title: B.thetaiotaomicron, raffinose, R3

city: Jouy-en-Josas

first: Paul

last: Biscarrat

address: 78352 Rue de la Manufacture,

institute: INRAE

description: Library name: BT_R_R3

data_processing:
bcl2fastq2-2.18.12 (demultiplex)
Cutadapt 3.2 (adapter trimming)
FastQC v0.11.5 (quality control)
Assembly: B.xylanisolvens:NZ_JH724294,NZ_JH724295,NZ_JH724296,NZ_JH724297,NZ_JH724298,NZ_JH724299,NZ_JH724300,NZ_JH724301,NZ_JH724302,NZ_JH724303,NZ_JH724304,NZ_JH724305,NZ_JH724306/B;thetaiotaomicron:NC_004663.1/R.intestinalis:NZ_LR027880.1/S.variabile:NZ_GG704769,NZ_GG704770,NZ_GG704771,NZ_GG704772,NZ_GG704773,NZ_GG704774,NZ_GG704775,NZ_GG704776,NZ_GG704777,NZ_GG704778,NZ_GG704779/A.rectalis NZ_AP012325.1 / B.adolescentis NC_008618.1 / B.uniformis RefSeq GCF_000154205.1/A.rectalis NC_012781
Supplementary files format and content: Table xxxx_DESeq_results.csv contains the raw, unfiltered results. There is one gene per row and in columns the metrics calculated by DEseq2 during the analysis: ID: gene name//baseMean: average of normalized counts for all samples/replicates involved in the comparison/log2FoldChange: log2 of the ratio of counts between the 2 conditions/lfcSE: standard error of this fold change/stat: the value of the statistical (Wald) test, used to calculate the pvalue. It is the ratio between log2FoldChange and lfcSE./pvalue: This value determines the significance of the statistical value or test. It indicates the probability that an observed fold change could be due to chance. The closer the p-value is to 0, the more significant the test, and the more real the differential in expression observed between the 2 conditions./- padj: adjusted (or corrected) pvalue, which takes into account multiple tests. As the statistical test is performed on each gene and each test is associated with a possible error, accumulating tests increases this error. We need to take this into account and make a correction for the number of tests performed. DEseq2 uses the Benjamini-Hochberg method./- then normalized counts for the samples involved in the comparison

organism: Bacteroides thetaiotaomicron

source_name: Bacteria

growth_protocol: Bacteria were cultured in Hungate tubes with a containing 90 % N2, 5 % CO2, 5 % H2 atmosphere. Cultures were performed in a minimum medium adapted from YCFA medium supplemented with 0.5 % carbohydrate. Cultures were stopped 12 h after inoculation.

extract_protocol:
RNA was harvested using RNeasy kit (Qiagen)
Directional RNA-Seq Libraries were constructed using the TruSeq Stranded Total RNA library prep kit, with bacteria Ribo-Zero reagents (Illumina), following the manufacturer’s instructions. After the Ribo-Zero step, the samples were checked on the Agilent Bioanalyzer for proper rRNA depletion. Final libraries quality was assessed on an Agilent Bioanalyzer 2100, using an Agilent High Sensitivity DNA Kit.

value: Bacteria

value: Raffinose


title: Mammary stem cells

status: Public on Jul 01 2025

type: SRA

city: Beijing

first: Pan

last: Jingyu

address: Haiding Street

department: School of basic medicine sciences

country: China

institute: Tsinghua university

description: Library name: Sample2

library_source: transcriptomic

data_processing:
Cutadapt--HISAT2--HTSEQ--DESeq2/EdgeR
Assembly: mm39, hg38
Supplementary files format and content: raw counts

molecule: total RNA

organism: Mus musculus

source_name: Mammary gland

extract_protocol:
RNA was extracted by RNAiso reagent. 0.1-1ug total RNA was used for constructing RNA-seq library
RNA-seq library was constructed by NEB kit according to the manufacturer's protocol

tag: tissue

value: Mammary gland

tag: cell line

value: Primary cell

tag: cell type

value: Normal mammary stem cell

tag: genotype

value: WT

tag: treatment

value: No


title: FFA180_02

city: Memphis

first: Richard

last: Lee

state: TN

address: 262 Danny Thomas Place

department: Department of Chemical Biology and Therapeutics

country: USA

institute: St. Jude Children's Research Hospital

data_processing:
Illumina Casava1.8 software used for basecalling.
The resulting reads were saved in FASTQ format and data was processed through the High-Performance Computing Facility at St. Jude.
Adapter content and quality trimming was performed using Cutadapt. The quality of the raw and trimmed reads was assessed using FastQC and MultiQC.
The resulting processed reads were aligned to the reference Mycobacterium abscessus ATCC19977 (Genome accession: NC_010397) using STAR2.7.1a and aligned reads were counted using featureCounts.
Differential gene expression analysis was analyzed using DESeq2 in the R statistical computing environment.
Assembly: Mycobacterium abscessus ATCC19977 (Genome accession: NC_010397)
Supplementary files format and content: Binary Alignment Map (.bam) files include aligned reads to M. abscessus ATCC19977 reference genome (Genome accession: NC_010397).
Supplementary files format and content: tab-delimitated text (.txt) files include raw counts for each Sample

organism: Mycobacteroides abscessus ATCC 19977

source_name: Planktonic

growth_protocol: M. abscessus ATCC19977 was cultured in cation-adjusted mueller hinton broth shaking at 225 rpm at 37 °C.

extract_protocol:
After treatment, 5 mL of Bacterial RNAprotect (Qiagen) was added for 5 minutes at room temperature. The culture was then centrifuged at 3214 xg for 10 minutes at 4 °C and the supernatant discarded. An RNAeasy Plus Mini Kit (Qiagen; Cat. No. 74134) was used to extract the RNA following the manufacturer’s instructions utilizing mechanical lysis for Gram-positive bacteria.
Libraries were prepared from ribosomal RNA-depleted total RNA using Illumina Stranded Total RNA Prep, ligation with Ribo-Zero Plus mRNA Library Prep Kit according to the manufacturer’s instructions (Illumina, PN 20037135). Libraries were analyzed for insert size distribution using the 2100 BioAnalyzer High Sensitivity kit (Agilent). Libraries were quantified using the Quant-iT PicoGreen ds DNA assay (ThermoFisher). Paired-end 100 cycle sequencing was performed on a NovaSeq X Plus (Illumina).

treatment_protocol: Five mL of mid-log cultures (OD600 0.4-0.6) were treated with 1/2 MIC of chloramphenicol (256 mg/L) for 30 minutes, 25µM of florfenicol for 30 minutes and 3 hours, 25µM of florfenicol amine for 30 minutes and 3 hours, or equilalent vehicle control (DMSO) for 30 minutes or 3 hours shaking at 225 rpm at 37 °C.

tag: strain

value: Planktonic

value: Florfenicol amine-0.025mM-3 hours


title: B12_PulledDown_S8

city: Seattle

middle: M

last: Jones Jr

state: WA

address: 750 Republican St

department: Microbiology

institute: University of Washington

data_processing:
DuffyTools R package used for processing
Assembly: ASM19595v2
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Mycobacterium tuberculosis

source_name: broth cultures

extract_protocol:
Trizol reagent used with bead beating in Lysing Matrix B tube followed by separation using Heavy Phase Lock tube and chloroform. Further purification using Qiagen RNeasy column was performed, including on-column DNase digest.
NEB Ultra II library prep kit was used

value: broth cultures


title: B.thetaiotaomicron, raffinose, R2

country: France

description: Library name: BT_R_R2


title: B11_PulledDown_S7


title: Cav3.1 KO mice with chronic stress 2

city: Kumamoto

first: Yasushi

last: Yabuki

state: Kumamoto

address: 2-2-1, Honjo, Chuo-ku

department: Genomic neurology

country: Japan

institute: Kumamoto University

description: Library name: KO with stress 2

data_processing:
Fastq files were processed for quality check and adapter trimming with Trimgalore! (0.6.6; https://github.com/FelixKrueger/TrimGalore). Trimmed reads were used for mapping the mouse genome (mm10) using STAR (2.7.9a). RSEM (1.3.1) was used to obtain read counts. The gene expression in each sample was further processed using DESeq2 (version 1.36.0) and expressed as normalized counts in a regularized logarithm (rlog). GO analysis was performed via over representation analysis in clusterProfiler v4.2.2.
Assembly: Mus Musculus
Supplementary files format and content: GeneMat_Count data

source_name: medial prefrontal cortex (mPFC)

growth_protocol: The generation of Cav3.1 KO mice with a C57BL/6J genetic background is described in a previous study (Anesthesiology. 2007;106(6):1177-1185. ). Cav3.1 KO mice (RBRC01465) were obtained from the RIKEN BioResource Research Center (RIKEN BRC, Japan). WT male and female C57BL/6J mice were purchased from Clea Japan, Inc. (Tokyo, Japan).  All experiments used adult male and female mice (aged 8–12 weeks). The animals were housed under conditions with a constant temperature at 23°C ± 2°C and humidity at 55% ± 5% in a 12-h light and dark cycle (light: 7:30 am–7:30 pm). The animals had unlimited access to food and water.

extract_protocol:
Total RNA was extracted from mPFC in WT and Cav3.1 KO with or without chronic stress  using an RNeasy Kit.
DNA libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kit

treatment_protocol: Chronic stress; The forced swim test (FST) and tail suspension test (TST) were performed. In the FST, the mice were placed individually in glass cylinders (height: 20 cm; diameter: 15 cm) filled with water with a temperature of 25℃. The total duration of animal immobility within the 5-min test period was scored. In the TST, acoustically and visually isolated mice were suspended 50 cm above the floor using an adhesive tape placed approximately 1 cm from the tip of the tail. The immobility time was recorded for 5 min. The mice were considered immobile only when they hung passively and remained completely motionless. The mouse was subjected to either behavioral test once a day for 5 days. Some opto-probe-implanted mice could not swim well and could drown during FST. Hence, the mice for the optogenetic experiments were only subjected to the TST. The mouse behaviors were recorded using a video camera, and their immobility time was measured by the recorded movies.

value: medial prefrontal cortex (mPFC)

value: brain tissue

value: Chronic stress


title: Cav3.1 KO mice with chronic stress 1

description: Library name: KO with stress 1


title: B.thetaiotaomicron, raffinose,  R1

description: Library name: BT_R_R1


title: FF180_03

value: Florfenicol-0.025mM-3 hours


title: FFA180_01


title: A17_PulledDown_S6


title: B.thetaiotaomicron, glucose, R3

description: Library name: BT_G_R3

value: Glucose


title: FF180_02


title: Cav3.1 KO mice without chronic stress 2

description: Library name: KO2


title: H3K9me3_CUTTag of shInts7 E14TG2a cells repeat 2

city: changsha

first: shen

last: yunfan

state: hunan

address: xiangya road

institute: central south university

description: Library name: shInts7_H3K9me3_CUTTag_rep2

library_source: genomic

data_processing:
For CUT&Tag analysis, the CUT&Tag Fastq read files were aligned to the mm10 reference genome using Bowtie2, utilizing the default parameters. To identify Dek-wt peaks, biological replicates were merged, and peak calling was carried out using MACS2 (version 2.2.6) with specific settings (--keep-dup all -g mm -P-value ≤ 1e–5) against the IgG data. The generation of CUT&Tag bedgraph files involved the subtraction of IgG signals from the experimental group signals using Deeptools' bamCompare, with the inclusion of --skipNAs and --scaleFactorsMethod readCount options. The CUT&Tag bedgraph files were then subjected to normalization by calculating the reads per million (RPM), and the resulting bigwig files were generated using bedGraphToBigWig.
For RNA-seq analysis, the RNA-seq data underwent initial quality assessment and adapter trimming utilizing Trim Galore (version 0.6.4_dev). Subsequently, the trimmed reads were aligned to the mm10 reference genome using STAR (version 2.7.2d). For the quantification of reads corresponding to genomic features, featureCounts (version 2.0.0) was employed.
Assembly: mm10
Supplementary files format and content: bigWig files were generated using bamCoverage.
Library strategy: CUT&Tag

molecule: genomic DNA

growth_protocol: Mouse E14TG2a ESCs were cultured on gelatin-coated dishes in DMEM (High Glucose, with Sodium Pyruvate, with L-Alanyl-L-Glutamine) (Vivacell) supplemented with 15% fetal bovine serum (Vistech), 1× non-essential amino acids (Gibco), 100 μM β-mercaptoethanol (Sigma), and 1000 U/mL of leukemia inhibitory factor (LIF) (Millipore). The cells were incubated at 37 °C in a humidified atmosphere with 5% CO2.

