum

description: 10x Genomics, v2 chemistry

source_name: Omentum

value: Omentum


title: cropseq_hek293T_library1_nih3t3_library2_0hr_grna

city: Durham

first: Charles

last: Gersbach

state: NC

address: 2127 Campus Drive

country: USA

institute: Duke University

description:
293T_LRB100_NTlib1-NIH3T3_LRB100_NTlib2_0hr_mix_barcodes.tsv.gz
293T_LRB100_NTlib1-NIH3T3_LRB100_NTlib2_0hr_mix_features.tsv.gz
293T_LRB100_NTlib1-NIH3T3_LRB100_NTlib2_0hr_mix_matrix.mtx.gz

data_processing:
Each lane of cells was processed using cellranger (version 6.0.1) count using default parameters and mapping to the GRCh38-and-mm10-2020 reference genome from 10x Genomics
Assembly: GRCh38-and-mm10-2020
Supplementary files format and content: Sparse matrices in Market Exchange (MEX) format for UMI counts for each barcode/gene or barcode/gRNA pair. Files are barcodes.tsv: This file contains the barcodes represented in the mtx file. genes.tsv: This file contains all annotated genes and gRNAs. matrix.mtx:  contained the "gene id" index, "cell id" index, and the total UMI count per cell and gene/gRNA combination.
Supplementary files format and content: R1/R2/I1/I2 .fastq files for lane 1 and 2 of the sequencing run. Read 1 contains UMI and cell barcode information. Read 2 contains the RNA transcript sequence.

molecule: polyA RNA

organism:
Homo sapiens
Mus musculus

growth_protocol: All cells were grown at 37°C. HEK293T/17 cells were cultured in DMEM + 10% FBS and NIH3T3 cells were cultured in DMEM + 10% CBS.

extract_protocol:
cells were washed three times, trypsinized, and strained through a 40 µm cell strainer
Approximately 10,000 cells were captured per lane of a 10x Chromium chip (Next GEM Chip G) using Chromium Next GEM Single Cell 3ʹ HT Reagent Kits v3.1 with Feature Barcoding technology for CRISPR Screening (10x Genomics, Inc, Document number CG000418, Rev D). CROP-seq protospacer sequences were amplified from barcoded cDNA.

tag: cell line


title: direct_capture_hek293T_library1_nih3t3_library2_72hr_gene_exp

description:
293T_MCH2_NTlib1-NIH3T3_MCH2_NTlib2_72hr_mix_barcodes.tsv.gz
293T_MCH2_NTlib1-NIH3T3_MCH2_NTlib2_72hr_mix_features.tsv.gz
293T_MCH2_NTlib1-NIH3T3_MCH2_NTlib2_72hr_mix_matrix.mtx.gz


title: skin, SMIR, 10 days, rep 1

source_name: skin

value: skin

value: replicated 1


title: direct_capture_hek293T_library1_nih3t3_library2_0hr_gene_exp

description:
293T_MCH2_NTlib1-NIH3T3_MCH2_NTlib2_0hr_mix_barcodes.tsv.gz
293T_MCH2_NTlib1-NIH3T3_MCH2_NTlib2_0hr_mix_features.tsv.gz
293T_MCH2_NTlib1-NIH3T3_MCH2_NTlib2_0hr_mix_matrix.mtx.gz


title: cropseq_hek293T_library1_nih3t3_library2_72hr_gene_exp

description:
293T_LRB100_NTlib1-NIH3T3_LRB100_NTlib2_72hr_mix_barcodes.tsv.gz
293T_LRB100_NTlib1-NIH3T3_LRB100_NTlib2_72hr_mix_features.tsv.gz
293T_LRB100_NTlib1-NIH3T3_LRB100_NTlib2_72hr_mix_matrix.mtx.gz


title: S009, IDS, Omentum

description: 10x Genomics, v2 chemistry

value: NACT


title: DRG, SMIR, 2 days, rep 4

source_name: DRG

value: DRG

value: 2 days


title: S008, chemo-naive, Omentum

description: 10x Genomics, v2 chemistry


title: cropseq_hek293T_library1_nih3t3_library2_0hr_gene_exp


title: skin, SMIR, 2 days, rep 3


title: S008, IDS, Ovary

description: 10x Genomics, v2 chemistry

source_name: Ovary

value: Ovary


title: muscle, SMIR, 2 days, rep 3


title: RAW264.7, LPS, Mdivi-1, 96 h-3

city: Kitakyushu

first: Jun-ichiro

last: Koga

state: --- Select One ---

address: 1-1, Iseigaoka, Yahatanishi-ku

country: Japan

institute: University of Occupatinal and Environmental Health, Japan

data_processing:
CLC genomic workbench (v10.1.1)
Assembly: Reads were mapped to reference genomes (hg19 for Human) using CLC Genomics Workbench.
Supplementary files format and content: xslx data including TPM data for each genes and samples

organism: Mus musculus

growth_protocol: DMEM medium with 10% FBS

extract_protocol:
RNA was extracted using TRIZOL and dissolved in RNase-free H2O according to the reagent's instructions.
100 ng of total RNA per sample was used for library preparation. Ribosomal RNA was removed using the NEBNext rRNA Depletion Kit, and libraries were constructed with the NEBNext Ultra II Directional RNA Library Prep Kit. Library quality was assessed with the Bioanalyzer DNA-sensitivity kit.

treatment_protocol: RAW264.7 cells were treated with 10 ng/mL LPS and 10 ng/mL mouse IFN-γ with or without 50 μM Mdivi-1,

value: 96 hr

tag: cell type

value: Macrophages

value: LPS, IFN-γ + Mdivi-1


title: RAW264.7, LPS, 96 h-3

value: LPS and IFN-γ


title: RAW264.7, LPS, 96 h-2


title: S007, chemo-naive, Ovary

description: 10x Genomics, v2 chemistry


title: DRG, SMIR, 2 days, rep 3

value: SMIR


title: cropseq_hek293T_library1_nih3t3_library2_72hr_grna


title: RAW264.7, LPS, 96 h-1


title: RAW264.7, LPS, Mdivi-1, 24 h-3

value: 24 hr


title: S005, chemo-naive, Omentum

description: 10x Genomics, v2 chemistry

value: Chemo-naive


title: muscle, SMIR, 2 days, rep 2

value: muscle

value: replicated 2


title: RAW264.7, LPS, 24 h-3


title: RAW264.7, LPS, Mdivi-1, 96 h-1


title: RAW264.7, LPS, Mdivi-1, 96 h-2


title: RAW264.7, LPS, Mdivi-1, 24 h-1


title: RAW264.7, LPS, Mdivi-1, 24 h-2


title: S006, chemo-naive, Mesentery

description: 10x Genomics, v2 chemistry

source_name: Mesentery

value: Mesentery


title: S004, chemo-naive, Ovary

description: 10x Genomics, v2 chemistry


title: DRG, SMIR, 2 days, rep 2


title: RAW264.7, LPS, 24 h-2


title: RAW264.7, LPS, 24 h-1


title: muscle, SMIR,  2 days, rep 1


title: skin, SMIR, 2 days, rep 1


title: S002, chemo-naive, Omentum

description: 10x Genomics, v2 chemistry

value: Omentum


title: skin, SMIR, 2 days, rep 2

value: skin


title: HC, Old3, 12M

city: Bronx

first: Dongsheng

last: Cai

state: NY

address: 1300 Morris Park Avenue, 1300 MORRIS PARK AVENUE

institute: ALBERT EINSTEIN COLLEGE OF MEDICINE

library_source: genomic

data_processing:
FASTQ files from bisulfite sequencing underwent quality control with FastQC. Reads were trimmed using Illumina's BaseSpace sequence hub (MethylSeq v2.0.0) and adapters using FASTQ Toolkit v2.2, retaining only reads with Q-scores >30. Trimmed reads were aligned to the mouse reference genome (GRCm38/mm10) using Bismark v0.14.4/Bowtie 2 v2.2.2, yielding over 25 million aligned reads per sample with 18-20X coverage. BAM files were processed with SAMtools v1.2, and methylation calling was performed using the Bismark methylation extractor. Differential methylation analysis was conducted using MethylKit v1.20.0 in R.
Assembly: GRCm38/mm10
Supplementary files format and content: CpG/CHG/CHH methylation call txt files

molecule: genomic DNA

source_name: Hippocampus

growth_protocol: All animal use and procedures were approved by the Institutional Animal Care and Use Committee of the Albert Einstein College of Medicine (Protocols #00001111, #00001385, #00001397, #00001398, #00001399 and their previously approved versions). C57BL/6 mice were obtained from Jackson Laboratory and housed under standard conditions in a 12-h light/12-h dark cycle with free access to food and water and were kept under standard, infection-free housing.

extract_protocol:
Hypothalamus, hippocampus and OB were dissected from 2 and 12 months of age (n=3 mice per group) in manner that it maintains the anatomic separation from the neighboring brain region. DNA was extracted from these tissues using a Qiagen kit.
The extracted DNA samples were sheared into fragments of 150-200 base pairs using sonication, and the fragment sizes were verified using the Agilent TapeStation with D1000 ScreenTape. The fragmented DNA underwent library preparation using the SureSelectXT Methyl-Seq Library Prep Kit, following the manufacturer’s instructions.
Bisulfite-Seq (Bisulfite oligonucleotide-captured sequencing)

value: Hippocampus

tag: strain

tag: Sex

value: Male

tag: age

value: 12 months


title: HT, Old3, 12M

source_name: Hypothalamus

value: Hypothalamus


title: OB, Old3, 12M

source_name: Olfactory bulb

value: Olfactory bulb


title: S003, chemo-naive, Peritoneum

description: 10x Genomics, v2 chemistry

source_name: Peritoneum

value: Peritoneum


title: HC, Old2, 12M


title: S001, IDS, Ovary

description: 10x Genomics, v2 chemistry

value: Ovary

value: NACT


title: skin, SMIR, 6 hours, rep 4

value: 6 hours

value: replicated 4


title: HT, Old2, 12M


title: muscle, SMIR, 6 hours, rep 4

value: SMIR


title: ED8, VDJ

city: Paris

first: Mickael

middle: Mathieu

last: Menager

address: 24 Boulevard du Montparnasse

country: France

institute: Institut Imagine

description: 10x Genomics 5’

data_processing:
Sequencing reads were demultiplexed and aligned to the human reference genome using the CellRanger Pipeline v5
Unfiltered RNA UMI counts were loaded into Seurat v4.0.1 (Stuart et al., 2019) for quality control, data integration and downstream analyses. Apoptotic cells and empty sequencing capsules were excluded by filtering out cells with fewer than 500 features or a mitochondrial content higher than 20%.
Data from each sample were SCT normalisedand scaled, before batch correction using Seurat’s FindIntegratedAnchors.
To evaluate the expression of the 11 surface protein, the antibody-derived tags (ADT) counts for the cells retained after filtering were loaded in the integrated seurat object and normalised using the CLR normalisation method.
BCR reads were aligned to the GRCh38 reference genome (vdj_GRCh38_alts_ensembl-5.0.0) and consensus BCR annotation was performed using the cellranger vdj program (v5.0.1)
Assembly: GRCh38-2020-A and vdj_GRCh38_alts_ensembl-5.0.0
Supplementary files format and content: h5 files contain the raw count matrix for each sample
Supplementary files format and content: the rds file contains the Seurat object of all integrated samples

source_name: Peripheral blood

extract_protocol:
PBMCs were isolated blood from five PAPS patients and two HD. Total B cells were isolated with the EasySep™ Human B-cell Isolation Kit (Stemcell Technologies). B cells were resuspended at 10x106/mL and incubated with Human TruStain FcX Fc Blocking reagent for 10min at 4°C. Cells were then incubated with the 10 following antibodies conjugated to an antibody-derived tag for 30 min at 4°C : CD19 (HIB19,TotalSeq, BioLegend) CD27 (0323), CD24 (ML5), CD38 (HIT2), CD5 (UCHT2), HLA-DR (L243), CD86 (IT2.2), IgM (MHM-88), IgD (IA6-2), CD21 (Bu32).
The scRNA-seq libraries were generated using Chromium Next GEM Single Cell 5’ V(D)J Reagent Kit v.1.1 with Feature Barcoding (10X Genomics) according to the manufacturer’s protocol. Gene expression (mRNA), ADT and VDJ BCR libraries were constructed. Briefly, cells were counted and up to 10 000 cells were loaded in the 10X Genomics Chromium Controller to generate single-cell gel-beads in emulsion. After reverse transcription, gel-beads in emulsion were disrupted. Barcoded complementary DNA was isolated and amplified by PCR. Following fragmentation, end repair and A-tailing, sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq S2 flowcell (Illumina).
CITE-Seq + VDJ-Seq

