title: A37S

city: Chengdu

first: Qian

last: Bu

address: No.24 South Section 1, Yihuan Road

department: Department of food and Technology

institute: Sichuan University

data_processing:
Paired-end reads were harvested from Illumina HiSeq 4000 sequencer, and were quality controlled by Q30.
After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3), the high quality clean reads were aligned to the reference genome (UCSC hg19) with hisat2 software (v2.0.4).
Then, guided by the Ensembl gtf gene annotation file, cuffdiff software (part of cufflinks) was used to get the gene level FPKM as the expression profiles of mRNA, and fold change and p-value were calculated based on FPKM, differentially expressed mRNA were identified.
GO and Pathway enrichment analysis were performed based on the differentially expressed mRNAs.
Genome_build: hg19

source_name: Brain tissue

extract_protocol:
Total RNA (1 μg) was used for removing the rRNAs using Ribo-Zero rRNA Removal Kits (Illumina, San Diego, CA, USA) following the manufacturer's instructions.
RNA libraries were constructed by using rRNA-depleted RNAs with TruSeq Stranded Total RNA Library Prep Kit (Illumina, San Diego, CA,  USA) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using  the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA).

value: Solid hemangioblastoma


title: A43N

status: Public on Apr 15 2020

type: SRA

country: China

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: tissue

value: Cystic hemangioblastoma


title: A35N


title: 1001200626_A4, pancreatic cells for patch-seq

city: Gothenburg

first: Joan

last: Camunas-Soler

address: Medicinaregatan 9C

country: Sweden

institute: University of Gothenburg

data_processing:
Mapped to Gch38 using STAR
Gene counts using htseq-count
Genome_build: GRCh38

source_name: pancreatic islets

extract_protocol: SmartSeq2 (21X-23X PCR cycles)

tag: cryopreserved

value: Yes

tag: diabetes

tag: Sex

value: M

tag: patched


title: A39S


title: BSC13rapa rep2

city: Rochester

first: Hu

last: Li

state: MN

address: 200 First Street, Gonda Building G19-408

department: Molecular Pharmacology & Experimental Therapeutics

country: USA

institute: Mayo Clinic

data_processing:
Fastq files of pair-end RNA-Seq reads were aligned with STAR 2.6.0a  to the reference genome GRCh38 using default parameters.
Gene level counts were obtained using htseq-count 0.5.3p9.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimted text file of gene-level raw counts

source_name: airway basal stem cells

growth_protocol: Tracheal aspirates collected from intubated infants were stored at 4 °C for no more than 24 hours prior to being cultured on plates pre-coated with laminin-enriched 804G-conditioned medium in Small Airway Epithelial Cell Growth Medium (PromoCell) with A-8301 (1mM) and Y27632 (5mM). Epithelial cell colonies were passaged when they became apparent.

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina TruSeq v2 protocols

treatment_protocol: cells were cultured with or without rapamycin (5nM)

tag: cell type

value: neonatal tracheal aspirate derived epithelial basal cell line

tag: developmental stage

value: term infant

tag: agent

value: rapamycin


title: A41S


title: 1001200626_A2, pancreatic cells for patch-seq


title: BSC13rapa rep1


title: 1001200626_A11, pancreatic cells for patch-seq


title: 1001200626_B10, pancreatic cells for patch-seq


title: 1001200626_B11, pancreatic cells for patch-seq


title: BSC13 rep2


title: 1001200626_A1, pancreatic cells for patch-seq


title: BSC11rapa rep2


title: 1001200626_A3, pancreatic cells for patch-seq


title: 1001200625_H8, pancreatic cells for patch-seq


title: 1001200625_H9, pancreatic cells for patch-seq


title: BSC11 rep1


title: BSC11rapa rep1


title: 1001200625_H7, pancreatic cells for patch-seq


title: 1001200625_H6, pancreatic cells for patch-seq

value: not applicable


title: BSC11 rep2


title: B16_TIL3_2

city: San diego

first: Ananda

last: Goldrath

state: CA

address: 9500 Gilman Dr

department: Molecular Biology

institute: UCSD

description: 3' Transcriptome sequencing (10X genomics V2)

data_processing:
data were processed by cellranger 2.1.0 with default parameter, using mm10 as reference.
Raw cell-reads were then loaded to R using the cellrangerRkit package. The scRNA-seq dataset was then further filtered based on gene numbers and mitochondria gene counts tototal counts ratio. Only cells with > 400 genes,UMI > 0,and 0.5% ~ 20% of their UMIs mappingto mitochondria genes were kept for downstream analysis.
For the scRNA-seq, the first 16 bp of R1 is the cell barcode and the next 10bp (17-26bp) is the UMI.
Genome_build: mm10
Supplementary_files_format_and_content: CellRanger output of filtered gene matrix with barcodes & features files

organism: Mus musculus

source_name: B16 Tumor CD8+ T cell

growth_protocol: No growth procedure was required.

extract_protocol:
For isolation of CD8+ T cells from spleen, spleens were collected and dissociated to yield a cell suspension prior to lysis of red blood cells. For isolation of CD8+ T cells from the tumors, tumors were digested with Collagenase I for 30 minutes then Percolled at 44%/67% gradient at 2000 rpm for 20 min (acceleration 4, brake 0)
Single cell libraries were prepared according to the protocol for 10X Genomics for 3’ Gene Expression. Approximately 10,000 sorted CD45.1+ Va2+ CD8+ CD44+ cells were loaded and partitioned into Gel Bead In-Emulsions (GEM). scRNA libraries were sequenced on a HiSeq4000 (Illumina).

treatment_protocol: These details are included in extraction protocol.

tag: time point

value: Cells sorted out at D15

value: tumor

tag: cell subtype surface markers

tag: cell subtype

value: CD8 T cells


title: B16_TIL3_1


title: 1001200625_H5, pancreatic cells for patch-seq


title: 1001200625_H2, pancreatic cells for patch-seq

value: No


title: 1001200625_H3, pancreatic cells for patch-seq


title: K_9483: Mettl5 KO rep 2

city: Neuherberg

first: Valentina

last: Ignatova

state: Select...

address: Institue of Functional Epigenetics, Ingolstädter Landstr. 1

department: IFE

country: Germany

institute: HMGU

data_processing:
fastq files were sorted against SortMerRNA to remove rRNA, after samples splited into several lines were merged and mapped to mm10 transcriptome using Kallisto
Gene-level analysis of changes in KO cells in comparision to wt were performed with Sleuth
Genome_build: mm10
Supplementary_files_format_and_content: csv  abundance measurements generated by Kallisto

molecule: polyA RNA

source_name: Embryonic stem cells

growth_protocol: mESC were grow in Serum Lif for 7 days before experiment

extract_protocol:
mESC were lysed in Trizol, total RNA were isolated by Trizol extraction followed by comunt purification, two tounds of polyA selection were performed with oligo dT beads follow by RNA fragmentation to 100 nt with NEB RNA fragmentation solution. Illumina TruSeq Stranded mRNA protocol was used with 0.1 ug RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using Illumina HiSeq 4000

tag: strain

value: mESC

tag: genotype

value: Mettl5 -/-


title: K_9484: Mettl5 KO rep 3


title: 1001200625_H4, pancreatic cells for patch-seq


title: 1001200626_A12, pancreatic cells for patch-seq


title: B16_Spleen3_1

source_name: Spleen CD8+ T cell

value: spleen


title: B16_Spleen3_2


title: 1001200625_H12, pancreatic cells for patch-seq


title: BSC13 rep1


title: 1001200625_H10, pancreatic cells for patch-seq


title: K_9482: Mettl5 KO rep 1


title: 1001200625_H11, pancreatic cells for patch-seq


title: 1001200625_H1, pancreatic cells for patch-seq


title: 1001200625_G9, pancreatic cells for patch-seq


title: K_9477: wt rep 1

value: wt


title: DC2 KO sample 1

city: New York

first: Gregory

last: Putzel

state: NY

address: 430 East 29th Street

department: Microbiology

institute: NYU Langone Health

data_processing:
Base calling and demultiplexing with Illumina Casava 1.8.2
Adapter trimming using FLEXBAR (v2.4)
Alignment to mm10 reference genome using STAR version 2.3.0 with default settings
Reads per gene counted using Rsubread R package
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text giving raw number of counts mapped to each gene (identified by Entrez ID) in each sample

source_name: Sorted DCs from colon lamina propria

extract_protocol:
Sorted cells were used to prepare RNAseq libraries using the Clontech SMARTer Ultra Low Input RNA Kit V4 (Clontech Laboratories).
Standard Illumina protocols