extract_protocol:
The CUT&Tag was performed following the protocol provided by the Hieff NGS® G-Type In-Situ DNA Binding Profiling Library Prep Kit (Yeasen). A total of 50,000 cells were harvested and subjected to two rounds of washing using washing buffer (composed of 20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, and 1× Protease inhibitor cocktail). Subsequently, the cells were incubated with activated Concanavalin A coated magnetic beads. To this, 0.5 μg of HA antibody was added and allowed to incubate on a rotating platform at 4 °C for a duration of 16 hours. Following this, 0.5 μL of Goat anti-Rabbit secondary antibody was introduced and incubated for an additional hour. After a thorough washing step, the cells were treated with pA/G-Tn5 transposase at 37°C for 1 hour. Subsequently, DNA extraction was carried out by DNA selection beads.
To amplify libraries, 16 μL CUT&Tag DNA was mixed with 1 μL of a uniquely barcoded i5, 1 μL a uniquely barcoded i7 primer, using a different barcode for each sample, 7 μL ddH2O, and 25 μL 2× Ultima Amplification Mix, and run the following cycling conditions with lid heat on: 72 °C for 3 min; 95 °C for 30 s; 12 cycles of 95 °C for 10 s, 55 °C for 30 s and 72 °C for 30 s; final extension at 72 °C for 5 min and hold at 4 °C. Post-PCR clean-up was performed by adding 1.2× volume of DNA selection beads (60 μL), and libraries were incubated with beads for 5 min at RT, washed twice gently in 80% ethanol, and eluted in 20 μL EB buffer.

treatment_protocol: Cells were infected with a lentivirus carrying shNT or shInts7 for 24 hours and then collected

value: mouse embryonic stem cell


title: B.thetaiotaomicron, glucose,  R2

description: Library name: BT_G_R2


title: FF180_01


title: B.thetaiotaomicron, glucose, R1

description: Library name: BT_G_R1


title: Cav3.1 KO mice without chronic stress 1

description: Library name: KO1


title: WT mice with chronic stress 3

description: Library name: WT with stress 3


title: H3K9me3_CUTTag of shInts7 E14TG2a cells repeat 1

description: Library name: shInts7_H3K9me3_CUTTag_rep1


title: H3K9me3_CUTTag of control E14TG2a cells repeat 2

description: Library name: shNT_H3K9me3_CUTTag_rep2

value: shNT


title: H3K9me3_CUTTag of control E14TG2a cells repeat 1

description: Library name: shNT_H3K9me3_CUTTag_rep1


title: Control180_03

value: DMSO-3 hours


title: Cav3.1 KO mice without chronic stress 3

description: Library name: KO3


title: Control180_02


title: WT mice with chronic stress 2

description: Library name: WT with stress 2


title: WT mice with chronic stress 1

description: Library name: WT with stress 1


title: H3K9me2_CUTTag of shInts7 E14TG2a cells repeat 2

description: Library name: shInts7_H3K9me2_CUTTag_rep2


title: FFA30_03

value: Florfenicol amine-0.025mM-30 minutes


title: H3K9me2_CUTTag of shInts7 E14TG2a cells repeat 1

description: Library name: shInts7_H3K9me2_CUTTag_rep1


title: WT mice without chronic stress 3

description: Library name: WT3


title: WT mice without chronic stress 2

description: Library name: WT2


title: H3K9me2_CUTTag of control E14TG2a cells repeat 2

description: Library name: shNT_H3K9me2_CUTTag_rep2


title: FFA30_02


title: H3K9me2_CUTTag of control E14TG2a cells repeat 1

description: Library name: shNT_H3K9me2_CUTTag_rep1


title: WT mice without chronic stress 1

description: Library name: WT1


title: FF30_03

value: Florfenicol-0.025mM-30 minutes


title: FF30_02


title: day 40 IAV_4  Blood endothelial cells

city: Glasgow

first: Graham

middle: Michael

last: Hamilton

state: Lanarkshire

address: University Avenue

department: MVLS Shared Research Facility - Molecular Analysis

country: United Kingdom

institute: University of Glasgow

data_processing:
Reads were aligned to the mouse genome mm10 with STAR version 2.4.2a (/doi.org/10.1093/bioinformatics/bts635) in two-pass mode, and on the second pass reads mapping to genes were quantified. Both the genomic DNA sequence (Mus_musculus. GRCm38 primary assembly) and gene annotations (GTF file GRCm38.86) were downloaded from Ensembl (Zerbino et al. doi:10.1093/nar/gkx1098). Quality control of the samples was carried out with FASTQC (bioinformatics.babraham.ac.uk/projects/fastqc) and FastP used for trimming, Hisat2 for aligning and FeatureCounts to count the reads aligning to the gene regions. Differential expression analysis was performed via DESeq2 and FDR with a p-value of less than 0.05 was considered statistically significant.  Further sample quality control, visualization and exploration were performed in R via SearchLight2
Assembly: mouse genome mm10 via STAR version 2.4.2a (/doi.org/10.1093/bioinformatics/bts635)
Supplementary files format and content: tab delimited csv file containing raw counts and for the indicated comparisons information on differential gene expression

molecule: polyA RNA

source_name: lung

extract_protocol:
Lungs were taken from C57BL/6 mice that were either naïve (control) or had been infected with influenza A virus 10 or 40 days previously. Lungs were digested with Collagenase P, Dispase and DNase and CD45+ cells removed using magnetic beads (Miltenyi Biotec). Cells were stained with antibodies to Epithelial cells (EpCAM1), Fibroblasts (CD140a) or blood endothelial cells (CD31) and live cells of each types sorted by FACS with CD45 and Ter119 used a dump gate. For each sample, cells were combined from 6-8 mice. Cells were pelleted, resuspended in a small volume and centrifuged through a QiaShredder. RNA was prepared using a mini or micro RNAeasy kit from Qiagen.
RNA was purified using RNAmicor or mini kits from Qiagen and total RNA (100ng) isolated using poly-T oligo‑attached magnetic beads (Life Technologies, CA, USA). Sequencing libraries were generated using NEB Next Ultra Directional RNA Library Prep Kit for Illumina (NEB) in accordance with the manufacturer's recommendations. Products were purified and quantified using the Agilent high sensitivity DNA assay on the Agilent Bioanalyzer 2100 system. After the clustering of the index-coded samples, each library preparation was sequenced on an Illumina NextSeq™ 500 platform with 2x75bp paired end sequencing. An average sequencing depth of 20M reads per sample was achieved.
Bulk sequencing of FACS sorted cells

value: lung

value: CD31+ Blood endothelial cells

value: Wild-type

value: Influenza A virus


title: Kap1_CUTTag of shInts7 E14TG2a cells repeat 2

description: Library name: shInts7_Kap1_CUTTag_rep2

value: WT


title: Kap1_CUTTag of shInts7 E14TG2a cells repeat 1

description: Library name: shInts7_Kap1_CUTTag_rep1


title: Control180_01

value: Planktonic


title: day 40 IAV_3  Blood endothelial cells


title: FF30_01


title: day 40 IAV_2  Blood endothelial cells


title: FFA30_01


title: Kap1_CUTTag of control E14TG2a cells repeat 2

description: Library name: shNT_Kap1_CUTTag_rep2


title: CAM30_03

value: Chloramphenicol-256 mg L-1-30 minutes


title: CAM30_02


title: day 40 IAV_1  Blood endothelial cells


title: Intestinal tissue, V600E_knock-in/knock-in, GGVB 5080 (5)

type: RNA

city: Leicester

first: Nicolas

last: Sylvius

address: University Road

department: CBS-Genetics

institute: University of Leicester

hyb_protocol: Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C .  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent)

source_name: Intestinal tissue

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was extracted on a Promega Maxwell 16 robot using the Maxwell 16 LEV simplyRNA Cells Kit (Reference AS1270). RNA quality and quantity was assessed using the 2100 Bioanalyzer Instrument (Agilent)

treatment_protocol: In all experimental mice, induction of 100 Cre activity was achieved by injection of 1 mg Tamoxifen (TM) into the 101 abdominal cavity of mice aged 8-12 weeks on 3 consecutive days at 24-hour intervals leading to the GSK3 alpha and beta isoforms knock-in/knock-in genotype (GSK3alphaS21A/S21A; GSK3betaS9A/S9A; VilCreERT+/+) and V600E_knock-in/knock-in genotype (GSK3alphaS21A/S21A; GSK3betaS9A/S9A; BrafLSL-V600E/+; VilCreERT+/+)

value: Intestinal tissue


title: YTa32−4_shRNA_4

city: Boston

first: Lai Ping

last: Wong

state: MA

address: 185 Cambridge St

department: Molecular Biology

institute: Massachusetts General Hospital

description: Library name: shRNA4

data_processing:
The STAR aligner was used to map sequencing reads to transcriptome in the mouse mm9 reference genome
Read counts for individual genes were produced using HTSeq v.0.6.0
Assembly: mm9
Supplementary files format and content: tab-delimited text file containing genome-wide gene expression counts

source_name: brain tissue

extract_protocol:
RNeasy Plus Micro Kit (Quiagen) was used
NGS libraries were constructed from total RNA using Clontech SMARTer v4 kit (Takara)

value: brain tissue


title: day 10 IAV_4  Blood endothelial cells


title: Intestinal tissue, V600E_knock-in/knock-in, GGVB 5077 (4)


title: Intestinal tissue, V600E_knock-in/knock-in, GGVB 5070 (5)


title: Intestinal tissue, V600E_knock-in/knock-in, GGVB 5075 (5)


title: CAM30_01


title: Intestinal tissue, knock-in/knock-in, GGVB 5169 (5)

value: knock-in/knock-in


title: day 10 IAV_3  Blood endothelial cells


title: YTa31−6_shRNA_3

description: Library name: shRNA3


title: Control30_03

value: DMSO-30 minutes


title: YTa31−5_shRNA_2

description: Library name: shRNA2


title: day 10 IAV_2  Blood endothelial cells


title: Control30_02


title: Intestinal tissue, V600E_knock-in/knock-in, GGVB 5079 (5)


title: OT1 CD8+ Tcells, repeat stimulation, d8, replicate 3

first: Tao

last: Gao

state: Beijing

address: No.38 Academy Road, Haidian District

department: Chemical Biology

institute: Peking University

description: Library name: Sample9

data_processing:
Data analysis was performed using using Hisat2, StringTie and DESeq2.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: Spleen

extract_protocol:
Total RNA was extracted using a total RNA isolation kit (Vazyme). 1 μg of total RNA was used for the construction of sequencing libraries.
For library preparation, 1 µg of total RNA was used with the Hieff NGS® Ultima Dual-mode mRNA Library Prep Kit (YEASEN) following manufacturer's protocol.

value: Spleen

value: CD8+ T cells

value: T cells

value: repeat stimulation

tag: time


title: Intestinal tissue, V600E_knock-in/knock-in, GGVB 5066 (4)


title: Intestinal tissue, knock-in/knock-in, GGVB 5164 (5)


title: day 10 IAV _1  Blood endothelial cells


title: YTa31−3_shRNA_1

description: Library name: shRNA1


title: Naïve 3  Blood endothelial cells


title: Control30_01


title: OT1 CD8+ Tcells, repeat stimulation, d8, replicate 2

description: Library name: Sample8


title: Kap1_CUTTag of control E14TG2a cells repeat 1

description: Library name: shNT_Kap1_CUTTag_rep1

value: mouse embryonic stem cell

value: shNT


title: Intestinal tissue, knock-in/knock-in, GGVB 5165 (5)


title: Intestinal tissue, knock-in/knock-in, GGVB 5142 (5)


title: YTa32−2_shNT_5

description: Library name: shNT5


title: Intestinal tissue, knock-in/knock-in, GGVB 5141 (5)


title: OT1 CD8+ Tcells, repeat stimulation, d8, replicate 1

description: Library name: Sample7


title: Naïve 2  Blood endothelial cells

value: lung


title: YTa32−1_shNT_4

description: Library name: shNT4


title: TMJ cartilage and disc cells

city: Pittsburgh

first: Alejandro

last: Almarza

address: 335 Sutherland Dr

institute: University of Pittsburgh

description:
Library name: TMJ tissues
Chromium Controller 10x Genomics

library_source: transcriptomic single cell

data_processing:
Doublet removal, rat genome alignment, and count matrix generation was done in Cell Ranger Count c7.0.1 pipeline. The count matrix was uploaded to R v3.4.0 where data was demultiplexed
TMJ cartilage cells, Healthy Control (CMO301). TMJ disc cells, Healthy Control (CMO302). TMJ cartilage cells, Splinted (CMO303). TMJ disc cells, Splinted (CMO304)
Assembly: mRatBN7.1
Supplementary files format and content: The file is an R .rds containing a Seurat object of the demultiplexed gene expression count matrix containing the assigned CMO tags in Seurat objects metadata. The data is not normalized and was filtered only to remove cells with less that 100 genes and more than 2500 genes.