value: Peripheral blood

value: Primary cells

value: B cells

tag: group

value: patient


title: OB, Old2, 12M


title: HC, Old1, 12M


title: MS7, VDJ

description: 10x Genomics 5’

tag: gender

value: F


title: DRG, SMIR, 6 hours, rep 4

value: DRG


title: skin, SMIR, 6 hours, rep 3

value: skin

value: replicated 3


title: CH5, VDJ

description: 10x Genomics 5’


title: OB, Young3, 2M

value: Male

value: 2 months


title: SS6, VDJ

description: 10x Genomics 5’

value: M


title: HT, Old1, 12M

value: Hypothalamus

value: 12 months


title: HC, Young2, 2M

value: Hippocampus


title: VG4, VDJ

description: 10x Genomics 5’


title: HT, Young3, 2M


title: HC, Young3, 2M


title: DRG, SMIR, 6 hours, rep 3

value: 6 hours


title: OB, Young2, 2M

value: Olfactory bulb


title: HT, Young2, 2M


title: DRG, SMIR, 2 days, rep 1

value: SMIR

value: 2 days

value: replicated 1


title: CR3, VDJ

description: 10x Genomics 5’

value: Peripheral blood

value: Primary cells

value: B cells


title: skin, SMIR, 6 hours, rep 2

value: replicated 2


title: HT, Young1, 2M


title: VP2, VDJ

description: 10x Genomics 5’

value: control


title: ChIPseq_Torin_30min_H4AC_Rep2_S12_R1_001.fastq.gz

city: Boston

first: Ryan

middle: Jared

last: Marina

state: MA

address: 45 Shattuck Street

department: Biological Chemistry and Molecular Pharmacology

institute: Harvard Medical School

data_processing:
Raw reads were filtered (mean quality score ≥20) and adapter sequences were removed using cutadapt (version 1.14)
Reads were mapped to the mm10 reference genome using bowtie (version 1.2.2)
Fragment midpoints were approximated by shifting mapped coordinates downstream by 75bp (approximating 150nt insert) and were converted to bedGraphs with both single bp bins or bin sizes of 50bp using the script (bowtie2stdBedGraph.pl)
Binned bedGraphs were then normalized by relative sequencing depth and converted to bigwig format
Assembly: mm10
Supplementary files format and content: BigWig
Supplementary files format and content: bigWigs representing depth-normalized read coverage

source_name: CY 2.4 Albino ES cells

extract_protocol:
Cells were fixed with 1% formaldehyde for 10min at room temperature. After quenching and cell lysis, chromatin was sonicated by using a E220 focused-ultrasonicator (Covaris).
ChIP-seq libraries were prepared with size selection step using NEBNext Ultra II DNA Library Prep Kit for Illumina (E7103S, NEB) complemented with NEBNext Multiplex Oligos for Illumina (Index Primers Set 1) (E7335S, NEB). 500ng DNA was used as starting material for input samples and 1.934-30.45ng DNA was used as starting material for ChIP samples. Libraries were amplified using 7-9 cycles for input samples and 12-14 cycles for ChIP samples on the thermocycler according to the protocol. Post amplification samples were beads purified and validated using Agilent High sensitivity DNA kit.

value: CY 2.4 Albino ES cells

value: Mouse embryonic stem cell

tag: chip antibody

value: ab177790,  Abcam


title: OB, Old1, 12M

value: Male


title: DRG, SMIR, 6 hours, rep 2

value: DRG


title: ChIPseq_Torin_15min_H4AC_Rep2_S11_R1_001.fastq.gz


title: muscle, SMIR, 6 hours, rep 3

value: muscle

value: replicated 3


title: ChIPseq_Torin_30min_H4AC_Input_S4_R1_001.fastq.gz


title: ED8, ADT

description: 10x Genomics 3’

library_source: other

molecule: protein

value: patient


title: ChIPseq_Torin_15min_H4AC_Rep1_S7_R1_001.fastq.gz


title: ED8, GEX

description: 10x Genomics 3’


title: muscle, SMIR,  6 hours, rep 1

value: 6 hours


title: ChIPseq_Torin_15min_H4AC_Input_S3_R1_001.fastq.gz


title: DRG, SMIR, 6 hours, rep 1

value: SMIR


title: MS7, ADT

description: 10x Genomics 3’

value: F


title: MS7, GEX

description: 10x Genomics 3’


title: ChIPseq_Control_H4AC_Rep2_S9_R1_001.fastq.gz

value: DMSO


title: ExVivoCell_72Hr_20μM_mRNA_rep3

type: RNA

city: Zhengzhou

first: Panpan

last: Wang

address: 郑州市高新区科学大道100号郑州大学

department: College of Public Health

institute: 郑州大学

description:
Gene expression after 72 h of exposure to 20 μM of CdCl2 in L-02 cell
[cd3](normalized)

hyb_protocol: Array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology). 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60°C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies).

source_name: L-02 cells,72hr, 20μM

label_protocol: Sample labeling were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology). Briefly, total RNA from each sample was linearly amplified and labeled with Cy3-UTP. The Labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: The total RNA of the cells was extracted by the TRIzol assay. The RNA purified was according to RNasey Mini Kit (Qiagen 74104, USA). The quantity of the total RNA from each sample was measured by NanoDrop® ND-1000 (Thermo-Fisher Scientific, USA) and the integrity of the total RNA and gDNA contamination were measured by agarose gel electrophoresis.

treatment_protocol: L-02 cells in logarithmic phase were divided into control and CdCl2 exposure group with the concentrations of 20 μM for 72 h in the RPMI 1640 medium containing 10% fetal bovine serum (Gibco, No. 10099-141) at 37℃ in 5% CO2., respectively. There were three replicate samples in each group.

value: human normal liver cell

value: female


title: skin, SMIR, 0 day, rep 4

value: skin

value: 0 day

value: replicated 4


title: ChIPseq_Control_H4AC_Rep1_S5_R1_001.fastq.gz

value: CY 2.4 Albino ES cells


title: skin, SMIR, 6 hours, rep 1

value: replicated 1


title: SS6, ADT

description: 10x Genomics 3’

value: Peripheral blood

value: Primary cells

value: B cells

value: M


title: ChIPseq_Torin_30min_H4AC_Rep1_S8_R1_001.fastq.gz

value: Mouse embryonic stem cell

value: ab177790,  Abcam


title: muscle, SMIR, 6 hours, rep 2

value: muscle

value: 6 hours

value: replicated 2


title: muscle, SMIR, 0 day, rep 4

value: SMIR


title: HC, Young1, 2M

value: Hippocampus

value: Male

value: 2 months


title: JT1, VDJ

description: 10x Genomics 5’

value: control


title: ChIPseq_Control_H4AC_Input_S1_R1_001.fastq.gz

value: DMSO


title: ExVivoCell_72Hr_20μM_mRNA_rep2

address: 郑州市高新区科学大道100号郑州大学

description:
Gene expression after 72 h of exposure to 20 μM of CdCl2 in L-02 cell
[cd2](normalized)

value: human normal liver cell

value: female


title: ExVivoCell_72Hr_20μM_mRNA_rep1

address: 郑州市高新区科学大道100号郑州大学

description:
Gene expression after 72 h of exposure to 20 μM of CdCl2 in L-02 cell
[cd1](normalized)


title: DRG, SMIR, 0 day, rep 4

value: DRG

value: 0 day

value: replicated 4


title: ChIPseq_Torin_30min_BRD4_abcam_Rep2_S12_R1_001.fastq.gz

value: CY 2.4 Albino ES cells

value: ab84776, Abcam


title: CH5, ADT

description: 10x Genomics 3’

value: Peripheral blood

value: Primary cells

value: B cells

value: patient

value: F


title: ExVivoCell_72Hr_0μM_mRNA_rep3

address: 郑州市高新区科学大道100号郑州大学

description:
Gene expression in L-02 cells were cultured normally after 72h
[N3](normalized)

source_name: L-02 cells,72hr, 0μM

value: cultured normally after 72h


title: ChIPSeq_12_SPI1_P54D

city: Sydney

first: Dominik

last: Beck

state: NSW

address: Level 10, UTS Building 11 (CB11 81-113, Broadway, Ultimo)

department: School of Biomedical Engineering

country: Australia

institute: University of Technology Sydney

data_processing:
Raw sequencing reads were processed as previously proposed (PMID: 23974199). Peaks were called with three publicly available peak-finding programs (MACS2, PMID: 18798982; FindPeaks, PMID: 20513432; SPP, PMID: 22533622), and peaks identified by at least two algorithms used for downstream analysis.
Assembly: hg19
Supplementary files format and content: hic and bed

source_name: ALL xenograft cells

extract_protocol: ChIP-seq were carried out as previously described (PMID: 30537513). Briefly, frozen PDX cells that were harvested from mice after dexamethasone or vehicle control treatment in vivo were revived from cryostorage, and fixed with 1% formaldehyde for 10 min at room temperature. Nuclei were extracted from fixed cells by 10 min incubation in lysis buffer (0.2% NP40 in 10 mM Tris buffer, pH 8.0) followed by centrifugation at 1250 × g for 5 min at 4 °C. Chromatin was fragmented using a Bioruptor sonicator (Diagenode SA, Belgium) on high power at 4 °C with 30 s on/off for 10 min. Separate immunoprecipitates were produced using immunoglobulin raised against the GR (Cell Signaling, Danvers, MA, USA), CTCF (Cell Signaling), Histone (N-terminal acetylated histone H3 in general, Millipore, Billerica, MA, USA; H3K4Me3, H3K27Ac and H3K27Me3, Cell Signaling) and processed according to the manufacturer’s instructions. DNA from protein-associated complexes and corresponding input samples was recovered using phenol/chloroform/isoamyl alcohol with phase lock gel tubes (5 Prime, Hilden, Germany). The ChIP DNA samples were dissolved in 20 µl water and sequenced using Hiseq2500 (50SE) platform with 20 M reads per sample.

treatment_protocol: ALL xenograft cells were inoculated by tail-vein injection into NSG mice, and engraftment was monitored weekly as previously described (PMID: 30537513). Mice were randomized and treated with either dexamethasone (15 mg/kg) or vehicle control by intraperitoneal injection when the %huCD45+ cells in the peripheral blood reached 70% for in vitro molecular biology experiments. Briefly, mice were treated when > 70% %huCD45+ cells in the peripheral blood, and sacrificed 8 hours thereafter. Cell suspensions of spleens were prepared, and mononuclear cells enriched to 97% human by density gradient centrifugation. After harvesting, cells were immediately resuspended in fetal calf serum (FCS) containing 10% DMSO, frozen and stored at liquid nitrogen for further use.

