title: Pinot noir berry sample collected at time point 5 (replicate 3) over ripening season 2012 - Crop thinned 50%

source_name: grape berry pericarp_time point 5_2012_Crop thinned 50%

tag: cultivar

tag: year

tag: time point


title: Pinot noir berry sample collected at time point 5 (replicate 2) over ripening season 2012 - Crop thinned 50%

status: Public on Dec 31 2022

type: SRA

city: San Pietro in Cariano

first: Marianna

last: Fasoli

state: Verona

address: Via della Pieve 70

department: Biotechnology

country: Italy

institute: University of Verona

library_source: transcriptomic

data_processing:
The reads were aligned onto the grapevine 12x reference genome PN40024 using TopHat v2.0.6 with default parameters
Mapped reads were used to reconstruct the transcripts using Cufflinks v2.0.2 and the reference genome annotation V1
The normalized expression of each transcript was calculated as RPKM (Reads Per Kilobase per Million mapped reads) for each sample.
Genome_build: 12X reference genome PN400024;
https://www.ncbi.nlm.nih.gov/assembly/GCF_000003745.3
Supplementary_files_format_and_content: tab delimited text file containing the normalized reads counts RPKM  for all the samples.

molecule: total RNA

organism: Vitis vinifera

growth_protocol: Vineyard Features: Vitis vinifera cultivar Pinot noir (clone FPS 23 grafted on rootstock Freedom and planted in 2001) was grown nearby Modesto (USA, CA) in sandy clay loam in an east-west orientation with 10 foot row spacing and 5 foot vine spacing.

extract_protocol:
Total RNA was isolated using the Spectrum Plant Total RNA kit (Sigma-Aldrich) following the manufacturer’s instructions with some modifications (Fasoli et al., 2012). RNA quality and quantity were determined using a Nanodrop 2000 spectrophotometer (Thermo Scientific) and a Bioanalyzer Chip RNA 7500 series II (Agilent).
165 non-directional cDNA libraries were prepared from 2.5 μg of total RNA using the Illumina TruSeq RNA Sample preparation protocol (Illumina Inc., San Diego, CA, USA). Library quality was determined using the Agilent High Sensitivity DNA kit on the Agilent 2100 bioanalyzer, and the quantity was determined by quantitative PCR using the KAPA Library Quantification kit (KapaBiosystems).

treatment_protocol: Cluster thinning treatments: Moderate thinning (50% crop load reduction) was achieved removing clusters to maintain one cluster per shoot; severe thinning (75% crop load reduction) consisted in mantaining one cluster every other shoot; control (0% crop load reduction) was unthinned vines.

value: cv Pinot noir

tag: time point replicate

tag: day after veraison

tag: sugar content (g/100ml)

tag: treatment (cluster thinning)

value: Crop thinned 50%

tag: tissue

value: grape berry pericarp


title: Pinot noir berry sample collected at time point 5 (replicate 1) over ripening season 2012 - Crop thinned 75%

source_name: grape berry pericarp_time point 5_2012_Crop thinned 75%

value: Crop thinned 75%


title: TJ1_1d_3_model_T_cell_1_tissue_Blood_day_35_NA [TJ_1d_3_B]

city: New York city

first: Zhi

last: Chai

state: NY

address: 1425 Madison Ave

country: USA

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Raw RNA-seq reads were aligned against the mm10 reference genome using STAR (version 2.4.0g1)
and gene- and exon-level read summarizations were performed with the featureCounts program in subRead
Ensembl annotations were used for both the alignment and the read summarization.
For the exon-level read summarization, a collapsed version of the annotations file where gene designs are described based on non-overlapping “counting- bins” was used to avoid over- or under-counting of reads.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include Raw Count values for each gene in each sample

organism: Mus musculus

source_name: Blood

extract_protocol:
The colons from 15 mice per group at each time point were collected for RNA analysis. 1 cm distal adjacent to rectum was used for histology and the remaining tissue was used for RNA. The remaining colon tissues were frozen in RNAlater at -80C for RNA extraction. Blood was collected by cardiac puncture from mice from every group at termination. Approximately 250ul of whole blood was collected into PAXgene tubes. Whole blood was assessed for RNA.  Colons from all groups were measured for length and weight. RNA was isolated with Qiagen RNeasy kits according to manufacturer’s instructions.
RNA TruSeq Kit by Illumina

treatment_protocol: DSS model. On Day 0, female C57Bl/6 mice were weighed and divided into 2 groups of 90 mice per group such that the average weight of each group is similar. Mice were enrolled onto study at body weight of 16-18 grams. Enrolling mice at a range of 16-18 grams ensures consistent disease across the groups while minimizing losses due to death. Mice in Group 1 received 2.5% DSS in drinking water at times shown below while mice in group 2 received plain drinking water at all times. Food was provided ad libitum.  At various times during the study (Day 5, 12, 17, 23, 27, and 34) 15 mice from each group were chosen randomly and sacrificed after an overnight fast; Adoptive Transfer model. CD45RBhigh CD4+T cells from C57Bl/6J mice were transferred to RAG1-/- mice which lack T and B cells. Induction. On study day 0, spleens for CD45RBhigh CD4+ T cell isolation were obtained from female C57Bl/6J mice using the RAG1-/- mice as recipient mice. After cells had been obtained and sorted, each female RAG1-/- mouse received an IP injection of 5X105 cells/ml (100μl/mouse injection). Control RAG1-/- mice served as a control.

tag: strain

tag: genotype

value: wildtype

tag: model

value: Blood

tag: bio region

value: B

tag: ctrl disease

value: C

tag: day

tag: hit rest


title: TJ1_1d_1_model_T_cell_1_tissue_Colon_day_35_NA [TJ_1d_1_PMC]

source_name: Colon

value: Colon

value: PMC


title: TJ1_1d_2_model_T_cell_1_tissue_Colon_day_35_NA [TJ_1d_2_PMC]


title: Pinot noir berry sample collected at time point 5 (replicate 2) over ripening season 2012 - Crop thinned 75%


title: Pinot noir berry sample collected at time point 5 (replicate 1) over ripening season 2012 - Crop thinned 50%


title: TJ1_1d_1_model_T_cell_1_tissue_Blood_day_35_NA [TJ_1d_1_B]


title: Pinot noir berry sample collected at time point 4 (replicate 3) over ripening season 2012 - Crop thinned 75%

source_name: grape berry pericarp_time point 4_2012_Crop thinned 75%


title: TJ1_1b_5_model_T_cell_1_tissue_Colon_day_21_NA [TJ_1b_5_PMC]


title: TJ1_1d_2_model_T_cell_1_tissue_Blood_day_35_NA [TJ_1d_2_B]


title: BT549-si-1

city: Wuhan

first: Li

last: Su

state: Hubei

address: Luoyu Road 1037

country: China

institute: Huazhong university of science and technology

data_processing:
Fastp(v 0.23.2) is used to control the quality of Raw Data, and Clean Data is obtained. Subsequent analysis is based on Clean Data
Use STAR(v 2.7.10a) to compare the Clean Data obtained after data quality control to the reference genome and sort it, and finally obtain the BAM format comparison result file .
Use Qualimap2(v2.2.2) to evaluate the quality of the comparison results of each sample
STAR was used to count the number of all genes compared to the reference genome annotation, and TPM (Transcripts Per Million) was used to standardize the gene count  as a measure of gene expression.
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

organism: Homo sapiens

growth_protocol: BT549 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using trizol. 1.3 ug of total RNA was used for the construction of sequencing libraries.
After the RNA sample is tested as qualified, the preparation of the entire library is completed through mRNA enrichment, fragmentation, cDNA one strand synthesis, two strand synthesis, end repair, adding A tail, adding sequencing connector, purification, PCR amplification and other steps.

tag: cell line

tag: cell type

value: breast cancer cells

value: SIPA1 knockdown


title: BT549-si-2


title: BT549-si-3


title: TJ1_1e_3_model_T_cell_1_tissue_Blood_day_42_NA [TJ_1e_3_B]


title: TJ1_1d_1_model_T_cell_1_tissue_Colon_day_35_NA [TJ_1d_1_DMC]

value: DMC


title: Pinot noir berry sample collected at time point 4 (replicate 2) over ripening season 2012 - Crop thinned 75%

tag: cultivar


title: BT549-dBD-3

value: SIPA1 knockdown and rescued the expression of the SIPA1-deleted DBR region (si-dDBR)


title: TJ1_1b_5_model_T_cell_1_tissue_Blood_day_21_NA [TJ_1b_5_B]


title: TJ1_1b_4_model_T_cell_1_tissue_Colon_day_21_NA [TJ_1b_4_DMC]


title: TJ1_1b_4_model_T_cell_1_tissue_Colon_day_21_NA [TJ_1b_4_PMC]


title: BT549-dBD-2


title: TJ1_1b_4_model_T_cell_1_tissue_Blood_day_21_NA [TJ_1b_4_B]


title: BT549-dBD-1


title: TJ1_1b_5_model_T_cell_1_tissue_Colon_day_21_NA [TJ_1b_5_DMC]


title: Pinot noir berry sample collected at time point 4 (replicate 1) over ripening season 2012 - Crop thinned 75%

tag: year


title: TJ1_2d_3_model_T_cell_1_tissue_Colon_day_35_NA [TJ_2d_3_PMC]

value: D


title: TJ1_1b_3_model_T_cell_1_tissue_Colon_day_21_NA [TJ_1b_3_PMC]


title: Pinot noir berry sample collected at time point 4 (replicate 3) over ripening season 2012 - Crop thinned 50%

source_name: grape berry pericarp_time point 4_2012_Crop thinned 50%

tag: time point


title: BT549-3

value: WT


title: TJ1_1b_3_model_T_cell_1_tissue_Colon_day_21_NA [TJ_1b_3_DMC]


title: TJ1_1b_3_model_T_cell_1_tissue_Blood_day_21_NA [TJ_1b_3_B]


title: TJ1_1b_2_model_T_cell_1_tissue_Colon_day_21_NA [TJ_1b_2_PMC]


title: Pinot noir berry sample collected at time point 4 (replicate 2) over ripening season 2012 - Crop thinned 50%

tag: time point replicate


title: Pinot noir berry sample collected at time point 4 (replicate 1) over ripening season 2012 - Crop thinned 50%

tag: day after veraison


title: TJ1_1b_2_model_T_cell_1_tissue_Colon_day_21_NA [TJ_1b_2_DMC]


title: TJ1_1b_2_model_T_cell_1_tissue_Blood_day_21_NA [TJ_1b_2_B]


title: BT549-2


title: BT549-1


title: Pinot noir berry sample collected at time point 1 (replicate 2) over ripening season 2013 - Crop thinned 75%

source_name: grape berry pericarp_time point 1_2013_Crop thinned 75%

tag: sugar content (g/100ml)


title: TJ1_1b_1_model_T_cell_1_tissue_Colon_day_21_NA [TJ_1b_1_DMC]


title: Pinot noir berry sample collected at time point 3 (replicate 3) over ripening season 2012 - Crop thinned 75%

source_name: grape berry pericarp_time point 3_2012_Crop thinned 75%

tag: treatment (cluster thinning)


title: TJ1_1b_1_model_T_cell_1_tissue_Blood_day_21_NA [TJ_1b_1_B]

tag: tissue


title: Pinot noir berry sample collected at time point 3 (replicate 2) over ripening season 2012 - Crop thinned 75%


title: P68

city: Delhi

first: Beena

last: Pillai

address: Mathura Road

country: India

institute: IGIB

data_processing:
Raw reads were trimmed using Trimmomatic software and the filtered reads those were ≥ Q30 values were taken for further analysis.
For RNA sequencing analysis , pipeline from the paper Trapnell et al. 2012 was used.
To find alternatively spliced isoforms “Altanalyze” was used which is an open source program that takes TopHat2 output- “junctions.bed” files and “aligned.bam” files for calculating  “Percent Spliced In” (PSI) values for all junctions present in the RNA Seq data.
Assembly: hg18
Supplementary files format and content: spreadsheet (xls file) having FPKM values of the samples

growth_protocol: Not applicable

extract_protocol:
PBMCs are isolated used Ficoll density gradient method. RNA was isolated using Trizol reagent. The cDNA libraries were prepared from 250ng total RNA from each sample, by using Illumina  TruSeq RNA sample preparation kit V2. The libraries were checked through Bioanalyzer 2100 (Agilent) and used for 2*100bp paired end sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Not applicable

value: PBMC

tag: patient class

value: Regular

tag: viral load

tag: age

tag: Sex

value: F


title: TJ1_1a_5_model_T_cell_1_tissue_Colon_day_14_NA [TJ_1a_5_DMC]

tag: strain

tag: genotype

tag: model

tag: bio region

tag: ctrl disease


title: TJ1_1a_5_model_T_cell_1_tissue_Colon_day_14_NA [TJ_1a_5_PMC]

tag: day

tag: hit rest


title: TJ1_1a_5_model_T_cell_1_tissue_Blood_day_14_NA [TJ_1a_5_B]


title: P65

tag: cell type


title: Pinot noir berry sample collected at time point 3 (replicate 3) over ripening season 2012 - Crop thinned 50%

source_name: grape berry pericarp_time point 3_2012_Crop thinned 50%

tag: cultivar

value: cv Pinot noir

tag: year

tag: time point

tag: time point replicate

value: Crop thinned 50%

value: grape berry pericarp


title: Pinot noir berry sample collected at time point 3 (replicate 1) over ripening season 2012 - Crop thinned 75%

tag: day after veraison

tag: sugar content (g/100ml)

tag: treatment (cluster thinning)

value: Crop thinned 75%

tag: tissue


title: P66

value: Blood

tag: patient class

tag: viral load

tag: age

tag: Sex


title: TJ1_1a_4_model_T_cell_1_tissue_Blood_day_14_NA [TJ_1a_4_B]

tag: strain

tag: genotype

value: wildtype

tag: model

tag: bio region

value: B

value: C


title: Pinot noir berry sample collected at time point 3 (replicate 2) over ripening season 2012 - Crop thinned 50%


title: TJ1_1a_3_model_T_cell_1_tissue_Blood_day_14_NA [TJ_1a_3_B]

tag: ctrl disease

tag: day

tag: hit rest


title: TJ1_1a_2_model_T_cell_1_tissue_Blood_day_14_NA [TJ_1a_2_B]


title: P46

tag: cell type

value: M


title: TJ1_1a_3_model_T_cell_1_tissue_Colon_day_14_NA [TJ_1a_3_DMC]

value: Colon


title: P37

value: LNC


title: P38

value: LTNP


title: TJ1_1a_1_model_T_cell_1_tissue_Colon_day_14_NA [TJ_1a_1_PMC]

value: PMC


title: TJ1_1a_1_model_T_cell_1_tissue_Colon_day_14_NA [TJ_1a_1_DMC]