title: 1001200625_G7, pancreatic cells for patch-seq


title: DC2 KO sample 2


title: 1001200625_G8, pancreatic cells for patch-seq


title: 1001200625_G6, pancreatic cells for patch-seq


title: 1001200625_G3, pancreatic cells for patch-seq


title: DC2 F/F sample 1

value: Hamp-floxed


title: 1001200625_G2, pancreatic cells for patch-seq


title: DC2 F/F sample 3


title: DC1 KO sample 3


title: 1001200626_A10, pancreatic cells for patch-seq


title: 1001200625_G12, pancreatic cells for patch-seq


title: K_9478: wt rep 2


title: K_9480: wt rep 3


title: 1001200625_G10, pancreatic cells for patch-seq


title: DC1 KO sample 1


title: 1001200626_C6, pancreatic cells for patch-seq


title: 1001200625_G1, pancreatic cells for patch-seq


title: DC1 F/F sample 2


title: DC2 F/F sample 4


title: DC1 F/F sample 3


title: DC2 F/F sample 5


title: DC1 F/F sample 1


title: 1001200625_G5, pancreatic cells for patch-seq


title: DC2 F/F sample 2


title: 1001200625_F7, pancreatic cells for patch-seq


title: 1001200625_F6, pancreatic cells for patch-seq


title: G2-GP2

city: Stanford

first: Natalina

last: Quarto

address: 257 Campus Drive

department: Surgery - Plastic and Reconstructive Surgery

institute: Stanford University School of Medicine

description: GP SSCs from Plate 2

data_processing:
RNA-Seq alignment to the reference was performed using STAR v2.5.3a using default conditions as described in Dobin et al., Bioinformatics, 2013.
Gene counts were tabulated from STAR v2.5.3a by mapping against mouse mm9 reference and used as input to Seurat. The counts coincide with those produced by htseq-count with default parameters.
The R package Seurat v2.3.0 was used for QC, analysis, and exploration of single-cell RNA-Seq data using R v3.4.4.
Genes expressed in at least 3 cells and cells with at least 200 expressed genes were retained for further analysis. Gene expression measurements for each cell were normalized by their total expression, scaled by 10,000, and log-transformed. Following normalization, genes that varied between single cells were identified.
PCA was performed on genes to output a set of genes that most strongly defined a set of principal components. Seurat’s graph-based clustering approach was used to cluster the cells. Seurat was further used to perform tSNE clustering which placed cells with similar local neighborhoods in high-dimensional space together in low-dimensional space. Positive and negative markers in each cluster were identified by comparing genes in cells of one cluster against genes in all other cells. Only genes that were detected in at least 25% of cells in either of the two populations were tested. Violin plots were used to visualize expression of top markers in each cluster. Finally, a heatmap of the top 20 marker genes across all cells in the 4 clusters was plotted.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include gene count values for each Sample.

source_name: Tibial Longbone Growth Plate

extract_protocol:
Total single cell RNA profiles of SSCs isolated post-natal day 3 posterior frontal (PF), sagittal (SAG), coronal (COR) sutures and the growth plate (GP) of the tibial long bone from CD-1, wild-type mice were purified using Qiagen MiRNeasy Kit (Cat #217084) following the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina single cell RNA seq protocols.