tag: antibody

value: ALL xenograft cells

value: dexamethasone


title: skin, SMIR, 0 day, rep 3

value: skin

value: SMIR

value: replicated 3


title: ChIPseq_Torin_30min_BRD4_abcam_Rep1_S8_R1_001.fastq.gz

value: Mouse embryonic stem cell


title: CH5, GEX

description: 10x Genomics 3’


title: muscle, SMIR, 0 day, rep 3

value: muscle


title: ChIPSeq_11_SPI1_P50D


title: ExVivoCell_72Hr_0μM_mRNA_rep1

address: 郑州市高新区科学大道100号郑州大学

description:
Gene expression in L-02 cells were cultured normally after 72h
[N1](normalized)

value: human normal liver cell

value: female


title: ChIPseq_Torin_30min_BRD4_abcam_Input_S4_R1_001.fastq.gz

value: CY 2.4 Albino ES cells


title: VG4, ADT

description: 10x Genomics 3’

value: M


title: ChIPSeq_10_SPI1_P54C


title: DRG, SMIR, 0 day, rep 3

value: DRG

value: 0 day


title: ChIPseq_Torin_15min_BRD4_abcam_Rep2_S11_R1_001.fastq.gz

value: ab84776, Abcam


title: VG4, GEX

description: 10x Genomics 3’

value: Peripheral blood

value: Primary cells

value: B cells

value: patient


title: SS6, GEX

description: 10x Genomics 3’


title: ChIPSeq_9_SPI1_P50C

value: ALL xenograft cells


title: CR3, ADT

description: 10x Genomics 3’


title: muscle, SMIR, 0 day, rep 2

value: replicated 2


title: skin, SMIR, 0 day, rep 2

value: skin

value: SMIR


title: ChIPseq_Torin_15min_BRD4_abcam_Rep1_S7_R1_001.fastq.gz

value: Mouse embryonic stem cell


title: OB, Young1, 2M

value: Olfactory bulb

value: Male

value: 2 months


title: ChIPseq_Control_BRD4_abcam_Rep1_S5_R1_001.fastq.gz

value: CY 2.4 Albino ES cells

value: DMSO


title: ChIPseq_Control_BRD4_abcam_Input_S1_R1_001.fastq.gz


title: VP2, GEX

description: 10x Genomics 3’

value: control


title: ChIPseq_Torin_15min_BRD4_abcam_Input_S3_R1_001.fastq.gz


title: muscle, SMIR, 0 day, rep 1

value: muscle

value: 0 day

value: replicated 1


title: VP2, ADT

description: 10x Genomics 3’

value: Peripheral blood

value: Primary cells


title: ChIPSeq_8_EBF1_E54D

value: dexamethasone


title: VGAT + PITX3 P0 - replicate 1

city: Utrecht

first: Özge

last: Düdükcü

address: Universiteitsweg 100

country: Netherlands

institute: University Medical Center Utrecht

data_processing:
The mapping process was carried out utilizing the MapAndGo255 STARmap pipeline. Briefly, the fastq files from different lanes were merged to consolidate the data, followed by the removal of reads without a CEL-Seq2 barcode during the demultiplexing step. To enhance the data quality, Illumina adaptor sequences and low-quality base calls from the 3'-end of the reads were trimmed. The subsequent step involved aligning the reads to a reference mouse genome (Ensemble GRC38 release 93) using STAR v-2.5.3a. This alignment procedure generated three distinct count files: the unspliced file containing reads mapped to intronic regions, the spliced file containing reads mapped to exons, and the total file comprising both types of reads.
Assembly: mm10
Supplementary files format and content: A tab-separated data file has been merged for all sequencing libraries, containing all genes (rows) and the number of sequenced transcripts for each sample. The first column includes the official gene symbol, followed by the gene's functional annotation and the chromosome name, separated by double underscores. Cells are labeled according to their IDs as listed under "sample name".
Supplementary files format and content: 3 metadata and 3 merged processed files. 1. unspliced, 2. spliced, 3. total

source_name: ventral midbrain

extract_protocol:
RNA was extracted by 2x heat lysis (65C) in 384 well, which were immediately used for downstream single cell RNA sequencing reactions (CELseq2) Single-cell RNA sequencing was conducted using CEL-seq2 at Single Cell Discoveries (Utrecht, NL), following the protocols by Hashimshony et al., 2016 and Muraro et al., 2016. The plates were preloaded with barcoded poly-T primers designed to specifically amplify mRNA and introduce a 6bp unique molecular identifier (UMI), an 8bp cell barcode, and a T7 RNA polymerase binding site. Additionally, ERCC spike-ins were preloaded into the plates to enable quality control of reactions in individual wells. Cells were lysed by heating at 65°C for 5 minutes, followed by rapid chilling on ice for 2 minutes, repeated twice. Superscript II (ThermoFisher Scientific) was used for reverse transcription of mRNA, which was then converted into second-stranded DNA by DNA polymerase I (ThermoFisher Scientific). The material from each plate was pooled, cleaned using Ampure beads (Beckman Coulter, #A63881), and amplified by in vitro transcription overnight with the MEGAscript T7 transcription kit (ThermoFisher Scientific, #AMB1334). After a second round of cleanup, the amplified RNA was measured with Agilent RNA 6000 pico chips (Agilent #5067-1513), reverse-transcribed using random hexamer primers to introduce Truseq Small RNA kit RP1 primer binding sites (Illumina), and finally converted into DNA libraries with custom rpi primers adapted from the Truseq Small RNA kit (Illumina)106. After two rounds of Ampure bead cleanup and quality control using the Agilent High Sensitivity DNA Kit (5067-4626), the libraries were sent for paired-end sequencing (26bp for read 1 and 50bp for read 2) on the Nextseq500 at the Utrecht Sequencing Facility (USEQ, Life Sciences faculty, Utrecht University).
Library was performed according to manufacturer's instructions. Illumina sequencing libraries were prepared with the TruSeq small RNA primers (Illumina) and sequenced paired-end at 75 bp read length the Illumina NextSeq.

value: ventral midbrain

tag: mouse line

tag: developmental stage


title: skin, LPI, 10 days, rep 4

value: LPI

value: 10 day

value: replicated 4


title: CR3, GEX

description: 10x Genomics 3’

value: B cells

value: patient

value: M


title: ChIPSeq_4_H3K4me1_ ALL54D

data_processing:
Raw sequencing reads were processed as previously proposed (PMID: 23974199). Peaks were called using SICER2 (PMID: 19505939).
Assembly: hg19
Supplementary files format and content: hic and bed

value: ALL xenograft cells


title: DRG, SMIR, 0 day, rep 1

value: DRG

value: SMIR


title: ChIPSeq_3_H3K4me1_ALL50D


title: ChIPseq_Control_BRD4_abcam_Rep2_S9_R1_001.fastq.gz

value: CY 2.4 Albino ES cells

value: Mouse embryonic stem cell

value: DMSO

value: ab84776, Abcam


title: DRG, SMIR, 0 day, rep 2

value: 0 day

value: replicated 2


title: ChIPSeq_6_EBF1_E54C


title: ChIPSeq_5_EBF1_E50C


title: BTSC475_ZBTB18_FL_3

city: Freiburg

first: Eyleen

last: Corrales

address: Breisacherstr. 153

department: Medizinische Fakultät

country: Germany

institute: Institut für Medizinische Bioinformatik und Systemmedizin

data_processing:
Adapter trimming and quality filtering of reads was performed with Trimmomatic, with parameters LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:25
Reads were mapped to the Ensembl GRCh38 reference genome with the STAR aligner, with parameters --twopassMode Basic --outReadsUnmapped None --outFilterMultimapNmax 10 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.05 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMatchNmin 16
Non-uniquely mapped reads were discarded
Genes that failed to achieve a minimum of one count-per-million (CPM) in at least two of the samples were filtered out as unexpressed
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes a matrix of raw counts for each sample

growth_protocol: BTSC268 and BTSC475 were maintained in Neurobasal medium containing B27 and N2 supplement, FGF (20ng/ml), EGF (20ng/ml), LIF (20ng/ml), Heparin (2mg/ml), and Glutamax in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted from the cell culture using miRNeasy Mini Kit (QIAGEN) according to the manufacturer’s instructions
Illumina TruSeq libraries were prepared at the Genomics and Proteomics Core Facility of the DKFZ, Heidelberg, using standard protocols

treatment_protocol: Lentiviral vector transduction with full length ZBTB18 (ZBTB18-FL), or empty vector (EV). Cells were GFP sorted and only the 20-30% strongest GFP positive cells were retained and used for sequencing

value: glioblastoma stem cell-like

tag: genotype


title: JT1, ADT

description: 10x Genomics 3’

value: Peripheral blood

value: Primary cells

value: control


title: skin, SMIR, 0 day, rep 1

value: skin

value: replicated 1


title: VGAT P0 - replicate 3

value: ventral midbrain


title: ChIPSeq_2_H3K4me1_ALL54C


title: ChIPSeq_7_EBF1_E50D

value: dexamethasone


title: ChIPSeq_1_H3K4me1_ALL50C

value: ALL xenograft cells


title: muscle, LPI, 10 days, rep 4

value: muscle

value: LPI

value: 10 day

value: replicated 4


title: JT1, GEX

description: 10x Genomics 3’

value: B cells


title: DRG, LPI, 10 days, rep 4

value: DRG


title: VGAT + PITX3 E16 - replicate 1


title: VGAT P0 - replicate 1


title: HiC_4 ALL54D

data_processing:
Raw sequencing reads were processed using HiC-Pro (PMID: 26619908) and the validpairs output was converted using HiC-Pro Utilities into Juicebox (PMID: 27467250) format.
Assembly: hg19
Supplementary files format and content: hic and bed

extract_protocol: Hi-C was performed using a modified version of a previously described protocol (PMID: 28435001). Briefly, 10 million cells were collected and cross-linked in 10 ml of PBS containing 1% formaldehyde for 10 minutes at room temperature. The reaction was stopped by 0.125M glycine solution. Cross-linked cell pellet was used to prepare nuclei, which were subjected to digestion with restriction enzyme followed by end-filling to create biotin-labeled blunt ends. Blunt ends were ligated by T4 DNA ligase at room temperature for 4 hours with rotation. Nuclei were digested with proteinase K and 10% sodium dodecyl sulfate (SDS) at 55°C for 30 minutes. Following sodium acetate and pure ethanol precipitation, DNA was isolated and dissolved in Tris buffer. DNA was sonicated using Bioruptor sonicator (Diagenode SA, Belgium), to obtain fragments ranging in size from 150 bp to 300 bp. Sonicated material was then size selected using AMPure XP beads with the 0.55X and 0.3X for HiC. HiC material was then biotinylated, washed, and purified using Dynabeads MyOne Streptavidin T1 beads (Life technologies, 65602). While on beads, DNA ends were blunt ended and dA tailed, followed by ligation of the Illumina sequencing adapter with the T4 DNA ligase. PCR reactions were performed on beads involving 8 cycles of amplification (95°C for 2 min, followed by 94°C for 80 s, 65°C for 30 s, 72°C for 30 s). DNA library was size selected using 1.5% agarose gel to obtain fragments ranging in size from 400bp to 700bp. Sequencing was performed on the Illumina HiSeq 2500 to obtain 150bp paired-end reads. Samples were sequenced to depth of 100 million reads.


title: skin, LPI, 10 days, rep 3

value: replicated 3


title: BTSC475_ZBTB18-FL_1


title: VGAT P0 - replicate 2


title: HiC_2 ALL54C


title: muscle, LPI, 10 days, rep 3


title: DRG, LPI, 10 days, rep 3


title: HiC_3 ALL50D


title: BTSC475_EV_3

value: EV


title: VGAT E16 - replicate 3


title: BTSC475_ZBTB18-FL_2

value: glioblastoma stem cell-like


title: BTSC475_EV_2


title: VGAT E16 - replicate 4


title: BTSC268_ZBTB18-FL_3


title: VGAT E16 - replicate 2


title: muscle, LPI, 10 days, rep 2

value: replicated 2


title: HiC_1 ALL50C


title: BTSC268_ZBTB18-FL_2


title: e11_5_rep1

city: San Francisco, CA

first: Rebecca

middle: Garrett

last: Jaszczak

state: California

address: 35 Medical Center Way, Room 913D

institute: UCSF

data_processing:
Initial processing of the v2 10x libraries was done through CellRanger v3.1.1. Libraries for all timepoints were aligned to the mouse genome (10× Genomics prebuilt mm10 version 3.0.0 reference genome) with all cellranger default parameters for demultiplexing and aligning. Our libraries were sequenced at a depth of 125,100 mean reads per cell for the E9.5 Anterior sample and 111,258 mean reads per cell for the E9.5 posterior sample. At E10.5, our anterior technical replicates 1 and 2 were 493,803 and 399,673, and our posterior replicates 3 and 4 492,512 and 556,014. At E11.5, our first biologic replicate was 15,542 mean reads per cell, and the second biologic replicate 20,967. Data was processed through SoupX (version 1.5.2) to remove ambient RNA contamination, as follows: E9.5 Anterior, 12%; E9.5 Posterior, autoEstCont; E10.5 Anterior, 19%, E10.5 Posterior, autoEstCont. The resulting gene by cell matrices were analyzed with the python package ScanPy v1.9.3 95. Cells were filtered to retain only high quality cells with a minimum of 2000 transcripts per cell barcode, a maximum of 10% mitochondrial transcripts, and a doublet score of 0.15 computed with Scrublet v0.2.3 96. Further downstream, any remaining cell populations lacking unique marker genes or with a high density of doublet scores near the 0.15 doublet score cutoff were also removed.
Assembly: mm10
Supplementary files format and content: h5ad with all somatic and germ cell populations
Supplementary files format and content: h5ad with only germ cell populations

source_name: E11.5 PGC migratory niche / AGM

extract_protocol:
Pou5f1-ΔPE-eGFP embryos were somite counted and age-matched. After microdissecting out the migratory region, samples were dissociated. After dissociation, cells were submitted for FACS to concentrate GFP+ migratory germ cells. Samples were reecombined with Oct4-GFP- somatic cells. These cell populations were used to create two 10X Chromium Single Cell 3' (v2 Chemistry) single cell RNA sequencing libraries.
10X ChromiumTM Single Cell 3' Reagent Kits v2 User Guide Rev A. Briefly, we used Single-Cell 3′ Reagent Version 2 Kit (10X Genomics) and used fluidics to create individual cells in gel bead-in-emulsions (GEMS). Samples were prepared directly according to the protocol, with the following steps tailored to maximize library yield: at the cDNA amplification step, we used 14 cycles, and at the sample index PCR step, we used 14 cycles. Samples were tested for quality on an Agilent Bioanalyzer High Sensitivity chip before sequencing. E9.5 and E11.5 libraries were sequenced on HiSeq 4000 (Illumina) with paired-end sequencing parameters: Read1, 98 cycles; Index1, 14 cycles; Index2, 8 cycles; and Read2, 10 cycles. E10.5 libraries were sequenced on Novaseq (Illumina) with paired-end sequencing parameters: Read1, 150 cycles; i7 Index, 8 cycles; i5 index, 0 cycles; and Read2, 150 cycles.