value: DMC


title: P30

value: PBMC


title: TJ2_2e_4_model_T_cell_2_tissue_Blood_day_42_NA [TB140]

value: D


title: TJ2_1d_4_model_T_cell_2_tissue_Blood_day_35_NA [TB139]


title: Pinot noir berry sample collected at time point 2 (replicate 2) over ripening season 2012 - Crop thinned 75%

source_name: grape berry pericarp_time point 2_2012_Crop thinned 75%

tag: cultivar

tag: year

tag: time point

tag: time point replicate


title: TJ1_1a_3_model_T_cell_1_tissue_Colon_day_14_NA [TJ_1a_3_PMC]

tag: tissue


title: P25

tag: patient class

value: F


title: TJ2_2a_1_model_T_cell_2_tissue_Blood_day_14_NA [TB138]


title: P14

tag: viral load


title: Pinot noir berry sample collected at time point 2 (replicate 3) over ripening season 2012 - Crop thinned 50%

source_name: grape berry pericarp_time point 2_2012_Crop thinned 50%

value: cv Pinot noir

tag: day after veraison

tag: sugar content (g/100ml)

tag: treatment (cluster thinning)


title: TJ2_2d_5_model_T_cell_2_tissue_Blood_day_35_NA [TB136]

tag: strain

tag: genotype


title: TJ2_1d_1_model_T_cell_2_tissue_Blood_day_35_NA [TB137]

tag: model

tag: bio region


title: Pinot noir berry sample collected at time point 2 (replicate 1) over ripening season 2012 - Crop thinned 75%


title: TJ2_1d_5_model_T_cell_2_tissue_Blood_day_35_NA [TB135]

tag: ctrl disease

tag: day


title: TJ2_1e_4_model_T_cell_2_tissue_Blood_day_42_NA [TB134]

tag: hit rest


title: Pinot noir berry sample collected at time point 3 (replicate 1) over ripening season 2012 - Crop thinned 50%

tag: cultivar

value: Crop thinned 50%


title: TJ2_2a_5_model_T_cell_2_tissue_Blood_day_14_NA [TB133]


title: P13

tag: cell type

tag: age

tag: Sex


title: TJ2_2d_1_model_T_cell_2_tissue_Blood_day_35_NA [TB132]

tag: tissue


title: Pinot noir berry sample collected at time point 2 (replicate 2) over ripening season 2012 - Crop thinned 50%

tag: year

tag: time point

tag: time point replicate

value: grape berry pericarp


title: TJ1_1a_1_model_T_cell_1_tissue_Blood_day_14_NA [TJ_1a_1_B]


title: TJ2_2d_2_model_T_cell_2_tissue_Blood_day_35_NA [TB131]


title: Pinot noir berry sample collected at time point 1 (replicate 3) over ripening season 2012 - Crop thinned 75%

source_name: grape berry pericarp_time point 1_2012_Crop thinned 75%

tag: day after veraison

tag: sugar content (g/100ml)

value: Crop thinned 75%


title: Pinot noir berry sample collected at time point 2 (replicate 1) over ripening season 2012 - Crop thinned 50%

tag: treatment (cluster thinning)


title: TJ2_2d_4_model_T_cell_2_tissue_Blood_day_35_NA [TB129]

tag: strain

tag: genotype

value: Blood


title: P6

tag: patient class

tag: viral load


title: TJ2_2c_3_model_T_cell_2_tissue_Blood_day_28_NA [TB130]

value: wildtype

tag: model

tag: bio region

tag: ctrl disease

tag: day


title: TJ2_2c_1_model_T_cell_2_tissue_Blood_day_28_NA [TB128]

value: B

tag: hit rest


title: Pinot noir berry sample collected at time point 1 (replicate 2) over ripening season 2012 - Crop thinned 75%

tag: cultivar


title: TJ2_2a_4_model_T_cell_2_tissue_Blood_day_14_NA [TB127]

tag: tissue


title: TJ2_2a_2_model_T_cell_2_tissue_Blood_day_14_NA [TB126]


title: TJ2_1c_2_model_T_cell_2_tissue_Blood_day_28_NA [TB125]

value: C


title: Pinot noir berry sample collected at time point 1 (replicate 1) over ripening season 2012 - Crop thinned 75%

tag: year


title: Pinot noir berry sample collected at time point 1 (replicate 3) over ripening season 2012 - Crop thinned 50%

source_name: grape berry pericarp_time point 1_2012_Crop thinned 50%

tag: time point


title: SW620 cell line, DMSO repeat 1

city: Shanghai

first: Hao

last: Zhang

address: No.555 Zuchongzhi Road

department: Chemical Biology

institute: Shanghai Institute of Materia Medica

description:
SW620 cells treated with DMSO repeat 1
SW_Gene_Exp_Cela_1uM.diff
SW_Gene_Exp_M048_1uM.diff
DMSO

data_processing:
tophat2 with default parameters
samtools to sort and convert the file format
cufflinks with default parameters
cuffmerge with default parameters
cuffdiff with default parameters
Assembly: ensembl GRch38
Supplementary files format and content: gene_exp.diff, generated by Cuffdiff, normalized values for each sample

growth_protocol: density 1e7 HCT116 and SW620 cells in 15cm dish, 24 hours, to 70% confluentence

extract_protocol:
2100 Bioanalyzer for quality check, DNaseI (Takara, Japan) for digestion at 37 C and 30 mins
100ng purified RNA, NEBNext® UltraTM RNA Library Prep Kit for Illumina (NEB, USA)

treatment_protocol: treatment with compounds or DMSO, after 24 hours

tag: cell type

value: colorectal cancer cells

tag: cell line

tag: treatment

value: DMSO


title: P12

tag: age

tag: Sex


title: TJ2_1d_3_model_T_cell_2_tissue_Blood_day_35_NA [TB124]

tag: strain

tag: genotype


title: TJ2_1a_4_model_T_cell_2_tissue_Blood_day_14_NA [TB121]


title: SW620 cell line, Compound 19-048 1uM repeat 1

description:
SW620 cells treated with Compound 19-048 1uM repeat 1
SW_Gene_Exp_M048_1uM.diff (sample_2 "A48_1U")
A48_1U

value: Compound 19-048 1uM


title: TJ2_1c_4_model_T_cell_2_tissue_Blood_day_28_NA [TB123]


title: SW620 cell line, Celastrol 1uM repeat 2

description:
SW620 cells treated with Celastrol 1uM repeat 2
SW_Gene_Exp_Cela_1uM.diff (sample_2 "L02_1U")
L02_1U

value: Celastrol 1uM


title: TJ2_2d_3_model_T_cell_2_tissue_Blood_day_35_NA [TB120]


title: SW620 cell line, Compound 19-048 1uM repeat 2

description:
SW620 cells treated with Compound 19-048 1uM repeat 2
SW_Gene_Exp_M048_1uM.diff (sample_2 "A48_1U")
A48_1U


title: SW620 cell line, Celastrol 1uM repeat 1

description:
SW620 cells treated with Celastrol 1uM repeat 1
SW_Gene_Exp_Cela_1uM.diff (sample_2 "L02_1U")
L02_1U


title: TJ2_1d_2_model_T_cell_2_tissue_Blood_day_35_NA [TB122]


title: TJ2_1e_2_model_T_cell_2_tissue_Blood_day_42_NA [TB117]


title: TJ2_2c_5_model_T_cell_2_tissue_Blood_day_28_NA [TB116]


title: TJ2_2a_3_model_T_cell_2_tissue_Blood_day_14_NA [TB119]


title: TJ2_1a_5_model_T_cell_2_tissue_Blood_day_14_NA [TB118]


title: TJ2_2c_2_model_T_cell_2_tissue_Blood_day_28_NA [TB115]


title: TJ2_1e_5_model_T_cell_2_tissue_Blood_day_42_NA [TB114]


title: TotalGC_Bcells_HTO

city: New York

first: Tiago

last: Castro

state: New York

address: 1230 York Avenue

institute: The Rockefeller University

library_source: transcriptomic single cell

data_processing:
Raw fastq files from our 10X libraries were processed with Cellranger count (v6.2.0). To identify fate-mapped cells from the sequence data, we used a customized mouse genome (mm39) that included the “Ai9” Rosa26tdTomato targeting plasmid sequence (Addgene plasmid #22799) as an artificial chromosome with the tdTomato and stop cassette sequences annotated as features to identify fate-mapped and non-fate-mapped cells, respectively. Quality control was performed by removing cells with high (> 10%) mitochondrial UMI content. Cells expressing either zero or more than one hashtag were removed from analyses. Additionally, we removed cells that contained both tdTomato and stop cassette counts. The BCR contig assembly and annotation were performed with the Cellranger vdj workflow from 10X Genomics. BCR clones were characterized by having identical V, (D), J, and CDR3 lengths for the paired Igh and Igk/Igl chains. Clones with a missing chain were considered part of a clonal group when matching 100% of its chain to the clone Igk and Igk/Igl pair.
The matrix of UMI counts was normalized by applying a regression model with a negative binomial distribution, available through the SCTransform function in the Seurat (v41.0) package55. The top 3000 variable genes were first used for dimensional reduction by PCA using the scaled data. The first 20 principal components were further used for visualization using the Manifold Approximation and Projection (UMAP) and cell clustering55,56. The Wilcoxon rank-sum test was used to detect significant gene markers between groups. P-values were adjusted for multiple testing using the Bonferroni correction method. Genes with adjusted p-values of less than 0.05 were considered downstream analysis. Gene signatures were scored by using the AddModuleScore available by the Seurat package. For the cell cycle signature, gene sets for the S and G2M phases57 were used to define cycling, and cells that did not score in at least one set were marked as in the G1 phase.
Assembly: GRCm39
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Lymph Nodes

extract_protocol:
For flow cytometry and cell sorting, disposable micropestles (Axygen) were used to mechanically disassociate LNs into cell suspensions. Cells from each tissue were resuspended in PBE 1X (PBS supplemented with 0.5% BSA + 1 mM EDTA) and incubated for 30 min on ice with fluorescently-labeled antibodies described in the Key Resources Table. Cells were filtered and washed with PBE again before analysis on BD FACS LSR II or FACS Symphony cytometers and sorting on FACS ARIA II cytometers. Analyses were performed using FlowJo v. 10 software.
Total GC B cells were sorted, counted for viability, and immediately subjected to library preparation. We produced gene expression and BCR single-cell libraries using the 10X Chromium Single Cell 5' and V(D)J Enrichment, according to the manufacturer’s instructions at the Genomics core of Rockefeller University. The scRNA and BCRseq libraries were sequenced on the Illumina NextSeq500 platform. The sequencing yielded 558 million reads with an average of 194,452 reads per cell using read lengths of R1: 26 bp [16bp cell barcode:10bp Unique Molecular Identifier (UMI)], R2: 57 bp read 2. In addition, single-cell BCR libraries yielded an average sequencing depth of 32,626 reads per cell using read lengths of 151 bp read 1 and 151 bp read 2.

value: Lymph Nodes

value: Total GC B cells

tag: library type

value: HTO


title: TotalGC_Bcells_VDJ

value: VDJ


title: Pinot noir berry sample collected at time point 2 (replicate 3) over ripening season 2012 - Crop thinned 75%

tag: time point replicate

tag: day after veraison

tag: sugar content (g/100ml)

tag: treatment (cluster thinning)


title: HCT116 cell line, Compound 19-048 2uM repeat 2

description:
HCT116 cells treated with Compound 19-048 2uM repeat 2
HCT_Gene_Exp_M048_2uM.diff (sample_2 "H048")
H048

value: Compound 19-048 2uM


title: HCT116 cell line, Compound 19-048 2uM repeat 1

description:
HCT116 cells treated with Compound 19-048 2uM repeat 1
HCT_Gene_Exp_M048_2uM.diff (sample_2 "H048")
H048


title: SW620 cell line, DMSO repeat 2

description:
SW620 cells treated with DMSO repeat 2
SW_Gene_Exp_Cela_1uM.diff
SW_Gene_Exp_M048_1uM.diff
DMSO


title: TotalGC_Bcells_RNA

value: RNA


title: TJ2_2c_4_model_T_cell_2_tissue_Blood_day_28_NA [TB112]

tag: model

tag: bio region

tag: ctrl disease

value: D

tag: day

tag: hit rest


title: HCT116 cell line, DMSO repeat 1

description:
HCT116 cells treated with DMSO repeat 1
HCT_Gene_Exp_Cela_2uM.diff
HCT_Gene_Exp_M048_2uM.diff
DMSO

tag: cell type


title: TJ2_1c_1_model_T_cell_2_tissue_Blood_day_28_NA [TB111]

tag: tissue


title: TJ2_2e_2_model_T_cell_2_tissue_Blood_day_42_NA [TB110]


title: HCT116 cell line, Celastrol 2uM repeat 2

description:
HCT116 cells treated with Celastrol 2uM repeat 2
HCT_Gene_Exp_Cela_2uM.diff (sample_2 "HLei")
HLei

tag: cell line

tag: treatment

value: Celastrol 2uM


title: Pinot noir berry sample collected at time point 1 (replicate 1) over ripening season 2012 - Crop thinned 50%

tag: cultivar

value: cv Pinot noir

tag: year

tag: time point

value: Crop thinned 50%

value: grape berry pericarp


title: Pinot noir berry sample collected at time point 1 (replicate 2) over ripening season 2012 - Crop thinned 50%


title: C57BL6/J T cells, GW CRISPR library, replicate B, GFP bin 3

city: San Francisco

first: William

last: Nyberg

state: CA

address: 513 Parnassus Ave., HSW 901

institute: UCSF

description:
Genome-wide CRISPR library
Column: B3

library_source: genomic

data_processing:
Fastq files were aligned to Teichmann (Addgene #104861) library using MAGeCK version 0.5.9.2 count command using --trim-5 22,23,24,25,26,28,29,30 argument
Supplementary files format and content: Raw counts of sgRNAs
Library strategy: CRISPR sgRNA amplicons

molecule: genomic DNA

source_name: Spleen

growth_protocol: Murine T cells were cultured in RPMI 1640 (Gibco #11875093) supplemented with FBS (10%), penicillin-streptomycin (100 U/ml), sodium pyruvate (1 mM), HEPES (10 mM), β-mercaptoethanol (Gibco #21985-023), MEM non-essential amino acids (1×; Gibco #11140050) and hIL-2 (200 U/ml: Peprotech #200-02).

extract_protocol:
Genomic DNA was extracted by phenol:chloroform:isoamyl alcohol DNA isolation.
Libraries were PCR amplified around the gRNA sequence from genomic DNA. A total of 5 ug of gDNA was used a template for each PCR reaction, six PCR reactios were run for each sample.