value: Bone

tag: age

value: post natal day 3

value: wild type

value: Skeletal Stem Cell


title: G4-GP2

description: GP SSCs from Plate 2


title: F9-GP2

description: GP SSCs from Plate 2


title: 1001200625_G4, pancreatic cells for patch-seq

value: Yes

value: M


title: DC1 KO sample 2


title: 1001200625_F4, pancreatic cells for patch-seq


title: 1001200625_F12, pancreatic cells for patch-seq


title: 1001200625_F5, pancreatic cells for patch-seq


title: 1001200625_F11, pancreatic cells for patch-seq


title: F8-GP2

description: GP SSCs from Plate 2


title: 1001200625_G11, pancreatic cells for patch-seq


title: 1001200625_F9, pancreatic cells for patch-seq


title: F6-GP2

description: GP SSCs from Plate 2


title: F10-GP2

description: GP SSCs from Plate 2


title: 1001200625_F2, pancreatic cells for patch-seq


title: F4-GP2

description: GP SSCs from Plate 2


title: F3-GP2

description: GP SSCs from Plate 2


title: F5-GP2

description: GP SSCs from Plate 2


title: F11-GP2

description: GP SSCs from Plate 2


title: 1001200625_F10, pancreatic cells for patch-seq


title: 1001200625_E7, pancreatic cells for patch-seq


title: 1001200625_E5, pancreatic cells for patch-seq


title: E2-GP2

description: GP SSCs from Plate 2


title: E3-GP2

description: GP SSCs from Plate 2


title: 1001200625_F1, pancreatic cells for patch-seq


title: 1001200625_E9, pancreatic cells for patch-seq


title: E12-GP2

description: GP SSCs from Plate 2


title: E9-GP2

description: GP SSCs from Plate 2


title: 1001200625_E8, pancreatic cells for patch-seq


title: 1001200625_E2, pancreatic cells for patch-seq


title: 1001200625_F8, pancreatic cells for patch-seq


title: E8-GP2

description: GP SSCs from Plate 2


title: E1-GP2

description: GP SSCs from Plate 2


title: D8-GP2

description: GP SSCs from Plate 2


title: D7-GP2

description: GP SSCs from Plate 2


title: 1001200625_E4, pancreatic cells for patch-seq


title: 1001200625_E11, pancreatic cells for patch-seq


title: 1001200625_F3, pancreatic cells for patch-seq


title: 1001200625_E6, pancreatic cells for patch-seq


title: 1001200625_E1, pancreatic cells for patch-seq


title: F1-GP2

description: GP SSCs from Plate 2


title: 1001200625_E3, pancreatic cells for patch-seq


title: 1001200625_E12, pancreatic cells for patch-seq


title: D4-GP2

description: GP SSCs from Plate 2


title: D9-GP2

description: GP SSCs from Plate 2


title: D3-GP2

description: GP SSCs from Plate 2


title: 1001200625_E10, pancreatic cells for patch-seq


title: D6-GP2

description: GP SSCs from Plate 2


title: 1001200625_D9, pancreatic cells for patch-seq


title: 1001200625_D6, pancreatic cells for patch-seq


title: E4-GP2

description: GP SSCs from Plate 2


title: 1001200625_D7, pancreatic cells for patch-seq


title: D5-GP2

description: GP SSCs from Plate 2


title: D2-GP2

description: GP SSCs from Plate 2


title: 1001200625_D8, pancreatic cells for patch-seq


title: 1001200625_D5, pancreatic cells for patch-seq


title: D11-GP2

description: GP SSCs from Plate 2


title: D1-GP2

description: GP SSCs from Plate 2


title: 1001200625_D2, pancreatic cells for patch-seq


title: C9-GP2

description: GP SSCs from Plate 2


title: 1001200625_D10, pancreatic cells for patch-seq


title: D12-GP2

description: GP SSCs from Plate 2


title: 1001200625_D1, pancreatic cells for patch-seq


title: D10-GP2

description: GP SSCs from Plate 2


title: C8-GP2

description: GP SSCs from Plate 2


title: C6-GP2

description: GP SSCs from Plate 2


title: 1001200625_D3, pancreatic cells for patch-seq


title: 1001200625_D4, pancreatic cells for patch-seq


title: 1001200625_D11, pancreatic cells for patch-seq


title: C7-GP2

description: GP SSCs from Plate 2


title: 1001200625_D12, pancreatic cells for patch-seq


title: 1001200625_C8, pancreatic cells for patch-seq


title: C2-GP2

description: GP SSCs from Plate 2


title: E11-GP2

description: GP SSCs from Plate 2


title: C10-GP2

description: GP SSCs from Plate 2


title: C3-GP2

description: GP SSCs from Plate 2


title: C5-GP2

description: GP SSCs from Plate 2


title: 1001200625_C7, pancreatic cells for patch-seq


title: 1001200625_C6, pancreatic cells for patch-seq


title: C1-GP2

description: GP SSCs from Plate 2


title: B9-GP2

description: GP SSCs from Plate 2


title: C11-GP2

description: GP SSCs from Plate 2


title: 1001200625_C2, pancreatic cells for patch-seq


title: C12-GP2

description: GP SSCs from Plate 2


title: 1001200625_C3, pancreatic cells for patch-seq


title: 1001200625_C5, pancreatic cells for patch-seq


title: B8-GP2

description: GP SSCs from Plate 2


title: C4-GP2

description: GP SSCs from Plate 2


title: 1001200625_B9, pancreatic cells for patch-seq


title: B7-GP2

description: GP SSCs from Plate 2


title: 1001200625_C9, pancreatic cells for patch-seq


title: B6-GP2

description: GP SSCs from Plate 2


title: 1001200625_C1, pancreatic cells for patch-seq


title: B5-GP2

description: GP SSCs from Plate 2


title: 1001200625_C10, pancreatic cells for patch-seq


title: B4-GP2

description: GP SSCs from Plate 2


title: B3-GP2

description: GP SSCs from Plate 2


title: 1001200625_B8, pancreatic cells for patch-seq


title: 1001200625_C4, pancreatic cells for patch-seq


title: 1001200625_B7, pancreatic cells for patch-seq


title: 1001200625_B6, pancreatic cells for patch-seq


title: B2-GP2

description: GP SSCs from Plate 2


title: 1001200625_C12, pancreatic cells for patch-seq


title: B11-GP2

description: GP SSCs from Plate 2


title: 1001200625_B4, pancreatic cells for patch-seq


title: B1-GP2

description: GP SSCs from Plate 2


title: 1001200625_C11, pancreatic cells for patch-seq


title: A9-GP2

description: GP SSCs from Plate 2


title: 1001200625_B2, pancreatic cells for patch-seq


title: A8-GP2

description: GP SSCs from Plate 2


title: 1001200625_B12, pancreatic cells for patch-seq


title: 1001200625_B11, pancreatic cells for patch-seq


title: A6-GP2

description: GP SSCs from Plate 2


title: A7-GP2

description: GP SSCs from Plate 2


title: 1001200625_B10, pancreatic cells for patch-seq


title: 1001200625_A9, pancreatic cells for patch-seq


title: 1001200625_A8, pancreatic cells for patch-seq


title: 1001200625_B1, pancreatic cells for patch-seq


title: 1001200625_A7, pancreatic cells for patch-seq


title: A3-GP2

description: GP SSCs from Plate 2


title: A5-GP2

description: GP SSCs from Plate 2


title: A12-GP2

description: GP SSCs from Plate 2


title: A11-GP2

description: GP SSCs from Plate 2


title: A4-GP2

description: GP SSCs from Plate 2


title: 1001200625_A6, pancreatic cells for patch-seq


title: 1001200625_A5, pancreatic cells for patch-seq


title: 1001200625_B5, pancreatic cells for patch-seq


title: 1001200625_B3, pancreatic cells for patch-seq


title: A10-GP2

description: GP SSCs from Plate 2


title: 1001200625_A3, pancreatic cells for patch-seq


title: E1-GP1

description: GP SSCs from Plate 1


title: 1001200625_A11, pancreatic cells for patch-seq


title: D7-GP1

description: GP SSCs from Plate 1


title: C8-GP1

description: GP SSCs from Plate 1


title: 1001200625_A12, pancreatic cells for patch-seq


title: 1001200625_A1, pancreatic cells for patch-seq


title: C12-GP1

description: GP SSCs from Plate 1


title: C5-GP1

description: GP SSCs from Plate 1


title: A2-GP2

description: GP SSCs from Plate 2


title: B9-GP1

description: GP SSCs from Plate 1


title: 1001200624_H8, pancreatic cells for patch-seq


title: 1001200625_A4, pancreatic cells for patch-seq


title: B6-GP1

description: GP SSCs from Plate 1


title: 1001200624_H7, pancreatic cells for patch-seq


title: 1001200624_H6, pancreatic cells for patch-seq


title: B12-GP1

description: GP SSCs from Plate 1


title: B2-GP1

description: GP SSCs from Plate 1


title: B4-GP1

description: GP SSCs from Plate 1


title: A1-GP2

description: GP SSCs from Plate 2


title: B11-GP1

description: GP SSCs from Plate 1


title: 1001200624_H2, pancreatic cells for patch-seq


title: 1001200624_H5, pancreatic cells for patch-seq


title: D5-GP1

description: GP SSCs from Plate 1


title: 1001200624_H4, pancreatic cells for patch-seq


title: 1001200625_A10, pancreatic cells for patch-seq


title: 1001200624_H3, pancreatic cells for patch-seq


title: 1001200625_A2, pancreatic cells for patch-seq


title: 1001200624_H12, pancreatic cells for patch-seq


title: A9-GP1

description: GP SSCs from Plate 1


title: 1001200624_H11, pancreatic cells for patch-seq


title: A5-GP1

description: GP SSCs from Plate 1


title: 1001200624_H9, pancreatic cells for patch-seq


title: A8-GP1

description: GP SSCs from Plate 1


title: A3-GP1

description: GP SSCs from Plate 1