value: E11.5 PGC migratory niche / AGM

value: CD1 dams crossed to sires homozygous for Pou5f1-deltaPE-eGFP (MGI:3057158)


title: Torin1 treated 360min biological replicate 3

description:
Matrix file_Column AS
Dataset3
RNAseq_all_raw_counts_combined_final.txt
RNAseq_TORIN_360m_F.bw
RNAseq_TORIN_360m_R.bw

data_processing:
Raw RNA-seq reads were quality filtered (mean quality score ≥20) and first mapped to ERCC spike sequences using STAR (version 2.7.3a)
Reads not mapping to spike-in sequences were aligned to the mm10 genome and deduplicated using STAR
Gene counts were generated using the featureCounts function of the Rsubread package (version 2.0.1)
Per-gene normalized counts values and differentially expressed genes were quantified using DESeq2 (version 1.26.0) using DESeq2 generated size factors
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample as calculated by featureCounts
Supplementary files format and content: BigWigs representing replicate-merged, size factor-normalized read coverage

extract_protocol:
RNA was harvested using TRIzol reagent (invitrogen). 200ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded Total RNA Library Prep Gold kit following manufacturer's protocol. Libraries for Control and I-BETR dataset as well as Control and starvations dataset were spiked-in with RNA Spike-In Mix (4456740, Thermo Fisher Scientific) following manufacturer’s recommendations. Control samples were engaged with Mix1 and the rest samples were engaged with Mix2.

value: CY 2.4 Albino ES cells

value: Mouse embryonic stem cell

value: Torin1 treated 360min


title: DRG, LPI, 10 days, rep 2


title: ExVivoCell_72Hr_0μM_mRNA_rep2

address: 郑州市高新区科学大道100号郑州大学

description:
Gene expression in L-02 cells were cultured normally after 72h
[N2](normalized)

value: human normal liver cell

value: female

value: cultured normally after 72h


title: skin, LPI, 10 days, rep 1

value: skin

value: LPI

value: replicated 1


title: BTSC268_EV_3


title: Torin1 treated 360min biological replicate 2

description:
Matrix file_Column AR
Dataset3
RNAseq_all_raw_counts_combined_final.txt
RNAseq_TORIN_360m_F.bw
RNAseq_TORIN_360m_R.bw


title: BTSC268_EV_2


title: e9_5_post

source_name: E9.5 posterior PGC migratory niche

value: E9.5 posterior PGC migratory niche


title: Post-stressed rat (S3)

city: Xi'an, Shaanxi Province

first: Yungang

last: Xu

state: Shaanxi

address: Xi'an, Shaanxi Province

institute: Xi'an Jiaotong University

description: Singleron MatrixTM Single cell RNA sequencing

data_processing:
The demultiplexing, barcoded processing and gene counting  were made using the Celescope v1.8.1
Assembly: mRatBN6.0
Supplementary files format and content: Tab-separated values files and matrix files

organism: Rattus norvegicus

source_name: Testicular tissue

extract_protocol:
Transfer fresh tissue to a culture dish containing HBSS buffer and wash it three time. Afterwards, remove the excess buffer and transfer the tissue to a 1.5mL low-adsorption centrifuge tube. Add 200 μL of Tissue Dissociation Mix, and use sterile ophthalmic scissors to cut the tissue to minced form. After adding 1 mL of Tissue Dissociation Mix, the minced tissue homogenate was transferred to a 15 mL low-adsorption centrifuge tube for tissue dissociation. The dissociated cell suspension was filtered through a 40um filter. And the Single-cell suspensions were prepared at a concentration of 1 × 105 cells/mL in PBS (HyClone).
Single-cell suspensions were loaded onto microfluidic devices and scRNA-seq libraries were constructed according to Singleron GEXSCOPE® protocol by GEXSCOPE® Single-Cell RNA Library Kit (Singleron Biotechnologies). Individual libraries were diluted to 4nM and pooled for sequencing. Pools were sequenced on Illumina NovaSeq with 150 bp paired end reads.

value: Testicular tissue

value: Terrified-sound induced psychological stress


title: Post-stressed rat (S2)


title: BTSC268_EV_1

value: EV


title: WT control for 360min Torin1 treatment biological replicate 3

description:
Matrix file_Column AP
Dataset3
RNAseq_all_raw_counts_combined_final.txt
RNAseq_CONT_360m_F.bw
RNAseq_CONT_360m_R.bw

value: WT control for 360min Torin1 treatment

value: DMSO


title: STEM, TCDD10nM-3

city: Stillwater,

first: Khursheed

last: Iqbal

state: OK

address: 310 N Monroe St,

institute: Oklahoma state university

data_processing:
Reads from *.fastq.gz files were mapped to the human reference genome (GRCh37) using CLC Genomics Workbench 12.0 (Qiagen, Redwood City, CA).
mRNA abundance was expressed in reads per kb of exon per million reads mapped.
A false discovery rate of 0.05 was used as a cutoff for significant differential expression.
Functional patterns of transcript expression were analyzed using Ingenuity Pathway Analysis (Qiagen).
Assembly: human reference genome (GRCh37)
Supplementary files format and content: RPKM

source_name: human trophoblast stem cell

extract_protocol:
Total RNA was isolated from cells and tissues using TRIzol reagent (cat no. 15596018, Thermo Fisher, Waltham, MA).
Transcript profiles were generated from vehicle control and TCDD (10 nM)  exposures in CT27 human TS cells (n=3 experiments per group). Complementary DNA libraries from total RNA samples were prepared with Illumina TruSeq RNA preparation kits according to the manufacturer’s instructions. RNA integrity was assessed using an Agilent 2100 Bioanalyzer. Barcoded cDNA libraries were multiplexed onto a TruSeq paired-end flow cell and sequenced (100-bp paired-end reads) with a TruSeq 200-cycle SBS kit (Illumina). Samples were run on Illumina sequencers located at the KUMC Genome Sequencing Facility. Reads from *.fastq.gz files were mapped to the human reference genome (GRCh37) using CLC Genomics Workbench 12.0 (Qiagen).

value: CT27 human TS cells

value: TCDD


title: Post-stressed rat (S1)


title: skin, LPI, 10 days, rep 2

source_name: skin

value: 10 day

value: replicated 2


title: Torin1 treated 360min biological replicate 1

description:
Matrix file_Column AQ
Dataset3
RNAseq_all_raw_counts_combined_final.txt
RNAseq_TORIN_360m_F.bw
RNAseq_TORIN_360m_R.bw

value: CY 2.4 Albino ES cells

value: Mouse embryonic stem cell

value: Torin1 treated 360min


title: STEM, TCDD10nM-2


title: DRG, LPI, 10 days, rep 1

source_name: DRG

value: DRG


title: skin, LPI, 2 days, rep 4

value: skin

value: 2 days

value: replicated 4


title: e11_5_rep2

value: E11.5 PGC migratory niche / AGM

value: CD1 dams crossed to sires homozygous for Pou5f1-deltaPE-eGFP (MGI:3057158)


title: VGAT E16 - replicate 1

value: ventral midbrain


title: Normal rat (C3)

value: Testicular tissue

value: Control


title: muscle, LPI, 2 days, rep 4

source_name: muscle

value: muscle

value: LPI


title: WT control for 360min Torin1 treatment biological replicate 1

description:
Matrix file_Column AN
Dataset3
RNAseq_all_raw_counts_combined_final.txt
RNAseq_CONT_360m_F.bw
RNAseq_CONT_360m_R.bw

value: WT control for 360min Torin1 treatment

value: DMSO


title: Torin1 treated 120min biological replicate 3

description:
Matrix file_Column AM
Dataset3
RNAseq_all_raw_counts_combined_final.txt
RNAseq_TORIN_120m_F.bw
RNAseq_TORIN_120m_R.bw

value: Torin1 treated 120min


title: DRG, LPI, 2 days, rep 4


title: muscle, LPI,  10 days, rep 1

value: 10 day

value: replicated 1


title: STEM, TCDD10nM-1

value: CT27 human TS cells

value: TCDD


title: Normal rat (C2)


title: BTSC475_EV_1

value: glioblastoma stem cell-like

value: EV


title: STEM, Vehicle3

value: control


title: skin, LPI, 2 days, rep 3

value: skin

value: 2 days

value: replicated 3


title: Normal rat (C1)

value: Testicular tissue


title: RNA_edc3scd6_Replicate_2

city: Bethesda

first: Alan

last: Hinnebusch

state: MD

address: 6 Center Drive, Building 6, Room 233

department: NICHD

institute: NIH

description:
RNA_edc3scd6_Replicate_2
RawCounts_SpikeIn_AllSamples_AllReplicates.txt

data_processing:
For ribo-seq/RNA-Seq samples, Fastq records are trimmed with fastxtoolkit (version 0.0.14) to remove adapters sequences. rRNA sequence was removed with Bowtie2 (version 2-2.3.5.1) then mapped to yeast genome (sacCer3) with HISAT2 (version 2.1.1). Perfect reads were extracted with samtools (version 1.9) for downstream analysis. Normalized wiggle files and reads counts are generated with RiboSeq tools (https://github.com/hzhanghenry/RiboProR). For RNA-seq, the same protocol mentioned above for ribo-seq analysis was followed.
Assembly: sacCer3 and Saccharomyces cerevisiae.R64-1-1 release 109
Supplementary files format and content: Processed data (.txt) files contain raw reads for each file. For Ribo and parallel RNA-Sequencing, each file contains five columns providing: systemmatic gene name (Gene_ID), total reads (trx), reads in CDS, reads in 5' UTR and reads in 3' UTR. For RNA-sequencing, with spike-in normalization, processed file is a matrix with 6 columns providing: systemmatic gene name (Gene_ID), chromosome (Chr), start and end coordinates of genes (Start and End), strand information (Strand), length of the gene in basepairs (length) and multiple columns with read counts for different samples.

organism: Saccharomyces cerevisiae

source_name: Yeast whole cells

growth_protocol: Yeast cells were cultured in liquid YPD medium at 30°C to OD600 = 0.6~0.8.

extract_protocol:
For RiboSeq library: Ribosome protected RNA 25-34 nt.  For RNASeq library: total RNA
Ribosome profiling (Rnase I footprinting, size selection, RNA extraction, preadenylated linker ligation, reverse transcription, cDNA circularization, PCR amplification) was done as described in "Hcr1/eIF3j Is a 60S Ribosomal Subunit Recycling Accessory Factor In Vivo". Young and Guydosh 2019, Cell Rep, 28, 39-50 e34. RNA sequencing libraries were produced in parallel from total RNA samples by the NHLBI DNA sequencing Core at NIH (Bethesda, MD) using the TruSeq Stranded mRNA Library Prep Kit (Illumina, single-end 100 bp reads).