treatment_protocol: Murine T cells were transduced with Ark313 at an MOI of 5E4 .

tag: strain

value: C57BL6/J H11-Cas9

value: Spleen

value: T cells

value: Transduced with Ark313


title: C57BL6/J T cells, GW CRISPR library, replicate B, GFP bin 4

description:
Genome-wide CRISPR library
Column: B4


title: C57BL6/J T cells, GW CRISPR library, replicate B, GFP bin 2

description:
Genome-wide CRISPR library
Column: B2


title: TJ2_2e_5_model_T_cell_2_tissue_Blood_day_42_NA [TB108]

tag: genotype

value: wildtype

value: Blood

value: B


title: TJ2_2e_3_model_T_cell_2_tissue_Blood_day_42_NA [TB106]


title: TJ2_1e_3_model_T_cell_2_tissue_Blood_day_42_NA [TB107]

value: C


title: TJ2_1e_1_model_T_cell_2_tissue_Blood_day_42_NA [TB104]


title: C57BL6/J T cells, GW CRISPR library, replicate B, GFP bin 1

description:
Genome-wide CRISPR library
Column: B1


title: JH31_HAEC_lane 8

city: Rochester

first: Akhilesh

last: Pandey

state: Minnesota

address: 200 First Street SW

department: Laboratory Medicine and Pathology

institute: Mayo Clinic

description: lane 8

data_processing:
Demultiplexed and base calling using bcl2fastq v1.8.4 of CASAVA v1.8
Alignment against hg38 using STAR-2.5.2
Alignment file processing using samtools-1.3.1
long non-coding RNA analysis using UClncR v1.0.9 (Mayo Clinic, Rochester, MN)
Genome_build: hg38
Supplementary_files_format_and_content: Read counts per gene

source_name: Aortic Endothelial Cells

growth_protocol: Primary human cells were acquired from Lonza and cultured following the manufacturer’s specifications.

extract_protocol:
Ribosomal RNA depletion
TruSeq stranded mRNA library

value: Endothelial

tag: tissue origin

value: Heart

tag: life stage

value: Adult


title: TJ2_1c_5_model_T_cell_2_tissue_Blood_day_28_NA [TB105]


title: TJ2_1c_3_model_T_cell_2_tissue_Blood_day_28_NA [TB103]


title: TJ2_2e_1_model_T_cell_2_tissue_Blood_day_42_NA [TB101]


title: HCT116 cell line, DMSO repeat 2

description:
HCT116 cells treated with DMSO repeat 2
HCT_Gene_Exp_Cela_2uM.diff
HCT_Gene_Exp_M048_2uM.diff
DMSO

value: colorectal cancer cells

value: DMSO


title: TJ2_1a_1_model_T_cell_2_tissue_Blood_day_14_NA [TB102]


title: C57BL6/J T cells, GW CRISPR library, replicate A, GFP bin 3

description:
Genome-wide CRISPR library
Column: A3


title: JH31_HAEC_lane 7

description: lane 7


title: TJ2_1a_3_model_T_cell_2_tissue_Blood_day_14_NA [TB109]


title: JH31_HAEC_lane 6

description: lane 6


title: HCT116 cell line, Celastrol 2uM repeat 1

description:
HCT116 cells treated with Celastrol 2uM repeat 1
HCT_Gene_Exp_Cela_2uM.diff (sample_2 "HLei")
HLei

value: Celastrol 2uM


title: DM_2_86_model_DSS_tissue_Colon_day_35_rest2 [DM_2_86_PC]

value: DSS

value: Colon

value: PC

value: D


title: DM_2_86_model_DSS_tissue_Blood_day_35_rest2 [DM_2_86_B]


title: JH31_HAEC_lane 5

description: lane 5


title: DM_2_84_model_DSS_tissue_Colon_day_35_rest2 [DM_2_84_WC]

value: DC


title: JH31_HAEC_lane 4

description: lane 4


title: C57BL6/J T cells, GW CRISPR library, replicate A, GFP bin 2

description:
Genome-wide CRISPR library
Column: A2

value: C57BL6/J H11-Cas9

value: Spleen

value: T cells


title: JH31_HAEC_lane 3

description: lane 3


title: C57BL6/J T cells, GW CRISPR library, replicate B, pre sort

description:
Genome-wide CRISPR library
Column: B_pre-sort

value: Transduced with Ark313


title: C57BL6/J T cells, GW CRISPR library, replicate A, GFP bin 1

description:
Genome-wide CRISPR library
Column: A1


title: DM_2_83_model_DSS_tissue_Blood_day_35_rest2 [DM_2_83_B]

value: wildtype

value: Blood

value: B


title: DM_2_84_model_DSS_tissue_Blood_day_35_rest2 [DM_2_84_B]


title: C57BL6/J T cells, GW CRISPR library, replicate A, pre sort

description:
Genome-wide CRISPR library
Column: A_pre-sort


title: DM_2_82_model_DSS_tissue_Colon_day_35_rest2 [DM_2_82_WC]


title: MSC.24hr.Il1bWT.Muscle.#2

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

data_processing:
Reads were mapped to the mouse reference genome (mm10) with STAR 2.7.3a.
Non-uniquely mapped reads were discarded.
The uniquely mapped reads were assigned to genes using featureCounts with GENCODE annotation (vM25).
Assembly: mm10 (GRCm38)
Supplementary files format and content: Genes_count_table.tsv: Tab-delimited text file includes raw read counts.

molecule: polyA RNA

source_name: MmSCs isolated from day 1 injured hindlimb skeletal muscle

extract_protocol: For flow-cytometrically sorted samples, cells were isolated by first enzymatically digesting the indicated tissue and then purified by fluorescence-activated cell sorting (two times to achieve enhanced purity). A total of 1,000 cells were sorted into TCL buffer with 1% 2-mercaptoethanol and submitted for library construction and sequencing. For whole muscle samples, tissue was homogenized in Trizol, and then RNA was isolated per manufacturer protocol. For each of these samples, 2 ng of purified RNA was added to TCL buffer with 1% 2-mercaptoethanol and submitted for library construction and sequencing.

value: MmSCs from day 1 injured hindlimb skeletal muscle

value: Cardiotoxin-induced hindlimb skeletal muscle injury


title: JH31_HAEC_lane 2

description: lane 2

value: Endothelial

value: Heart

value: Adult


title: DM_2_84_model_DSS_tissue_Colon_day_35_rest2 [DM_2_84_PC]

value: DSS


title: TJ2_1a_2_model_T_cell_2_tissue_Blood_day_14_NA [TB113]

value: C


title: DM_2_83_model_DSS_tissue_Colon_day_35_rest2 [DM_2_83_WC]

value: Colon


title: DM_2_86_model_DSS_tissue_Colon_day_35_rest2 [DM_2_86_WC]

value: D


title: JH31_HAEC_lane 1

description: lane 1


title: DM_2_82_model_DSS_tissue_Colon_day_35_rest2 [DM_2_82_PC]

value: PC


title: DM_2_9_model_DSS_tissue_Colon_day_5_hit1 [DM_2_9_WC]

value: DC


title: JH30_BdSMC_lane 8

description: lane 8

source_name: Bladder Smooth Muscle Cells

value: SmoothMuscle

value: Bladder


title: DM_2_81_model_DSS_tissue_Colon_day_35_rest2 [DM_2_81_WC]


title: MSC.24hr.Il1bKO.Muscle.#3


title: DM_2_82_model_DSS_tissue_Blood_day_35_rest2 [DM_2_82_B]


title: C57BL6/J T cells, GW CRISPR library, replicate A, GFP bin 4

description:
Genome-wide CRISPR library
Column: A4

value: C57BL6/J H11-Cas9

value: Spleen

value: T cells

value: Transduced with Ark313


title: DM_2_81_model_DSS_tissue_Colon_day_35_rest2 [DM_2_81_PC]

value: wildtype


title: DM_2_81_model_DSS_tissue_Blood_day_35_rest2 [DM_2_81_B]

value: Blood

value: B


title: MSC.24hr.Il1bKO.Muscle.#2

value: MmSCs from day 1 injured hindlimb skeletal muscle

value: Cardiotoxin-induced hindlimb skeletal muscle injury


title: DM_2_6_model_DSS_tissue_Colon_day_5_hit1 [DM_2_6_WC]

value: DSS


title: DM_2_83_model_DSS_tissue_Colon_day_35_rest2 [DM_2_83_PC]


title: MSC.24hr.Il1bKO.Muscle.#1


title: MSC.MDX.12wk.Muscle.#2

source_name: MmSCs isolated from hindlimb skeletal muscle of 12.5-wk-old mice

value: DMDmdx

value: MmSCs from hindlimb skeletal muscle of 12.5-wk-old mice


title: JH30_BdSMC_lane 6

description: lane 6

value: Adult


title: DM_2_5_model_DSS_tissue_Blood_day_5_hit1 [DM_2_5_B]

source_name: Blood

value: D


title: DM_2_44_model_DSS_tissue_Colon_day_17_hit2 [DM_2_44_PC]

source_name: Colon

value: Colon

value: PC


title: DM_2_6_model_DSS_tissue_Blood_day_5_hit1 [DM_2_6_B]


title: MSC.24hr.Il1bWT.Muscle.#1


title: DM_2_44_model_DSS_tissue_Blood_day_17_hit2 [DM_2_44_B]


title: DM_2_43_model_DSS_tissue_Blood_day_17_hit2 [DM_2_43_B]


title: DM_2_43_model_DSS_tissue_Colon_day_17_hit2 [DM_2_43_WC]

value: DC


title: JH30_BdSMC_lane 3

description: lane 3

value: SmoothMuscle

value: Bladder


title: JH30_BdSMC_lane 2

description: lane 2


title: JH30_BdSMC_lane 4

description: lane 4


title: DM_2_43_model_DSS_tissue_Colon_day_17_hit2 [DM_2_43_PC]


title: DM_2_42_model_DSS_tissue_Colon_day_17_hit2 [DM_2_42_WC]


title: DM_2_42_model_DSS_tissue_Colon_day_17_hit2 [DM_2_42_PC]


title: JH30_BdSMC_lane 1

description: lane 1


title: JH30_BdSMC_lane 7

description: lane 7


title: DM_2_42_model_DSS_tissue_Blood_day_17_hit2 [DM_2_42_B]


title: DM_2_41_model_DSS_tissue_Colon_day_17_hit2 [DM_2_41_WC]


title: JH29_PrSMC_lane 8

description: lane 8

source_name: Prostate Smooth Muscle Cells

value: Prostate


title: MSC.MDX.7wk.Muscle.#1

source_name: MmSCs isolated from hindlimb skeletal muscle of 7-wk-old mice

value: MmSCs from hindlimb skeletal muscle of 7-wk-old mice


title: MSC.MDX.2.5wk.Muscle.#3

source_name: MmSCs isolated from hindlimb skeletal muscle of 2.5-wk-old mice

value: MmSCs from hindlimb skeletal muscle of 2.5-wk-old mice


title: MSC.MDX.7wk.Muscle.#3


title: MSC.MDX.7wk.Muscle.#2


title: DM_2_44_model_DSS_tissue_Colon_day_17_hit2 [DM_2_44_WC]

value: wildtype


title: DM_2_41_model_DSS_tissue_Blood_day_17_hit2 [DM_2_41_B]

value: Blood

value: B


title: JH30_BdSMC_lane 5

description: lane 5


title: DM_2_41_model_DSS_tissue_Colon_day_17_hit2 [DM_2_41_PC]


title: MSC.MDX.12wk.Muscle.#1


title: DM_2_40_model_DSS_tissue_Colon_day_17_hit2 [DM_2_40_WC]


title: JH29_PrSMC_lane 6

description: lane 6


title: MSC.MDX.2.5wk.Muscle.#1


title: MSC.MDX.2.5wk.Muscle.#2


title: DM_2_40_model_DSS_tissue_Colon_day_17_hit2 [DM_2_40_PC]


title: JH29_PrSMC_lane 5

description: lane 5


title: Muscle.7d.IgG.Muscle.#3

source_name: Day 7 injured tibialis anterior muscle (whole muscle sample)

value: Cardiotoxin-induced hindlimb skeletal muscle injury

value: i.p. IgG


title: Muscle.7d.IgG.Muscle.#2

value: Day 7 injured tibialis anterior muscle (whole muscle sample)


title: DM_2_29_model_DSS_tissue_Blood_day_12_rest1 [DM_2_29_B]

value: DSS


title: DM_2_28_model_DSS_tissue_Colon_day_12_rest1 [DM_2_28_WC]


title: DM_2_29_model_DSS_tissue_Colon_day_12_rest1 [DM_2_29_WC]


title: DM_2_28_model_DSS_tissue_Colon_day_12_rest1 [DM_2_28_PC]


title: JH29_PrSMC_lane 3

description: lane 3

value: Adult


title: DM_2_28_model_DSS_tissue_Blood_day_12_rest1 [DM_2_28_B]

value: D


title: DM_2_40_model_DSS_tissue_Blood_day_17_hit2 [DM_2_40_B]


title: DM_2_29_model_DSS_tissue_Colon_day_12_rest1 [DM_2_29_PC]

value: Colon


title: Muscle.7d.IgG.Muscle.#1


title: DM_2_27_model_DSS_tissue_Colon_day_12_rest1 [DM_2_27_WC]


title: JH29_PrSMC_lane 2

description: lane 2


title: JH29_PrSMC_lane 7

description: lane 7


title: JH28_InMyoFib_lane 8

description: lane 8

source_name: Intestinal Myofibroblasts

value: Myofibroblasts

value: Intestine

value: Fetus


title: DM_2_24_model_DSS_tissue_Colon_day_12_rest1 [DM_2_24_WC]

value: DC


title: Muscle.7d.aCxcl5.Muscle.#3

value: i.p. aCxcl5


title: DM_2_27_model_DSS_tissue_Blood_day_12_rest1 [DM_2_27_B]


title: Muscle.7d.aCxcl5.Muscle.#2


title: Muscle.7d.aCxcl5.Muscle.#1


title: JH28_InMyoFib_lane 7

description: lane 7


title: JH29_PrSMC_lane 4

description: lane 4

value: SmoothMuscle

value: Prostate


title: MSC.12hr.Thy1.1-.Muscle.#3

source_name: Thy1.1- MmSCs isolated from day 0.5 injured hindlimb skeletal muscle

value: Thy1.1- MmSCs from day 0.5 injured hindlimb skeletal muscle


title: DM_2_24_model_DSS_tissue_Colon_day_12_rest1 [DM_2_24_PC]

value: wildtype

value: PC


title: DM_2_21_model_DSS_tissue_Colon_day_12_rest1 [DM_2_21_PC]


title: DM_2_21_model_DSS_tissue_Colon_day_12_rest1 [DM_2_21_WC]