organism: Rattus norvegicus

source_name: TMJ cartilage and disc

extract_protocol:
Cartilage and disc  tissues were minced and then digested in 1mg/mL Liberase DL (Sigma, USA) for 45 minutes, followed by enzyme inactivation via 2% fetal bovine serum (FBS) in PBS. The samples were centrifuged, supernatant was removed, and each group (cartilage and disc) was resuspended in their respective (naïve and splinted) Cell Multiplexing Oligo (CMO) provided by the University of Pittsburgh Single Cell Core. After five minutes of CMO incubation at room temperature,cells were washed three times with culture media containing 10% FBS.
Single-cell RNA sequencing libraries were prepared using the Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10x Genomics) following the manufacturer’s protocol. Briefly, single-cell suspensions were loaded into a Chromium Controller, where cells were encapsulated with barcoded Gel Beads in oil emulsion droplets (GEMs). Within each GEM, cells were lysed and reverse transcription occurred, incorporating unique cell barcodes and UMIs into the cDNA. Following reverse transcription, emulsions were broken and barcoded cDNA was purified using Dynabeads Silane magnetic beads to remove excess primers and enzymes. The barcoded cDNA was then amplified by PCR to generate sufficient material for downstream library construction. Amplified cDNA was enzymatically fragmented, end-repaired, A-tailed, and ligated to adapters, followed by a sample indexing PCR step. Cleanup steps between enzymatic reactions were performed using SPRIselect magnetic beads to ensure library purity and size selection. Final libraries were quantified, pooled, and sequenced on a the Chromium Controller using paired-end reads across four lanes. Read 1 captured the 3′ gene expression, Read 2 contained UMI information, and dual index reads (I1 and I2) enabled sample multiplexing and demultiplexing.

treatment_protocol: Cells come from rats that have had no experimental procedure or from rats that have been incisor-splinted to induce a bite shift and robust condylar remodeling for 4 weeks

value: TMJ cartilage and disc

value: control (CMO301,CMO302), incisor-splinted bite shift (CMO303,CMO304)

tag: age

value: 15 weeks

tag: Sex

value: female


title: B. uniformis, raffinose, R3

description: Library name: BU_R_R3

organism: Bacteroides uniformis

value: Bacteria

value: ATCC 8492

value: Raffinose


title: Intestinal tissue, knock-in/knock-in, GGVB 5143 (5)

value: Intestinal tissue


title: OT1 CD8+ Tcells, single stimulation, d8, replicate 3

description: Library name: Sample6

value: single stimulation


title: B. uniformis, raffinose, R2

description: Library name: BU_R_R2


title: OT1 CD8+ Tcells, single stimulation, d8, replicate 2

description: Library name: Sample5


title: Naïve 1 Blood endothelial cells

value: CD31+ Blood endothelial cells

value: Wild-type


title: YTa31−4_shNT_3

description: Library name: shNT3

value: brain tissue


title: day 40 IAV_4  Fibroblasts

value: CD140a+ fibroblast

value: Influenza A virus


title: OT1 CD8+ Tcells, single stimulation, d8, replicate 1

description: Library name: Sample4

value: Spleen

value: CD8+ T cells

value: T cells


title: YTa31−2_shNT_2

description: Library name: shNT2


title: day 40 IAV_3  Fibroblasts

value: lung


title: B. uniformis, raffinose, R1

description: Library name: BU_R_R1


title: YTa31−1_shNT_1

description: Library name: shNT1


title: B. uniformis, glucose, R3

description: Library name: BU_G_R3

value: Glucose


title: B. adolescentis, raffinose, R3

description: Library name: BA_R_R3

organism: Bifidobacterium adolescentis


title: day 40 IAV_2  Fibroblasts


title: OT1 CD8+ Tcells, d0, replicate 3

description: Library name: Sample3

value: No treatment


title: day 40 IAV_1  Fibroblasts


title: OT1 CD8+ Tcells, d0, replicate 1

description: Library name: Sample1


title: B. uniformis, glucose, R2

description: Library name: BU_G_R2


title: day 10 IAV_4  Fibroblasts


title: OT1 CD8+ Tcells, d0, replicate 2

description: Library name: Sample2


title: Fcmr KO3-6h

city: Shanghai

first: Zichao

last: Wen

address: 130 Dongan Road, Xuhui District

department: school of basic medical sciences

institute: Fudan University

description:
Library name: sample12
Fcmr3-6h

data_processing:
Before read mapping, clean reads were obtained from the raw reads by removing the adaptor sequences and low-quality reads. The clean reads were then aligned to mouse genome (mm10, Ensembl100) using the Star. [STAR: ultrafast universal RNA-seq aligner, Bioinformatics, Volume 29, Issue 1, January 2013, Pages 15–21] HTseq [Anders S, Pyl P T, Huber W. HTSeq–A Python framework to work with high-throughput sequencing data[J]. Bioinformatics, 2014: btu638.] was used to get gene counts and FPKM method was used to determine the gene expression.
Assembly: The clean reads were aligned to mouse genome (mm10, Ensembl100) using the Star.
Supplementary files format and content: Matrix table includ gene FPKM values for each sample

extract_protocol:
Total RNA was extracted using RNAiso Plus (Takara) according to the manufacturer’s instructions. Triplicate biological replicate RNA samples of each time point were sent to the Novel Bioinformatic Co., Ltd for sequencing and analysis. In brief, RNA quality was assessed using an Agilent 2200 Bioanalyzer, and samples with an RNA integrity number (RIN) > 7.0 were deemed acceptable for cDNA library construction.
Total RNA was extracted from the samples by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Agilent 2200 and kept at −80°C. The RNA with RIN (RNA integrity number) > 7.0 is acceptable for cDNA library construction. The cDNA libraries were constructed for each RNA sample using the VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina (vazyme, Inc.) according to the manufacturer’s instructions. Generally, the protocol consists of the following steps: Poly-A containing mRNA was purified from 1ug total RNA using oligo(dT) magnetic beads and fragmented into 200-600 bp using divalent cations at 85℃ for 6 min. The cleaved RNA fragments were used for first- and second-strand complementary DNA (cDNA) synthesis . dUTP mix was used for second-strand cDNA synthesis, which allows for the removal of the second strand. The cDNA fragments were end repaired, A-tailed and ligated with indexed adapters. The ligated cDNA products were purified and treated with uracil DNA glycosylase to remove the second-strand cDNA. Purified first-strand cDNA was enriched by PCR to create the cDNA libraries. The libraries were quality controlled with Agilent 2200 and sequenced by DNBSEQ-T7 on a 150 bp paired-end run.

treatment_protocol: Purified B cells from WT and Fcmr KO mice were cultured with 10 μg/mL F(ab’)2 anti-IgM and harvested at 1 or 6 h for RNA-seq

value: B cells

value: Naive B cells

value: Fcmr KO

value: F(ab’)2 anti-IgM


title: B. uniformis, glucose, R1

description: Library name: BU_G_R1

value: Bacteria

value: ATCC 8492


title: day 10 IAV_3  Fibroblasts


title: B. adolescentis, raffinose, R2

description: Library name: BA_R_R2

value: Raffinose


title: MC-TM3 rep3

city: Wageningen

first: Xiaobing

last: Jiang

address: Droevendaalsesteeg 1

department: Bioscience

country: Netherlands

institute: Wageningen University

description:
MC-TM3_merged_normalized.bigwig
Narrow_peaks_MC-TM3_0_0001.bed

data_processing:
Read trimming with Trim Galore
Read mapping with HISAT2
Merging files with MergeSamFiles
Peakcalling with MACS2
Annotating peaks with ChIPseeker
Differential peak analysis with MACS2 bdgdiff
Assembly: MbTMVv1, MbTMV_gene_models4_1_polished
Supplementary files format and content: Narrow peaks representing peaks for p<0,0001
Supplementary files format and content: Bedgraphs representing normalized read files
Library strategy: DAP-seq

organism: Solanum lycopersicum

source_name: young leaf

growth_protocol: young leaf oftomato cv Moneyberg

extract_protocol:
Recombinant proteins were produced with the TnT SP6 protein expression system from Promega, while the genomic DNA was extracted with a CTAB protocol from tomato young leaf.
The libraries were constructed with the Truseq Illumina kit and unique adaptors were used for each sample. 400ng of DNA library was used per sample. Libraries were amplified using 20 cycles on the thermocycler. Post-amplification libraries were size selected at 250-650bp in length using Agencourt AMPure XP beads from Beckman Coulter

value: young leaf

tag: cultivar

value: Moneyberg

value: WT


title: B. adolescentis, glucose, R3

description: Library name: BA_G_R3


title: MC-TM3 rep2


title: day 10 IAV_2  Fibroblasts

value: CD140a+ fibroblast

value: Wild-type

value: Influenza A virus


title: B. adolescentis, glucose, R2

description: Library name: BA_G_R2


title: day 10 IAV _1  Fibroblasts


title: Fcmr KO2-6h

description:
Library name: sample11
Fcmr2-6h

value: Spleen


title: Fcmr KO1-6h

description:
Library name: sample10
Fcmr1-6h


title: WT3-6h

description:
Library name: sample9
W3-6h


title: MC-J2 rep3

description:
MC-J2_merged_normalized.bigwig
Narrow_peaks_MC-J2_0_0001.bed


title: Naïve 4  Fibroblasts

value: lung


title: WT2-6h

description:
Library name: sample8
W2-6h


title: leaves,  PagSUPa overexpression (OE) line 7 , rep4

city: Hangzhou

first: Dan

last: Hou

address: 666 Wusu street, Lin'an District, Hangzhou

institute: A&F university

data_processing:
A cDNA library was sequenced run with DNBSEQ sequence platform.
Firstly, Cutadapt [1] and perl scripts in house were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). including the Q20, Q30 and GC-content of the clean data.
Populus trichocarpa genome assembly of the transcriptome was performed with Trinity 2.4.0 [2]. Trinity groups transcripts into clusters based on shared sequence content. Such a transcript cluster is very loosely referred to as a 'gene'. The longest transcript in the cluster was chosen as the 'gene' sequence (aka Unigene).
Salmon [4] was used to perform expression level for Unigenes by calculating TPM
Assembly: Populus trichocarpa genome assembly
Supplementary files format and content: xlsx files include TPM values for each Sample

organism: Populus alba x Populus glandulosa

source_name: leaves

extract_protocol:
SMARTer cDNA synthesis starts with picogram amounts of total RNA or single cell/several cells. A modified oligo(dT) primer (the SMART CDS Primer) primes the first-strand synthesis reaction. When SMARTScribe™ Reverse Transcriptase reaches the 5’ end of the mRNA, the enzyme’s terminal transferase activity adds a few additional nucleotides to the 3’ end of the cDNA. The carefully-designed SMARTer Oligonucleotide base-pairs with the non-template nucleotide stretch, creating an extended template to enable SMARTScribe RT continue replicating to the end of the oligonucleotide. The resulting full-length, single-stranded (ss) cDNA contains the complete 5’ end of the mRNA, as well as sequences that are complementary to the SMARTer Oligonucleotide. Amplify sscDNA by LD PCR and get enough dscDNA for library construction.
the mRNA was hybridized with Oligo（dT）probe and Captured by Magnetic Beads. The mRNA was fragmented by high temperature，then reverse-transcripted to first strand DNA. First strand DNA was used as template to synthesis second strand DNA, obtaining dsDNA. The dTTP tailed adaptor was ligated to both ends of the dsDNA fragments. The ligation product was amplified by PCR, and circularized to get single-stranded circular(ssCir) library. The ssCir library was then amplified through rolling circle amplification (RCA) to obtain DNA nanoball(DNB).