value: Yeast whole cells

value: MATa ade2-1 ura3-1 his3-11,15 trp1-1 leu2-3,112 can1-100 edc3::KanMX4 scd6::hphMX4


title: WT control for 120min Torin1 treatment biological replicate 3

description:
Matrix file_Column AJ
Dataset3
RNAseq_all_raw_counts_combined_final.txt
RNAseq_CONT_120m_F.bw
RNAseq_CONT_120m_R.bw

value: CY 2.4 Albino ES cells

value: Mouse embryonic stem cell

value: WT control for 120min Torin1 treatment


title: Torin1 treated 120min biological replicate 1

description:
Matrix file_Column AK
Dataset3
RNAseq_all_raw_counts_combined_final.txt
RNAseq_TORIN_120m_F.bw
RNAseq_TORIN_120m_R.bw

value: Torin1 treated 120min


title: Torin1 treated 120min biological replicate 2

description:
Matrix file_Column AL
Dataset3
RNAseq_all_raw_counts_combined_final.txt
RNAseq_TORIN_120m_F.bw
RNAseq_TORIN_120m_R.bw


title: STEM, Vehicle1


title: WT control for 120min Torin1 treatment biological replicate 2

description:
Matrix file_Column AI
Dataset3
RNAseq_all_raw_counts_combined_final.txt
RNAseq_CONT_120m_F.bw
RNAseq_CONT_120m_R.bw

value: DMSO


title: RNA_edc3scd6_Replicate_1

description:
RNA_edc3scd6_Replicate_1
RawCounts_SpikeIn_AllSamples_AllReplicates.txt


title: DRG, LPI, 2 days, rep 3

data_processing:
sequencing was carried out using the Illumina Novaseq 6000 instrument.
The raw data was handled by Skewer and data quality was checked by FastQC v0.11.2.
Clean reads were aligned to the Human genome hg38 using STAR. StringTie.
The expression of the transcript was calculated by FPKM using Perl.
Assembly: rn6
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample.
Supplementary files format and content: Tab-delimited text file includes FPKM values for each sample.

value: DRG

value: LPI


title: ST3D_103 (TCDD)

extract_protocol:
Total RNA was isolated from cells and tissues using TRIzol reagent (cat no. 15596018, Thermo Fisher, Waltham, MA).
Transcript profiles were generated from vehicle control and TCDD (10 nM)  exposures in CT27 human TS cells cultured in conditions promoting ST3D cell differentiation (n=3 experiments per group). Complementary DNA libraries from total RNA samples were prepared with Illumina TruSeq RNA preparation kits according to the manufacturer’s instructions. RNA integrity was assessed using an Agilent 2100 Bioanalyzer. Barcoded cDNA libraries were multiplexed onto a TruSeq paired-end flow cell and sequenced (100-bp paired-end reads) with a TruSeq 200-cycle SBS kit (Illumina). Samples were run on Illumina sequencers located at the KUMC Genome Sequencing Facility. Reads from *.fastq.gz files were mapped to the human reference genome (GRCh37) using CLC Genomics Workbench 12.0 (Qiagen).

value: CT27 human TS cells

value: TCDD


title: muscle, LPI, 2 days, rep 2

extract_protocol:
Rats were deeply anesthetized with isoflurane, transcardially perfused with nuclease-free saline (pH 7.4). The incised skin and muscle tissue were rapidly dissected, the C3-C6 DRGs of LPI and C2-C5 DRGs of SMIR were then extracted. All samples were immediately transferred to ice-cold RNAlater solution and refrigerated at 4°C for 48 hours. Then samples were removed from RNAlater solution, placed into fresh 1.5 mL conical tubes and stored at -80℃. Total RNA was isolated, then Gel electrophoresis and Qubit were used to exam the RNA quality and RNA integrity number (RIN). For RNA sequencing, RNA samples from seven to nine biological replicates at each time point were separated into three independent pools. Strand-specific libraries were constructed using the TruSeq RNA sample preparation kit, and sequencing was carried out using the Illumina Novaseq 6000 instrument.
Strand-specific libraries were constructed using the TruSeq RNA sample preparation kit (RS-122-2001, Illumina, San Diego, CA, USA)

value: muscle

value: replicated 2


title: BTSC268_ZBTB18-FL_1

value: glioblastoma stem cell-like


title: skin, LPI, 2 days, rep 2

value: skin

value: 2 days


title: RNA_scd6_Replicate_2

description:
RNA_scd6_Replicate_2
RawCounts_SpikeIn_AllSamples_AllReplicates.txt


title: STEM, Vehicle2

value: control


title: ST3D_102 (TCDD)


title: WT control for 120min Torin1 treatment biological replicate 1

description:
Matrix file_Column AH
Dataset3
RNAseq_all_raw_counts_combined_final.txt
RNAseq_CONT_120m_F.bw
RNAseq_CONT_120m_R.bw


title: ST3D_101 (TCDD)


title: RNA_scd6_Replicate_1

description:
RNA_scd6_Replicate_1
RawCounts_SpikeIn_AllSamples_AllReplicates.txt

value: Yeast whole cells


title: RNA_edc3_Replicate_2

description:
RNA_edc3_Replicate_2
RawCounts_SpikeIn_AllSamples_AllReplicates.txt


title: skin, LPI, 2 days, rep 1

value: replicated 1


title: Torin1 treated 60min biological replicate 3

description:
Matrix file_Column AG
Dataset3
RNAseq_all_raw_counts_combined_final.txt
RNAseq_TORIN_60m_F.bw
RNAseq_TORIN_60m_R.bw

value: CY 2.4 Albino ES cells

value: Torin1 treated 60min


title: ST3D_V3


title: Torin1 treated 60min biological replicate 2

description:
Matrix file_Column AF
Dataset3
RNAseq_all_raw_counts_combined_final.txt
RNAseq_TORIN_60m_F.bw
RNAseq_TORIN_60m_R.bw

value: Mouse embryonic stem cell


title: muscle, LPI,  2 days, rep 1


title: Torin1 treated 60min biological replicate 1

description:
Matrix file_Column AE
Dataset3
RNAseq_all_raw_counts_combined_final.txt
RNAseq_TORIN_60m_F.bw
RNAseq_TORIN_60m_R.bw


title: RNA_edc3_Replicate_1

description:
RNA_edc3_Replicate_1
RawCounts_SpikeIn_AllSamples_AllReplicates.txt


title: WT control for 60min Torin1 treatment biological replicate 3

description:
Matrix file_Column AD
Dataset3
RNAseq_all_raw_counts_combined_final.txt
RNAseq_CONT_60m_F.bw
RNAseq_CONT_60m_R.bw

value: WT control for 60min Torin1 treatment


title: ST3D_V2


title: RNA_WT_Replacte_2

description:
RNA_WT_Replacte_2
RawCounts_SpikeIn_AllSamples_AllReplicates.txt


title: DRG, LPI, 2 days, rep 1


title: skin, LPI, 6 hours, rep 4

value: 6 hours

value: replicated 4


title: WT control for 60min Torin1 treatment biological replicate 2

description:
Matrix file_Column AC
Dataset3
RNAseq_all_raw_counts_combined_final.txt
RNAseq_CONT_60m_F.bw
RNAseq_CONT_60m_R.bw

value: DMSO


title: Ribo_edc3scd6_Replicate_1

data_processing:
For ribo-seq/RNA-Seq samples, Fastq records are trimmed with fastxtoolkit (version 0.0.14) to remove adapters sequences. rRNA sequence was removed with Bowtie2 (version 2-2.3.5.1) then mapped to yeast genome (sacCer3) with HISAT2 (version 2.1.1). Perfect reads were extracted with samtools (version 1.9) for downstream analysis. Normalized wiggle files and reads counts are generated with RiboSeq tools (https://github.com/hzhanghenry/RiboProR). For RNA-seq, the same protocol mentioned above for ribo-seq analysis was followed.
Assembly: sacCer3 and Saccharomyces cerevisiae.R64-1-1 release 109
Supplementary files format and content: Processed data (.txt) files contain raw reads for each file. For Ribo and parallel RNA-Sequencing, each file contains five columns providing: systemmatic gene name (Gene_ID), total reads (trx), reads in CDS, reads in 5' UTR and reads in 3' UTR. For RNA-sequencing, with spike-in normalization, processed file is a matrix with 6 columns providing: systemmatic gene name (Gene_ID), chromosome (Chr), start and end coordinates of genes (Start and End), strand information (Strand), length of the gene in basepairs (length) and multiple columns with read counts for different samples.
Library strategy: Ribo-seq

molecule: other

value: MATa ade2-1 ura3-1 his3-11,15 trp1-1 leu2-3,112 can1-100 edc3::KanMX4 scd6::hphMX4


title: EVT_TCDD102

extract_protocol:
Total RNA was isolated from cells and tissues using TRIzol reagent (cat no. 15596018, Thermo Fisher, Waltham, MA).
Transcript profiles were generated from vehicle control and TCDD (10 nM)  exposures in CT27 human TS cells cultured in conditions promoting EVT cell differentiation (n=3 experiments per group). Complementary DNA libraries from total RNA samples were prepared with Illumina TruSeq RNA preparation kits according to the manufacturer’s instructions. RNA integrity was assessed using an Agilent 2100 Bioanalyzer. Barcoded cDNA libraries were multiplexed onto a TruSeq paired-end flow cell and sequenced (100-bp paired-end reads) with a TruSeq 200-cycle SBS kit (Illumina). Samples were run on Illumina sequencers located at the KUMC Genome Sequencing Facility. Reads from *.fastq.gz files were mapped to the human reference genome (GRCh37) using CLC Genomics Workbench 12.0 (Qiagen).

value: CT27 human TS cells

value: TCDD


title: RNA_WT_Replicate_1

description:
RNA_WT_Replicate_1
RawCounts_SpikeIn_AllSamples_AllReplicates.txt


title: Ribo_edc3scd6_Replicate_2


title: Torin1 treated 30min biological replicate 3

description:
Matrix file_Column AA
Dataset3
RNAseq_all_raw_counts_combined_final.txt
RNAseq_TORIN_30m_F.bw
RNAseq_TORIN_30m_R.bw

value: Torin1 treated 30min


title: EVT_TCDD101


title: DRG, LPI, 6 hours, rep 4

value: DRG

value: LPI


title: ST3D_V1


title: WT control for 360min Torin1 treatment biological replicate 2

description:
Matrix file_Column AO
Dataset3
RNAseq_all_raw_counts_combined_final.txt
RNAseq_CONT_360m_F.bw
RNAseq_CONT_360m_R.bw

value: WT control for 360min Torin1 treatment


title: skin, LPI, 6 hours, rep 3

value: skin

value: replicated 3


title: Torin1 treated 30min biological replicate 2

description:
Matrix file_Column Z
Dataset3
RNAseq_all_raw_counts_combined_final.txt
RNAseq_TORIN_30m_F.bw
RNAseq_TORIN_30m_R.bw


title: EVT_V3

value: control


title: muscle, LPI, 6 hours, rep 4

value: muscle


title: muscle, LPI, 6 hours, rep 3


title: Ribo_scd6_Replicate_2

value: Yeast whole cells


title: Ribo_scd6_Replicate_1


title: EVT_V2


title: EVT_TCDD103


title: Torin1 treated 30min biological replicate 1

description:
Matrix file_Column Y
Dataset3
RNAseq_all_raw_counts_combined_final.txt
RNAseq_TORIN_30m_F.bw
RNAseq_TORIN_30m_R.bw

value: CY 2.4 Albino ES cells

value: Mouse embryonic stem cell


title: EVT_V1


title: WT control for 30min Torin1 treatment biological replicate 3

description:
Matrix file_Column X
Dataset3
RNAseq_all_raw_counts_combined_final.txt
RNAseq_CONT_30m_F.bw
RNAseq_CONT_30m_R.bw

value: WT control for 30min Torin1 treatment


title: Ribo_edc3_Replicate_1


title: WT control for 30min Torin1 treatment biological replicate 2

description:
Matrix file_Column W
Dataset3
RNAseq_all_raw_counts_combined_final.txt
RNAseq_CONT_30m_F.bw
RNAseq_CONT_30m_R.bw


title: skin, LPI, 6 hours, rep 2

value: 6 hours

value: replicated 2


title: muscle, LPI, 6 hours, rep 2


title: Ribo_WT_Replicate_2


title: WDR4_03

city: Jena

first: Marco

last: Groth

address: Beutenbergstraße 11

department: Core Facility - Next Generation Sequencing

institute: Leibniz Institute on Aging - FLI

description:
WDR4_03
counts_RPMs_RPKMs.xls

data_processing:
Reads were extracted in FastQ format using Illumina’s bcl2FastQ v2.20.0.422. RNA-specific and UMIs-specific reads were separated in individual FastQ files.
UMIs were added to read headers using umi_tools v1.1.1.
Reads were mapped using TopHat2 v2.1.0 (--no-convert-bam --no-coverage-search -x 1 -g 1)
PCR duplicons occurred in library preparation were removed after mapping of reads based on UMIs (unique molecular identifier) using umi_tools v1.1.1.
Counting of reads per gene was done using featureCounts v2.0.3
RPMs and RPKMs were calculated using the statistical environment R (v 4.1.3).
Assembly: GRCh38.92
Supplementary files format and content: xls file containing read counts/RPMs/RPKMs per gene

source_name: Skin

growth_protocol: Cells were cultivated in MEM alpha medium supplemented with 15% FCS and 1% penicillin/streptomycin before serum-starvation.