title: DM_2_21_model_DSS_tissue_Blood_day_12_rest1 [DM_2_21_B]

value: Blood

value: B


title: DM_2_24_model_DSS_tissue_Blood_day_12_rest1 [DM_2_24_B]


title: DM_2_14_model_DSS_tissue_Blood_day_5_hit1 [DM_2_14_B]


title: MSC.12hr.Thy1.1-.Muscle.#2

value: Cardiotoxin-induced hindlimb skeletal muscle injury


title: DM_2_27_model_DSS_tissue_Colon_day_12_rest1 [DM_2_27_PC]

value: DSS


title: DM_1_93_model_DSS_tissue_Colon_day_35_control [DM_1_93_WC]

value: C

value: control


title: JH29_PrSMC_lane 1

description: lane 1

value: Adult


title: DM_1_93_model_DSS_tissue_Blood_day_35_control [DM_1_93_B]


title: DM_1_93_model_DSS_tissue_Colon_day_35_control [DM_1_93_PC]

value: Colon


title: JH28_InMyoFib_lane 3

description: lane 3

value: Myofibroblasts

value: Intestine


title: DM_1_89_model_DSS_tissue_Colon_day_35_control [DM_1_89_PC]


title: DM_1_89_model_DSS_tissue_Colon_day_35_control [DM_1_89_WC]

value: DC


title: MSC.12hr.Thy1.1+.Muscle.#3

source_name: Thy1.1+ MmSCs isolated from day 0.5 injured hindlimb skeletal muscle

value: Thy1.1+ MmSCs from day 0.5 injured hindlimb skeletal muscle


title: JH28_InMyoFib_lane 2

description: lane 2

value: Fetus


title: DM_1_88_model_DSS_tissue_Colon_day_35_control [DM_1_88_PC]


title: DM_1_88_model_DSS_tissue_Colon_day_35_control [DM_1_88_WC]


title: MSC.12hr.Thy1.1+.Muscle.#1


title: DM_1_88_model_DSS_tissue_Blood_day_35_control [DM_1_88_B]


title: DM_1_87_model_DSS_tissue_Colon_day_35_control [DM_1_87_WC]


title: MuSC.inj.d1.Muscle.#3

source_name: MuSCs isolated from day 1 injured hindlimb skeletal muscle

value: MuSCs from day 1 injured hindlimb skeletal muscle


title: JH27_InEpC_lane 8

description: lane 8

source_name: Intestinal Epithelial Cells

value: Epithelial


title: DM_1_87_model_DSS_tissue_Colon_day_35_control [DM_1_87_PC]

value: wildtype


title: JH28_InMyoFib_lane 5

description: lane 5


title: JH27_InEpC_lane 7

description: lane 7


title: DM_1_87_model_DSS_tissue_Blood_day_35_control [DM_1_87_B]


title: JH28_InMyoFib_lane 6

description: lane 6


title: JH28_InMyoFib_lane 1

description: lane 1


title: DM_1_86_model_DSS_tissue_Colon_day_35_control [DM_1_86_WC]


title: MSC.12hr.Thy1.1-.Muscle.#1

value: Thy1.1- MmSCs from day 0.5 injured hindlimb skeletal muscle


title: MuSC.inj.d1.Muscle.#2


title: DM_1_86_model_DSS_tissue_Colon_day_35_control [DM_1_86_PC]

value: PC


title: MuSC.inj.d1.Muscle.#1


title: JH27_InEpC_lane 6

description: lane 6


title: DM_2_10_model_DSS_tissue_Blood_day_5_hit1 [DM_2_10_B]

value: Blood

value: B

value: D


title: MSC.12hr.Thy1.1+.Muscle.#2

value: Cardiotoxin-induced hindlimb skeletal muscle injury


title: DM_1_6_model_DSS_tissue_Colon_day_5_control [DM_1_6_WC]

value: DSS

value: C

value: control


title: DM_1_86_model_DSS_tissue_Blood_day_35_control [DM_1_86_B]


title: MuSC.d0.Muscle.#3

source_name: MuSCs isolated from uninjured hindlimb skeletal muscle

value: MuSCs from uninjured hindlimb skeletal muscle


title: JH27_InEpC_lane 5

description: lane 5

value: Intestine


title: DM_1_43_model_DSS_tissue_Colon_day_17_control [DM_1_43_WC]

value: Colon

value: DC


title: DM_1_6_model_DSS_tissue_Blood_day_5_control [DM_1_6_B]


title: MuSC.d0.Muscle.#2


title: MuSC.d0.Muscle.#1


title: JH27_InEpC_lane 4

description: lane 4

value: Fetus


title: DM_1_43_model_DSS_tissue_Colon_day_17_control [DM_1_43_PC]


title: DM_1_43_model_DSS_tissue_Blood_day_17_control [DM_1_43_B]


title: DM_1_42_model_DSS_tissue_Colon_day_17_control [DM_1_42_WC]


title: JH27_InEpC_lane 3

description: lane 3


title: MSC.inj.d1.Muscle.#3

value: MmSCs from day 1 injured hindlimb skeletal muscle


title: JH27_InEpC_lane 2

description: lane 2

value: Epithelial


title: MSC.inj.d1.Muscle.#2


title: DM_1_40_model_DSS_tissue_Colon_day_17_control [DM_1_40_WC]

value: wildtype


title: JH27_InEpC_lane 1

description: lane 1


title: DM_1_42_model_DSS_tissue_Blood_day_17_control [DM_1_42_B]


title: DM_1_42_model_DSS_tissue_Colon_day_17_control [DM_1_42_PC]


title: DM_1_40_model_DSS_tissue_Colon_day_17_control [DM_1_40_PC]


title: DM_1_40_model_DSS_tissue_Blood_day_17_control [DM_1_40_B]


title: DM_1_4_model_DSS_tissue_Blood_day_5_control [DM_1_4_B]


title: DM_1_39_model_DSS_tissue_Blood_day_17_control [DM_1_39_B]


title: DM_1_36_model_DSS_tissue_Colon_day_17_control [DM_1_36_WC]


title: DM_1_36_model_DSS_tissue_Colon_day_17_control [DM_1_36_PC]


title: MSC.inj.d1.Muscle.#1


title: MSC.d0.Muscle.#3

source_name: MmSCs isolated from uninjured hindlimb skeletal muscle

value: MmSCs from uninjured hindlimb skeletal muscle


title: JH26_AoSMC_lane 8

description: lane 8

source_name: Aortic Smooth Muscle Cells

value: SmoothMuscle

value: Heart

value: Adult


title: JH26_AoSMC_lane 7

description: lane 7


title: JH26_AoSMC_lane 6

description: lane 6


title: JH26_AoSMC_lane 5

description: lane 5


title: MSC.d0.Muscle.#1


title: CD45+.inj.d1.Muscle.#3

source_name: CD45+ cells isolated from day 1 injured hindlimb skeletal muscle

value: CD45+ cells from day 1 injured hindlimb skeletal muscle


title: DM_1_21_model_DSS_tissue_Colon_day_12_control [DM_1_21_WC]


title: DM_1_36_model_DSS_tissue_Blood_day_17_control [DM_1_36_B]

value: Blood

value: B


title: DM_1_23_model_DSS_tissue_Blood_day_12_control [DM_1_23_B]

value: DSS

value: C


title: CD45+.inj.d1.Muscle.#2

value: Cardiotoxin-induced hindlimb skeletal muscle injury


title: DM_1_23_model_DSS_tissue_Colon_day_12_control [DM_1_23_PC]

value: PC

value: control


title: DM_1_21_model_DSS_tissue_Blood_day_12_control [DM_1_21_B]


title: JH26_AoSMC_lane 3

description: lane 3


title: JH26_AoSMC_lane 4

description: lane 4


title: DM_1_21_model_DSS_tissue_Colon_day_12_control [DM_1_21_PC]

value: Colon


title: CD45+.inj.d1.Muscle.#1


title: MSC.d0.Muscle.#2


title: DM_1_20_model_DSS_tissue_Colon_day_12_control [DM_1_20_PC]


title: DM_1_20_model_DSS_tissue_Colon_day_12_control [DM_1_20_WC]

value: DC


title: DM_1_89_model_DSS_tissue_Blood_day_35_control [DM_1_89_B]


title: JH28_InMyoFib_lane 4

description: lane 4

value: Myofibroblasts

value: Intestine

value: Fetus


title: CD45+.d0.Muscle.#3

source_name: CD45+ cells isolated from uninjured hindlimb skeletal muscle

value: CD45+ cells from uninjured hindlimb skeletal muscle


title: JH26_AoSMC_lane 1

description: lane 1

value: SmoothMuscle


title: DM_1_18_model_DSS_tissue_Colon_day_12_control [DM_1_18_PC]

value: wildtype


title: DM_1_18_model_DSS_tissue_Colon_day_12_control [DM_1_18_WC]


title: JH26_AoSMC_lane 2

description: lane 2

value: Heart

value: Adult


title: JH24_HSMM_lane 8

description: lane 8

source_name: Skeletal Muscle Myoblasts

value: Myoblasts

value: Muscle


title: DM_1_20_model_DSS_tissue_Blood_day_12_control [DM_1_20_B]

source_name: Blood

value: DSS

value: Blood

value: B


title: DM_1_18_model_DSS_tissue_Blood_day_12_control [DM_1_18_B]

value: C


title: CD45+.d0.Muscle.#2


title: JH24_HSMM_lane 7

description: lane 7


title: CD31+.inj.d1.Muscle.#3

source_name: CD31+ cells isolated from day 1 injured hindlimb skeletal muscle

value: CD31+ cells from day 1 injured hindlimb skeletal muscle

value: Cardiotoxin-induced hindlimb skeletal muscle injury


title: DM_1_17_model_DSS_tissue_Colon_day_12_control [DM_1_17_WC]

source_name: Colon

value: Colon

value: DC

value: control


title: DM_1_17_model_DSS_tissue_Blood_day_12_control [DM_1_17_B]


title: DM_1_17_model_DSS_tissue_Colon_day_12_control [DM_1_17_PC]

value: PC


title: CD31+.inj.d1.Muscle.#2


title: JH24_HSMM_lane 6

description: lane 6


title: DM_1_13_model_DSS_tissue_Blood_day_5_control [DM_1_13_B]


title: DM_1_12_model_DSS_tissue_Colon_day_5_control [DM_1_12_WC]


title: JH24_HSMM_lane 5

description: lane 5


title: CD31+.inj.d1.Muscle.#1


title: JH24_HSMM_lane 4

description: lane 4


title: CD31+.d0.Muscle.#3

source_name: CD31+ cells isolated from uninjured hindlimb skeletal muscle

value: CD31+ cells from uninjured hindlimb skeletal muscle


title: DJ_2_89_model_DSS_tissue_Colon_day_36_rest2 [DJ_2_89_WC]

value: WC

value: D


title: DM_1_11_model_DSS_tissue_Blood_day_5_control [DM_1_11_B]

value: wildtype


title: DM_1_12_model_DSS_tissue_Blood_day_5_control [DM_1_12_B]


title: DJ_2_90_model_DSS_tissue_Blood_day_36_rest2 [DJ_2_90_B]


title: JH24_HSMM_lane 3

description: lane 3

value: Adult


title: DJ_2_85_model_DSS_tissue_Colon_day_36_rest2 [DJ_2_85_WC]


title: DJ_2_85_model_DSS_tissue_Blood_day_36_rest2 [DJ_2_85_B]


title: CD31+.d0.Muscle.#2


title: JH24_HSMM_lane 2

description: lane 2

value: Myoblasts


title: DJ_2_89_model_DSS_tissue_Blood_day_36_rest2 [DJ_2_89_B]


title: DJ_2_84_model_DSS_tissue_Blood_day_36_rest2 [DJ_2_84_B]


title: JH24_HSMM_lane 1

description: lane 1

value: Muscle


title: DJ_2_83_model_DSS_tissue_Colon_day_36_rest2 [DJ_2_83_WC]

value: DSS


title: DJ_2_84_model_DSS_tissue_Colon_day_36_rest2 [DJ_2_84_WC]


title: DJ_2_80_model_DSS_tissue_Colon_day_36_rest2 [DJ_2_80_WC]


title: MSC.2hr.Osm-Il17a.Muscle.#2

value: MmSCs from uninjured hindlimb skeletal muscle

value: i.p. Oncostatin M and Il-17A


title: CD31+.d0.Muscle.#1


title: JH23_PrSC_lane 8

description: lane 8

source_name: Prostate Stromal Cells

value: Stromal

value: Prostate


title: MSC.2hr.Osm-Il17a.Muscle.#1


title: JH23_PrSC_lane 7

description: lane 7


title: JH23_PrSC_lane 6

description: lane 6


title: DJ_2_80_model_DSS_tissue_Blood_day_36_rest2 [DJ_2_80_B]

value: Blood

value: B


title: DJ_2_65_model_DSS_tissue_Blood_day_17_hit2 [DJ_2_65_B]


title: DJ_2_58_model_DSS_tissue_Colon_day_12_rest1 [DJ_2_58_WC]

value: Colon


title: DJ_2_5_model_DSS_tissue_Colon_day_5_hit1 [DJ_2_5_WC]


title: MSC.2hr.Osm-TNFa.Muscle.#1

value: i.p. Oncostatin M and TNFa


title: DJ_2_5_model_DSS_tissue_Blood_day_5_hit1 [DJ_2_5_B]


title: DJ_2_44_model_DSS_tissue_Colon_day_12_rest1 [DJ_2_44_WC]


title: CD45+.d0.Muscle.#1

value: CD45+ cells from uninjured hindlimb skeletal muscle


title: JH23_PrSC_lane 5

description: lane 5


title: DJ_2_40_model_DSS_tissue_Colon_day_17_hit2 [DJ_2_40_WC]


title: JH23_PrSC_lane 4

description: lane 4


title: MSC.2hr.Osm-TNFa.Muscle.#2


title: DJ_2_58_model_DSS_tissue_Blood_day_12_rest1 [DJ_2_58_B]


title: MSC.2hr.Osm-Il1b.Muscle.#1

value: i.p. Oncostatin M and Il-1b


title: MSC.2hr.Il17a.Muscle.#2

value: i.p. Il-17A


title: DJ_2_4_model_DSS_tissue_Blood_day_5_hit1 [DJ_2_4_B]

value: D


title: JH23_PrSC_lane 2

description: lane 2


title: DJ_2_38_model_DSS_tissue_Colon_day_17_hit2 [DJ_2_38_WC]

value: wildtype

value: WC


title: DJ_2_38_model_DSS_tissue_Blood_day_17_hit2 [DJ_2_38_B]


title: DJ_2_4_model_DSS_tissue_Colon_day_5_hit1 [DJ_2_4_WC]