value: leaves


title: MC-J2 rep2


title: leaves,  PagSUPa overexpression (OE) line 7 , rep3


title: WT1-6h

description:
Library name: sample7
W1-6h


title: Naïve 3 Fibroblasts


title: B. adolescentis, raffinose, R1

description: Library name: BA_R_R1


title: MC-J2 rep1


title: Naïve 2  Fibroblasts


title: Naïve 1 Fibroblasts


title: leaves,  PagSUPa overexpression (OE) line 7 , rep2


title: Fcmr KO3-1h

description:
Library name: sample6
Fcmr3-1h


title: MC-J  rep3

description:
MC-J_merged_normalized.bigwig
Narrow_peaks_MC-J_0_0001.bed


title: Fcmr KO2-1h

description:
Library name: sample5
Fcmr2-1h


title: MC-J  rep2


title: Fcmr KO1-1h

description:
Library name: sample4
Fcmr1-1h


title: B. adolescentis, glucose, R1

description: Library name: BA_G_R1

value: Glucose


title: MC-TM3 rep1


title: day 40 IAV_3  Epithelial cells

value: EpCAM+ Epithelial cells


title: leaves,  PagSUPa overexpression (OE) line 2, rep2


title: leaves,  PagSUPa overexpression (OE) line 7 , rep1


title: day 40 IAV_4  Epithelial cells


title: leaves,  PagSUPa overexpression (OE) line 2, rep3


title: FUL2-TM3 rep2

description:
FUL2-TM3_merged_normalized.bigwig
Narrow_peaks_FUL2-TM3_0_0001.bed


title: day 40 IAV_1  Epithelial cells


title: leaves,  PagSUPa overexpression (OE) line 2, rep4


title: day 40 IAV_2  Epithelial cells


title: leaves,  PagSUPa overexpression (OE) line 2 , rep1


title: FUL2-TM3 rep3


title: WT1-1h

description:
Library name: sample1
WT1-1h

value: B cells

value: Naive B cells


title: FUL2-TM3 rep1


title: D7,Smarca5,33

first: Jing

last: Han

address: qinghuayuan

description: Library name: RNA_D7_Smarca5_33

data_processing:
The adaptors of paired-end reads were trimmed by trim-galore (v.0.6.4) with the parameters set as: -q 25 --phred33 --length 50 -e 0.1 --fastqc --stringency 5 --paired.
Adaptor-trimmed reads were aligned to the mm10 genome with the following parameters: --readFilesCommand zcat --outFilterMismatchNoverLmax 0.2 by STAR (v.2.7.9a)
Aligned reads stored in SAM format were converted to BAM files using SAMtools with parameter: samtools view -bS -h -F 4 -f 2 -q 7.
FeatureCounts counted reads stored in BAM format to exon sites of genes included in GTF files from Ensembl
Assembly: mm10/hg19
Supplementary files format and content: raw counts

source_name: pancreas

extract_protocol:
300 GFP-positive cells and 10,000 GFP-positive cells were sorted by FACS for small scale RNA-seq and ATAC-seq. 10% HEK-293T cells were mixed in ATAC-seq samples for spike-in normalization. ATAC-seq was performed with Chromatin Profile Kit for Illumina (Novoprotein, N248-01A). Small scale RNA-seq library was constructed using Smart-seq2 method with modifications allowing higher quality library generation from pancreatic cells. Briefly, mouse pancreatic cells were directly sorted into 8 μl of denaturing lysis buffer (6 M guanidine HCl, 0.2% (vol/vol) Triton X-100 and 1% (vol/vol) β-mercaptoethanol). RNA SPRI beads (RNA Clean XP beads, Beckman A63987) were added (2.2X) to the lysis buffer and RNA was purified, followed by library preparation by the standard Smart-seq2 protocol, except with a 12-cycle PCR pre-amplification step.
Smart-seq2 protocol.

value: pancreas

value: pancreatitis


title: FUL2-J2 rep3

description:
FUL2-J2_merged_normalized.bigwig
Narrow_peaks_FUL2-J2_0_0001.bed


title: leaves, nontransgenic control (CK), rep4


title: day 10 IAV_3  Epithelial cells


title: MC-J  rep1


title: leaves, nontransgenic control (CK), rep3


title: WT3-1h

description:
Library name: sample3
WT3-1h

value: F(ab’)2 anti-IgM


title: FUL2-J2 rep2


title: D7,Runx1,27

description: Library name: RNA_D7_Runx1_27


title: leaves, nontransgenic control (CK), rep2


title: day 10 IAV_2  Epithelial cells


title: FUL2-J2 rep1


title: WT2-1h

description:
Library name: sample2
WT2-1h


title: day 10 IAV _1  Epithelial cells


title: Naïve 4  Epithelial cells


title: leaves, nontransgenic control (CK) , rep1


title: hiPS_SFC086_03_03, Passage 3, Replicate 1

city: Basel

first: Martina

last: Pigoni

address: Grenzacherstrasse 124

department: NRD

country: Switzerland

institute: Hoffmann-La Roche

description: Library name: MP23-018-iBEC-REPLATE-3-MP-20-04-23_S23

data_processing:
Base calling was conducted using the BCL to FASTQ file converter bcl2fastq2 version 2.20.0 (Illumina).
Quality assessment of FASTQ files was performed with FastQC version 0.12.1 (Andrews et al. 2010). Paired-end reads were aligned to the human genome (build "hg38") using the STAR read aligner version 2.7.11b with default mapping parameters (Dobin et al. 2013).
Alignment metrics were determined using Picard version 3.1.1 (Broad Institute).
Quality of read sequences and alignments was assessed with MultiQC version 1.21.
The number of reads mapped to all RefSeq transcript variants of a gene were combined into a single count value (i.e., read count) assuming a reverse-stranded library, using featureCounts version 2.0.6.
Assembly: hg38
Supplementary files format and content: count matrix with RefSeq gene IDs, GCT file format
Supplementary files format and content: log2tpm per gene using RefSeq gene IDs, GCT file format

organism: Homo sapiens

source_name: iPSC-derived endothelial cells

extract_protocol:
At least 300,000 iCE-BEC per condition  were collected and pellets were snap frozen.
RNA was extracted and preparation of Illumina stranded TruSeq RNA libraries, including poly(A) enrichment, was performed (2*100 bp paired-end reads).

value: iPSC-derived endothelial cells


title: FUL2-J rep3

description:
FUL2-J_merged_normalized.bigwig
Narrow_peaks_FUL2-J_0_0001.bed

value: young leaf


title: FUL2-J rep2

value: Moneyberg


title: hiPS_SFC086_03_03, Passage 2, Replicate 1

description: Library name: MP23-018-iBEC-REPLATE-2-MP-17-04-23_S22


title: tumor,Smarca5,212

description: Library name: RNA_tumor_Smarca5_212

value: PDAC


title: D2,H3K27ac,Rosa

description: Library name: CUTTag_H3K27ac_D2_Rosa_941

data_processing:
The adaptors of paired-end reads were trimmed by trim-galore (v.0.6.4) with the parameters set as: -q 25 --phred33 --length 50 -e 0.1 --fastqc --stringency 5 --paired.
Adaptor-trimmed reads were aligned to the mm10 genome with the following parameters: --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700 by Bowtie2.
Aligned reads stored in SAM format were converted to BAM files and PCR duplicates were removed using SAMtools.
Peaks were called by MACS2(v.2.2.7.1)56 using the parameters: macs2 callpeak -g mm -B -p 0.01 -f BEDPE.
Assembly: mm10
Supplementary files format and content: bigwig
Library strategy: CUT&Tag

extract_protocol:
50,000-100,000 GFP-positive cells were sorted by FACS. CUT&Tag was performed using Hyperactive Universal CUT&Tag Assay Kit for Illumina Pro kit (Vazyme, TD904-01). Antibody of H3K27ac from Abcam (ab4729, 0.5 μL) was used
CUT&Tag was performed using Hyperactive Universal CUT&Tag Assay Kit for Illumina Pro kit (Vazyme, TD904-01).

value: control


title: FUL2-J rep1

value: WT


title: hiPS_SFC086_03_03, Passage 0, Replicate 2

description: Library name: MP23-012-SFC860303-D14-RNA-MP190323_S18


title: day 10 IAV_4  Epithelial cells

value: Wild-type

value: Influenza A virus


title: input rep3


title: Naïve 3  Epithelial cells

value: lung


title: hiPS_SFC086_03_03, Passage 1, Replicate 1

description: Library name: MP23-012-REPLATED-1-14-04-23_S21


title: input rep2


title: Naïve 1 Epithelial cells


title: D7,Rosa,33

description: Library name: RNA_D7_Rosa_25


title: BIONi010-C13, Passage 0, Replicate 1

description: Library name: MP23-012-BION10C-D14-RNA-MP190324_S19


title: input rep1


title: D2,SMARCA5,Rosa,727

description: Library name: D2_SMARCA5_Rosa_727

data_processing:
The adaptors of paired-end reads were trimmed by trim-galore (v.0.6.4) with the parameters set as: -q 25 --phred33 --length 50 -e 0.1 --fastqc --stringency 5 --paired.
Adaptor-trimmed reads were aligned to the mm10 genome with the following parameters: --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700 by Bowtie2.
Aligned reads stored in SAM format were converted to BAM files and PCR duplicates were removed using SAMtools.
Peaks were called by MACS2(v.2.2.7.1)56 using the parameters: macs2 callpeak -g mm -B -p 0.01 -f BEDPE.
Assembly: mm10/hg19
Supplementary files format and content: bigwig
Library strategy: CUT&RUN

extract_protocol:
30,000-60,000 GFP-positive cells were sorted by FACS and the CUT&RUN sequencing was performed as previously described44 with minor modifications. 10% Kasumi-1 cells were added as spike-in. Concanavalin-A (ConA) beads were activated by washed twice using activation buffer (20 mM HEPES–KOH pH 7.9, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2). Sorted cells were resuspended in room temperature (RT) wash buffer (20 mM HEPES–KOH pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, protease inhibitor cocktail) and added into ConA beads. After incubating 10 min in RT, ConA-beads-bound cells were incubated overnight at 4 °C in antibody buffer (wash buffer supplemented with 0.01% digitonin and 2 mM EDTA) and antibody. The following primary antibodies were used: SMARCA5 (EpiCypher, 13-2007, 2.5 μl) and CTCF (CST, 3418S, 1μl). After antibody incubation, ConA-beads-bound nuclei were washed once with Digitonin buffer (wash buffer supplemented with 0.01% digitonin) then resuspended and incubated at 4 °C for 1 h in Digitonin buffer and 0.1 μl pAG-MNase (a gift from Dr. Wei Xie, Tsinghua University). ConA-beads-bound nuclei were then washed twice with Digitonin buffer and resuspended in 98 μl of Digitonin buffer and incubated on ice for 5 min. Then, 2 μl 100 mM CaCl2 was added and mixed gently to each 100 μl ConA-bound nuclei. The reaction was then incubated at 4 °C for 30 min. The reaction was stopped by addition of 100 μl 2× stop buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.02% Digitonin and 50 μg/ml RNaseA, 50 μg/ml Glycogen) and incubated at 37 °C for 10 min. All buffers mentioned above were filtered with 0.22 μm filter before use. After incubation, ConA-bound nuclei were captured using a magnet and supernatant containing CUT&RUN DNA fragments were collected. Supernatant was incubated at 70 °C for 10 min with 2 μl 10% sodium dodecyl sulfate, 3 μL 10 mg/ml proteinase K and 2 μL 20ng/μL carrier RNA (Qiagen, 1068337). DNA was purified using PCI reagent (Solarbio, P1012) and overnight ethanol precipitation with glycogen at -20 °C.
DNA was resuspended in water and repaired to 5´phosphorylated and 3´ dA-tailed DNA with NEBNext® Ultra™ II End Repair/dA-Tailing Module (NEB, E7546S). Barcodes (BIOO Scientific, 514153) were ligated with Quick Ligation kit (NEB, M2200). After size selection, 16 cycles of PCR were used to amplify the library. PCR-amplified libraries were purified using KAPA beads (Kapa biosystems) and sent for sequencing.


title: eNPCs, wt, 48h differentiation, rep6

city: Bonn

first: Daniele

last: Bano

state: NRW

address: Venusberg Campus 1, Gebaeude 99

country: Germany

institute: DZNE, German Center for Neurodegenerative Diseases

data_processing:
Samples were demultiplexed and base call files were converted into Fastq format using bcl2fastq2 v2.20 software (Illumina) before alignment to the mouse genome mm10 build GRCm38 using kallisto aligner (v.0,440).
Assembly: mm10
Supplementary files format and content: tsv (est_counts, tpm)

source_name: primary cells

growth_protocol: Cells were grown under standard cell culture conditions

extract_protocol:
At the indicated time points, cells were scraped, collected and pelleted in PBS. Cell pellets of approximately 500,000 cells were then lysed in Trizol, snap-frozen and stored at -80 °C until use RNA was quantified via HS RNAassay on a Tapestation4200 instrument (Agilent).
RNA was extracted from wt and Hq mutant eNPCs collected at the indicated time points. Approximately 100 ng of extracted RNA were used as input for RNA‐Seq library preparation according to the TruSeq Stranded mRNA kit (Illumina). Next generation sequencing libraries were quantified via Qubit HS dsDNA assay (Invitrogen) and library size distribution was determined using a HS D1000 assay on a Tapestation4200 instrument (Agilent). Libraries were equimolarly pooled, clustered at 1200 pM concentration, and sequenced SR 75 cycles on a NovaSeq6000 instrument (Illumina) using an S1 v1.5 chemistry.