extract_protocol:
Total RNA from was isolated with the Qick-RNA MicroPrep Kit (Zymo Research), which includes a DNAse-Digestion step.
Libraries were prepared using NEBNext Ultra II Directional RNA Library Preparation Kit in combination with NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Multiplex Oligos for Illumina (Unique Dual Index UMI Adaptors RNA) following the manufacturer's instructions (NewEngland Biolabs).

treatment_protocol: Cells were serum starved in MEM alpha medium supplemented with 0.1% FCS and 1% penicillin/streptomycin during 3 days before RNA isolation.

value: Skin

value: fibroblasts

value: serum-starved (3 days)


title: Ribo_WT_Replicate_1


title: skin, LPI, 6 hours, rep 1

value: replicated 1


title: I-BETR ES cells biological replicate 4

description:
Matrix file_Column I
Dataset1
RNAseq_all_raw_counts_combined_final.txt
RNAseq_IBETR_F.bw
RNAseq_IBETR_R.bw

value: I-BETR


title: Rpb1ChIP_edc3scd6_Replicate_2

data_processing:
For ChIP-Seq: Sequence data were aligned to the SacCer3 version of the genome sequence using Bowtie2 with parameters -X 1000 -very-sensitive, to map sequences up to 1 kb with maximum accuracy. PCR duplicates from ChIP-seq data were removed using the samtools rmdup package.
Assembly: sacCer3
Supplementary files format and content: Processed data (csv) files contain raw reads for each sample.  Rpb1 average occupancy over gene bodies file contains two columns: systemmatic gene name (ORF) and avg occupancy.

extract_protocol:
Briefly, for ChIP assays, chromatin was prepared from formaldehyde-crosslinked cells, immunoprecipitated with Rpb1 antibodies, and the DNA was extracted.
DNA libraries for Illumina paired-end sequencing were prepared using DNA Library Prep Kit for Illumina from New England Biolabs

treatment_protocol: In additional columns of the SAMPLES section

value: anti-Rpb1 (Biolegend #664906)

value: MATa ade2-1 ura3-1 his3-11,15 trp1-1 leu2-3,112 can1-100 edc3::KanMX4 scd6::hphMX4


title: I-BETR ES cells biological replicate 3

description:
Matrix file_Column H
Dataset1
RNAseq_all_raw_counts_combined_final.txt
RNAseq_IBETR_F.bw
RNAseq_IBETR_R.bw


title: I-BETR ES cells biological replicate 2

description:
Matrix file_Column G
Dataset1
RNAseq_all_raw_counts_combined_final.txt
RNAseq_IBETR_F.bw
RNAseq_IBETR_R.bw


title: WT control for 30min Torin1 treatment biological replicate 1

description:
Matrix file_Column V
Dataset3
RNAseq_all_raw_counts_combined_final.txt
RNAseq_CONT_30m_F.bw
RNAseq_CONT_30m_R.bw

value: DMSO


title: Ribo_edc3_Replicate_2


title: Rpb1ChIP_edc3scd6_Replicate_3


title: WT control for 60min Torin1 treatment biological replicate 1

description:
Matrix file_Column AB
Dataset3
RNAseq_all_raw_counts_combined_final.txt
RNAseq_CONT_60m_F.bw
RNAseq_CONT_60m_R.bw

value: WT control for 60min Torin1 treatment


title: DRG, LPI, 6 hours, rep 3

value: DRG

value: LPI

value: replicated 3


title: muscle, LPI,  6 hours, rep 1

value: muscle


title: DRG, LPI, 2 days, rep 2

value: 2 days


title: WDR4_02

description:
WDR4_02
counts_RPMs_RPKMs.xls


title: WDR4_01

description:
WDR4_01
counts_RPMs_RPKMs.xls


title: Rpb1ChIP_edc3scd6_Replicate_1

value: Yeast whole cells


title: WDR4_04

description:
WDR4_04
counts_RPMs_RPKMs.xls


title: 1BR3_03

description:
1BR3_03
counts_RPMs_RPKMs.xls

value: wild type


title: I-BETR ES cells biological replicate 1

description:
Matrix file_Column F
Dataset1
RNAseq_all_raw_counts_combined_final.txt
RNAseq_IBETR_F.bw
RNAseq_IBETR_R.bw

value: CY 2.4 Albino ES cells

value: Mouse embryonic stem cell


title: skin, LPI, 0 day, rep 4

value: skin

value: 0 day

value: replicated 4


title: DRG, LPI, 6 hours, rep 2

value: 6 hours

value: replicated 2


title: Control for I-BETR ES cells biological replicate 4

description:
Matrix file_Column E
Dataset1
RNAseq_all_raw_counts_combined_final.txt
RNAseq_WT_CONT_F.bw
RNAseq_WT_CONT_R.bw

value: WT control for I-BETR


title: Rpb1ChIP_WT_Replicate_2

value: anti-Rpb1 (Biolegend #664906)


title: muscle, LPI, 0 day, rep 4


title: DRG, LPI, 0 day, rep 4


title: Control for I-BETR ES cells biological replicate 1

description:
Matrix file_Column B
Dataset1
RNAseq_all_raw_counts_combined_final.txt
RNAseq_WT_CONT_F.bw
RNAseq_WT_CONT_R.bw

value: DMSO


title: MNPs from unaffected intestinal mucosa, SI4

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 28+90 or 28+91 base paired-end mode.
Illumina RTA3 v3.4.4 software was used for base calling.
Generated reads were input into the cellranger pipeline (Cell Ranger v.6.0.0, 10x Genomics) for UMI counting for each gene - cell (barcode) combination.
Assembly: refdata-gex-GRCh38-2020-A
Supplementary files format and content: genematrix.csv: comma-delimited text files including UMI counts for all cells detected

source_name: intestinal tract

extract_protocol:
Sinlge cell droplets were generated by 10x Genomics Chromium Controller, and cDNAs with UMIs were generated at single-cell level.
The single cell libraries were prepared following the protocol outlined in the Chromium Single Cell 5' Reagent Kits v2 User Guide.

value: intestinal tract

value: mononuclear phagocytes

tag: disease

value: unaffected intestinal mucosa from patients with right-sided colon cancer

value: Male


title: CK176-SI

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 101+101 base paired-end mode.
Illumina RTA 3.4.4 software was used for base calling.
Generated reads were input into the BD Rhapsody Targeted Analysis Pipeline (Revision 13) for UMI counting for each cell(index)-gene combination.
Assembly: the fasta file ("1329_Osaka_University_Mari_Murakami_20200512_amplicons.fasta") based on the customized BD Rhapsody Immune Response Panel Hs
Supplementary files format and content: comma-delimited text files including UMI count for each cell(index)-gene combination

extract_protocol:
Single-cell RNA-seq analysis was conducted using BD Rhapsody Single-Cell Analysis System (BD BioScience) following the manufacture’s protocol.
For library construction, we used a customized BD Rhapsody Immune Response Panel Hs.

tag: tissue

tag: disease state


title: 1BR3_04

description:
1BR3_04
counts_RPMs_RPKMs.xls

value: Skin

value: fibroblasts

tag: treatment

value: serum-starved (3 days)


title: MNPs from unaffected intestinal mucosa, SI2

value: Female


title: 1BR3_01

description:
1BR3_01
counts_RPMs_RPKMs.xls

value: wild type


title: Control for I-BETR ES cells biological replicate 2

description:
Matrix file_Column C
Dataset1
RNAseq_all_raw_counts_combined_final.txt
RNAseq_WT_CONT_F.bw
RNAseq_WT_CONT_R.bw

value: CY 2.4 Albino ES cells

value: Mouse embryonic stem cell


title: Rpb1ChIP_WT_Replicate_1

value: Yeast whole cells


title: cropseq_nih3t3_library2_grna

data_processing:
fastqs were trimmed using FASTX-toolkit
trimmed fastqs were aligned using bowtie2
Assembly: gRNA library
Supplementary files format and content: text file containing gRNA counts
Library strategy: CRISPR library

extract_protocol:
cells were washed three times, trypsinized, and strained through a 40 µm cell strainer
Up to 20 μg of genomic DNA per sample was used to amplify the U6-3’ to gRNA hairpin region. PCR2 was performed to add full-length Illumina sequencing adapters using internally ordered primers with equivalent sequences to NEBNext Index Primer Sets 1 and 2 (New England Biolabs). All PCRs were performed using Q5UltraII polymerase (NEB). Pooled samples were sequenced using MiSeq (Illumina), using 50-nt reads and collecting greater than 100 reads per gRNA in the library.  The library prep primers were as follows: PCR1: U6_BcA_r1seq_halftail  5' ACTCTTTCCCTACACGACGCTCTTCCGATCTACTAGGGAAAGGACGAAACACCG 3' gRNAFE_r2seq_halftail 5' GACTGGAGTTCAGACGTGTGCTCTTCCGATCTGCCTTATTTAAACTTGCTATGCTGT 3' PCR2: r1seq_fulltail 5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTC 3’ r2seq_fulltail (Two distinct indexed versions of this primer were used to allow for pooling) 5' CAAGCAGAAGACGGCATACGAGATNNNNNNNNGTGACTGGAGTTCAGACGTGTGCT 3'


title: DRG, LPI, 6 hours, rep 1

value: DRG

value: LPI

tag: time

value: 6 hours

tag: replicated animal_number

value: replicated 1


title: Control for I-BETR ES cells biological replicate 3

description:
Matrix file_Column D
Dataset1
RNAseq_all_raw_counts_combined_final.txt
RNAseq_WT_CONT_F.bw
RNAseq_WT_CONT_R.bw

tag: cell line

tag: cell type

value: WT control for I-BETR

value: DMSO


title: skin, LPI, 0 day, rep 2

value: skin

value: 0 day

value: replicated 2


title: MNPs from unaffected intestinal mucosa, SI3

value: intestinal tract

value: mononuclear phagocytes

value: unaffected intestinal mucosa from patients with right-sided colon cancer

tag: Sex


title: skin, LPI, 0 day, rep 3

value: replicated 3


title: Rpb1ChIP_WT_Replicate_3

value: anti-Rpb1 (Biolegend #664906)

tag: strain


title: DRG, LPI, 0 day, rep 3


title: MGHS, replicate3, scRNAseq

city: Beijing

first: hua

middle: xiu

last: ma

address: NO.2 Yuanmingyuan weat road

institute: China Agriclutural university

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1  (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/atest/what-is-cell-ranger)
Assembly: GCF_016772045.2
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

organism: Ovis aries

source_name: rumen epithelial

extract_protocol:
Three sheep from each experimental group were selected randomly for scRNA-seq. Epithelial tissues from the ventral bursa region of the rumen were collected post-slaughter, washed with saline to remove digestive fluids, and stored in liquid nitrogen.Rumen epithelial tissues (≥0.2 g) were prepared by absorbing residual liquid, placing the tissues in sterile petri dishes, and chopping them into 1-2 mm³ pieces on ice.The pieces were transferred to freezing tubes, frozen in liquid nitrogen for 5 minutes, and stored in an ultra-low temperature freezer. A quality control (QC) sample was similarly prepared but frozen without chopping. Before nucleus isolation, the QC sample was thawed, and RNA was extracted to confirm integrity.
Gel beads containing the barcode information bind to a mixture of cells and enzymes and enter the reservoir separated by oil to form GEMs (Gel Beads-In-Emulsions). Afterwards, the gel beads are dissolved to release the capture sequence containing the Barcode sequence, reverse transcribe the cDNA fragments, and label the sample. The gel beads were crushed and the oil droplets were broken up and PCR amplification was performed using cDNA as a template. The products of all GEMs were mixed to construct a standard sequencing library.