title: DJ_2_36_model_DSS_tissue_Colon_day_17_hit2 [DJ_2_36_WC]


title: DJ_2_36_model_DSS_tissue_Blood_day_17_hit2 [DJ_2_36_B]


title: MSC.2hr.Il17a.Muscle.#1


title: MSC.2hr.Osm.Muscle.#2

value: i.p. Oncostatin M


title: DJ_2_34_model_DSS_tissue_Colon_day_17_hit2 [DJ_2_34_WC]


title: JH23_PrSC_lane 3

description: lane 3

value: Adult


title: DJ_2_40_model_DSS_tissue_Blood_day_17_hit2 [DJ_2_40_B]

value: DSS


title: MSC.2hr.TNFa.Muscle.#2

value: MmSCs from uninjured hindlimb skeletal muscle

value: i.p. TNFa


title: MSC.2hr.TNFa.Muscle.#1


title: MSC.2hr.Osm-Il1b.Muscle.#2


title: JH22_HPdLF_lane 6

description: lane 6

source_name: Periodontal Ligament Fibroblasts

value: Fibroblasts

value: Bone


title: JH22_HPdLF_lane 7

description: lane 7


title: DJ_2_31_model_DSS_tissue_Blood_day_12_rest1 [DJ_2_31_B]

value: Blood


title: MSC.2hr.Il1b.Muscle.#1

value: i.p. Il-1b


title: DJ_2_33_model_DSS_tissue_Blood_day_17_hit2 [DJ_2_33_B]

value: B


title: JH22_HPdLF_lane 5

description: lane 5


title: DJ_2_33_model_DSS_tissue_Colon_day_17_hit2 [DJ_2_33_WC]

value: Colon


title: JH22_HPdLF_lane 8

description: lane 8


title: JH22_HPdLF_lane 4

description: lane 4


title: DJ_2_26_model_DSS_tissue_Colon_day_12_rest1 [DJ_2_26_WC]


title: MSC.PBS.Muscle.#2

value: i.p. PBS


title: DJ_2_26_model_DSS_tissue_Blood_day_12_rest1 [DJ_2_26_B]


title: DJ_2_20_model_DSS_tissue_Colon_day_12_rest1 [DJ_2_20_WC]


title: DJ_2_14_model_DSS_tissue_Colon_day_5_hit1 [DJ_2_14_WC]


title: DJ_2_18_model_DSS_tissue_Blood_day_12_rest1 [DJ_2_18_B]


title: DJ_2_12_model_DSS_tissue_Blood_day_5_hit1 [DJ_2_12_B]


title: DJ_2_15_model_DSS_tissue_Blood_day_5_hit1 [DJ_2_15_B]


title: JH22_HPdLF_lane 2

description: lane 2


title: JH23_PrSC_lane 1

description: lane 1

value: Stromal

value: Prostate


title: MSC.2hr.Osm.Muscle.#1


title: DJ_2_18_model_DSS_tissue_Colon_day_12_rest1 [DJ_2_18_WC]

value: D


title: MSC.2hr.Il1b.Muscle.#2


title: DJ_2_12_model_DSS_tissue_Colon_day_5_hit1 [DJ_2_12_WC]

value: wildtype


title: MSC.PBS.Muscle.#1


title: DJ_2_1_model_DSS_tissue_Blood_day_5_hit1 [DJ_2_1_B]


title: JH22_HPdLF_lane 3

description: lane 3


title: JH21_AoAF_lane 8

description: lane 8

source_name: Aortic Adventitial Fibroblasts

value: Heart


title: JH22_HPdLF_lane 1

description: lane 1


title: MSC.8hr.4IPstim.Muscle.#2

value: i.p. Il-1b, TNFa, Oncostatin M, Il-17A


title: MSC.4hr.4IPstim.Muscle.#2


title: MSC.2hr.4IPstim.Muscle.#2


title: JH21_AoAF_lane 7

description: lane 7

value: Adult


title: DJ_1_78_model_DSS_tissue_Blood_day_36_control [DJ_1_78_B]

value: DSS

value: C

value: control


title: DJ_1_79_model_DSS_tissue_Blood_day_36_control [DJ_1_79_B]


title: DJ_1_80_model_DSS_tissue_Colon_day_36_control [DJ_1_80_WC]

value: WC


title: DJ_1_84_model_DSS_tissue_Colon_day_36_control [DJ_1_84_WC]


title: DJ_2_1_model_DSS_tissue_Colon_day_5_hit1 [DJ_2_1_WC]


title: MSC.2hr.4IPstim.Muscle.#1

value: MmSCs from uninjured hindlimb skeletal muscle


title: DJ_1_90_model_DSS_tissue_Colon_day_36_control [DJ_1_90_WC]


title: DJ_1_77_model_DSS_tissue_Colon_day_36_control [DJ_1_77_WC]


title: DJ_1_90_model_DSS_tissue_Blood_day_36_control [DJ_1_90_B]

value: Blood


title: DJ_1_79_model_DSS_tissue_Colon_day_36_control [DJ_1_79_WC]


title: DJ_1_7_model_DSS_tissue_Colon_day_5_control [DJ_1_7_WC]


title: JH21_AoAF_lane 6

description: lane 6

value: Fibroblasts


title: JH21_AoAF_lane 5

description: lane 5


title: JH21_AoAF_lane 3

description: lane 3


title: DJ_1_7_model_DSS_tissue_Blood_day_5_control [DJ_1_7_B]

value: B


title: DJ_1_5_model_DSS_tissue_Colon_day_5_control [DJ_1_5_WC]

value: Colon


title: MSC.8hr.4IPstim.Muscle.#1


title: DJ_1_84_model_DSS_tissue_Blood_day_36_control [DJ_1_84_B]


title: JH21_AoAF_lane 2

description: lane 2


title: DJ_1_44_model_DSS_tissue_Blood_day_17_control [DJ_1_44_B]


title: 1090B-miRNA

city: Helsinki

first: Piet

last: Finckenberg

address: Haartmaninkatu 8

department: Medicum

country: Finland

institute: University of Helsinki

data_processing:
The library pool(s) were  sequenced by Illumina NextSeq500 (3 days follow up samples) or Illumina HiSeq2000 (21 days follow up samples)
Data was mapped with Bowtie2 v.2.2.2 and annotated against the reference (GRCm38; miRbase_20)
Differential expression analysis was performed using the EdgeR statistical software package (Bioconductor, http://bioconductor.org/). For normalization, the trimmed mean of M-values method based on LogF and absolute gene-wise changes in expression levels between samples (TMM normalization) was used.
Assembly: GRCm38; miRbase_20
Supplementary files format and content: Animal number….."expr" file, contains individual miRNA identifiers and  counts (TextEdit document). Animal number….."align" file, shows how the individual miRNAs were aligned against the mature miRNA sequences (TextEdit document).

source_name: Cardiac muscle

growth_protocol: Neonatal mice were housed with their original litter and mother until sacrificed and cardiac samples were taken

extract_protocol:
Cardiac samples from the remote zone of the left ventricle for RNASeq and miRNASeq were collected, frozen in liquid nitrogen and stored at −80 °C. The samples were then homogenized and RNA was isolated with TRIzol reagent.
Cardiac samples from the left ventricle for RNASeq and miRNASeq were collected, frozen in liquid nitrogen and stored at −80 °C. The samples were then homogenized and RNA was isolated with TRIzol reagent.
3 days follow up samples. Library preparation was done using the Qiagen QIAseq miRNA Library Kit. 100ng of total RNA was converted into miRNA NGS libraries. Quality was analyzed using either Agilent Bioanalyzer 2100 or TapeStation 4200. The library pool(s) were then sequenced on Illumina NextSeq500.
21 days follow up samples. Library preparation was done using the Illumina TruSeq Small RNA Sample Prep kit. 100ng of total RNA was converted into miRNA NGS libraries. Quality was analyzed using either Agilent Bioanalyzer 2100 or TapeStation 4200. The library pool(s) were then sequenced on Illumina HiSeq2000 (2x100 cycles).

treatment_protocol: Mice were subjected to LAD ligation or SHAM operation at the postnatal day 1 or 7. After the operation, the follow-up period lasted 3 or 21 days until the cardiac samples were collected

value: Left ventricular wall from the remote zone

tag: age (operation day + follow up time)

value: 7 + 3 days

value: MI at postnatal day 7


title: DJ_1_77_model_DSS_tissue_Blood_day_36_control [DJ_1_77_B]

tag: model


title: JH21_AoAF_lane 4

description: lane 4


title: DJ_1_45_model_DSS_tissue_Blood_day_17_control [DJ_1_45_B]

tag: bio region


title: JH21_AoAF_lane 1

description: lane 1


title: DJ_1_41_model_DSS_tissue_Blood_day_17_control [DJ_1_41_B]

tag: ctrl disease


title: 1075G-miRNA

value: SHAM at postnatal day 7


title: 1075F-miRNA


title: DJ_1_39_model_DSS_tissue_Colon_day_17_control [DJ_1_39_WC]

value: wildtype

tag: day


title: JH20_HRPE_lane 6

description: lane 6

source_name: Retinal Pigment Epithelial Cells

value: Epithelial

value: Eye

value: Fetus


title: DJ_1_40_model_DSS_tissue_Blood_day_17_control [DJ_1_40_B]

value: DSS

tag: hit rest


title: DJ_1_44_model_DSS_tissue_Colon_day_17_control [DJ_1_44_WC]

value: C


title: 1075E-miRNA


title: DJ_1_37_model_DSS_tissue_Colon_day_17_control [DJ_1_37_WC]

value: control


title: DJ_1_37_model_DSS_tissue_Blood_day_17_control [DJ_1_37_B]


title: DJ_1_28_model_DSS_tissue_Colon_day_12_control [DJ_1_28_WC]

value: WC


title: JH20_HRPE_lane 5

description: lane 5

tag: cell type


title: DJ_1_5_model_DSS_tissue_Blood_day_5_control [DJ_1_5_B]

tag: tissue


title: JH20_HRPE_lane 4

description: lane 4


title: DJ_1_45_model_DSS_tissue_Colon_day_17_control [DJ_1_45_WC]


title: JH20_HRPE_lane 8

description: lane 8


title: 1088D-miRNA


title: DJ_1_41_model_DSS_tissue_Colon_day_17_control [DJ_1_41_WC]


title: DJ_1_28_model_DSS_tissue_Blood_day_12_control [DJ_1_28_B]


title: DJ_1_27_model_DSS_tissue_Colon_day_12_control [DJ_1_27_WC]


title: 1075D-miRNA


title: JH20_HRPE_lane 7

description: lane 7


title: DJ_1_26_model_DSS_tissue_Colon_day_12_control [DJ_1_26_WC]


title: DJ_1_27_model_DSS_tissue_Blood_day_12_control [DJ_1_27_B]


title: DJ_1_26_model_DSS_tissue_Blood_day_12_control [DJ_1_26_B]


title: 1086C-miRNA

value: 1 + 3 days

value: MI at postnatal day 1


title: 1086A-miRNA


title: JH20_HRPE_lane 2

description: lane 2


title: 1059E-miRNA


title: DJ_1_20_model_DSS_tissue_Blood_day_12_control [DJ_1_20_B]

value: Blood


title: JH19_RPTEC_lane 8

description: lane 8

source_name: Renal Proximal Tubule Epithelial Cells

value: Kidney

value: Adult


title: 1090A-miRNA

value: Left ventricular wall from the remote zone


title: DJ_1_20_model_DSS_tissue_Colon_day_12_control [DJ_1_20_WC]

value: Colon


title: JH20_HRPE_lane 1

description: lane 1


title: DJ_1_2_model_DSS_tissue_Colon_day_5_control [DJ_1_2_WC]


title: DJ_1_2_model_DSS_tissue_Blood_day_5_control [DJ_1_2_B]

value: B


title: JH19_RPTEC_lane 7

description: lane 7


title: 1103E-miRNA

value: SHAM at postnatal day 1


title: 1086D-miRNA


title: DJ_1_11_model_DSS_tissue_Colon_day_5_control [DJ_1_11_WC]

value: wildtype


title: DJ_1_11_model_DSS_tissue_Blood_day_5_control [DJ_1_11_B]


title: 1103D-miRNA


title: JH20_HRPE_lane 3

description: lane 3

value: Epithelial


title: JH19_RPTEC_lane 6

description: lane 6


title: DJ_1_1_model_DSS_tissue_Colon_day_5_control [DJ_1_1_WC]


title: 1078F-miRNA


title: DJ_1_23_model_DSS_tissue_Colon_day_12_control [DJ_1_23_WC]


title: DJ_1_24_model_DSS_tissue_Blood_day_12_control [DJ_1_24_B]


title: M295_Fibroblast_HC_011122

city: Chicago

first: Ziyou

last: Ren

state: IL

address: 303 E Chicago Ave

institute: Northwestern University

data_processing:
Reads were demultiplexed using bcl2fastq (version 2.17.1.14).
Quality was assessed with FastQC. Reads were then trimmed and aligned to the Mus musculus reference genome (with mm10 assembly) using TopHat2 (version 2.1.0)
Read counts were associated with genes using HTSeq
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files including raw htseq count

growth_protocol: 9-11 weeks old male mice were obtained from Jackson Laboratories

extract_protocol:
Total RNA from fibroblasts cells was extracted using Qiagen RNeasy Plus Mini kit (Qiagen) and quality and quantity were assessed 4200 TapeStation  Agilent
RNA-Seq libraries were prepared using a full-length transcript coverage NEBNext Ultra RNA (New England Biolabs)
DNA libraries sequencing was performed using an Illumina NextSeq 500 instrument (Illumina) of the average dept of 5–7.5 million aligned reads per sample

treatment_protocol: 9  mice were kept at room air (3 mice were used per replicate), 9 mice were exposed to 10% CO2( 3 mice were used per replicate) for 10 days . Mice were ansthetized and both lungs were harvested for flow-sorting of fibroblast cells

value: flow-sorted PDGFR+ lung  fibroblast cells

tag: organ

value: Lung


title: 1078G-miRNA

tag: treatment


title: 20_LXR-aKO_CTRL_(H3K27ac)_rep3

city: Madrid

first: ANTONIO

last: CASTRILLO

address: Arturo Duperier 4

department: metabolism and cellular signaling

country: Spain

institute: Instituto Investigaciones Biomedicas Alberto Sols CSIC

data_processing:
Basecalls performed using Casava version 1.8.4
For ChIP-Seq, reads were aligned to the mm10 genome using default parameter for bowtie2 (v2.2.9).
Aligned read files were analyzed with HOMER software (v4.9) to find peaks, perform sequence motif finding and other analyses in the study.
Each ChIP-Seq experiment was normalized to a total of 10^7 uniquely mapped tags by adjusting the number of tags at each position in the genome to the correct fractional amount given the total tags mapped.
annotation was performed with HOMER software v4.9 annotatePeaks.pl using default parameters
Assembly: mm10
Supplementary files format and content: Processed files include bed files.