title: 1001200624_H1, pancreatic cells for patch-seq


title: A2-GP1

description: GP SSCs from Plate 1


title: 1001200624_H10, pancreatic cells for patch-seq


title: A12-GP1

description: GP SSCs from Plate 1


title: 1001200624_G9, pancreatic cells for patch-seq


title: 1001200624_G8, pancreatic cells for patch-seq


title: A11-GP1

description: GP SSCs from Plate 1


title: A1-GP1

description: GP SSCs from Plate 1


title: H9-COR2

description: COR SSCs from Plate 2

source_name: Cranial Coronal Suture

value: Suture complex:bone/mesenchyme


title: 1001200624_G7, pancreatic cells for patch-seq


title: H8-COR2

description: COR SSCs from Plate 2


title: 1001200624_G6, pancreatic cells for patch-seq


title: 1001200624_G5, pancreatic cells for patch-seq


title: 1001200624_G4, pancreatic cells for patch-seq


title: 1001200624_G3, pancreatic cells for patch-seq


title: 1001200624_G2, pancreatic cells for patch-seq


title: 1001200624_G11, pancreatic cells for patch-seq


title: 1001200624_F9, pancreatic cells for patch-seq


title: 1001200624_G10, pancreatic cells for patch-seq


title: 1001200624_G1, pancreatic cells for patch-seq


title: 1001200624_G12, pancreatic cells for patch-seq


title: H10-COR2

description: COR SSCs from Plate 2


title: H4-COR2

description: COR SSCs from Plate 2


title: H5-COR2

description: COR SSCs from Plate 2


title: G5-COR2

description: COR SSCs from Plate 2


title: G8-COR2

description: COR SSCs from Plate 2


title: G11-COR2

description: COR SSCs from Plate 2


title: F9-COR2

description: COR SSCs from Plate 2


title: G12-COR2

description: COR SSCs from Plate 2


title: G10-COR2

description: COR SSCs from Plate 2


title: 1001200624_F7, pancreatic cells for patch-seq


title: 1001200624_F8, pancreatic cells for patch-seq


title: 1001200624_F6, pancreatic cells for patch-seq


title: F5-COR2

description: COR SSCs from Plate 2


title: 1001200624_F5, pancreatic cells for patch-seq


title: F3-COR2

description: COR SSCs from Plate 2


title: 1001200624_F4, pancreatic cells for patch-seq


title: F2-COR2

description: COR SSCs from Plate 2


title: H3-COR2

description: COR SSCs from Plate 2


title: F12-COR2

description: COR SSCs from Plate 2


title: F11-COR2

description: COR SSCs from Plate 2


title: F1-COR2

description: COR SSCs from Plate 2


title: 1001200624_F12, pancreatic cells for patch-seq


title: 1001200624_F2, pancreatic cells for patch-seq


title: 1001200624_F11, pancreatic cells for patch-seq


title: E9-COR2

description: COR SSCs from Plate 2


title: E8-COR2

description: COR SSCs from Plate 2


title: 1001200624_E9, pancreatic cells for patch-seq


title: F6-COR2

description: COR SSCs from Plate 2


title: E6-COR2

description: COR SSCs from Plate 2


title: 1001200624_E5, pancreatic cells for patch-seq


title: E7-COR2

description: COR SSCs from Plate 2


title: E5-COR2

description: COR SSCs from Plate 2


title: 1001200624_E6, pancreatic cells for patch-seq


title: 1001200624_E7, pancreatic cells for patch-seq


title: E4-COR2

description: COR SSCs from Plate 2


title: 1001200624_F1, pancreatic cells for patch-seq


title: E12-COR2

description: COR SSCs from Plate 2


title: 1001200624_F10, pancreatic cells for patch-seq


title: 1001200624_E8, pancreatic cells for patch-seq


title: 1001200624_E3, pancreatic cells for patch-seq


title: E3-COR2

description: COR SSCs from Plate 2


title: E11-COR2

description: COR SSCs from Plate 2


title: E1-COR2

description: COR SSCs from Plate 2


title: 1001200624_F3, pancreatic cells for patch-seq


title: 1001200624_E2, pancreatic cells for patch-seq


title: 1001200624_E12, pancreatic cells for patch-seq


title: 1001200624_E4, pancreatic cells for patch-seq


title: 1001200624_E11, pancreatic cells for patch-seq


title: D8-COR2

description: COR SSCs from Plate 2


title: 1001200624_E10, pancreatic cells for patch-seq


title: D7-COR2

description: COR SSCs from Plate 2


title: D6-COR2

description: COR SSCs from Plate 2


title: 1001200624_E1, pancreatic cells for patch-seq


title: D5-COR2

description: COR SSCs from Plate 2


title: 1001200624_D9, pancreatic cells for patch-seq


title: 1001200624_D8, pancreatic cells for patch-seq


title: D3-COR2

description: COR SSCs from Plate 2


title: 1001200624_D6, pancreatic cells for patch-seq


title: D4-COR2

description: COR SSCs from Plate 2


title: D1-COR2

description: COR SSCs from Plate 2


title: C8-COR2

description: COR SSCs from Plate 2


title: 1001200624_D2, pancreatic cells for patch-seq


title: C7-COR2

description: COR SSCs from Plate 2


title: C9-COR2

description: COR SSCs from Plate 2


title: D12-COR2

description: COR SSCs from Plate 2


title: 1001200624_D7, pancreatic cells for patch-seq


title: C6-COR2

description: COR SSCs from Plate 2


title: C5-COR2

description: COR SSCs from Plate 2


title: 1001200624_D4, pancreatic cells for patch-seq


title: 1001200624_D11, pancreatic cells for patch-seq


title: 1001200624_D5, pancreatic cells for patch-seq


title: 1001200624_D10, pancreatic cells for patch-seq


title: 1001200624_D3, pancreatic cells for patch-seq


title: 1001200624_D12, pancreatic cells for patch-seq


title: D9-COR2

description: COR SSCs from Plate 2


title: 1001200624_D1, pancreatic cells for patch-seq


title: C2-COR2

description: COR SSCs from Plate 2


title: C12-COR2

description: COR SSCs from Plate 2


title: C11-COR2

description: COR SSCs from Plate 2


title: 1001200624_C9, pancreatic cells for patch-seq


title: C1-COR2

description: COR SSCs from Plate 2


title: 1001200624_C7, pancreatic cells for patch-seq


title: B9-COR2

description: COR SSCs from Plate 2


title: 1001200624_C6, pancreatic cells for patch-seq


title: 1001200624_C5, pancreatic cells for patch-seq


title: B8-COR2

description: COR SSCs from Plate 2


title: B7-COR2

description: COR SSCs from Plate 2


title: C3-COR2

description: COR SSCs from Plate 2


title: B3-COR2

description: COR SSCs from Plate 2


title: 1001200624_C3, pancreatic cells for patch-seq


title: 1001200624_C11, pancreatic cells for patch-seq


title: B10-COR2

description: COR SSCs from Plate 2


title: 1001200624_C10, pancreatic cells for patch-seq


title: B12-COR2

description: COR SSCs from Plate 2


title: 1001200624_C2, pancreatic cells for patch-seq


title: 1001200624_C1, pancreatic cells for patch-seq


title: 1001200624_B8, pancreatic cells for patch-seq


title: 1001200624_B9, pancreatic cells for patch-seq


title: 1001200624_C8, pancreatic cells for patch-seq


title: hr288.FGF10

city: Baltimore

first: Carlo

last: Colantuoni

state: MD

address: 733 N Broadway

department: Neurology

institute: Johns Hopkins Univ. School of Medicine

data_processing:
After sequencing run the Illumina Real Time Analysis (RTA) module was used to perform image analysis, base calling, and the BCL Converter (bcl2fastq v2.17.1.14) were followed to generate FASTQ files which contain the sequence reads.
Read-level Q/C was performed by FastQC (v0.11.5). Pair-end reads of cDNA sequences are aligned back to the human genome (UCSC hg19 from Illumina iGenome) by the spliced read mapper TopHat (v2.0.9) with default option with “--mate-innder-dist 160” and “--library-type fr-firststrand” parameters based on known transcripts of Ensembl Build GRCh37.75.
To achieve gene-level expression profile, the properly paired and mapped reads are achieved by “samtools sort –n” option, and these reads are counted by htseq-count v0.9.1 (with intersection-strict mode and stranded option) according to gene annotation (Ensembl Build GRCh37.75) and RPKM is calculated.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each sample

source_name: primary mouse neural stem cell

growth_protocol: Embryonic day (E)11.5 embryos were isolated from pregnant C57BL/6 mice (Charles River) and dorsal telencephalic cortex was collected. 1 x 106 cells were plated and expanded in 10 ng/ml FGF2.  NSCs were lifted and frozen.

extract_protocol:
RNeasy Mini Kit (Qiagen, Ct# 74106)
RNAseq libraries were constructed using Illumina TruSeq Stranded Total RNA RiboZero Gold sample Prep Kit (RS-122-2303) following the manufacturer’s protocol. The concentration of RNA was measured by Qubit (Life Technologies). Quality of RNAseq library was measured by LabChipGX (Caliper) using HT DNA 1K/12K/HiSens Labchip. The final cDNA libraries were sequenced using HiSeq 3000 for high-throughput DNA sequencing.

treatment_protocol: Thawed NSCs were expanded for 4 days in 10 ng/ml and passaged into varying concentration of FGF2 without astrocytes. Differentiation of mouse NSCs was induced 2 days after plating, by FGF2 withdrawal. At DIV 4, N2 was replaced with NeuroBasal medium and neurotrophins.