value: primary cells

value: neural progenitor cells

value: wt

value: 48h differentiation


title: eNPCs, wt, 48h differentiation, rep5


title: Bioni037-A, Passage 0, Replicate 2

description: Library name: MP23-012-BIO37A-D14-RNA-MP190325_S20


title: eNPCs, wt, 48h differentiation, rep4


title: FoxO OE 30-6

city: Kiel

first: Judith

last: Bossen

address: Am Botanischen Garten 3-9

department: Molecular Physiology

institute: CAU Kiel, Zoological Institute

data_processing:
transcriptomic analysis was performed with CLC workbench 9.5.2, Illumina files (fastq) were importet and failed reads were removed
the reads were mapped to gene regions only using the Drosophila melanogaster genome (assembly Release 6 plus ISO1 MT) using the following parameters: mismatch cost = 2, insertion cost = 2, deletion cost = 2, length fraction = 0.8, similarity fraction = 0.85, global alignment = no, strand specific = both, maximum number of hits for a read = 10, count paired reads as two = no, expression value = RPKM, calculate RPKM for genes without transcripts = no, use EM estimation = yes
Differential expression for RNA-Seq was perfomed by compairing against a control group (Control; FoxO OE 18)
Assembly: Drosophila melanogaster Release 6 plus ISO1 MT
Supplementary files format and content: tab delimited text files include differential expression values based on comparison to the control group

organism: Drosophila melanogaster

source_name: Trachea

growth_protocol: yw; foxo21/21 and y[1] w[1118] animals were incubated at 25 °C until 3rd instar stage before dissection. Gal4-ppk4;tubGal80>UAS-foxo animals were incubated at the permissive temperature (18 °C) for the control or  shifted to the restrictive temperature (30 °C) for 4 h before dissection in 3rd instar stage.

extract_protocol:
whole RNA from dissected trachea was extracted using RNAmagic (Bio-Budget Technologies GmbH, Germany)
Samples were quantified with a fluorometric dye (Quant-IT, Thermofisher, USA) and between 187 and 500 ng per sample were used as input for theTruSeq stranded mRNA library kit (Illumina, USA) following the manufacturers manual.
Resulting libraries showed a fragment size distribution of around 350 bp and were sequenced on a HiSeq 4000 (Illumina, USA) with 50bp single-end reads

value: Trachea


title: tumor,Rosa,211

description: Library name: RNA_tumor_Rosa_211

value: pancreas


title: D7,BRG1,Rosa,8

description: Library name: D7_BRG1_Rosa_8

value: pancreatitis


title: D2,BRG1,Rosa,22

description: Library name: D2_BRG1_Rosa_22


title: Bioni037-A, Passage 0, Replicate 1

description: Library name: MP23-007-APOE3-3-LB23022-D14-030324_S28


title: FoxO OE 30-5


title: Naïve 2  Epithelial cells

value: EpCAM+ Epithelial cells


title: PDAC_cell,SMARCA5

description: Library name: ChIP_PDAC_cell_SMARCA5

data_processing:
The adaptors of paired-end reads were trimmed by trim-galore (v.0.6.4) with the parameters set as: -q 25 --phred33 --length 50 -e 0.1 --fastqc --stringency 5 --paired.
Adaptor-trimmed reads were aligned to the mm10 genome with the following parameters: --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700 by Bowtie2.
Aligned reads stored in SAM format were converted to BAM files and PCR duplicates were removed using SAMtools.
Peaks were called by MACS2(v.2.2.7.1)56 using the parameters: macs2 callpeak -g mm -B -p 0.01 -f BEDPE.
Assembly: mm10
Supplementary files format and content: bigwig

extract_protocol:
Cells were resuspended in 6mL DMEM and 375ml 16% Formaldehyde (w/v) (Pierce, 28908) was added at room temperature for 8 min with gentle shaking. For inactivation, 319 mL 2.5M Glycine was added. Cells were washed with cold PBS twice and centrifuged at 400g for 5 min 3mL ChIP lysis buffer (50 mMHEPES/KOH pH 7.5, 140 mM NaCl, 0.1% sodium deoxycholate, 1% Triton X-100, 1 mM EDTA, 0.1% SDS, 0.25% sarkosyl and proteinase inhibitor cocktail) was added into the cell precipitate. After sonicated, the supernatant was collected by centrifugation at 13000g for 10min. The supernatant was diluted with dilution buffer (50 mM HEPES/KOH pH 7.5, 140 mM NaCl, 1% Triton X-100, 1 mM EDTA and 13proteinase inhibitor cocktail). DNA was isolated from supernatant by IP with antibodies . IPed DNA was washed with high salt buffer (20 mM Tris pH 7.9, 500 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS and 13proteinase inhibitor cocktail) 7 times and TE buffer (1M Tris-HCl pH 8.0, 0.5M EDTA) once. After treated with RNase A (Qiagen, 19101) and proteinase K (TIANGEN, RT403), transfer DNA was purified using phenol/chloroform (pH 7.0) and ethanol precipitation.
The End-It DNA End-Repair Kit (Lucigen, ER81050) was used to convertpurified DNA to 50-phosphorylated, blunt-end DNA. After treated with Klenow Fragment (3’/50 exo-), barcodes (BIOO Scientific, 514120) were ligated with Quick Ligation kit (NEB, M2200). After size selection, 15 cycles of PCR were used to amplify the library.


title: D7,RUNX1,Rosa,14

description: Library name: D7_RUNX1_Rosa_14


title: eNPCs, wt, proliferating, rep3

value: proliferating


title: FoxO OE 30-3


title: R.intestinalis, raffinose, R3

first: Paul

last: Biscarrat

address: 78352 Rue de la Manufacture,

institute: INRAE

description: Library name: RR_R_R3

data_processing:
bcl2fastq2-2.18.12 (demultiplex)
Cutadapt 3.2 (adapter trimming)
FastQC v0.11.5 (quality control)
Assembly: B.xylanisolvens:NZ_JH724294,NZ_JH724295,NZ_JH724296,NZ_JH724297,NZ_JH724298,NZ_JH724299,NZ_JH724300,NZ_JH724301,NZ_JH724302,NZ_JH724303,NZ_JH724304,NZ_JH724305,NZ_JH724306/B;thetaiotaomicron:NC_004663.1/R.intestinalis:NZ_LR027880.1/S.variabile:NZ_GG704769,NZ_GG704770,NZ_GG704771,NZ_GG704772,NZ_GG704773,NZ_GG704774,NZ_GG704775,NZ_GG704776,NZ_GG704777,NZ_GG704778,NZ_GG704779/A.rectalis NZ_AP012325.1 / B.adolescentis NC_008618.1 / B.uniformis RefSeq GCF_000154205.1/A.rectalis NC_012781
Supplementary files format and content: Table xxxx_DESeq_results.csv contains the raw, unfiltered results. There is one gene per row and in columns the metrics calculated by DEseq2 during the analysis: ID: gene name//baseMean: average of normalized counts for all samples/replicates involved in the comparison/log2FoldChange: log2 of the ratio of counts between the 2 conditions/lfcSE: standard error of this fold change/stat: the value of the statistical (Wald) test, used to calculate the pvalue. It is the ratio between log2FoldChange and lfcSE./pvalue: This value determines the significance of the statistical value or test. It indicates the probability that an observed fold change could be due to chance. The closer the p-value is to 0, the more significant the test, and the more real the differential in expression observed between the 2 conditions./- padj: adjusted (or corrected) pvalue, which takes into account multiple tests. As the statistical test is performed on each gene and each test is associated with a possible error, accumulating tests increases this error. We need to take this into account and make a correction for the number of tests performed. DEseq2 uses the Benjamini-Hochberg method./- then normalized counts for the samples involved in the comparison

organism: Roseburia intestinalis

extract_protocol:
RNA was harvested using RNeasy kit (Qiagen)
Directional RNA-Seq Libraries were constructed using the TruSeq Stranded Total RNA library prep kit, with bacteria Ribo-Zero reagents (Illumina), following the manufacturer’s instructions. After the Ribo-Zero step, the samples were checked on the Agilent Bioanalyzer for proper rRNA depletion. Final libraries quality was assessed on an Agilent Bioanalyzer 2100, using an Agilent High Sensitivity DNA Kit.

value: Bacteria

value: Raffinose


title: D7,RUNX1,Rosa,8

institute: Tsinghua university

description: Library name: D7_RUNX1_Rosa_8


title: FoxO OE 30-4


title: R.intestinalis, raffinose,  R2

description: Library name: RR_R_R2


title: eNPCs, wt, 48h differentiation, rep3


title: PDAC cell,sgSrcap,rep2

description: Library name: ATAC_SCF_sgSrcap_2

data_processing:
The adaptors of paired-end reads were trimmed by trim-galore (v.0.6.4) with the parameters set as: -q 25 --phred33 --length 50 -e 0.1 --fastqc --stringency 5 --paired.
Trimmed reads were aligned to the mm10 genome with the following parameters: --very-sensitive -k 10 by Bowtie2 (v.2.3.5.1)
Aligned reads stored in SAM format were manipulated to generate BAM files and PCR duplicates were removed using SAMtools (v.1.10)
ATAC-seq peaks were called by Genrich (v.0.6) using the parameters: -j -y -r -e chrM -v.
All peaks from all samples were merged and raw counts of merged peaks in each sample were counted by featureCounts (v.2.0.1). Size factor for each sample were calculated using DESeq2 (v.1.24.0). Normalized bigwig files were generated with 1/(size factor) using bamCoverage from deepTools (v.3.4.3).
Assembly: mm10/hg19
Supplementary files format and content: bigwig

extract_protocol:
10,000 GFP-positive cells were sorted by FACS for ATAC-seq. 10% HEK-293T cells were mixed in ATAC-seq samples for spike-in normalization. ATAC-seq was performed with Chromatin Profile Kit for Illumina (Novoprotein, N248-01A).
ATAC-seq was performed with Chromatin Profile Kit for Illumina (Novoprotein, N248-01A).

value: PDAC

value: SrcapKO


title: eNPCs, wt, proliferating, rep2


title: R.intestinalis, raffinose, R1

description: Library name: RR_R_R1


title: FoxO OE 30-2


title: R.intestinalis, glucose, R3

description: Library name: RI_G_R3

value: Glucose


title: PDAC cell,sgSrcap,rep1

description: Library name: ATAC_SCF_sgSrcap_1


title: FoxO OE 30-1


title: PDAC cell,sgSmarca5,rep2

description: Library name: ATAC_SCF_sgSmarca5_2


title: eNPCs, Hq, 48h differentiation, rep4

value: Hq


title: FoxO OE 18-4


title: R.intestinalis, glucose,  R2

description: Library name: RI_G_R2


title: hiPS_SFC086_03_03, Passage 0, Replicate 1

description: Library name: MP23-007-SFC860303-D14-030323_S27

value: iPSC-derived endothelial cells


title: eNPCs, wt, proliferating, rep4


title: eNPCs, Hq, 48h differentiation, rep3


title: PDAC cell,sgSmarca5,rep1

description: Library name: ATAC_SCF_sgSmarca5_1


title: PDAC_cell,SMARCA4

description: Library name: ChIP_PDAC_cell_SMARCA4

value: control


title: FoxO OE 18-2


title: R.intestinalis, glucose, R1

description: Library name: RI_G_R1


title: eNPCs, Hq, proliferating, rep4

value: primary cells


title: PDAC cell,sgChd4,rep2

description: Library name: ATAC_SCF_sgChd4_2


title: FoxO OE 18-1


title: MEF cells, 30mins treated with LLOMe

city: Hyderabad

first: Nitesh

middle: Kumar

last: Singh

state: Telangana

address: Habsiguda

department: Bioinformatics

country: India

institute: Center for Cellular and Molecular Biology

description: Library name: LLOMe_30mins_hac

data_processing:
NanoStat was used to perform read quality check
Dorado was used to basecall the long-read data with methylation basecalling to capture base modification data
The reads were aligned to the GRCm39 mouse reference genome
modkit was used calculate the position-wise methylation scores from read wise methylation information
Assembly: GRCm39
Supplementary files format and content: bed file, tab delimited text file containing position wise methylation information

source_name: Mouse Embryonic Fibroblast Cell

extract_protocol:
DNA was extracted using NucleoSpin Tissue, Mini kit for DNA from cells and tissue (Macherey-Nagel,#740952.50). The quality and quantity of total DNA was checked using Qubit.
After assessing the quality of DNA, it was subjected to Ligation Sequencing Kit V14 (SQK-LSK114). Tape station and Qubit was used to assess the library QC.