source_name: Bone marrow

growth_protocol: For bone marrow-derived macrophage (BMDM) cell differentiation, bone marrow from femurs and tibias of 8-10 week-old WT or LXRβ-/- mice were isolated and cultured for 7 days in RPMI supplemented with 10% conditioned media from L-929 cells expressing M-CSF and 1% antibiotics (penicillin and streptomycin). To analyze LXRα-dependent response, cells were cultured in RPMI supplemented with 10% FBS, 1% antibiotics (penicillin and streptomycin) and 100 nM of Lipopolysachaaride (LPS). Genome-wide locations of LXRα and H3K27ac acetylation mark were analized in response to treatment with  LPS.

extract_protocol:
Cells were fixed with DSG (2 mM) for 30 minutes and 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a Biorruptor plus (Diagenode) and LXR-DNA or H3K27ac-DNA complexes were isolated with indicated antibodies.
to create the sequencing library, DNA was end-repaired and ligated to stem-loop adaptors (DNA Library Prep kit for Illumina (Ref.:#7370) following the manufacture instructions). Then DNA was PCR amplified with Illumina-compatible primers for 7-11 cycles and library fragments of 200 to 400 bp were selected using Ampure XP beads.

value: Bone marrow

value: bone marrow-derived macrophage

value: LXR-aKO

tag: chip antibody

value: H3K27ac (Abcam catalog#ab4729)

value: Vehicle


title: JH19_RPTEC_lane 3

description: lane 3


title: M294_Fibroblast_HC_011122

value: flow-sorted PDGFR+ lung fibroblast cells


title: 18_LXR-aKO_CTRL_(H3K27ac)_rep1


title: 19_LXR-aKO_CTRL_(H3K27ac)_rep2


title: M293_Fibroblast_HC_011122


title: JH19_RPTEC_lane 1

description: lane 1


title: 14_LXR-WT_CTRL_(H3K27ac)_rep3

value: WT


title: 13_LXR-WT_CTRL_(H3K27ac)_rep2


title: JH18_HRE_lane 8

description: lane 8

source_name: Renal Epithelial Cells

value: Kidney

value: Fetus


title: JH19_RPTEC_lane 5

description: lane 5

value: Adult


title: M291_Fibroblast_RA_011122

value: Naïve (Room Air exposure)

value: flow-sorted PDGFRA+ lung fibroblast cells


title: 12_LXR-WT_CTRL_(H3K27ac)_rep1


title: M290_Fibroblast_RA_011122

value: flow-sorted PDGFRa+ lung fibroblast cells


title: 6_LXR-bKO_CTRL_(LXRa)_rep1

value: LXR-bKO

value: A polyclonal antibody raised against LXRα and LXRβ was obtained from their original creators (Pehkonen 2012)


title: JH18_HRE_lane 6

description: lane 6

value: Epithelial


title: Ribo-seq_sh-Dhps_Dox+_2

city: TAmpa

first: Yonghong

state: FL

address: 12902 USF Magnolia Drive

department: Biomedical Informatics

institute: Moffitt Cancer Center

data_processing:
Library strategy: Ribo-seq
Illumina BaseSpace software (bcl2fastq v2.20.0.422) used for basecalling.
Sequenced reads were trimmed for adaptor sequence and Clippered 6 bases from the 5' end using FASTX-Toolkitg19 reference genome using star v2.5.3a with default settings.
Ribosomal reads were removed using bowtie2
Pressed reads are aligned mouse genome mm10 with tophat (v2.0.13)
Aligned reads analysis for ribo-score
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw read count for each sample

source_name: Em-Myc lymphoma cells

growth_protocol: Em-Myc lymphoma cells  in culture in 1:1 Dulbecco's modified eagle medium and Iscove's Modified Dulbecco's medium supplementedwith 10%FBC, 1mM sodium pyrubate, glutamax, 2-mercaptoethanol and penicillin/streptomycin.

extract_protocol:
Cells were washed and follwed by cell lysis, RNAase treatment, ribosome recovery and purification of the ribosome footprints according to Ingoria et al., Nature Protocol (2012).
Libraries were generated according to Ingoria et al., Nature Protocol (2012) and followed by rRNA depletion and PCR amplification steps.

treatment_protocol: Cells were treated with or without 0.9 μg/mL of doxycline for 72 hours to induce shRNA expression. Cells were treated with cycloheximide to stabilize the ribosomes prior to cell harvest.

tag: cancer type

value: Emicro-Myc lymphoma

tag: cell line

value: Suspension cell line

tag: shRNA

value: sh-Dhps

tag: dox status

value: Dox+


title: JH18_HRE_lane 5

description: lane 5

tag: tissue origin


title: ICR393-3-miRNA

tag: strain

value: Left ventricular wall from the remote zone

value: 7 + 21 days

value: MI at postnatal day 7


title: Ribo-seq_sh-Dhps_Dox+_1


title: ICR393-1-miRNA

tag: age (operation day + follow up time)


title: JH19_RPTEC_lane 2

description: lane 2

tag: life stage


title: ICR380-3-miRNA

value: SHAM at postnatal day 7


title: ICR380-2-miRNA


title: JH18_HRE_lane 4

description: lane 4

value: Kidney


title: M292_Fibroblast_RA_011122

value: flow-sorted PDGFRa+ lung  fibroblast cells

value: Lung


title: Ribo-seq_sh-EiF5A_Dox+_2


title: 1077B-miRNA

value: 7 + 3 days


title: ICR380-1-miRNA


title: JH18_HRE_lane 3

description: lane 3

value: Fetus


title: Ribo-seq_sh-EiF5A_Dox+_1


title: ICR405-2 -miRNA

value: 1 + 21 days

value: MI at postnatal day 1


title: JH18_HRE_lane 2

description: lane 2


title: ICR405-1-miRNA


title: ICR392-5-miRNA

value: SHAM at postnatal day 1


title: JH18_HRE_lane 1

description: lane 1

value: Epithelial


title: Ribo-seq_sh-Ren_Dox+_1

value: Emicro-Myc lymphoma

value: shRen


title: ICR392-3-miRNA


title: ICR392-2-miRNA


title: JH17_HRCE_lane 8

description: lane 8

source_name: Renal Cortical Epithelial Cells

value: Adult


title: sh-Dhps_Dox+_2

data_processing:
Illumina BaseSpace software (bcl2fastq v2.20.0.422) used for basecalling.
Sequenced reads were trimmed for adaptors, and mapped to mm10 mouse reference genome using tophat v2.0.13.
Uniquely mapped reads were counted at transcript level by htseq-count using Refseq GRCh38 (mm10) transcript annotations for mouse
Genome_build: GRCh38(mm10)
Supplementary_files_format_and_content: tab-delimited text files include raw read count for each sample

extract_protocol:
Cells were washed and follwed by total RNA extraction using mirRNeasy kit (Qiagen). Genomic DNA was removed by DNase treatment.
Libraries were prepared for sequencing using Epicentre ScriptSeq Complete Gold Library kit and the quality was evaluated by BioAnalyzer.

treatment_protocol: Cells were treated with or without 0.9 μg/mL of doxycline for 72 hours.

value: Suspension cell line

value: sh-Dhps

value: Dox+


title: ICR393-3-RNA

data_processing:
Basecalls by Illumina NextSeq550 (3 days follow up samples) or Illumina HiSeq2000 (21 days follow up samples)
Sequence reads were aligned to the reference genome (GRCm38; Ensembl_81)  with Tophat (v2.0.11) and Bowtie2 (v. 2.2.2)
Cufflinks (v2.2.1) was used to assemble the transcriptome from the aligned  sequences followed by feature summation and normalization of expression estimates
Cuffdiff2 was used to calculate the FPKM (number of fragments per kilobase of transcript per million mapped fragments) and test for differential expression and regulation among the assembled transcripts across the submitted samples using the Cufflinks output.
The expression profiles of different treatment groups were compared and the transcript ratios between the average FPKMs were calculated. Transcripts showing a LogFC ≥1 and a False Discovery Rate (FDR) <0.05 were classified as differentially expressed.
Assembly: GRCm38; Ensembl_81
Supplementary files format and content: Animal number."gene.annotated.counts.txt" (Individual data containing gene locations, ensemble identifiers, gene names and counts) as TextEdit Documents

extract_protocol:
Cardiac samples from the remote zone of the left ventricle for RNASeq and miRNASeq were collected, frozen in liquid nitrogen and stored at −80 °C. The samples were then homogenized and RNA was isolated with TRIzol reagent.
3 days follow up samples.  Library preparation was done using Illumina TruSeq stranded total RNA sample Library Prep Kit with the starting material of 500 ng total RNA. Library quality was inspected on Agilent Bioanalyzer 2100 or BioAnalyzer 4200 TapeStation. The library pool was quantified using qPCR and sequenced on Illumina NextSeq550 (2x75 cycles).
21 days follow up samples.  Library preparation was done using Illumina ScriptSeqV2 Library Prep Kit with the starting material of 500 ng total RNA. Library quality was inspected on Agilent Bioanalyzer 2100 or BioAnalyzer 4200 TapeStation. The library pool was quantified using qPCR and sequenced on Illumina HiSeq 2000 instrument (2x100 cycles).

value: Left ventricular wall from the remote zone

value: 7 + 21 days

value: MI at postnatal day 7


title: JH18_HRE_lane 7

description: lane 7

value: Kidney


title: sh-Dhps_Dox+_1


title: ICR405-3-miRNA


title: JH17_HRCE_lane 7

description: lane 7


title: JH17_HRCE_lane 5

description: lane 5


title: ICR380-2-RNA

value: SHAM at postnatal day 7


title: ICR405-3-RNA


title: ICR380-1-RNA


title: sh-EiF5A_Dox+_1


title: ICR393-2-RNA


title: ICR393-2-miRNA


title: ICR405-2 -RNA


title: sh-EiF5A_Dox+_2


title: ICR393-1-RNA


title: Ribo-seq_sh-Ren_Dox+_2


title: JH17_HRCE_lane 4

description: lane 4


title: sh-Ren_Dox+_2

value: sh-Ren


title: JH17_HRCE_lane 3

description: lane 3


title: ICR392-5-RNA


title: ICR380-3-RNA


title: sh-Ren_Dox+_1


title: sh-Ren_Dox-_2

value: Dox-


title: ICR392-3-RNA

value: 1 + 21 days


title: JH17_HRCE_lane 6

description: lane 6


title: ICR392-2-RNA


title: ChIP_MEF_Ola_Input_IFNb_0h_Rep2

city: Heidelberg

first: Markus

last: Muckenhuber

address: Im Neuenheimer Feld 280

country: Germany

institute: DKFZ

data_processing:
ChIP bed files: Raw reads were mapped with Bowtie (v1.2.2). The mapped reads were sorted, duplicates and reads in blacklisted regions removed with bedtools (v2.27.1).
ChIP Norm counttables: Bam files were used to count reads around peaks of STAT1p701 and STAT2 by bedtools (v2.27.1). Reads were normalized by sequencing depth, fragment length and enrichment to control. For histon marks H3 signal was the control. For STAT ChIPs IgG_Rb_CST.
Genome_build: mm10

source_name: Mouse embryonic fibroblasts

growth_protocol:
Embryonic stem cells: Cultured on 0.1 % gelatinized tissue flasks in ESC media. Cells were incubated at 37 °C and 5 % CO2. Media was PowerStem ESPro1 (PAN-Biotech; P04-77510K) with self-made LIF (1:1000).
Mouse embryonic fibroblasts: Cells were incubated at 37 °C and 5 % CO2. Media was DMEM (Gibco, 11880-28), 10% FCS (PAN-Biotech; P30-3602), 1x L-Glutamine (PAN-Biotech, P04-80050), 1x PenStrep (PAN-Biotech, P06-07050).
Neural progenitor cells: ESCs were differentiated into NPCs based on the Bible-protocol Bibel et al. 2007. 4-5*10^6 cultured ESCs were split onto a T75 UltraLow-BindingPlates (Corning, 3814) in 15 ml StemPAN media (PAN-biotech, P08-50500). After 4 days 5µM retinoic acid (Sigma-Aldrich, R2625) was added. On day 8, cells were platted on plates coated with 1% Matrigel (Corning, 356230) in neuronal base medium (Gibco, 211103049), G5 supplements (Gibco, 17503012), NSC supplements (Gibco, 17502048). Experiments were performed five days after neuronal plating.