tag: hours

tag: fgf


title: hr288.FGF100


title: A7-COR2

description: COR SSCs from Plate 2


title: hr288.FGF1


title: A6-COR2

description: COR SSCs from Plate 2


title: A5-COR2

description: COR SSCs from Plate 2


title: A9-COR2

description: COR SSCs from Plate 2


title: A4-COR2

description: COR SSCs from Plate 2


title: A3-COR2

description: COR SSCs from Plate 2


title: 1001200624_C4, pancreatic cells for patch-seq


title: 1001200624_B6, pancreatic cells for patch-seq


title: 1001200624_B5, pancreatic cells for patch-seq


title: B2-COR2

description: COR SSCs from Plate 2


title: A12-COR2

description: COR SSCs from Plate 2


title: hr216.FGF10


title: hr216.FGF0.1


title: hr144.FGF100


title: 1001200624_B3, pancreatic cells for patch-seq


title: A11-COR2

description: COR SSCs from Plate 2


title: 1001200624_B7, pancreatic cells for patch-seq


title: hr144.FGF1


title: D5-COR1

description: COR SSCs from Plate 1


title: hr144.FGF0.1


title: 1001200624_B2, pancreatic cells for patch-seq


title: hr144.FGF10


title: D11-COR1

description: COR SSCs from Plate 1


title: D12-COR1

description: COR SSCs from Plate 1


title: 1001200624_B12, pancreatic cells for patch-seq


title: hr108.FGF100


title: hr108.FGF1


title: A2-COR2

description: COR SSCs from Plate 2


title: hr288.FGF0.1


title: hr108.FGF0.1


title: hr108.FGF10


title: hr216.FGF1


title: hr102.FGF100


title: C9-COR1

description: COR SSCs from Plate 1


title: hr102.FGF10


title: hr102.FGF1


title: 1001200624_B10, pancreatic cells for patch-seq


title: 1001200624_B11, pancreatic cells for patch-seq


title: 1001200624_B4, pancreatic cells for patch-seq


title: C6-COR1

description: COR SSCs from Plate 1


title: 1001200624_B1, pancreatic cells for patch-seq


title: hr102.FGF0.1


title: 1001200624_A9, pancreatic cells for patch-seq


title: hr96.FGF10


title: hr96.FGF100


title: hr96.FGF0.1


title: 1001200624_A8, pancreatic cells for patch-seq


title: C3-COR1

description: COR SSCs from Plate 1


title: hr60.FGF100


title: C10-COR1

description: COR SSCs from Plate 1


title: hr60.FGF10


title: 1001200624_A7, pancreatic cells for patch-seq


title: hr60.FGF1


title: hr216.FGF100


title: 1001200624_A6, pancreatic cells for patch-seq


title: hr60.FGF0.1


title: C1-COR1

description: COR SSCs from Plate 1


title: hr54.FGF100


title: hr54.FGF10


title: B9-COR1

description: COR SSCs from Plate 1


title: 1001200624_A5, pancreatic cells for patch-seq


title: 1001200624_C12, pancreatic cells for patch-seq


title: hr54.FGF1


title: 1001200624_A4, pancreatic cells for patch-seq


title: hr48.FGF100


title: hr54.FGF0.1


title: C4-COR1

description: COR SSCs from Plate 1


title: hr48.FGF10


title: B8-COR1

description: COR SSCs from Plate 1


title: hr48.FGF1


title: B7-COR1

description: COR SSCs from Plate 1


title: hr48.FGF0.1


title: hr96.FGF1


title: 1001200624_A3, pancreatic cells for patch-seq


title: B3-COR1

description: COR SSCs from Plate 1


title: B12-COR1

description: COR SSCs from Plate 1


title: hr24.FGF10


title: 1001200624_A2, pancreatic cells for patch-seq


title: hr24.FGF1


title: 1001200624_A12, pancreatic cells for patch-seq


title: B11-COR1

description: COR SSCs from Plate 1


title: hr24.FGF0.1


title: 1001200624_A11, pancreatic cells for patch-seq


title: hr12.FGF100


title: hr12.FGF10


title: 1001200624_A10, pancreatic cells for patch-seq


title: A11-COR1

description: COR SSCs from Plate 1


title: hr12.FGF1


title: F8-SAG2

description: SAG SSCs from Plate 2

source_name: Cranial Sagittal Suture


title: hr12.FGF0.1


title: 1001200624_A1, pancreatic cells for patch-seq


title: F7-SAG2

description: SAG SSCs from Plate 2


title: hr6.FGF10


title: hr6.FGF100


title: F5-SAG2

description: SAG SSCs from Plate 2


title: F6-SAG2

description: SAG SSCs from Plate 2


title: hr6.FGF1


title: 2_Lo

city: Montreal

first: Heather

last: Melichar

state: Quebec

address: 5415 Boulevard de l'Assomption

department: Immunology-Oncology Unit

country: Canada

institute: Maisonneuve-Rosemont Hospital Research Center

data_processing:
Performed single-end RNA-seq using the Illumina NextSeq500 platform for 75 cycles (NextSeq500 Mid Output Kit).
Sequences were trimmed for sequencing adapters and low quality 3' bases using Trimmomatic version 0.35 and aligned to the reference human genome version GRCh38 (gene annotation from Gencode version 24, based on Ensembl 88) using STAR version 2.5.1
FPKM values for gene and transcript level expression for these stranded RNA libraries were obtained both as readcounts directly from STAR as well as computed using RSEM
DESeq2 version 1.18.1 was then used to normalize gene readcounts. Benjamini-Hochberg adjusted P values (Padj) were used to compute differential expression between groups.
Genome_build: GRCh38
Supplementary_files_format_and_content: abundance measurments

extract_protocol:
3x10^5 naïve CD4+ T cells were sorted directly into Trizol LS (Thermo Fisher Scientific) based on CD5 expression (top and bottom 15%) and used for library preparation.
Library was prepared using the Illumina Nextera XT Kit according to Illumina's instructions

treatment_protocol: Total T cells were enriched from human PBMCs by negative selection using the EasySep Human T cell Enrichment Kit (StemCell Technologies).

value: Peripheral Blood Mononuclear Cells (PBMC)

value: Naïve CD4+ T cells

tag: sorting strategy

value: Sorted on bottom 15% of CD5 expression


title: 2_Hi

value: Sorted on top 15% of CD5 expression


title: 1_Hi


title: hr24.FGF100


title: F4-SAG2

description: SAG SSCs from Plate 2

tag: tissue


title: 1_Lo


title: F3-SAG2

description: SAG SSCs from Plate 2


title: CLIP-seq mock

city: Copenhagen

first: Nicolai

last: Krogh

address: Blegdamsvej 3B

department: Department of Cellular and Molecular Medicine

country: Denmark

institute: University of Copenhagen

description: Whole cell RNA from pull-down

data_processing:
Library strategy: RNA adapter ligation using a modifed tRNA ligase.
Barcode separation using python scripts
Adaptor trimming using Cutadapt v. 2.0
Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1
Counting reads using python scripts
Genome_build: Human rDNA (18S, 28S). The reference sequences are in rDNA_sequence.fasta
Supplementary_files_format_and_content: MS Excel file containing read count normalized to total mapped reads.

extract_protocol:
After pull-down, RNA was extracted using PCI and chloroform and precipitated with 96% ethanol.
Adaptors were added to the fragmented RNA using a system relying on a modified Arabidopsis tRNA ligase joining 2',3' cyclic phosphate and 5' phosphate ends. The library fragments were then sequenced on the Ion Proton platform.

tag: cell line


title: CLIP-seq ZAK-alpha-RBR

description: Whole cell RNA from pull-down


title: E9-SAG2

description: SAG SSCs from Plate 2


title: hr6.FGF0.1


title: Id3lo.Blimp1lo.TIL#2

data_processing:
Tophat
HT-Seq Count
DESeq from BioConductor
Genome_build: UCSC mm10
Supplementary_files_format_and_content: gct

source_name: D14 TIL P14

extract_protocol:
Total RNA was extracted in TRIZoL reagent
PrepX RNA-seq library preperation kit (Integenex)

value: 6-16 Weeks

value: Tumor


title: Id3lo.Blimp1lo.TIL#1


title: E7-SAG2

description: SAG SSCs from Plate 2


title: E5-SAG2

description: SAG SSCs from Plate 2


title: UNINF_3

city: Iowa City

first: Stanley

last: Perlman

state: Iowa

address: 3-712 BSB, 51 Newton Rd

department: Department of Microbiology and Immunology

institute: University of Iowa

data_processing:
Index of reference genome was built using Bowtie v2.3.5.1.
FPKM of each gene was calculated on the length of gene and reads count mapped to this gene.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Uninfected_Ols in CNS

extract_protocol:
Brains and spinal cords were harvested at day 30 p.i. and processed as described above. After Live/Dead staining and treatment with Fc block, OLs were identified using APC-anti-O4 (1:50; Miltenyi). RNA was extracted from sorted OLs using an RNeasy Micro Kit (Qiagen).
Total RNA samples were converted to sequencing libraries using Takara Bio’s SMARTer Stranded Total RNA-Seq – Pico Mammalian Kit v2 (Cat. #634414).

tag: treatment

value: uninfected

value: Brain and spinal cord

value: mock oligodendrocytes (Ols)


title: Id3lo.Blimp1hi.TIL#1


title: UNINF_4


title: OLR1 transfected, UVPAPC treated, rep2

type: RNA

city: Vienna

first: Markus

last: Jeitler

address: Lazarettgasse 14

country: Austria

institute: Medical University Vienna

description: OLR1si UVPAPC 2

hyb_protocol: Affymetrix GeneChip® Human Gene 1.0 ST arrays were washed, stained and scanned according to the protocol described in GeneChip® WT Terminal Labeling and Hybridization User Manual (Fluidics Protocol FS450_0007).

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 3000 7G, software AGCC 3.1.1.

data_processing: RMA (Robust Multiarray average) Signal extraction using Affymetrix Expression Console Version 1.3.1.187.

label: Biotin

source_name: SZ95 sebocytes

label_protocol: 100ng of total RNA were amplified and labeled using the GeneChip® WT PLUS Reagent Kit (Catalog Number 902281, Affymetrix, Santa Clara, CA).

growth_protocol: Sebomed medium.

extract_protocol: Trifast / Qiaex purification.

treatment_protocol: siRNA scramble or siRNA OLR1, lipofection with lipofectamine 2000. After 24h, treatment with 25µg/ml UV oxidized PAPC.

value: sebocytes

tag: sirna

value: UVPAPC


title: OLR1 transfected, untreated, rep3

description: OLR1si control 3

value: untreated


title: OLR1 transfected, UVPAPC treated, rep3

description: OLR1si UVPAPC 3


title: OLR1 transfected, UVPAPC treated, rep1

description: OLR1si UVPAPC 1


title: OLR1 transfected, untreated, rep1

description: OLR1si control 1


title: Scramble transfected, UVPAPC treated, rep3

description: scramble UVPAPC 3

value: scramble


title: Scramble transfected, untreated, rep3

description: scramble control 3


title: E4-SAG2

description: SAG SSCs from Plate 2

value: post natal day 3

value: wild type

value: Skeletal Stem Cell


title: OLR1 transfected, untreated, rep2

description: OLR1si control 2


title: Id3lo.Blimp1hi.TIL#2


title: Scramble transfected, UVPAPC treated, rep2

description: scramble UVPAPC 2


title: UNINF_2


title: F2-SAG2

description: SAG SSCs from Plate 2

value: Suture complex:bone/mesenchyme


title: Scramble transfected, untreated, rep1

description: scramble control 1


title: Scramble transfected, UVPAPC treated, rep1

description: scramble UVPAPC 1


title: Id3hi.Blimp1lo.TIL#2


title: UNINF_1


title: E3-SAG2

description: SAG SSCs from Plate 2


title: Scramble transfected, untreated, rep2

description: scramble control 2


title: tdtomato_P3

source_name: tdtomato_P_Ols in CNS

value: rMHV-infected

value: tdTomato+ oligodendrocytes (Ols)