value: Mouse Embryonic Fibroblast Cell

value: 30mins treated with LLOMe


title: MEF cells, untreated

description: Library name: LLOMe_control_hac

value: untreated


title: PDAC cell,sgBrg1,rep2

description: Library name: ATAC_SCF_sgBrg1_2


title: Control 4

value: Trachea


title: PDAC cell,sgChd4,rep1

description: Library name: ATAC_SCF_sgChd4_1

value: pancreas


title: eNPCs, wt, 48h differentiation, rep2

value: neural progenitor cells

value: wt

value: 48h differentiation


title: PDAC cell,sgBrg1,rep1

description: Library name: ATAC_SCF_sgBrg1_1


title: MEF cells, 24hrs treated with LLOMe

description: Library name: LLOMe_24hrs_hac

value: 24hrs treated with LLOMe


title: MEF cells, 3hrs treated with LLOMe

description: Library name: LLOMe_03hrs_hac

value: 3hrs treated with LLOMe


title: Control 2


title: PDAC cell,Control,rep2

description: Library name: ATAC_SCF_sg9270

value: PDAC


title: FoxO OE 18-3


title: eNPCs, Hq, proliferating, rep2

value: proliferating


title: PDAC cell,Control,rep1

description: Library name: ATAC_SCF_sg4841


title: Control 3


title: eNPCs, Hq, 48h differentiation, rep2


title: Control 1


title: eNPCs, Hq, 48h differentiation, rep1


title: eNPCs, wt, 48h differentiation, rep1


title: DSM10D_2

city: Santa Fe

first: Jenifer

last: Castro Estrada

state: Santa Fe

address: Pedro Ferré 1277

country: Argentina

institute: Littoral Agrobiotechnology Institute

description: Library name: Sample 29

data_processing:
AgriGO v2.0 - GO Analysis Toolkit and Database for Agricultural Community
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: Stem

growth_protocol: Seeds were sown in soil using 0.5 l pots filled with GROWMIX® Multipro™, one plant per pot. The pots were placed in a greenhouse under a long day photoperiod (16/8 h light/dark cycles), with daily temperatures of about 28 °C.

extract_protocol:
Total RNA was isolated from stems using Trizol reagent (Invitrogen, https://www.thermofisher.com/ar/), following the manufacturer's instructions. The experiment was performed with biological replicates of each treatment. Isolated RNA was lyophilised before shipment.
RNA libraries for RNA-seq were prepared using HISAT to align the clean reads to the reference genome AND Bowtie2 to align the clean reads to the reference genes.

treatment_protocol: A wooden clamp (3 g) was suspended from the top of 4.5-5 cm tall stems. The weight was applied over a period of 48h.

value: Stem

value: Ailsa Craig

value: DSM

tag: batch

value: 10 Days Post Treatment (DPT)


title: PDAC cell,SMARCA5WT,sgSmarca5,6

city: Beijing

description: Library name: ATAC_rescue_WT_sgSmarca5_6


title: FoxO KO 4

value: yw; foxo21/21


title: eNPCs, Hq, proliferating, rep3

value: primary cells

value: Hq


title: DSM10D_1

description: Library name: Sample 10


title: PDAC cell,SMARCA5WT,sgSmarca5,5

description: Library name: ATAC_rescue_WT_sgSmarca5_5


title: eNPCs, Hq, proliferating, rep1


title: FoxO KO 3


title: eNPCs, wt, proliferating, rep1


title: C10D_3

description: Library name: Sample 27

value: Control


title: C10D_2

description: Library name: Sample 23


title: PDAC cell,SMARCA5WT,sg9270

description: Library name: ATAC_rescue_WT_sg9270

value: control


title: Exp6, Vancomycin, with Candida

city: Birmingham

first: Rebecca

last: Drummond

state: Edgbaston

address: IBR 437, University of Birmingham

institute: University of Birmingham

data_processing:
Read counts were quantified using HTSeq-count. Differentially expressed genes between biological conditions were detected using DESeq2 analysis pipeline in R (Padj<0.05).
Assembly: mm10
Supplementary files format and content: Raw read counts in FASTQ files

source_name: Bone-marrow Macrophage

growth_protocol: Bone marrow was flushed from the femurs and tibias of mice (8–12-week-old C57BL/6JCrl males and females) into sterile PBS supplemented with 2mM EDTA. Collected bone marrow was filtered through a 70mm filter and centrifuged (1500rpm 5 minutes at 4⁰C) to pellet the cells. The pellet was resuspended in Roswell Park Memorial Institute (RPMI) media with GlutaMAX and HEPES, further supplemented with 20% heat-inactivated foetal bovine serum and 40ng/mL M-CSF (Biolegend). Half of the cell suspension was further supplemented with 20mg/mL vancomycin hydrochloride (Fisher BioReagents). The cell suspension (10mL per flask) was incubated in T75 flasks (Corning) for 3 days at 37C at 5% CO2, before removing the media and replacing with 10mL fresh media (supplemented with FBS and M-CSF with/without vancomycin, as above), before continuing the incubation for a further 2 days. On day 5 of the culture, adherent macrophages were collected by harvesting in ice-cold 2mM EDTA/PBS. Briefly, the media was removed and cell layer flooded with ice-cold 2mM EDTA/PBS before incubation on ice for 5 minutes. Cells were gently lifted with a cell scraper (Corning) and collected by centrifugation. Macrophages were counted using a haemocytometer and Trypan blue exclusion. Macrophages were cultured in RPMI supplemented with 10% FBS without antibiotics or with 20mg/mL vancomycin in subsequent assays.

extract_protocol:
Macrophages were seeded overnight in 24-well plates at 1x106 cells/well, and infected with C. albicans for 2 hours (MOI 2:1) or mock infected with PBS. Media was then removed from wells and 1mL of Trizol (Life Technologies) added to each well. Lysed cells were lifted from the wells, transferred to RNAse-free Eppendorfs and stored at -80°C. Samples were thawed at room temperature and 200μL of chloroform was added to each tube, mixed by inverting several times and allowed to settle for 5 minutes. Samples were centrifuged at 12,000g for 15 minutes at 4°C. The top layer containing RNA was transferred to RNAse-free Eppendorf tubes and an equal volume of 70% ethanol was added to each sample. Samples were then added to Qiagen columns (RNeasy kit, Qiagen) to be washed and perform a DNAse digest step (Qiagen). RNA was eluted in RNAse-free water, and then QC-tested using the Qubit Fluorometer TapeStation.
RNA libraries were then prepared using the Lexogen QuantSeq 3’ mRNA-Seq kit according to the manufacturers’ instructions. Illumina sequencing was performed on the NextSeq 500 sequencing platform using the v2.5 150 cycles mid output flow cell, which produced 75 bp single reads. Reads where mapped to the Mus musculus reference genome. Read counts were quantified using HTSeq-count. Differentially expressed genes between biological conditions were detected using DESeq2 analysis pipeline in R (Padj<0.05).
Lexogen 3' QuantSeq FWD

tag: experiment group

tag: stimulus

value: Candida albicans

value: Bone-marrow Macrophage

value: Vancomycin


title: FoxO KO 1

value: Trachea


title: FoxO KO 2


title: C10D_1

description: Library name: Sample 9


title: Exp6, Control, with Candida

value: Untreated (control)


title: Exp6, Vancomycin, no infection


title: DSM10D_3

description: Library name: Sample 32


title: PDAC cell,vector,sgSmarca5,5

description: Library name: ATAC_rescue_V_sgSmarca5_5

value: pancreas


title: PDAC cell,vector,sgSmarca5,6

description: Library name: ATAC_rescue_V_sgSmarca5_6

value: PDAC


title: Information of vdj from C05 and MG05

city: Chiba

first: Hiroyuki

last: Akamine

address: chuoku inohana 1-8-1

institute: Chiba university

description:
Library name: vdj_C05_MG05
Rhapsody

library_source: other

data_processing:
The BCL file after sequencing was converted to a FASTQ file using bcl2fastq. The multiplex FASTQ was output as adata using sample tags and index information in sevenbridges. Subsequently, to facilitate analysis, files were created that were completely divided by sample as adata.The RNA expression matrix was analyzed with scanpy (v1.9.8).
Assembly: GRCh38
Supplementary files format and content: adata file of RNA and Abseq for each sample, vdj data as xlsx

molecule: other

source_name: PBMC

extract_protocol:
Peripheral blood was collected from all participants, and SepMate (STEMCELL Technologies, ST-8645, Vancouver, Canada) was used for PBMC isolation.
T and B cells were sorted from PBMC using a BD Melody cytometer. After 30-min incubation at 4 °C with sample tags and Abseq antibodies, the cells were washed and enumerated using a hemocytometer with Trypan blue. Cell viability was assessed, and the total cell number was quantified using a BD Rhapsody Scanner. A total of 20,000 cells were targeted and loaded onto BD Rhapsody cartridges, allowing single cells to remain stationary. If sample tags were used for pooled cells from two samples, we adjusted the target cell number accordingly. The libraries were prepared according to the BD Rhapsody protocol using the WTA amplification kit. They were then quantified and quality-assessed on an Agilent TapeStation.

value: PBMC


title: DSM6H_1

description: Library name: Sample 20

value: Stem

value: 6 Hours Post Treatment


title: Exp5, Vancomycin, with Candida


title: Exp6, Control, no infection


title: PDAC cell,vector,sg9270

description: Library name: ATAC_rescue_V_sg9270


title: DSM6H_2

description: Library name: Sample 22

value: Ailsa Craig

value: DSM


title: DSM6H_3

description: Library name: Sample 5


title: PDAC cell,vector,sg4841

description: Library name: ATAC_rescue_V_sg4841


title: S9_2

city: shanghai

first: Yang

last: Ming

address: No.600 yishan road

institute: Shanghai jiao tong universiay affiliated sixth people's hospital

description: Library name: SAMPLES8

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count
Assembly: NCBI_UM_NZW_1.0
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: Matrix table with FPKM values for every gene and every sample

organism: Oryctolagus cuniculus

source_name: urethral

extract_protocol:
RNA was harvested using Rneasy mini plus kit ( Qiagen ).1.3 ug of total RNA was used for the construction of sequencing libraries
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: urethral


title: S9_4

description: Library name: SAMPLES9


title: PDAC cell,SMARCA5WT,sg4841

description: Library name: ATAC_rescue_WT_sg4841


title: C6H_3

description: Library name: Sample 16


title: Exp5, Vancomycin, no infection


title: Exp5, Control, with Candida


title: S9_1

description: Library name: SAMPLES7


title: Information of vdj from C04 and MG04

description:
Library name: vdj_C04_MG04
Rhapsody


title: C6H_2

description: Library name: Sample 14


title: C6H_1

description: Library name: Sample 3


title: Exp5, Control, no infection


title: PDAC cell,SMARCA5K211R,sg9270

description: Library name: ATAC_rescue_K211R_sg9270


title: PDAC cell,SMARCA5K211R,sgSmarca5,5

description: Library name: ATAC_rescue_K211R_sgSmarca5_5


title: S7_3

description: Library name: SAMPLES5


title: Exp4, Vancomycin, with Candida


title: RNA_∆atpB_rep3

city: Jena

first: Rabea

last: Ghandour

address: Winzerlaer Straße 2

department: Institute of Microbiology

institute: Friedrich Schiller University

description: Library name: RNA_datpB_rep3

data_processing:
The quality of the obtained footprint reads was checked with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Adapters were removed using cutadapt.
All alignments were performed with STAR aligner v2.7.1a, using a sequential mapping approach where unmapped reads were used as input for the proceeding alignment. The alignment order is as follows: 1) rRNA and tRNA contaminants; 2) chloroplast genome; 3) mitochondrial genome; and 4) nuclear genome. The following sequences were obtained from NCBI (with following annotation): 5.8S rRNA (AJ300215.1), 5S rRNA (AJ222659.1), 18S rRNA (AJ236016.1), and 26S rRNA (AF479172.1), chloroplast genome (Z00044.2), mitochondrial genome (NC_006581.1). Sequences for the nuclear genome and tRNAs were obtained from solgenomics (ftp://ftp.solgenomics.net/genomes/Nicotiana_tabacum/).
Additional processing and sorting of alignment data were done using samtools and bedtools.
Assembly: Z00044.2
Supplementary files format and content: xlsx file including total reads, RPKM from each sample for chloroplast transcripts

organism: Nicotiana tabacum

source_name: Petit Havana

growth_protocol: Knockout tobacco mutants of essential photosynthetic genes were grown heterotrophically in Magenta boxes containing solidified Murashige and Skoog (MS) medium supplemented with 3% sucrose. Tissue was harvested once equivalent developmental stage of a four leaf old tobacco seedling was reached.

extract_protocol:
For Ribo-Seq, the ribosome footprints were generated using 250 U RNase I per 1 ml of plant lysate (derived from 100 mg of plant fresh weight). The lysate was then layered on a sucrose cushion to purify monosomes. Ribosome footprints from ~20 nt to ~39 nt were size-selected from polyacrylamide gels. For total RNA samples, RNA was isolated with the TRIzol® Reagent (Thermo Fisher Scientific) according to manufacturer’s instructions, gDNA was removed using TURBO™ DNase.
For Ribo-seq, cDNA was synthesized by using NEXTflex™ Small RNA-Seq Kit v3. For RNA-seq, cDNA libraries were generated using Zymo-Seq RiboFree total RNA library kit. The quality and quantity of cDNA libraries was measured by Bioanalyzer and Qubit, respectively.