value: rumen epithelial

value: male

value: rumen epithelial cells

value: MGHS


title: MGNS, replicate2, scRNAseq

description: 10x Genomics

value: MGNS


title: MGHS, replicate1, scRNAseq

description: 10x Genomics


title: MGHS, replicate2, scRNAseq

description: 10x Genomics


title: MGNS, replicate3, scRNAseq

description: 10x Genomics


title: muscle, LPI, 0 day, rep 2

city: Shanghai

first: xiaoyan

last: Meng

institute: eastern hepatobililary surgical hospital

value: muscle

value: LPI


title: 1BR3_02

description:
1BR3_02
counts_RPMs_RPKMs.xls

value: Skin

value: fibroblasts

value: wild type

value: serum-starved (3 days)


title: MNPs from unaffected intestinal mucosa, SI1

tag: age

value: Male


title: muscle, LPI, 0 day, rep 3

value: 0 day


title: direct_capture_nih3t3_library2_grna

city: Durham

first: Charles

last: Gersbach

institute: Duke University


title: cDC1 cells, 12-HETE_4

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 101-base single-end mode.
Illumina RTA v3.4.4 software was used for base calling.
Generated reads were mapped to the human (hg19) reference genome using TopHat v2.1.1 in combination with Bowtie2 ver. 2.2.8 and SAMtools ver. 0.1.18.
Raw count data of mapped reads were calculated using featureCounts software included in subread-2.0.0 tool package.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include raw count values for each sample

source_name: ileum

extract_protocol:
Total RNA was harvested using TRIzol reagent.
Full-length cDNA was prepared using a SMART-Seq HT Kit (Takara Bio, Japan) according to the manufacturer's instructions. According to the SMARTer kit instructions, an Illumina library was then prepared using a NexteraXT DNA Library Preparation Kit (Illumina).

value: ileum

tag: individual

value: individual 4

value: type1 conventional dendritic cells

value: Female


title: MGNS, replicate1, scRNAseq

description: 10x Genomics

value: rumen epithelial


title: DRG, LPI, 0 day, rep 2

value: DRG

value: replicated 2


title: cDC1 cells, LA_4

value: LA


title: BM_Rep1_Untreated

first: Robert

last: Policastro

state: Massachusetts

address: 451 D St Unit #600

institute: Ensoma Inc.

description: TRACE

data_processing:
For computational analyses, unless otherwise stated default parameters are used for all commands. All code for the below initial TRACE processing is provided on github (https://github.com/ensoma/andrelieber-trace-isa-wf). Briefly, fastq trimming using cutadapt [https://doi.org/10.14806/ej.17.1.200] (v4.4) was performed in four steps to ensure proper read structure: 1) R1 and R2 adapter trimming (-g ”^NNNNCGAGTTTTAATGACTCCAACT” -G ”^AGTGGCACAGCAGTTAGGNNNNNNNNAGATGTGTATAAGAGACAG” -m20 –e5), 2) IR trimming (-g ”^TAAGTGTATGTAAACTTCCGACTTCAACTG” -m20 -e4), 3) R1 and R2 adapter readthrough trimming (-a ”CTGTCTCTTATACACATCTNNNNNNNNCCTAACTGCTGTGCCACT” -A ”AGTTGGAGTCATTAAAACTCGNNNN” -m20 -e4), and IR readthrough trimming (-A ”CAGTTGAAGTCGGAAGTTTACATACACTTA” -m20 –e3). FastQC [https://www.bioinformatics.babraham.ac.uk/projects/fastqc/] (v0.12.1) is then used for read QC before and after each processing step
The ENSEMBL mouse GRCm39 hard-masked assembly (https://ftp.ensembl.org/pub/release-111/fasta/mus musculus/dna/Mus musculus.GRCm39.dna rm.primary assembly.fa.gz) and v111 annotation (https://ftp.ensembl.org/pub/release-111/gtf/mus musculus/Mus musculus.GRCm39.111.chr.gtf.gz) were concatenated to the payload sequence, indexed with bwa [https://doi.org/10.48550/arXiv.1303.3997] (0.7.17), and the previously trimmed and filtered reads aligned to the index with bwa-mem.
There are three samtools [PMID: 19505943] (v1.17) alignment filtering steps to ensure accurate insertion sites: 1) Flag and quality score filtering (samtools view –q30 –F 3852 –f3; samtools sort –n; samtools fixmate –m; samtools view –f2; samtools sort), 2) Removal of PCR duplicates (samtools sort –n; samtools fixmate –m; samtools sort; samtools markdup –r), 3) Removing read-pairs with more than 5 soflcip reads on the 5’ end of R1 (a custom python (v3.10.13) and pysam [https://github.com/pysam-developers/pysam] (v0.21.0) script; samtools sort –n; samtools fixmate; samtools view –f3; samtools sort). Samtools flagstat and idstat are used before and after each filtering step to collect various metrics about the alignments.
Insertion sites are called using a custom Python and Pysam script that finds the genomic coordinate of the 5’-most non-sofclipped base on the R1 read. Insertion sites within 5 bases are summed and the new location set at the position with the largest read number, or given equal read numbers for multiple positions the median position of those sites. Insertion sites with a score ≥ 2 in 2 or more samples are removed using bedtools [PMID: 20110278] (2.31.0) due to their likely status of being artifacts of the TRACE method. Insertion sites are annotated to the nearest gene using a custom R (4.3.1) script that utilizes ChIPseeker [PMID: 25765347] (v1.36.0) with the settings: tssRegion=c(-2000, 200), level=”transcript”, sameStrand=TRUE. Insertion sites were retained if present in at least 2 of 3 technical replicates.
Assembly: GRCm39
Supplementary files format and content: HDAd_tHMGA2_GFP.fasta contains the sequence of the tHMGA2-containing vector.
Supplementary files format and content: annotated_insertion_sites.tsv is a table containing the post-filtering integration sites for all samples, as well as their summed scores and annotations to the nearest gene and transcript.
Library strategy: TRACE Insertion Site Analysis

source_name: Bone Marrow

extract_protocol:
Genomic DNA (gDNA) from week 44 bone marrow cells were extracted using the Quick-DNA miniprep kit (Zymo Research).
TRACE sequencing was performed as previously described [PMID: 35705805] with the following modifications. Tagmentation was done in an 80 µL reaction by incubating 500 ng of genomic DNA (gDNA) with 3 µL of Tn5 transposase (Diagenode; C01070010) and 4.8 µL of annealed Tn5 adapter top and bottom oligos at 45 µM in 5X TAPs buffer (50 mM TAPS-NaOH, pH 8.5, 25 mM MgCl2) with 8 µL DMF for 10 mins at 55°C. The reaction was quenched with 160 µL RLT buffer (Qiagen; 79216) followed by a 0.7X SPRI bead cleanup (Beckman Coulter; B23318). Tagmented DNA was eluted with 30 µL of nuclease-free water and 20 µL was used in the first round of PCR at 20 cycles with the Tn1c and LCI primers and Q5 High-Fidelity DNA Polymerase (NEB; M0494S), and the product was cleaned with 0.7X SPRI beads and eluted into 20 µL of nuclease-free water. 12 µL was then used for nested PCR at 20 cycles with primers MA-F and MA-LCII, and the product was purified with 0.7X SPRI-beads and eluted into 20 µL of nuclease-free water. 2 µL was used as input to indexing PCR with the NEBNext Multiplex Oligos for Illumina (Dual Index Primers Set 1) (NEB; E7600S) followed by a 0.7X SPRI bead cleanup. Final libraries were sequenced paired-end 150 x 2 (MiSeq Reagent Kit v2 300-cycles; Ms-102-2002) on an Illumina MiSeq.

value: Bone Marrow

value: Mononuclear Cells

value: untreated

value: Week 44


title: cDC1 cells, PA_4

value: PA


title: BM_257_Rep3_tHMGA2-GFP

description: TRACE


title: BM_Rep2_Untreated

description: TRACE


title: skin, LPI, 0 day, rep 1

address: Changhai road 225. Shanghai, China

value: skin

value: LPI

value: replicated 1


title: Plasmid library, rep 5

city: Salt Lake City

first: Justin

last: English

state: UT

address: 15 N Medical Drive East, Rm 4100

department: Biochemistry

institute: University of Utah

data_processing:
Barcodes were obtained by collecting the first 24 nucleotides of each read from demultiplexed fastq files.
Paired-end reads were trimmed using TrimGalore and joined using FastQ-Join.
Barcodes were clustered within each sample via Starcode using a Levenshtein distance of one.
Assembly: Custom barcode dictionary.
Supplementary files format and content: finalBarcodeMap.csv contains the barcode sequences and associated candidate transcriptional response elements
Supplementary files format and content: rpms.csv contains the barcode reads per million for each treatment and plasmid library

organism: synthetic construct

source_name: Synthetic (input plasmid)

growth_protocol: Cell lines were maintained in maintenance media (typically DMEM supplemented with 10% FBS and antibiotics) in a 37C humidified incubator with 5% carbon dioxide.

extract_protocol:
RNA was isolated from cell pellets using the AllPrep DNA/RNA Mini Kit (Qiagen) with QIAshredder columns (Qiagen).
RNA libraries were prepared using the Superscript IV One-Step RT-PCR System (Invitrogen) with custom primers. DNA libraries from plasmid inputs were prepared using the Platinum SuperFI II Green PCR Master Mix (Invitrogen) with custom primers.

treatment_protocol: Cells on 10 cm dishes were transfected with 10 micrograms of the TRE-MPRA plasmid library when subconfluent.Six hours after transfection, the maintenance media was replaced with serum-free media. The following day, cells were treated for six hours. Cells were then trypsinied and pellets were frozen at -80 C until processing.

value: Synthetic (input plasmid)


title: BM_Rep3_Untreated

description: TRACE


title: BM_257_Rep1_tHMGA2-GFP

description: TRACE


title: Plasmid library, rep 3


title: cDC1 cells, control_4

value: ileum

value: control


title: DRG, LPI, 0 day, rep 1

value: 0 day


title: Plasmid library, rep 1


title: BM_256_Rep3_tHMGA2-GFP

description: TRACE


title: Plasmid library, rep 2


title: BM_257_Rep2_tHMGA2-GFP

description: TRACE


title: cDC1 cells, 12-HETE_3

value: individual 3

value: type1 conventional dendritic cells

value: Male


title: Plasmid library, rep 4


title: e9_5_ant

source_name: E9.5 anterior PGC migratory niche

extract_protocol:
Pou5f1-ΔPE-eGFP embryos were somite counted and age-matched. After microdissecting out the migratory region, samples were dissociated. After dissociation, cells were submitted for FACS to concentrate GFP+ migratory germ cells. Samples were reecombined with Oct4-GFP- somatic cells. These cell populations were used to create two 10X Chromium Single Cell 3' (v2 Chemistry) single cell RNA sequencing libraries.
10X ChromiumTM Single Cell 3' Reagent Kits v2 User Guide Rev A. Briefly, we used Single-Cell 3′ Reagent Version 2 Kit (10X Genomics) and used fluidics to create individual cells in gel bead-in-emulsions (GEMS). Samples were prepared directly according to the protocol, with the following steps tailored to maximize library yield: at the cDNA amplification step, we used 14 cycles, and at the sample index PCR step, we used 14 cycles. Samples were tested for quality on an Agilent Bioanalyzer High Sensitivity chip before sequencing. E9.5 and E11.5 libraries were sequenced on HiSeq 4000 (Illumina) with paired-end sequencing parameters: Read1, 98 cycles; Index1, 14 cycles; Index2, 8 cycles; and Read2, 10 cycles. E10.5 libraries were sequenced on Novaseq (Illumina) with paired-end sequencing parameters: Read1, 150 cycles; i7 Index, 8 cycles; i5 index, 0 cycles; and Read2, 150 cycles.