extract_protocol:
ChIP-seq for histone marks in MEFs: Cells were crosslinked by 1 % Formaldehyde for 10 min at room temperature and stopped with 125 mM Glycine for 5 min. Samples of around 40 million cells were treated with 40 U of MNase for 15 min at 37 °C. The samples were shared for 15 min (Burst 200; Cycle 20%; Intensity 8). Replicate 1 was shared for 30 min and no MNase treatment was performed. 4µg of antibody was used per sample and incubated for 2 hours at 4 °C. Protein G-beads were added over night. Multiple low and high salt washes were performed and the samples were eluted. Samples were reverse crosslinked and stored at -20°C.
ChIP-seq for histone marks in MEFs: Libraries were made using NEBNext Ultra™ II DNA Library Prep Kit for Illumina (New England Biolabs, E7645)

treatment_protocol: All cells were treated with 500U/ml of self-made interferon beta (16.6U/µl) for 1 hour or 6 hours

value: Mouse embryonic fibroblasts


title: JH17_HRCE_lane 2

description: lane 2


title: ChIP_MEF_Ola_H3K9me3_IFNb_0h_Rep2


title: ChIP_MEF_Ola_Input_IFNb_0h_Rep1


title: JH17_HRCE_lane 1

description: lane 1


title: sh-Ren_Dox-_1


title: ICR405-1-RNA

value: MI at postnatal day 1


title: JH15_NHOST_lane 8

description: lane 8

source_name: Osteoblast cells

value: Osteoblast

value: Bone


title: ChIP_MEF_Ola_H3K9me3_IFNb_0h_Rep1


title: JH15_NHOST_lane 7

description: lane 7


title: JH15_NHOST_lane 6

description: lane 6


title: ChIP_MEF_Ola_H3K9ac_IFNb_0h_Rep2


title: ChIP_MEF_Ola_H3K4me3_IFNb_0h_Rep2


title: ChIP_MEF_Ola_H3K9ac_IFNb_0h_Rep1


title: ChIP_MEF_Ola_H3K4me3_IFNb_0h_Rep1


title: ChIP_MEF_Ola_H3K4me1_IFNb_0h_Rep2


title: aged mouse 6 (72 weeks) [Illumina NextSeq 500]

city: NORWICH

first: Laura

last: mincarelli

state: County (optional)

address: Norwich Research Park, Colney Lane, Colney

country: United Kingdom

institute: Earlham Institute

description: single cell fulllenght cDNA (10x Genomics)

data_processing:
Illumina data
Raw Illumina sequencing data were analysed with the 10X Genomics CellRanger pipeline (version 3.0.2) to obtain a single-cell expression matrix object.
Using Seurat v3 in R data were normalised using NormalizeData
data from multiple samples were merged using the FindIntegrationAnchors and IntegrateData commands
count matrices produced by short-read sequencing for individual libraries were combined in Seurat using FindIntegrationAnchors and IntegrateData functions
Illumina and PacBio reads were integrated in Seurat using the CreateAssayObject command to add the long-read data to an existing Seurat object already containing the short-read data
Pacbio data
Circular Consensus reads (CCS) were generated using smrtlink-6.0.0.47841 amnd the command "ccs --numThreads=24 --noPolish --minLength=50 --maxLength=15000 --minPasses=1 --minPredictedAccuracy=0.8"
Reads with identified polydA or polydT were demultiplexed using bbduk and the 10X genomics barcodes identified from the short-read analysis
Long-reads were mapped to the mouse genome (mm10) using Minimap 2 (v2.17), and to the gencode (vM19) transcriptome. De novo transcript annotation was performed with TALON  v.5 was used to generate custom transcriptome using gencode v.M24 and GRCm38.p6. Minimum identity threshold 0.9, coverage 0.8. Novel features filtered with N=5 reads in K=3 samples. Transcriptome then filtered for mis-called antisense transcripts. Novel features were merged with v.M24 reference to make custom annotation. Count matrices were generated using HTSeq, the alignments to the genome (GRCm38.p6, Minimap2) and the TALON annotation
Novel exons were identified by investigating the alignment of the reads to the transcriptome
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: gene level counts
Supplementary_files_format_and_content: de novo annotation
Supplementary_files_format_and_content: gene levels counts

source_name: bone marrow cells

extract_protocol:
Bone marrow was isolated from spine, femora, tibiae, and ilia,blood cell depletion was performed with ammonium chloride lysis  and lineage negative cells were isolated using the EasySep Mouse Hematopoietic Progenitor Cell Isolation Kit
3’ end single cell RNA-Seq using the 10X Genomics Chromium (V2 Kit) according to manufacturer’s protocol
Libraries compatible for Illumina platform and for Pacific Biosciences Sequel/Sequel II systems were prepared from input cDNA

value: Lineage negative, cKit (Cd117) positive (LK) cell fraction

tag: Sex

value: female

tag: age

value: 72 weeks


title: aged mouse 4 (72 weeks) [Illumina NextSeq 500]


title: young  mouse 5 ( 8 weeks) [Illumina NextSeq 500]

value: 8 weeks


title: JH15_NHOST_lane 5

description: lane 5

value: Adult


title: ChIP_MEF_Ola_H3K4me1_IFNb_0h_Rep1


title: ChIP_MEF_Ola_H3K27me3_IFNb_0h_Rep2


title: ChIP_MEF_Ola_H3K27ac_IFNb_0h_Rep2


title: ChIP_MEF_Ola_H3K27me3_IFNb_0h_Rep1


title: aged mouse 2 (72 weeks) [Illumina NextSeq 500]


title: young  mouse 3 ( 8 weeks) [Illumina NextSeq 500]


title: JH15_NHOST_lane 4

description: lane 4


title: ChIP_MEF_Ola_H3K27ac_IFNb_0h_Rep1


title: ChIP_MEF_Ola_H3_IFNb_0h_Rep2


title: JH15_NHOST_lane 3

description: lane 3


title: young  mouse 1 ( 8 weeks) [Illumina NextSeq 500]


title: JH15_NHOST_lane 2

description: lane 2


title: KO-5-R3

city: Goyaongsi

first: Charny

last: Park

state: Gyeonggi-do

address: 323 Ilsan-ro,

country: South Korea

institute: National Cancer Center

data_processing:
Quality filtering and adapter trimming: FASTQC and Trimmomatic(Version 0.39) (standard parameters)
Mapping with STAR(version 2.7.0a)
Quantification with RSEM (v1.2.31 )
Genome_build: mm9
Supplementary_files_format_and_content: Tab delimited matrix of FPKM

source_name: Knockout mouse five month bone marrow cells

growth_protocol: Lineage- cells isolated from WT and Txnip-/- mice were expanded for 3 days in Serum-Free Expansion Medium II (SFEMII; StemCell Technologies, #09655) supplemented with 10% FBS, 1% 1% penicillin/streptomycin, 100 ng/mL murine (m) Scf, and 20 ng/mL mTpo.

extract_protocol:
On day 3 of growth, CD41+ cells were sorted using flow cytometry sorter and RNA was isolated using NEB RNA extraction kit (NEB #T2010S)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: BM Lineage- cells-derived CD41+ cells

tag: genotype

value: Txnip -/-


title: KO-5-R2


title: KO-5-R1


title: H3K27me3_Rep2

city: Bronx

first: Deyou

last: Zheng

address: 1300 Morris Park Ave

institute: Albert Einstein College of Medicine

data_processing:
The ChIP-seq reads were aligned to the mouse reference genome (mm10) using the bowtie2 software (v2.3.3.1). Uniquely aligned reads to the mouse genome were kept for downstream analysis, after duplicate reads removed by the software samtools (v1.9).  Genomic regions broadly enriched with ChIP-seq singling were determined using a sliding window approach with the input as controls. Peaks consistently called in both replicates were used as the final peaks.
Genome_build: mm10
Supplementary_files_format_and_content: text file of peaks called in both replicates in minimal bed format, the three columns are chromosome, peak start and peak end.

source_name: Skin epidermis

extract_protocol:
Basal layer epidermal progenitors were isolated from K14-RFP;K10-H2B-GFP mice. The basal layer epidermal progenitors were isolated from adult back skin. Back skins were collected and washed with 1x DPBS and incubated for 0.25% Trypsin/EDTA at 37℃ for 1 hour. Crosslinking was stopped by the addition of Glycine (final concentration 125mM) for 5 minutes at room temperature, followed by 2 washes with 1x DPBS.  Cells were stained with 1:200 Sca1-PerCP-Cy5.5 (Biolegend) and Zombie violet (Biolegend) for 30 minutes on ice and washed twice with 1x DPBS before cell sorting. Epidermal progenitors were sorted as Sca1(+), RFP(high) and GFP(-).
For high-throughput ChIP sequencing, libraries were constructed from 5ng of purified DNA using the NEBnext Ultra II DNA Library Prep Kit (New England Biolabs) according to the manufacturer’s instructions. Constructed ChIP-seq libraries were sequenced on Illumina NextSeq 500 platform with 75-single end reads.

value: Epidermal cells

value: Epidermis

value: Postnatal day 71

value: Control

value: H3K27me3 (Sigma-Aldrich, Cat#07-449)


title: H3K27me3_Rep1


title: JH14_NHMC_lane 8

description: lane 8

source_name: Mesangial Cells

value: Mesangial

value: Kidney


title: WT-5-R1

source_name: Wild-type mouse five month bone marrow cells

value: Wild type


title: WT-5-R3


title: H2AK119ub_Rep2

value: H2AK119ub (Cell Signaling, Cat# 8240S)


title: JH14_NHMC_lane 7

description: lane 7


title: H2AK119ub_Rep1


title: JH14_NHMC_lane 6

description: lane 6


title: RNA_ESC_Ola_IFNb_6h_Rep4

description: RNA_ESC_Ola_IFNb_Counttable_Raw.txt, RNA_ESC_Ola_IFNb_Counttable_TPM_FPKM.txt

data_processing:
ATAC-seq bam files: Raw reads were trimmed by Trimmomatic (v0.36) and mapped using Bowtie2 (v2.3.3.1). The mapped reads were with bedtools (v2.27.1) sorted, shifted by +4/-5bp to correct for transposase intragtion bias, duplicates and reads in blacklisted reads removed. Reads with quality score below 30 were removed.
ATAC-seq bed files: The sorted and quality filtered bam files were used for peak calling by MACS2 (v2.1.2).
ATAC Norm counttables: Bam files were used to count reads around peaks of STAT1p701 and STAT2 by bedtools (v2.27.1). Reads were normalized by sequencing depth, fragment length and enrichment to control.
ChIP bed files: Raw reads were mapped with Bowtie (v1.2.2). The mapped reads were sorted, duplicates and reads in blacklisted regions removed with bedtools (v2.27.1).
ChIP Norm counttables: Bam files were used to count reads around peaks of STAT1p701 and STAT2 by bedtools (v2.27.1). Reads were normalized by sequencing depth, fragment length and enrichment to control. For histon marks H3 signal was the control. For STAT ChIPs IgG_Rb_CST.
RNA-seq raw counttable: Ribosomal RNAs were removed by SortMeRNA (v2.1). Raw reads were aligned with STAR (v2.5.3a) and Aligned.sorted.ByCoord.out.bam and Aligned.to.Transcriptome.out.bam were created. STAR counted reads per genes in ReadsPerGene.out.tab files. These files were combined and the resulting raw count-table was the input for DESeq2.
RNA-seq count table TPM and FPKM: Ribosomal RNAs were removed by SortMeRNA (v2.1). Raw reads were aligned with STAR (v2.5.3a) and Aligned.sorted.ByCoord.out.bam and Aligned.to.Transcriptome.out.bam were created. The  Aligned.to.Transcriptome.out.bam files from STAR were used as input for RSEM (v1.3.0) to create TPM and FPKM values.
RNA-seq DESeq result tables: Result tables for DESeq2 (1.24.0) for the comparisons of 1h IFNb with 0h; 6h IFNb with 0h and 6h with 1h IFNb.
scATAC-seq: Raw reads were applied to CellRanger (v1.1.0), a full automatic pipeline especially for scATAC-seq data done by the 10x Chromium.
scATAC-seq: The default output counttable for downstream analysis.
scRNA-seq: Raw reads were applied to CellRanger (v1.3.1), a full automatic pipeline especially for scRNA-seq data done by the 10x Chromium.
scRNA-seq counttable: The default output folders with the counttable for downstream analysis.
Genome_build: mm10
Supplementary_files_format_and_content: ATAC-seq bam files: Quality filtered mapped read files
Supplementary_files_format_and_content: ATAC-seq bed files: File containing coordinates of peaks and enrichment scores by MACS2
Supplementary_files_format_and_content: ChIP-seq bed files: File containing coordinates of peaks and enrichment scores by MACS2
Supplementary_files_format_and_content: ChIP-seq peak list for STAT1 and STAT2 by DiffBind: Peak lists for STAT1p701 and STAT2 replicates were anaylzed by DiffBind (v2.12.0) to create list of robust binding sites over replicates. Peaks at 1h and 6h of IFNb treatment were combined
Supplementary_files_format_and_content: RNA-seq raw counttable: Counttable containing ENSEMBL gene ID and the raw read counts for each gene over the replicates in ESCs, MEFs and NPCs
Supplementary_files_format_and_content: RNA-seq count table TPM and FPKM: Counttable with normalized TPM and FPKM values for each samples of ESCs, MEFs and NPCs. In addtition, the ENSEMBL gene ID, all transcript Ids and the annotated gene length.
Supplementary_files_format_and_content: RNA-seq DESeq result tables: Results table from DESeq2 of all genes for the three compariosns of 1h vs 0h, 6h vs 0h and 6h vs 1h. Each files contains the ENSEMBL gene ID, the normalized counts for all used samples, the base mean expression, the log2 fold change of the comaprison, the standard error of the log2 fold change, the Wald statistic, pvalue and adjusted pvalue.
Supplementary_files_format_and_content: scATAC: Counttable with a the coordinates of mapped fragments, the barcode of the fragment and the counts.
Supplementary_files_format_and_content: scRNA-seq: The folder contains the deault output of Cellranger. A list of detected barcodes in the sample. A List of identified genes in the sample as ENSEMBL ID and gene symbole. And a matix which is the counttable.

extract_protocol:
ATAC-seq: . For ESCs, the cell pellet was resuspended in 200 µl ATAC lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl2, 3 mM MgCl2, 0.1 % NP-40) and incubate for at room temperature for 2 min. 20 µl ATAC reaction buffer containing 10 µl 2x transposase buffer and 2.5 µl Tn5 enzyme (Illumina) was added and samples were incubated at 37 °C for 30 min. Samples were purified. For MEFs, the lysis buffer contained additionally 1 % digitonin.
ATAC-seq: Purified samples were directly amplifed, barcoded and purified.
ChIP-seq for histone marks in ESC: Cells were crosslinked by 1 % Formaldehyde for 10 min at room temperature and stopped with 125 mM Glycine for 5 min. Samples of around 40 million cells were treated with 40 U of MNase for 15 min at 37 °C. The samples were shared for 15 min (Burst 200; Cycle 20%; Intensity 8). Replicate 1 was shared for 30 min and no MNase treatment was performed. 4µg of antibody was used per sample and incubated for 2 hours at 4 °C. Protein G-beads were added over night. Multiple low and high salt washes were performed and the samples were eluted. Samples were reverse crosslinked and stored at -20°C.
ChIP-seq for histone marks in ESCs: Libraries were made using NEBNext Ultra™ II DNA Library Prep Kit for Illumina (New England Biolabs, E7645)
ChIP-seq for STATs in ESCs and MEFs: The isolation of the chromatin was done with Simple ChIP Enzymatic Chromatin IP Kit (Cell Signaling Technology, 9003)
ChIP-seq for STATs in ESCs and MEFs: Libraries were made using NEBNext Ultra™ II DNA Library Prep Kit for Illumina (New England Biolabs, E7645)
RNA-seq: Total RNA was isolated using NucleoSpin RNA Plus Kit (Macherey-Nagel, 740984.250). Depletion of rRNA was done with Ribo-Zero rRNA Removal Kit (Illumina, 15066012) for ESCs and MEFs and with NEBNext® rRNA Depletion Kit (New England Biolabs, E6350).
RNA-seq: Libraries were prepared using NEBNext Ultra II Directional  RNA Library Prep Kit for Illumina (New England Biolabs, E7760).
scATAC-seq: The experiment was performed based on the standard manufacturer’s protocol Chromium Single Cell ATAC Reagent Kits (PN-1000110).
scRNA-seq: The experiment was performed based on the standard manufacturer’s protocol of Chromium Single Cell 3’ Reagent Kits v2 (PN-120237).