value: Petit Havana

value: delta atpB


title: Exp4, Vancomycin, no infection


title: RNA_D7_Runx1_741

data_processing:
The adaptors of paired-end reads were trimmed by trim-galore (v.0.6.4) with the parameters set as: -q 25 --phred33 --length 50 -e 0.1 --fastqc --stringency 5 --paired.
Adaptor-trimmed reads were aligned to the mm10 genome with the following parameters: --readFilesCommand zcat --outFilterMismatchNoverLmax 0.2 by STAR (v.2.7.9a)
Aligned reads stored in SAM format were converted to BAM files using SAMtools with parameter: samtools view -bS -h -F 4 -f 2 -q 7.
FeatureCounts counted reads stored in BAM format to exon sites of genes included in GTF files from Ensembl
Assembly: mm10
Supplementary files format and content: raw counts

value: pancreatitis


title: PDAC cell,SMARCA5K211R,sg4841

description: Library name: ATAC_rescue_K211R_sg4841

value: control


title: S7_2

description: Library name: SAMPLES4


title: RNA_∆atpB_rep2

description: Library name: RNA_datpB_rep2


title: S6_4

description: Library name: SAMPLES3


title: RNA_D7_Runx1_737


title: RNA_WT_SNN_rep3

description: Library name: RNA_WT_SNN_rep3


title: S6_3

description: Library name: SAMPLES2


title: Exp4, Control, with Candida

value: Candida albicans


title: RNA_∆atpB_rep1

description: Library name: RNA_datpB_rep1


title: Exp4, Control, no infection

value: Bone-marrow Macrophage


title: RNA_WT_SNN_rep2

description: Library name: RNA_WT_SNN_rep2


title: RNA_D7_Rosa_738


title: RNA_D7_Rosa_55


title: SDT400, timepoint4, rep2

city: Kongens Lyngby

first: Pascal

middle: Aldo

last: Pieters

state: Region Hovedstaden

address: Building 220, Kemitorvet

department: Novo Nordisk Foundation Center for Biosustainability

country: Denmark

institute: DTU

data_processing:
First, raw read trimming was performed using Trim Galore with default options, followed by FastQC on the trimmed reads. Next, reads were aligned to the E. coli K-12 MG1655 reference genome (NC_000913.3) using Bowtie. The read direction was inferred using RSeQC. Read counts were generated using featureCounts. All quality control metrics were compiled using MultiQC. Finally, the expression dataset was reported in units of log-transformed transcripts per million (log(TPM).
Assembly: NC_000913.3
Supplementary files format and content: Comma-separated file, where the first column contains locus tags, and subsequent columns correspond to the log_tpm values of the samples (see description).

organism: Escherichia coli K-12

growth_protocol: Bioreactor fed-batch cultivations were performed in 0.25 L Ambr® fermenters (Sartorius, Germany) with the strains SDT400 and SDT387. Prior to feeding phase, batch phase cultivation was started with 150 mL cultivation volume with the batch medium containing 5 g L-1 D-(+)-glucose monohydrate, 7.6 g L-1 (NH4)2SO4, 15.7 g L-1 KH2PO4, 1.86 g L-1 citric acid monohydrate,  0.493 g L-1 MgSO4, 100 mg L-1 thiamine hydrochloride, 0.5 mL L-1 Antifoam 204 and 3.5 mL L-1 of trace metal solution A  (containing 0.48 g L-1 CuSO4·5H2O, 0.54 g L-1 CoCl·7H2O, 0.54 g L-1 ZnSO4·7H2O, 2 g L-1 CaCl2·2H2O, 41.8 g L-1 FeCl3·6H2O, 0.3 g L-1 MnSO4·H2O, 33.4 g L-1 Na2EDTA, 0.5 g L-1 Na2MoO4·2H2O), 1 mL L-1 trace metal solution B (containing 41.8 g L-1 FeCl3·6H2O)  and 4 mL L-1 of trace metal solution C (containing 5.4 g L-1 ZnSO4·5H2O). Initial batch fermentations were performed until complete glucose consumption, marked by a 50% decline in the rate of CO2 formation, triggering an automatic switch to an exponential fed-batch operation with continuous supply of the feed medium (550 g L-1 D-(+)-glucose monohydrate, 13.7 g L-1 MgSO4·7H2O), where the initial feed rate (0.16 mL h-1); µset is the set specific growth rate (0.11 h-1); and t is the process time. In our experiments, temperature was set at 37°C, dissolved O2 was controlled at 40% (cascade control with stirring speed from 1000 - 4000 rpm or 1500 - 4500 rpm, air flow from 0.15 to 0.35 L min-1, and O2 flow from 0.0 to 0.05 L min-1), pH was maintained at 6.5 with ammonium hydroxide (8% v/v). Throughout the cultivation, samples were taken periodically by an automated liquid handler for transcriptome analysis, as well as offline analysis of biomass, tyrosine, glucose, and organic acid concentrations.

extract_protocol:
All transcriptome samples were collected and prepared in biological duplicates, whereby either 2 mL of culture (low cell density culture, batch phase) or 0.5 mL of culture (high cell density culture, fed batch phase) was added to 6 mL of Qiagen RNA-protect Bacteria Reagent immediately after sample collection. This solution was then vortexed for 30 seconds, incubated at room temperature for 5 minutes, and then centrifuged. The supernatant was then removed and the cell pellet was stored at -80°C. The RNase-Free DNase Set (Qiagen) was used to extract and purify RNA from the cell pellets per vendor protocol, including on-columns DNase treatment for 30 minutes at room temperature. RNA was quantified using qubit fluorometer (Thermofisher) and integrity was assessed using fragment analyzer (Agilent Technologies). Ribosomal RNA was removed using QIAseq FastSelect –5S/16S/23S kit (Qiagen).
Sequencing libraries were prepared with the KAPA Stranded RNA-Seq Library Preparation Kit (Kapa Biosystems) and assessed using fragment analyzer (Agilent Technologies). The libraries were then subjected to paired end sequencing on Illumina NovaSeq.

treatment_protocol: Add other strains later

value: Timepoint 4

tag: cultivation phase

value: Fed-batch

value: {delta}ptsHIcrr


title: Exp3, Vancomycin, no infection

value: Vancomycin


title: Exp3, Vancomycin, with Candida


title: PDAC cell,SMARCA5K211R,sgSmarca5,6

description: Library name: ATAC_rescue_K211R_sgSmarca5_6

value: pancreas

value: PDAC


title: RNA_WT_SNN_rep1

description: Library name: RNA_WT_SNN_rep1


title: S7_4

description: Library name: SAMPLES6


title: RNA_D7_Rosa_22


title: Exp3, Control, with Candida

value: Untreated (control)


title: RNA_as_ATPC_rep3

description: Library name: RNA_as_ATPC_rep3


title: SDT400, timepoint2, rep2

value: Timepoint 2


title: RNA_as_ATPC_rep2

description: Library name: RNA_as_ATPC_rep2


title: SDT400, timepoint3, rep2

value: Timepoint 3


title: Exp2, Vancomycin, with Candida


title: CUTTag_H3K27ac_tumor_Rosa_195


title: Exp3, Control, no infection


title: CUTTag_H3K27ac_D7_Rosa_22


title: S6_2

description: Library name: SAMPLES1


title: RNA_as_ATPC_rep1

description: Library name: RNA_as_ATPC_rep1


title: SDT400, timepoint1, rep2

value: Timepoint 1

value: Batch


title: SDT400, timepoint4, rep1


title: RNA_∆psaB_rep3

description: Library name: RNA_dpsaB_rep3

value: Petit Havana

value: delta psaB


title: CUTRUN_SMARCA5_D7_Rosa_55

value: pancreatitis


title: SDT400, timepoint3, rep1


title: Exp2, Control, with Candida


title: SDT400, timepoint2, rep1


title: CUTRUN_CTCF_D2_Smarca5_361


title: RNA_∆psaB_rep2

description: Library name: RNA_dpsaB_rep2


title: Exp2, Vancomycin, no infection


title: SDT400, timepoint1, rep1


title: RNA_∆psaB_rep1

description: Library name: RNA_dpsaB_rep1


title: Exp2, Control, no infection


title: CUTRUN_CTCF_D2_Smarca5_359


title: Exp1, Vancomycin, with Candida


title: RNA_∆petN_rep3

description: Library name: RNA_dpetN_rep3

value: delta petN


title: CUTRUN_SMARCA5_D7_Runx1_737


title: SDT387, timepoint4, rep2

value: {delta}ptsHIcrr aroGfbr tyrAfbr aroBCO


title: CUTRUN_CTCF_D2_Rosa_362

value: control


title: Exp1, Vancomycin, no infection

value: Bone-marrow Macrophage


title: RNA_∆petN_rep1

description: Library name: RNA_dpetN_rep1


title: SDT387, timepoint3, rep2

value: Fed-batch


title: RNA_∆petB/D_rep3

description: Library name: RNA_dpetB_D_rep3

value: delta petB/D


title: Exp1, Control, with Candida

value: Candida albicans


title: Exp1, Control, no infection


title: SDT387, timepoint1, rep2


title: SDT387, timepoint2, rep2


title: CUTRUN_CTCF_D2_Rosa_357

value: pancreas


title: ATAC_Kca_D7_Rosa_55

data_processing:
The adaptors of paired-end reads were trimmed by trim-galore (v.0.6.4) with the parameters set as: -q 25 --phred33 --length 50 -e 0.1 --fastqc --stringency 5 --paired.
Trimmed reads were aligned to the mm10 genome with the following parameters: --very-sensitive -k 10 by Bowtie2 (v.2.3.5.1)
Aligned reads stored in SAM format were manipulated to generate BAM files and PCR duplicates were removed using SAMtools (v.1.10)
ATAC-seq peaks were called by Genrich (v.0.6) using the parameters: -j -y -r -e chrM -v.
All peaks from all samples were merged and raw counts of merged peaks in each sample were counted by featureCounts (v.2.0.1). Size factor for each sample were calculated using DESeq2 (v.1.24.0). Normalized bigwig files were generated with 1/(size factor) using bamCoverage from deepTools (v.3.4.3).
Assembly: mm10
Supplementary files format and content: bigwig

value: no


title: ATAC_Kca_D7_Runx1_741


title: KO-6

city: Chicago

first: Cambrian

middle: Yangshao

last: Liu

state: IL

address: 5841 S Maryland Ave

department: Department of Medicine

institute: The University of Chicago

description: Primary TNFR1-/- CMFs - mouse 6

data_processing:
Illumina software was used for basecalling.
Transcript abundances were obtained from cellranger 5.0.0
Matrix files were loaded into monocle 3.0 for sample merging and normalization.
Analysis scripts are available at: https://github.com/stalepig/2021-mesenchyme-scrnaseq
Genome_build: mm10
Supplementary_files_format_and_content: Sparse Matrix (mtx) file of merged UMI counts with each row representing a gene and each column a cell barcode, can be read into R with readMM function in the Matrix package
Supplementary_files_format_and_content: Tab-delimited text (txt) files providing gene names (row data) or cell clustering and sample information (column data), matched to the sparse Matrix file

source_name: Cultured murine colonic mesenchyme

growth_protocol: Primary colonic myofibroblasts (CMFs) were isolated from the distal end of 16w old control (TNFR1+/-) and TNFR1-/- mice. The colon (1cm from the dentate line), cut horizontally, was stirred at 250 rpm in 5 mM EDTA/HBSS medium (without Ca++ and Mg++) at 37°C for 15 min and repeated for a total of 5 washes. Following two washes of ice-cold PBS, the tissue was digested in DMEM, low glucose, GlutaMAX™ Supplement, pyruvate plus Penicillin-Streptomycin (10,000 U/mL) with, 0.31 mg/mL Dispase and 0.25mg/mL collagenase Type XI for up to 60 minutes at 250 rpm at 37°C, until the tissue appeared stringy. Digested tissue was treated with ACK lysis buffer (4.15 g NH4Cl, 0.5 g KHCO3, 18.6 mg Na2EDTA, 400 ml H2O, pH 7.2-7.4) for 5 min and then passed through a 100‐μm cell strainer into 6-well dishes of CMF-growth medium (DMEM, low glucose, GlutaMAX™ Supplement, pyruvate plus Penicillin-Streptomycin (10,000 U/mL) with 10% FBS and 1X recombinant human insulin, human transferrin and sodium selenite (ITS) solution, and 20 ng/mL recombinant murine epidermal growth factor. After 24‐h incubation, non‐adherent cells were washed away. One week later, only myofibroblasts divided, and macrophages and epithelial cells had senesced after the first passage.