title: tdtomato_P5


title: E8-SAG2

description: SAG SSCs from Plate 2


title: BMDC, Eco3

hyb_protocol: Array was performed at the University of Pennsylvania Microarray core

data_processing: affymetrix-algorithm-name = rma-gene-default; affymetrix-algorithm-version = 1.0; program-name = Expression Console; program-version = 1.3.1.187

label: biotin

source_name: E. coli infected BMDCs, Day 4

growth_protocol: bone marrow cells were cultured in the presence of GM-CSF

extract_protocol: Cells were lysed in Trizol

treatment_protocol: cells were treated with live E. coli

value: BMDC

tag: infection

value: E. coli


title: BMDC, Eco1

scan_protocol: Array was performed at the University of Pennsylvania Microarray core

tag: cell type


title: BMDC, Eco2

label_protocol: Array was performed at the University of Pennsylvania Microarray core


title: Id3lo.Blimp1lo.Spl#2

source_name: D14 Spleen P14

value: 6-16 Weeks

value: Spleen


title: tdtomato_P1


title: tdtomato_N5

source_name: tdtomato_N_Ols in CNS

value: tdTomato- oligodendrocytes (Ols)


title: E12-SAG2

description: SAG SSCs from Plate 2


title: E10-SAG2

description: SAG SSCs from Plate 2


title: tdtomato_N1

value: Brain and spinal cord


title: tdtomato_N2


title: Id3lo.Blimp1hi.Spl#1


title: tdtomato_N4


title: RMB2970

city: SINGAPORE

first: JIA CHI

last: TAN

address: 8a Biomedical Grove

country: Singapore

institute: SIgN

data_processing:
Raw reads were aligned to the mouse reference genome GRCm38 from GENCODE using RSEM program version 1.2.19 with default parameters. Gene expression values in transcripts per million (TPM) were calculated using the same RSEM program and the mouse GENCODE annotation version 4.
Genome_build: GRCm38
Supplementary_files_format_and_content: TPM

extract_protocol:
Cell lysis, reverse transcription and cDNA amplification were performed on the C1 Single-Cell Auto Prep IFC, as specified by the manufacturer (Fluidigm Inc. protocol no. 100-5950 B1). The SMARTer Ultra Low RNA Kit (Clontech) was used for cDNA synthesis from the single cells. The resulting cDNA was quantified with a Quant-iT PicoGreen dsDNA Assay Kit (PN P11496; Life Technologies), and quality was checked with High Sensitivity DNA Reagents (PN 5067-4626) according to the manufacturer’s instructions (Agilent Technologies). Only cells with high-quality cDNA and concentration higher than 0.05 ng/μl were processed for subsequent library preparation.
Illumina NGS library was constructed with Nextera XT DNA Sample Prep kit (Illumina), according to the manufacturer’s recommendations (protocol 100-7168 E1). Sequencing was performed on Illumina HiSeq2000 (Illumina) high output mode by multiplexed single-read run with 51 cycles.

tag: developmental stage

value: brain

value: Microglia cell

tag: markers


title: E11-SAG2

description: SAG SSCs from Plate 2


title: Id3hi.Blimp1lo.Spl#2


title: Id3lo.Blimp1hi.Spl#2


title: E1-SAG2

description: SAG SSCs from Plate 2


title: RMB2969


title: D9-SAG2

description: SAG SSCs from Plate 2


title: RMB2967


title: Id3hi.Blimp1lo.Spl#1


title: E2-SAG2

description: SAG SSCs from Plate 2


title: D8-SAG2

description: SAG SSCs from Plate 2


title: RMB2966


title: RMB2965


title: D7-SAG2

description: SAG SSCs from Plate 2


title: tdtomato_P2


title: RMB2963


title: RMB2964


title: RMB2962


title: D6-SAG2

description: SAG SSCs from Plate 2


title: RMB2971


title: RMB2961


title: Id3lo.Blimp1lo.Spl#1


title: RMB2968


title: RMB2958


title: RMB2960


title: RMB2956


title: RMB2955


title: D4-SAG2

description: SAG SSCs from Plate 2


title: RMB2957


title: D2-SAG2

description: SAG SSCs from Plate 2


title: RMB2954


title: RMB2953


title: RMB2952


title: D12-SAG2

description: SAG SSCs from Plate 2


title: RMB2951


title: RMB2949


title: RMB2950


title: RMB2948


title: Sp.D35.Id3loBlimp1hi#2

source_name: D35 spleen P14

value: spleen


title: D11-SAG2

description: SAG SSCs from Plate 2


title: D10-SAG2

description: SAG SSCs from Plate 2


title: D5-SAG2

description: SAG SSCs from Plate 2


title: RMB2947


title: RMB2945


title: D1-SAG2

description: SAG SSCs from Plate 2


title: RMB2946


title: RMB2959


title: Sp.D35.Id3loBlimp1hi#1


title: RMB2944


title: D3-SAG2

description: SAG SSCs from Plate 2


title: RMB2942


title: C9-SAG2

description: SAG SSCs from Plate 2


title: Sp.D35.Id3loBlimp1lo#1


title: RMB2941


title: Sp.D35.Id3hiBlimp1lo#2


title: C8-SAG2

description: SAG SSCs from Plate 2


title: Sp.D35.Id3hiBlimp1lo#1


title: RMB2938


title: RMB2940


title: C7-SAG2

description: SAG SSCs from Plate 2


title: RMB2939


title: mLN.D35.Id3loBlimp1hi#2

source_name: D35 mLN P14

value: mesenteric lymph node


title: RMB2936


title: C5-SAG2

description: SAG SSCs from Plate 2


title: mLN.D35.Id3hiBlimp1lo#2


title: C4-SAG2

description: SAG SSCs from Plate 2


title: RMB2933


title: Sp.D35.Id3loBlimp1lo#2


title: C2-SAG2

description: SAG SSCs from Plate 2


title: IEL.D35.Id3loBlimp1hi#2

source_name: D35 siIEL P14

value: Small Intestine Epithelium


title: RMB2934


title: RMB2932


title: RMB2930


title: RMB2943


title: RMB2928


title: C3-SAG2

description: SAG SSCs from Plate 2

value: post natal day 3


title: RMB2929


title: RMB2926


title: C11-SAG2

description: SAG SSCs from Plate 2

value: wild type


title: RMB2927


title: C12-SAG2

description: SAG SSCs from Plate 2

value: Skeletal Stem Cell


title: IEL.D35.Id3loBlimp1hi#1


title: mLN.D35.Id3hiBlimp1lo#1


title: RMB2937


title: RMB2935


title: C6-SAG2

description: SAG SSCs from Plate 2

value: Suture complex:bone/mesenchyme


title: RMB2923


title: RMB2924


title: RMB2925


title: C10-SAG2

description: SAG SSCs from Plate 2


title: RMB2931


title: IEL.D35.Id3loBlimp1lo#2


title: mLN.D35.Id3loBlimp1hi#1


title: IEL.D35.Id3loBlimp1lo#1


title: RMB2922


title: C1-SAG2

description: SAG SSCs from Plate 2


title: RMB2921


title: B9-SAG2

description: SAG SSCs from Plate 2


title: RMB2919


title: IEL.D35.Id3hiBlimp1lo#1


title: B8-SAG2

description: SAG SSCs from Plate 2


title: RMB2918


title: Sp.D7.Id3loBlimp1hi#2

source_name: D7 spleen P14


title: RMB2917


title: RMB2920


title: RMB2916


title: B5-SAG2

description: SAG SSCs from Plate 2


title: Sp.D7.Id3loBlimp1hi#1


title: RMB2912


title: RMB2915


title: RMB2911


title: Sp.D7.Id3hiBlimp1lo#2


title: Sp.D7.Id3loBlimp1lo#2


title: B6-SAG2

description: SAG SSCs from Plate 2


title: RMB2914


title: B4-SAG2

description: SAG SSCs from Plate 2


title: RMB2910


title: RMB2913


title: B3-SAG2

description: SAG SSCs from Plate 2


title: IEL.D35.Id3hiBlimp1lo#2


title: RMB2909


title: B2-SAG2

description: SAG SSCs from Plate 2


title: RMB2908


title: RMB2906


title: Sp.D7.Id3hiBlimp1lo#1


title: IEL.D7.Id3loBlimp1hi#2

source_name: D7 siIEL P14


title: IEL.D7.Id3loBlimp1hi#1


title: RMB2905


title: RMB2907


title: RMB2903


title: RMB2904


title: B10-SAG2

description: SAG SSCs from Plate 2


title: RMB2902


title: IEL.D7.Id3loBlimp1lo#1


title: IEL.D7.Id3loBlimp1lo#2


title: RMB2898


title: IEL.D7.Id3hiBlimp1lo#1


title: RMB2900


title: RMB2896


title: RMB2897


title: RMB2901


title: RMB2899


title: B1-SAG2

description: SAG SSCs from Plate 2


title: IEL.D7.Id3hiBlimp1lo#2


title: A7-SAG2

description: SAG SSCs from Plate 2


title: A9-SAG2

description: SAG SSCs from Plate 2


title: Id3hi.Blimp1lo.TIL#1

value: Tumor


title: RMB2895


title: RMB2894


title: CIC-3 (CIC ChIP)

city: New york

first: Jihye

last: Paik

address: 1300 York Ave.