value: E9.5 anterior PGC migratory niche

value: CD1 dams crossed to sires homozygous for Pou5f1-deltaPE-eGFP (MGI:3057158)


title: BM_256_Rep2_tHMGA2-GFP

description: TRACE

value: Bone Marrow


title: cDC1 cells, PA_3


title: Gulf pipefish frontal jaws scRNAseq atlas (sample 2)

city: Eugene

first: William

last: Cresko

state: Oregon

address: 1505 Franklin Blvd #131

institute: University of Oregon

description: 10X Genomics

data_processing:
We ran Cell Ranger (10X Genomics 3.0.2) using our scRNAseq reads, the Gulf pipefish genome assembly (ROL_Ssco_1.1) with mitochondrial genome (NC_065499.1), and modified gene annotations (RefSeq annotations were integrated with scISOseq to increase 3' UTR lengths). We analyzed Cell Ranger’s output using Seurat (v4.1.0) on R on R (v4.0.2). To remove extraneous RNA counts from the dataset, we used SoupX (v1.5.2). We identified doublet scores for our dataset using scrublet (v0.2.3). We finally removed cells with less than 500 features, greater than 9000 features, greater than 1E5 RNA counts, with a scrublet score greater than the detected threshold (.76 for sample 2 and .21 for sample 2), or greater than 10% mitochondrial reads. We normalized the datasets with SCTransform (v0.3.3). We used Seurat’s integration tools, SelectIntegrationFeatures using 3,000 feature genes, FindIntegrationAnchors using SCT normalization, and IntegrateData using SCT normalization, to integrate the two datasets. We then used the integrated dataset to complete PCA analysis. We next clustered the cells using 30 PCs and plotted the data on a UMAP with Seurat.
Assembly: ROL_Ssco_1.1
Supplementary files format and content: Individual processed files have each libraries data after removing doublets and extraneous RNA. The combined processed file has the integrated data after cell clustering.

organism: Syngnathus scovelli

source_name: Entire Embryo

growth_protocol: Wild caught pregnant males

extract_protocol:
Embryos were dissociated in 460ul of .25% trypsin and 40ul 100mg/ml collagenase I. Cells were filtered using a 40uM cell strainer. Cell concentratoins were quantified with the TC20 Automated Cell Counter then diluted to 800 cells/ul in .04%. The University of Oregon Genomics and Cell Characterization Core prepared single cell libraries for the two samples using the 10X Genomics Single Cell 3' Genome Expression mRNAseq kit with NextGEM v3.1 chemistry.
10X Genomics Single Cell 3' Genome Expression mRNAseq kit with NextGEM v3.1 chemistry

value: Entire Embryo

value: All cells from embryo


title: muscle, LPI, 2 days, rep 3

value: muscle

value: 2 days

value: replicated 3


title: ExVivoCell_72Hr_20μM_miRNA_rep2

address: 郑州市高新区科学大道100号郑州大学

description:
Gene expression after 72 h of exposure to 20 μM of CdCl2 in L-02 cell
[cd2](normalized)

hyb_protocol: Array hybridization were performed according to the Agilent miRNA Microarray System with miRNA Complete Labeling and Hyb Kit protocol (Agilent Technology, Agilent p/n 5190-0456).1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60°C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (Agilent p/n G2505C) using scan settings for one-color scans(Scan region Agilent HD (61 x 21.6 mm), Scan resolution 3μm, Tiff file dynamic range 20bit, Dye channel is set to Green and Green PMT gain is set to 100%).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v14.9 software package (Agilent Technologies).

source_name: L-02 cells,72hr, 20μM

label_protocol: Sample labeling were performed according to the Agilent miRNA Microarray System with miRNA Complete Labeling and Hyb Kit protocol (Agilent Technology, Agilent p/n 5190-0456). Briefly, total miRNA from each sample was labeled with Cyanine 3-pCp under the action of T4 RNA ligase. The labeled cRNA over the procession of  inspissation and desiccation and then redissolved with water.

extract_protocol: The total RNA of the cells was extracted by the TRIzol assay. The RNA purified was according to RNasey Mini Kit (Qiagen 74104, USA). The quantity of the total RNA from each sample was measured by NanoDrop® ND-1000 (Thermo-Fisher Scientific, USA) and the integrity of the total RNA and gDNA contamination were measured by agarose gel electrophoresis.

value: human normal liver cell

value: female


title: ExVivoCell_72Hr_20μM_miRNA_rep3

address: 郑州市高新区科学大道100号郑州大学

description:
Gene expression after 72 h of exposure to 20 μM of CdCl2 in L-02 cell
[cd3](normalized)


title: cDC1 cells, LA_3

value: LA


title: BM_256_Rep1_tHMGA2-GFP

description: TRACE

value: Mononuclear Cells

value: Week 44


title: BM_254_Rep3_tHMGA2-GFP

description: TRACE


title: cDC1 cells, 12-HETE_2

value: ileum

value: individual 2


title: cDC1 cells, LA_2

value: type1 conventional dendritic cells


title: BM_254_Rep2_tHMGA2-GFP

description: TRACE


title: knockout strain, 0.5mM-2

city: Shenzhen

first: Jinquan

last: Li

state: Guangdong

address: 3688 Nanhai Avenue

institute: Shenzhen University

data_processing:
Raw reads were quality filtered and adapter trimmed with fastp.
Trimmed reads were then mapped to the genome of H. volcanii DS2 using Bowtie2.
Assembly: GCF_000025685.1
Supplementary files format and content: tab-delimited text files include TPM values for each sample

organism: Haloferax volcanii DS2

source_name: cell culture

growth_protocol: Strains were grown in Hv-YPC medium at 45°C until OD600 reach 0.5.

extract_protocol:
Total RNA was extracted using Direct-zol RNA MiniPrep Kits (Zymo) according to the manufacturer’s instructions.
Sequencing libraries were generated using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB) following manufacturer’s recommendations.

treatment_protocol: Sodium bisulfite was added to the final concentration of 0.1 or 0.5 mM and continuously cultured for 48 h.

value: cell culture

value: HVO_RS06830 gene knockout

value: 0.5mM sodium bisulfite


title: knockout strain, 0.5mM-1


title: ExVivoCell_72Hr_20μM_miRNA_rep1

first: Panpan

last: Wang

address: 郑州市高新区科学大道100号郑州大学

institute: 郑州大学

description:
Gene expression after 72 h of exposure to 20 μM of CdCl2 in L-02 cell
[cd1](normalized)


title: ExVivoCell_72Hr_0μM_miRNA_rep1

address: 郑州市高新区科学大道100号郑州大学

description:
Gene expression in L-02 cells were cultured normally after 72h
[N1](normalized)

source_name: L-02 cells,72hr, 0μM

value: cultured normally after 72h


title: Day4 pregnant uterus

city: Bunkyo-ku

first: Shizu

last: Aikawa

state: Tokyo

address: 7-3-1 Hongo

institute: The University of Tokyo

data_processing:
Raw reads were processed by Cell Ranger with default setting.
Assembly: mm10
Supplementary files format and content: filtered_feature_bc_matrix.h5.gz:The filtered feature count matrix generated from Cell Ranger.
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg.gz: image of tissue and spots
Supplementary files format and content: scalefactors_json.json.gz: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png.gz: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png.gz: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv.gz: list of spatial barcodes and the coodinates specifying spots
Library strategy: Spatial transcriptomics

source_name: uterus

extract_protocol:
After reaction with Proteinase K for 40 min, the sections were hybridized with spatial tags on the slides according to manufacturer's protocol.
Following the hybridization with spatial tags, reverse-transcribed in situ according to manufacturer's protocol.

value: uterus

value: wildtype

value: pregnancy day 4


title: Day 6 pregnant uterus, implantation site

value: pregnancy day 6


title: cDC1 cells, 12-HETE_1

value: individual 1

value: Male


title: BM_254_Rep1_tHMGA2-GFP

city: Boston

description: TRACE

value: Bone Marrow


title: ExVivoCell_72Hr_0μM_miRNA_rep3

city: Zhengzhou

address: 郑州市高新区科学大道100号郑州大学

description:
Gene expression in L-02 cells were cultured normally after 72h
[N3](normalized)

value: human normal liver cell

value: female


title: cDC1 cells, PA_2

value: PA


title: ExVivoCell_72Hr_0μM_miRNA_rep2

address: 郑州市高新区科学大道100号郑州大学

description:
Gene expression in L-02 cells were cultured normally after 72h
[N2](normalized)


title: knockout strain, 0.1mM-2

value: 0.1mM sodium bisulfite


title: BM_253_Rep3_tHMGA2-GFP

description: TRACE

value: Mononuclear Cells

value: Week 44


title: direct_capture_hek293T_library1_nih3t3_library2_72hr_grna

address: 2127 Campus Drive


title: cDC1 cells, control_2

value: ileum

value: individual 2

value: type1 conventional dendritic cells

value: control


title: cropseq_hek293T_library1_nih3t3_library2_72hr_grna


title: BM_253_Rep2_tHMGA2-GFP

description: TRACE


title: cDC1 cells, control_3

value: individual 3


title: BM_253_Rep1_tHMGA2-GFP

description: TRACE


title: cDC1 cells, LA_1

value: LA


title: BM_251_Rep3_tHMGA2-GFP

description: TRACE


title: cDC1 cells, PA_1


title: Gulf pipefish frontal jaws scRNAseq atlas (sample 1)

description: 10X Genomics

value: Entire Embryo

value: All cells from embryo


title: knockout strain, 0.1mM-1

value: cell culture

value: HVO_RS06830 gene knockout


title: escherichia coli, BL21(DE3), NmGNAT-3

city: Nanjing

first: Jinyuan

address: No. 138, Xianlin Street, Qixia District, Nanjing City, Jiangsu Province

institute: Nanjing University of Traditional Chinese Medicine

description: fpkm all samples(NmY_3)

data_processing:
Illumina NovaSeq6000 reads were trimmed and clipped for quality control in Fastp v0.22.0
High quality reads in each sample were mapped to the reference genome Escherichia coli BL21(DE3)  GCF_000022665.1 using analysis tool: Hisat2
rRNA contamination assessment using Blast
Expression analysis Quantify gene and transcript abundances from paired-end RNA-Seq data using RSEM
Differential expression analysis was performed using the DESeq2 v1.4.5
Assembly: BL21(DE3)(https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000022665.1/)
Supplementary files format and content: table-delimited text file includes raw counts for each sample
Supplementary files format and content: table-delimited text files include FPKM values for each sample

organism: Escherichia coli

growth_protocol: BL21 (DE3) cells grown on LB-agar plates containing 50 μg/mL kanamycin overnight at 37 ˚C.

extract_protocol:
When the OD600 reached 0.1-0.2, the cells were induced with 0.2 mM IPTG, and the AcK group was supplied with 5 mM AcK. Subsequently, the cells were moved to 30 ˚C and harvested when the OD600 reached 0.5-0.6.
RNA was harvested using FreeZol Reagent (vazyme, catalog no. R711) and Bacteria RNA Enhancement Reagent (vazyme, catalog no. R412-C5) .

treatment_protocol: The resulting colonies were inoculated into seed cultures, which were then diluted 1:100 into LB media containing 50 μg/mL kanamycin and incubated at 37 ˚C.

tag: transformed with

value: NmGNAT


title: escherichia coli, BL21(DE3), NmGNAT-2

description: fpkm all samples(NmY_2)


title: cDC1 cells, control_1

value: individual 1

value: Male


title: escherichia coli, BL21(DE3), NmGNAT-1

description: fpkm all samples(NmY_1)


title: H26 strain, 0.5mM-2

value: H26 strian

value: 0.5mM sodium bisulfite


title: knockout strain, control-1

value: no treatment


title: escherichia coli, BL21(DE3), 5mM AcK-2

description: fpkm all samples(Kac_2)

value: 5mM AcK


title: muscle, LPI, 0 day, rep 1

extract_protocol:
Rats were deeply anesthetized with isoflurane, transcardially perfused with nuclease-free saline (pH 7.4). The incised skin and muscle tissue were rapidly dissected, the C3-C6 DRGs of LPI and C2-C5 DRGs of SMIR were then extracted. All samples were immediately transferred to ice-cold RNAlater solution and refrigerated at 4°C for 48 hours. Then samples were removed from RNAlater solution, placed into fresh 1.5 mL conical tubes and stored at -80℃. Total RNA was isolated, then Gel electrophoresis and Qubit were used to exam the RNA quality and RNA integrity number (RIN). For RNA sequencing, RNA samples from seven to nine biological replicates at each time point were separated into three independent pools. Strand-specific libraries were constructed using the TruSeq RNA sample preparation kit, and sequencing was carried out using the Illumina Novaseq 6000 instrument.
Strand-specific libraries were constructed using the TruSeq RNA sample preparation kit (RS-122-2001, Illumina, San Diego, CA, USA)

value: muscle

value: LPI

value: 0 day

value: replicated 1