extract_protocol:
Control (TNFR1+/-) and TNFR1-/- primary CMFs were seeded at a density of 1x103 cells/50µL of Matrigel into 24-well plates and were grown to 70% confluency. At Day 5, CMFs were extracted from Matrigel after brief incubation at 4⁰C via centrifugation at 1200rpm for 5 min. Cells were reconstituted in 10mL of HBS/1% BSA solution and were passsed through a 40 µm filter to suspend into single cells. To remove dead cells for the final flow, single cell suspensions of control of TNFR1-/- CMFs were stained with the EasySep™ Dead Cell Removal (Annexin V) Kit (Thermofisher) according to manufacturer's guidelines. Live cells were quantified and reconstituted in 100-200 µL of HBS/1% BSA solution. Samples with live cell counts of 95% and above only were processed for scRNA-Seq.
Single-cell 3' libraries were generated using the 10X Chromium platform. Paired-end sequencing with index reads was performed on a NextSeq 500.

treatment_protocol: scRNA-Seq was performed on control (TNFR1+/-) and TNFR1-/- primary CMFs grown in vitro.

tag: days post passage


title: ATAC_Kca_D7_Runx1_737


title: SDT387, timepoint4, rep1

value: Timepoint 4


title: KO-5

description: Primary TNFR1-/- CMFs - mouse 5


title: RNA_∆petB/D_rep2

description: Library name: RNA_dpetB_D_rep2


title: ATAC_Kca_D7_Rosa_22


title: SDT387, timepoint3, rep1


title: RNA_∆petB/D_rep1

description: Library name: RNA_dpetB_D_rep1


title: RNA_∆psbJ_rep3

description: Library name: RNA_dpsbJ_rep3

value: delta psbJ


title: SDT387, timepoint2, rep1

value: Timepoint 2


title: KO-4

description: Primary TNFR1-/- CMFs - mouse 4


title: Con-3

description: Primary control (TNFR1-/+) CMFs - mouse 3


title: RNA_∆petN_rep2

description: Library name: RNA_dpetN_rep2


title: castrated3

first: Jingdong

last: Xue

address: No.389 XInCun Road

institute: tongji university Tongji Hospital

description: Library name: sample6

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2)
(1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
The clean reads were mapped to the reference genome using HISAT2 (v2.0.4)
Bowtie2 (v2.2.5) [3] was applied to align the clean reads to the reference coding gene set，then expression level of gene was calculated by StringTie (v2.1.2)
Assembly: UM_NZW_1.0
Supplementary files format and content: tab-delimited xls file includes raw counts for each Sample
Supplementary files format and content: Xls files include FPKM values for each Sample

source_name: urethra

extract_protocol:
RNA was harvested using TRIzol™ Reagent (Invitrogen). 1.3 ug of total RNA was used for theconstruction of sequencing libraries.
RNA libraries for RNA-seg were prepared using VAHTS Universal V6 RNA-seq Library Prep Kit followingmanufacturer's protocols.

treatment_protocol: Adult male New Zealand rabbits castrated control (0 mg/kg), physiological dose (2.5 mg/kg). Rabbits in the castrated received intramuscular injections of sterile water without testosterone, while the physiological dose group (2.5 mg/kg) received 2.5 mg/kg of testosterone propionate, respectively. Injections were administered in the right thigh muscle every 48 hours. All rabbits underwent bulbar urethroplasty via end-to-end anastomosis and were sacrificed one month postoperatively. For transcriptomic analysis, urethral tissues were randomly collected from three rabbits in each group. Tissues were harvested from the site of urethral reconstruction.

value: urethra

value: castrated control+physiological dose androgen supplementation(2.7 mg/kg)


title: RNA_∆psbJ_rep2

description: Library name: RNA_dpsbJ_rep2

value: Petit Havana


title: castrated2

description: Library name: sample5

value: castrated control+physiological dose androgen supplementation(2.6 mg/kg)


title: SDT387, timepoint1, rep1

value: Timepoint 1

value: Batch


title: RNA_∆psbJ_rep1

description: Library name: RNA_dpsbJ_rep1


title: RNA_∆3'psbD_rep3

description: Library name: RNA_dpsbD_rep3

value: delta 3'psbD


title: castrated1

description: Library name: sample4

value: castrated control+physiological dose androgen supplementation(2.5 mg/kg)


title: Con-1

description: Primary control (TNFR1-/+) CMFs - mouse 1


title: mOocyte, FloxFloxZp3Cre, rep2

city: Fukuoka

first: Tappei

last: Mishina

address: 744 Motooka Nishi-ku

institute: Kyushu University

description: Library name: zp3cre_02

data_processing:
Sequence reads were trimmed adaptor and low-quality bases using fastp with the option '-3 -q 15 -l 15'.
Hisat2 v2.2.1 was used to align the reads to the mouse genome (GRCm38).
The featureCounts v2.0.3 tool implemented in the Subread software was used to generate counts of reads uniquely mapped to annotated genes using the Ensembl (release 93) annotation gtf file.
In order to quantify the first exon of Kif11, as proxy for the full-length mRNA, reads were counted using the custom annotation gtf file with all Kif11 exons removed except for the exon 1.
Assembly: mouse genome GRCm38
Supplementary files format and content: tab-delimited text file including raw count or TPM for each sample.

source_name: oocytes

extract_protocol:
The isolated full-grown oocytes at the germinal vesicle (GV) stage were washed in washing medium [0.1% PBA in PBS] and collected manually with 0.5 μL of the washing medium in 2.125 μl cell lysis buffer [10X Lysis Buffer (TAKARA), RNase Inhibitor (TAKARA), and RNase-free water (Nacalai)] in 0.2 mL 8-strip tubes. Three oocytes were collected in each tube with one or two replicates from each mouse.
The SMART-seq v4 Ultra Low Input RNA Kit for Sequencing (Takara) was used to reverse transcribe poly(A) RNA and amplify full-length cDNA. Samples were amplified for 13 cycles in 8-strip tubes. After the cDNA was adjusted to 0.5 ng in 1.25 μL of elution buffer [10mM Tris-HCl, pH8.5], Tn5 tagmentation-based reaction was performed with 1/4 volume of the Nextera XT DNA Library Preparation Kit (Illumina) with Nextera XT Index Kit (Illumina) according to manufacturer's protocol. Library DNA was amplified with 12 cycles of PCR and purified using 1.8× volume of SPRISelect (Beckman Coulter) and eluted into 12 μL of the elution buffer [10mM Tris-HCl, pH8.5].

value: oocytes

value: FloxFlox, Zp3-Cre


title: RNA_∆3'psbD_rep1

description: Library name: RNA_dpsbD_rep1


title: mOocyte, FloxFloxGdfCre, rep2

description: Library name: gdf9cre_02

value: FloxFlox, Gdf9-Cre


title: 4367TGP-POS, Low Serum #1

city: Paris

first: Elodie

last: Girard

address: 11-13 rue Pierre et Marie Curie

institute: Institut Curie

description: Library name: 436_P1

data_processing:
Raw counts were generated using Star (v2.6.1a) gene quantification mode (--quantMode GeneCounts) on the Gencode v19 gene database.
Raw counts were normalized using  the TMM method using EdgeR (v3.22.5) and Limma's voom function (v3.36.5).
Assembly: hg19
Supplementary files format and content: Tab-delimited text file containing raw counts for each sample
Supplementary files format and content: Tab-delimited text file containing TPM for each sample

growth_protocol: MDA-MB-2317TGP-POS and MDA-MB-2317TGP-NEG cells were propagated in DMEM supplemented with 10% FBS under standard cell culture conditions, maintained at 37.5°C in a humidified atmosphere containing 5% CO2. MDA-MB-4367TGP-POS and MDA-MB-4367TGP-NEG cells were propagated in DMEM supplemented with 10% FBS under standard cell culture conditions, maintained at 37.5°C in a humidified atmosphere containing 5% CO2.

extract_protocol:
Extraction was performed using the RNAeasy Mini Kit (Qiagen, Courtaboeuf, France), according to the manufacturer’s instructions
TruSeq Stranded mRNA

treatment_protocol: WNT activity reporter cell lines were generated by liposome-mediated transfection of the 7TGP plasmid, followed by stable selection with puromycin (3 μg/mL) for a minimum of five passages. The 7TGP reporter vector contains seven copies of TCF-binding sites upstream of a minimal promoter that drives eGFP expression in response to WNT pathway activation. Upon nuclear translocation of β-catenin and subsequent binding to TCF/LEF1 transcription factors, eGFP is expressed. Reporter activity (7TGP/eGFP status) was assessed by flow cytometry and fluorescence microscopy under optimal growth conditions. Sequential FACS sorting was performed on the stably transfected lines to enrich for either 7TGP-positive or 7TGP-negative subpopulations.

value: Mesenchymal Cell line

value: Wnt-positive cell Line

value: 7TGP vector transfected MDA-MB-4367TGP-POS


title: castrated+T1

city: Shanghai

description: Library name: sample1

value: castrated control (0mg/kg)


title: mOocyte, FloxFloxZp3Cre, rep1

description: Library name: zp3cre_01


title: castrated+T2

description: Library name: sample2


title: 4367TGP-NEG, Low Serum #2

description: Library name: 436_N2

value: Wnt-negative cell line

value: 7TGP vector transfected MDA-MB-4367TGP-NEG


title: mOocyte, FloxFloxGdfCre, rep1

description: Library name: gdf9cre_01


title: castrated+T3

description: Library name: sample3

value: urethra


title: RNA_RB70_rep3

description: Library name: RNA_RB70_rep3


title: unlabel_NC_2

first: Rui

last: Cheng

state: Shanghai

address: No. 1630 East Road, Pudong New Area

institute: Shanghai Jiao Tong University

description: Library name: SAMPLES 17

data_processing:
FASTQ files were processed using the DynamicST pipeline to extract UMIs (47–58 bp) and spatial barcodes (X: 1–8 bp, Y: 39–46 bp) from Read 1 for spatial location identification. cDNA from Read 2 was aligned to the mouse genome (mm10, Gencode vM13) using STAR 2.7.11a. Spots outside tissue regions, defined by H&E staining, were excluded.
Assembly: mm10
Supplementary files format and content: The spatial transcriptomics file in .h5ad format, including the raw matrices of both new and old total RNA.

source_name: kidney

extract_protocol:
First, the nucleoside analog 4sU is administered to mice via tail vein injection. 4sU is rapidly diffused throughout the body via blood flow and is incorporated into new RNA during transcription. After labeling, the tissue is sectioned and attached to a DNA coordinate barcoding array for spatial transcriptome indexing. Following hematoxyling and eosin (H&E) and permeabilization, the released RNAs with poly (A) tails from the tissue are in situ captured by the spatial barcoding oligo(dT) sequence in each spot. By iodoacetamide (IAA)-based alkylation treatment, the 4sU in mRNA is transformed into a cytosine analog by covalently attaching a carboxyamidomethyl group, altering its hydrogen-bonding properties. During reverse transcription, this chemical modification leads to T-to-C substitutions at single-base resolution, marking the newly synthesized RNAs, while the spatial barcoding sequences added to the cDNAs record the coordinate of captured mRNAs. Subsequently, second-strand cDNA synthesis, library construction, and next-generation sequencing are performed.
RNA-Seq

treatment_protocol: To induce renal ischemia, mice were first anesthetized via intraperitoneal injection of 30 mg/ml pentobarbital sodium. Ischemia was initiated by clamping the renal artery, thereby obstructing blood flow to the kidney. After a 50-minute ischemic period, reperfusion was initiated by releasing the clamp, allowing blood flow to return to the kidney. The renal artery remained clamped for 50 minutes during the ischemic phase, and following the release of the clamp, blood circulation was restored. Kidneys were harvested at three different time points following reperfusion: 4.5 hours, 12 hours, and 24.8 hours.

value: kidney


title: A. rectalis, raffinose, R2

city: Jouy-en-Josas

description: Library name: AR_R_R2

organism: Agathobacter rectalis

source_name: Bacteria

value: Bacteria

value: Raffinose


title: A. rectalis, raffinose, R3

description: Library name: AR_R_R3


title: RNA_RB70_rep2

description: Library name: RNA_RB70_rep2

value: Petit Havana


title: 2317TGP-POS, Low Serum #2

description: Library name: 231_P2

value: 7TGP vector transfected MDA-MB-2317TGP-POS


title: 4367TGP-NEG, Low Serum #1

description: Library name: 436_N1


title: unlabel_NC_1

description: Library name: SAMPLES 16


title: RNA_RB70_rep1

description: Library name: RNA_RB70_rep1


title: A. rectalis, raffinose, R1

description: Library name: AR_R_R1


title: 2317TGP-POS, Low Serum #1

description: Library name: 231_P1


title: label_NC_3

description: Library name: SAMPLES 15