department: Pathology

institute: Weill Cornell Medical College

description: CIC ChIP

library_source: genomic

data_processing:
Basecalls performed using BaseCall version 1.1.2
ChIP-seq reads were aligned to the mm9 genome assembly using SOAPaligner/soap2 version 2.21 with the following configurations：-v 2 -s 35 -m 50 -x 600
Data were filtered using the following specifications：Sequenced reads with adaptor sequence or low-quality sequence (we define the low quality read as the percentage of base which quality is lesser than 5 is greater than 50% in a read) are discarded
Peaks were called using macs2 version 2.1.0 with the following setting: --bw 200 -g mm -s 49 -p 1e-5 -m 10 30
Genome_build: mm9
Supplementary_files_format_and_content: Bw files were transformed from wig files generated using macs2

molecule: genomic DNA

source_name: Mouse brain P1

growth_protocol: We harvested mouse brains at indicated ages and cross-linked with 1% paraformaldehyde.

extract_protocol:
After isolation of nucleus with lysis buffer (50 mM HEPES-KOH, 135 mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, and 0.25% TritonX100), the chromatin was digested with micrococcal nuclease. The pellet was resuspended with IP buffer (50 mM Tris-HCl, 100 mM NaCl, 10 mM EDTA, 0.1% SDS, and 1% TritonX100) and the nuclear membrane was broken with sonication. IP was performed with respective antibody overnight at  cold room. The antibody-antigen was precipitated with magnetic beads. The ChIPed DNA was eluted and extracted with DNA extraction kit (MN #740609.250).
Libraries were made using KAPA Hyper Prep kit (KAPABiosystems #KR0961) following manufacturer’s instructions. Briefly, 30 ng from each immunoprecipitated or Input DNA, were end-repaired, phosphorylated, A-tailed and ligated to adaptors (Roche SeqCap Adapter kit A #07141530001). Ligated products were size selected with 0.8X SPRI beads to obtain 250~350 bp of DNA. After purification, 8-cycle PCR amplification reaction was performed. PCR product was cleaned by the use of 1X SPRI beads. Final product was resuspended in 30 ul of Tris buffer.

value: Brain

value: Postnatal day 1

tag: mouse genotype

value: Nes-Cre;CIC+/+

tag: chip antibody

value: Home-made


title: B11-SAG2

description: SAG SSCs from Plate 2


title: A6-SAG2

description: SAG SSCs from Plate 2


title: RMB2892


title: CIC-2 (CIC ChIP)

description: CIC ChIP


title: RMB2893


title: RMB2891


title: A8-SAG2

description: SAG SSCs from Plate 2


title: A5-SAG2

description: SAG SSCs from Plate 2


title: CIC-1 (input)

description: input DNA


title: A3-SAG2

description: SAG SSCs from Plate 2


title: RMB2888


title: RMB2890


title: A4-SAG2

description: SAG SSCs from Plate 2


title: RMB2887


title: RMB2889


title: RMB2886


title: RMB2884


title: RMB2882


title: RMB2880


title: RMB2881


title: A11-SAG2

description: SAG SSCs from Plate 2


title: A10-SAG2

description: SAG SSCs from Plate 2


title: RMB2883


title: Uninfected castor bean rep3

city: Castanet tolosan

first: Sylvain

last: Raffaele

address: 28 chemin de borde rouge

country: France

institute: INRAE

data_processing:
HiSeq control software 2.2.58, RTA 1.18.64.0, Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genomes using the RNA-seq analysis function of the CLC genomics software with default settings.
Read count per gene were calculated using the RNA-seq analysis function of the CLC genomics software with default settings.
Genome_build: Helianthus annuus HanXRQr1.0; Beta vulgaris BETVU1.2.2; Ricinus communis RICCO1.1; Phaseolus vulgaris PVULG_BAT93
Supplementary_files_format_and_content: tab-delimited text files include total count of uniquely mapped reads per gene for each Sample

organism: Ricinus communis

source_name: ~20mm leaf disk from uninfected plants

growth_protocol: Plants were  grown in Jiffy pots under controlled conditions at 23°C, with a 9 hour light period at intensity of 120 μmol/m²/s.

extract_protocol:
The edge and center of developed mycelial colonies (~20 mm diameter) was harvested and stored in liquid nitrogen. Samples were ground with metal beads (2.5 mm) in a Retschmill apparatus (24hertz for 2x1min) before solubilizing in 1mL Trizol reagent (ThermoFisher) and left for 5 min at RT. Chloroform (200 µL) was added and mixed thoroughly before incubating for 3 min at RT. After centrifugation at ~12,000g (4°C) for 15min, the upper aqueous phase was recovered and nucleic acids were precipitated by adding 2µL GlycoBlue (Ambion) and 500µL isopropanol (10 min at -20°C). After centrifugation at ~15,000g (4°C) for 15min, pellets were washed twice with 70% ethanol before drying and resuspended in RNAse-free water. To eliminate chloroform traces, water resuspended nucleic acids were further cleaned using an RNA extraction kit (Quiagen) following manufacturer’s instructions. Genomic DNA was removed by DNase treatment (TURBO DNase; Ambion) following manufacturer’s instructions. The quality and concentrations of RNAs preparations were assessed with an Agilent apparatus and chips (nano).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: S. sclerotiorum strain 1980 was subcultured on Potato Dextrose Agar plates at 22°C. For inoculations, a 5-mm wide agar plug containing actively growing S. sclerotiorum mycelium was placed at the center of a Petri dish or on the adaxial surface of leaves on 5-week old plants. The border (ring of ~5mm wide) and center of colonies were collected with a scalpel and frozen in liquid nitrogen.

tag: cultivar

value: Hale

value: Leaves of 5-week old plants

value: control (uninfected)


title: RMB2885

tag: strain

value: brain


title: A1-SAG2

description: SAG SSCs from Plate 2

tag: genotype


title: A12-SAG2

description: SAG SSCs from Plate 2

tag: age


title: RMB2878

value: Microglia cell


title: Uninfected castor bean rep2


title: RMB2879


title: Uninfected castor bean rep1


title: RMB2877


title: RMB2875


title: RMB2876


title: D5-SAG1

description: SAG SSCs from Plate 1


title: RMB2873


title: RMB2874


title: A2-SAG2

description: SAG SSCs from Plate 2


title: RMB2872


title: D3-SAG1

description: SAG SSCs from Plate 1


title: RMB2871


title: D2-SAG1

description: SAG SSCs from Plate 1


title: RMB2870


title: Uninfected beetroot rep3

organism: Beta vulgaris subsp. vulgaris


title: RMB2869


title: RMB2868


title: RMB2866


title: D1-SAG1

description: SAG SSCs from Plate 1


title: RMB2867


title: RMB2864


title: C6-SAG1

description: SAG SSCs from Plate 1


title: shNUDT21 2

city: Houston,

first: Hari Krishna

last: Yalamanchili

state: TX

address: 1250 Moursund St #1125,

institute: Baylor College of Medicine

data_processing:
Raw reads were trimmed using fastp.
PolyA tails were trimmed using hts_PolyATTrim.
Trimmed reads were aligned to the reference genome using bowtie2.
Samtools were used to sort, convert and index alignment files.
Deeptools were used to generate bigwig files.
Genome_build: GRCh38
Supplementary_files_format_and_content: bigwig

source_name: Excitatory neurons

growth_protocol: We used WA09 (H9; RRID:CVCL_9773) female embryonic stem cells (ESCs) to generate human neurons. We differentiated neural progenitors into human neurons over three weeks, changing the media every 3 d. Afterwards, we passaged the neurons with trypsin. Three days after passaging, we infected the neurons with lentiviruses containing pGIPZ shRNA clones at a multiplicity of infection of 10. We verified the tropism and infectivity of the virus using the tGFP reporter signal. At day 3 after infection, we treated the neurons with puromycin (0.75–1.25 g/ml) for 6 days to select for infected cells. We cultured the cells for 60 days after infection, changing the media three times per week.