value: Embryonic stem cells


title: RNA_ESC_Ola_IFNb_6h_Rep3


title: RNA_ESC_Ola_IFNb_6h_Rep2


title: JH14_NHMC_lane 5

description: lane 5


title: Py230 derived turmors growing in lean mice  (Sample 370)

city: Geneva

first: Isabelle

last: Dupanloup

address: Rue Michel-Servet, 1

country: Switzerland

institute: University of Geneva

data_processing:
Software for basecalling: Illumina Casava v1.8
Software to demultiplex Illumina data and generate fastq files: bcl2fastq v2.18.0.12
Software to remove adapter sequences and low quality bases: cutadapt v1.12
Software to map the reads to the mm10 reference genome: STAR v2.5.2b
Software to estimate the read counts for each gene: htseq-count
Genome_build: mm10
Supplementary_files_format_and_content: Table of raw gene counts for each gene (rows) and each sample (columns)

source_name: Primay mammary turmor, 4th mammary gland

growth_protocol: 10E6 Py230 tumor cells were injected in the 4th mammary fat pad of mice to form tumor. Tumor growth was monitored clinically and turmors were resected at day 56 after initiation.

extract_protocol:
Total RNA was extracted from tumors using the RNeasy® Mini kit (Qiagen).
Library preparation with TruSeq Stranded RNA HT Kit (Illumina)

treatment_protocol: Resected tumors were snap-frozen in liquid nitrogen and stored at -80°C until RNA extraction.

tag: condition

value: Lean

value: Py230 mouse breast adenocarcinoma cell line


title: RNA_ESC_Ola_IFNb_6h_Rep1

tag: cell type


title: RNA_ESC_Ola_IFNb_1h_Rep4


title: ChIP_MEF_Ola_H3_IFNb_0h_Rep1

value: Mouse embryonic fibroblasts


title: JH14_NHMC_lane 4

description: lane 4


title: Py230 derived turmors growing in lean mice  (Sample 358)

tag: tissue


title: RNA_ESC_Ola_IFNb_1h_Rep2


title: JH15_NHOST_lane 1

description: lane 1

value: Osteoblast

value: Bone


title: RNA_ESC_Ola_IFNb_1h_Rep3


title: WT-5-R2

value: BM Lineage- cells-derived CD41+ cells


title: RNA_ESC_Ola_IFNb_0h_Rep4


title: JH14_NHMC_lane 3

description: lane 3

value: Adult


title: Skin epidermis P71 control- Input

description: Input

value: Epidermal cells


title: Py230 derived turmors growing in lean mice  (Sample 356)


title: RNA_ESC_Ola_IFNb_0h_Rep2


title: RNA_ESC_Ola_IFNb_1h_Rep1


title: Py230 derived turmors growing in lean mice  (Sample 355)


title: RNA_ESC_Ola_IFNb_0h_Rep3


title: RNA_ESC_Ola_IFNb_0h_Rep1


title: Py230 derived turmors growing in obese mice  (Sample 375)

value: Obese


title: JH14_NHMC_lane 1

description: lane 1


title: ChIP_ESC_Ola_Input_IFNb_6h_Rep2


title: ChIP_ESC_Ola_Input_IFNb_6h_Rep3


title: JH13_HMEC_lane 8

description: lane 8

source_name: Mammary Epithelial cells

value: Epithelial

value: Mammary


title: Py230 derived turmors growing in obese mice  (Sample 362)


title: JH13_HMEC_lane 7

description: lane 7


title: ChIP_ESC_Ola_Input_IFNb_1h_Rep3


title: ChIP_ESC_Ola_Input_IFNb_6h_Rep1


title: Py230 derived turmors growing in obese mice  (Sample 359)


title: ChIP_ESC_Ola_Input_IFNb_1h_Rep1


title: ChIP_ESC_Ola_Input_IFNb_1h_Rep2


title: JH13_HMEC_lane 6

description: lane 6


title: ChIP_ESC_Ola_Input_IFNb_0h_Rep3


title: Py230 derived turmors growing in obese mice  (Sample 349)


title: ChIP_ESC_Ola_Input_IFNb_0h_Rep2


title: JH13_HMEC_lane 5

description: lane 5


title: JH14_NHMC_lane 2

description: lane 2


title: ChIP_ESC_Ola_Input_IFNb_0h_Rep1


title: ChIP_ESC_Ola_IgG_Rb_IFNb_6h_Rep3


title: JH13_HMEC_lane 4

description: lane 4


title: JH19_RPTEC_lane 4

description: lane 4


title: VertX.in vitro.D8.rep1.Input

city: Vancouver

first: Martin

last: Hirst

state: British Columbia

address: 2125 East Mall

department: Microbiology and Immunology

country: Canada

institute: University of British Columbia

description: VertX.in vitro.D8.rep1.Input

data_processing:
Sequence reads were aligned to GRCm38/mm10 using Burrows-Wheeler Aligner 0.7.6a and converted to bam format by Sambamba 0.5.5.
Tracks for Input libraries were generated by converting bam files to Wiggle tracks and UCSC Wig2Bigwig was used to convert Wiggle tracks to BigWig for display on the UCSC browser.
Input control normalized tracks ChIPseq libraries were generated using MACS2.
Genome_build: GRCm38
Supplementary_files_format_and_content: bigWig, Input and ChIP libraries tracks

source_name: Spleen

extract_protocol:
Cells were lysed in non-ionic detergents and protease inhibitor cocktail. Cells were digested  by Micrococcal nuclease (MNase) at room temperature for 5 minutes and 0.25mM EDTA was used to stop the reaction. Antibodies, H3K27me3 and H3K4me3 were incubated with anti-IgA magnetic beads for 2 hours. Digested chromatin was incubated with magnetic beads alone for 1.5 hours. Digested chromatin was separated from beads and incubated with antibody-bead complex overnight in IP buffer. IPs were washed twice and eluted for 1.5 hours. Histones were digested by Protease for 30min and DNA fragments were purified using Sera Mag magnetic beads in 30% PEG.
Illumina sequencing libraries were generated by end repair, 3’ A-addition, and Illumina sequencing adaptor ligation.

treatment_protocol:
naïve cells: Single cell suspensions were prepared from spleens of VertX or VertX TCCR mice. CD4+ T cells were purified using negative selection kits and live CD4+ CD44lo populations isolated by cell sorting.
in vitro activated D8 cells: Purified CD4+ T cells were activated in vitro for 4 days in the presence of IL-27. Activated CD44hi cells were isolated by cell sorting and cultured in IL-2 for 4 additional days.

value: VertX

value: post natal day 56

value: Control

value: IL-10 GFP reporter


title: VertX.TCCR.naive.rep1.Input

value: VertX IL-27Ra-/-

value: IL-10 GFP reporter/IL-27Ra-/-


title: VertX.TCCR.in vitro.D8.rep1.Input

description: VertX.TCCR.in vitro.D8.rep1.Input


title: ChIP_ESC_Ola_IgG_Rb_IFNb_6h_Rep1

value: Embryonic stem cells


title: ChIP_ESC_Ola_IgG_Rb_IFNb_1h_Rep3


title: ChIP_ESC_Ola_IgG_Rb_IFNb_6h_Rep2


title: JH13_HMEC_lane 3

description: lane 3


title: JH13_HMEC_lane 2

description: lane 2


title: ChIP_ESC_Ola_IgG_Rb_IFNb_1h_Rep2


title: VertX.naive.rep1.Input


title: ChIP_ESC_Ola_IgG_Rb_IFNb_0h_Rep3


title: DJ_1_13_model_DSS_tissue_Blood_day_5_control [DJ_1_13_B]

city: New York city

first: Zhi

last: Chai

address: 1425 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Raw RNA-seq reads were aligned against the mm10 reference genome using STAR (version 2.4.0g1)
and gene- and exon-level read summarizations were performed with the featureCounts program in subRead
Ensembl annotations were used for both the alignment and the read summarization.
For the exon-level read summarization, a collapsed version of the annotations file where gene designs are described based on non-overlapping “counting- bins” was used to avoid over- or under-counting of reads.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include Raw Count values for each gene in each sample

source_name: Blood

extract_protocol:
The colons from 15 mice per group at each time point were collected for RNA analysis. 1 cm distal adjacent to rectum was used for histology and the remaining tissue was used for RNA. The remaining colon tissues were frozen in RNAlater at -80C for RNA extraction. Blood was collected by cardiac puncture from mice from every group at termination. Approximately 250ul of whole blood was collected into PAXgene tubes. Whole blood was assessed for RNA.  Colons from all groups were measured for length and weight. RNA was isolated with Qiagen RNeasy kits according to manufacturer’s instructions.
RNA TruSeq Kit by Illumina

value: wildtype

tag: model

value: DSS

value: Blood

tag: bio region

value: B

tag: ctrl disease

value: C

tag: day

tag: hit rest

value: control


title: ChIP_ESC_Ola_IgG_Rb_IFNb_1h_Rep1

tag: treatment

tag: chip antibody


title: JH13_HMEC_lane 1

description: lane 1

tag: tissue origin

value: Adult


title: JH12_NHEM-Ad_lane 8

description: lane 8

source_name: Melanocyte

value: Melanocytes

value: Skin


title: ChIP_ESC_Ola_IgG_Rb_IFNb_0h_Rep1

tag: strain


title: ChIP_ESC_Ola_IgG_Rb_IFNb_0h_Rep2


title: VertX.TCCR.in vitro.D8.rep1.H3K4me1

description: VertX.TCCR.in vitro.D8.rep1.H3K4me1

value: H3K4me1 (Diagenode, Cat# C15410037)


title: VertX.in vitro.D8.rep1.H3K4me1

description: VertX.in vitro.D8.rep1.H3K4me1

value: VertX


title: ChIP_ESC_Ola_H3K9me3_IFNb_6h_Rep3


title: JH12_NHEM-Ad_lane 7

description: lane 7


title: ChIP_ESC_Ola_H3K9me3_IFNb_6h_Rep2


title: VertX.TCCR.naive.rep1.H3K4me1

value: post natal day 56


title: ChIP_ESC_Ola_H3K9me3_IFNb_1h_Rep3


title: ChIP_ESC_Ola_H3K9me3_IFNb_6h_Rep1


title: JH12_NHEM-Ad_lane 6

description: lane 6


title: ChIP_ESC_Ola_H3K9me3_IFNb_1h_Rep2


title: ChIP_ESC_Ola_H3K9me3_IFNb_1h_Rep1


title: VertX.naive.rep1.H3K4me1


title: JH12_NHEM-Ad_lane 5

description: lane 5


title: ChIP_ESC_Ola_H3K9me3_IFNb_0h_Rep3


title: ChIP_ESC_Ola_H3K9me3_IFNb_0h_Rep2


title: JH12_NHEM-Ad_lane 4

description: lane 4


title: VertX.in vitro.D8.rep1.H3K27Ac

description: VertX.in vitro.D8.rep1.H3K27Ac

value: H3K27Ac (Kimura et al, 2008)


title: ChIP_ESC_Ola_H3K9me3_IFNb_0h_Rep1


title: JH12_NHEM-Ad_lane 3

description: lane 3


title: VertX.TCCR.rep1.H3K27Ac


title: ChIP_ESC_Ola_H3K9ac_IFNb_6h_Rep3


title: JH12_NHEM-Ad_lane 2

description: lane 2


title: ChIP_ESC_Ola_H3K9ac_IFNb_6h_Rep1


title: ChIP_ESC_Ola_H3K9ac_IFNb_1h_Rep2


title: VertX.TCCR.in vitro.D8.rep1.H3K27me3

description: VertX.TCCR.in vitro.D8.rep1.H3K27me3

value: post natal day 60

value: H3K27me3 (Diagenode, Cat# pAb-069-050)


title: VertX.naive.rep1.H3K27Ac

value: IL-10 GFP reporter


title: JH11_NHEK-Neo_lane 8

description: lane 8

source_name: Epidermal Keratinocytes Neonatal

value: Keratinocytes

value: Neonatal


title: ChIP_ESC_Ola_H3K9ac_IFNb_1h_Rep1

value: Embryonic stem cells


title: VertX.in vitro.D8.rep1.H3K27me3

description: VertX.in vitro.D8.rep1.H3K27me3

value: post natal day 57


title: ChIP_ESC_Ola_H3K9ac_IFNb_0h_Rep2


title: ChIP_ESC_Ola_H3K4me3_IFNb_6h_Rep2


title: VertX.TCCR.in vitro.D8.rep1.H3K4me3

description: VertX.TCCR.in vitro.D8.rep1.H3K4me3

value: VertX IL-27Ra-/-

value: H3K4me3 (Cell Signaling Technology, Cat# 9751S)

value: IL-10 GFP reporter/IL-27Ra-/-


title: JH11_NHEK-Neo_lane 7

description: lane 7


title: ChIP_ESC_Ola_H3K4me3_IFNb_6h_Rep1


title: ChIP_ESC_Ola_H3K4me3_IFNb_1h_Rep2


title: JH11_NHEK-Neo_lane 6

description: lane 6


title: VertX.in vitro.D8.rep1.H3K4me3

description: VertX.in vitro.D8.rep1.H3K4me3


title: ChIP_ESC_Ola_H3K9ac_IFNb_0h_Rep1


title: ChIP_ESC_Ola_H3K9ac_IFNb_6h_Rep2


title: JH11_NHEK-Neo_lane 5

description: lane 5


title: VertX.TCCR.naive.rep1.H3K27Ac


title: VertX.TCCR.naive.rep1.H3K27me3


title: ChIP_ESC_Ola_H3K4me3_IFNb_0h_Rep1


title: ChIP_ESC_Ola_H3K4me3_IFNb_0h_Rep2


title: ChIP_ESC_Ola_H3K9ac_IFNb_1h_Rep3


title: ChIP_ESC_Ola_H3K4me3_IFNb_1h_Rep1


title: JH11_NHEK-Neo_lane 4

description: lane 4


title: VertX.naive.rep1.H3K27me3


title: JH12_NHEM-Ad_lane 1

description: lane 1

value: Adult


title: ChIP_ESC_Ola_H3K4me1_IFNb_6h_Rep1


title: ChIP_ESC_Ola_H3K9ac_IFNb_0h_Rep3


title: ChIP_ESC_Ola_H3K4me1_IFNb_1h_Rep2


title: JH11_NHEK-Neo_lane 2

description: lane 2


title: VertX.TCCR.naive.rep1.H3K4me3


title: ChIP_ESC_Ola_H3K4me1_IFNb_0h_Rep2


title: ChIP_ESC_Ola_H3K4me1_IFNb_1h_Rep1


title: ChIP_ESC_Ola_H3K4me1_IFNb_0h_Rep1


title: VertX.naive.rep1.H3K4me3


title: JH10_NHEK-Ad_lane 8

description: lane 8

source_name: Epidermal Keratinocytes Adult


title: ChIP_ESC_Ola_H3K27me3_IFNb_1h_Rep3


title: ChIP_ESC_Ola_H3K27me3_IFNb_6h_Rep2