extract_protocol:
After 60 days of culturing after infection, we aspirated all the media and washed the cells with PBS before freezing them at -80C for later RNA extraction. We extracted RNA from shRNA-infected, human ESC-derived neurons in a 12-well plate. We lysed the neurons in the tissue-culture plate with TRIzol Reagent (ThermoFisher Scientific) and immediately transferred the lysate to microfuge tubes for trituration. We then isolated the RNA by chloroform phase separation, precipitation with 2-propanol, washing with 75% ethanol, and eluting in water.
We reverse transcribed 1 ug of total RNA with the partial P7 adapter (Illumina_4N_21T) and dNTPs with the addition of spiked-in azido-nucleotides (AzVTPs) at 5:1. We click-ligated the p5 adapter (IDT) to the 5′ end of the cDNA with CuAAC. We then amplified the cDNA for 21 cycles with Universal primer and 3′ indexing primer and purified it on a 2% agarose gel by extracting amplicon from 200-300 base pairs. We pooled the libraries and sequenced single-end, 75 base-pair reads on a Nextseq 550 (Illumina).

treatment_protocol: We infected the neurons at a multiplicity of infection of 10 with pGIPZ lentiviral shRNA clones: RHS4348 and V2LHS_253272 (Dharmacon).

value: WA09 embryonic stem cell-derived excitatory neurons

tag: culture duration

value: 60 days

tag: shRNA


title: D4-SAG1

description: SAG SSCs from Plate 1


title: RMB2862


title: Uninfected beetroot rep1


title: Uninfected beetroot rep2


title: C4-SAG1

description: SAG SSCs from Plate 1


title: shNUDT21 1


title: RMB2858


title: Scramble 3

value: Scramble


title: RMB2863


title: RMB2857


title: C3-SAG1

description: SAG SSCs from Plate 1

value: post natal day 3


title: RMB2856


title: C2-SAG1

description: SAG SSCs from Plate 1

value: wild type


title: RMB2860


title: RMB2861


title: C7-SAG1

description: SAG SSCs from Plate 1

value: Skeletal Stem Cell


title: RMB2865


title: Scramble 1


title: Scramble 2


title: C12-SAG1

description: SAG SSCs from Plate 1

value: Suture complex:bone/mesenchyme


title: RMB2853


title: RMB2854


title: RMB2859


title: Sample195

city: Atlanta

first: Angela

last: Mo

state: GA

address: 950 Atlantic Drive

department: School of Biological Sciences

institute: Georgia Institute of Technology

data_processing:
Reads were mapped to the human genome (GrCh37) with hisat2
aligned reads were transformed with SAMtools to quantify number of reads at the gene level with HTSeq-0.6.1 using default “union” mode
counts were normalized using TMM normalization with edgeR
confounding effects were adjusted with SVA and SNM
Genome_build: GrCh37
Supplementary_files_format_and_content: tab-delimited text file include normalized read counts at the gene level for each sample

source_name: Crohn's Disease_Ileum

extract_protocol:
Ileal biopsy specimens were obtained via pinch endoscopy forceps. Biopsies were stored in RNAlater, and RNA was extracted using Qiagen AllPrep DNA/RNA Mini Kit.
RNA sequencing (RNA-seq) libraries were prepared using the Lexogen QuantSeq 3' Library Prep Kit FWD for Illumina and sequenced by the Molecular Evolution Core at GT on the Illumina NextSeq single-end 150-bp or 75-bp reads.

tag: gender

value: Male

tag: age at diagnosis

tag: ancestry

value: White

tag: diagnosis

value: Crohn's Disease

value: Ileum


title: shNUDT21 3


title: C11-SAG1

description: SAG SSCs from Plate 1

source_name: Cranial Sagittal Suture

tag: tissue


title: RMB2855


title: Sample193

value: Female


title: RMB2851


title: Sample194


title: RMB2849


title: B9-SAG1

description: SAG SSCs from Plate 1


title: C10-SAG1

description: SAG SSCs from Plate 1


title: RMB2847


title: tKO_C1_DM3_BR2_RNAseq

city: Charlottesville

first: Roza

middle: Kamila

last: Przanowska

state: Virginia

department: Biomedical Engineering

institute: University of Virginia

data_processing:
STAR
DESeq
Genome_build: mm10
Supplementary_files_format_and_content: .txt: table with fpkm for all samples

source_name: Murine myotubes C2C12

growth_protocol: C2C12 PAX7 NEG cells were maintained in HyClone Dulbecco’s High Glucose Modified Eagles Medium (GE #SH30081.01) with 20% FBS. For differentiation to myotubes serum was exchanged to 2%HS.

extract_protocol:
Cells were grown to ~80% confluency for GM or differentiated for 3 days for DM3 and washed briefly twice with ice-cold PBS. Total RNA was extracted by Trizol reagent (Invitrogen #15596018) and purified with column-based Direct-zol RNA Miniprep kit (Zymo Research #R2051).
RNA-seq libraries were prepared by Beijing Novogene Co., Ltd. on poly(A) enriched RNA using the Illumina HiSeq instrument.

tag: cell line

value: miR-206, miR-1a-1 and miR-1a-2 triple KO

value: Myotubes


title: C5-SAG1

description: SAG SSCs from Plate 1

tag: cell type


title: Sample192


title: B7-SAG1

description: SAG SSCs from Plate 1


title: RMB2848

tag: developmental stage


title: Control_2_DM3_BR2_RNAseq

value: Wild-type


title: B5-SAG1

description: SAG SSCs from Plate 1


title: B6-SAG1

description: SAG SSCs from Plate 1


title: Control_1_DM3_BR2_RNAseq


title: B4-SAG1

description: SAG SSCs from Plate 1


title: tKO_C2_DM3_BR2_RNAseq


title: RMB2850

value: brain

tag: markers


title: RMB2852

value: Microglia cell


title: Control_2_GM_BR2_RNAseq

source_name: Murine myoblasts C2C12

value: Myoblasts


title: Sample188

value: African American


title: tKO_C2_GM_BR2_RNAseq


title: Control_1_GM_BR2_RNAseq


title: B3-SAG1

description: SAG SSCs from Plate 1


title: Sample189


title: RMB2846


title: tKO_C1_DM3_BR1_RNAseq


title: tKO_C2_DM3_BR1_RNAseq


title: Sample191


title: Sample190


title: B2-SAG1

description: SAG SSCs from Plate 1


title: Sample187


title: Control_2_DM3_BR1_RNAseq


title: Sample186

source_name: Ulcerative Colitis_Ileum

value: Ulcerative Colitis


title: tKO_C2_GM_BR1_RNAseq


title: B11-SAG1

description: SAG SSCs from Plate 1

value: post natal day 3


title: Control_1_DM3_BR1_RNAseq


title: tKO_C1_GM_BR1_RNAseq


title: Control_2_GM_BR1_RNAseq


title: Sample185

value: Control


title: Sample184


title: Control_1_GM_BR1_RNAseq


title: A7-SAG1

description: SAG SSCs from Plate 1

value: wild type

value: Skeletal Stem Cell


title: Sample183

value: Male


title: tKO_C1_GM_BR2_RNAseq


title: Sample182


title: A3-SAG1

description: SAG SSCs from Plate 1

value: Suture complex:bone/mesenchyme


title: 183_ileum_NI

city: Chapel Hill

first: Terry

last: Furey

state: NC

address: 120 Mason Farm Road

department: Genetics

institute: University of North Carolina, Chapel Hill

description:
intestinal bacteria 16S rRNA
UNC_abundance_genera.txt
UNC_abundance_species.txt

data_processing:
Library strategy: 16s rRNA seq
Illumina MiSeq software used for basecalling
Barcodes removed with in-house script
Data filtered and trimmed using DADA2
Paired reads merged using DADA2
Chimeric sequences removed using DADA2
Taxonomy assigned using RDP bacterial genome database.
Genome_build: None
Supplementary_files_format_and_content: Amplicon sequence variant (ASV) count table

source_name: mucosal biopsy

extract_protocol:
PCR products were normalized using a SequalPrepTM kit (Invitrogen, Carlsbad, CA), pooled, lyophilized, purified and concentrated using a DNA Clean and Concentrator Kit (Zymo, Irvine, CA). Pooled amplicons were quantified using Qubit Fluorometer 2.0 (Invitrogen, Carlsbad, CA). The pool was diluted to 4nM and denatured with 0.2 N NaOH at room temperature. The denatured DNA was diluted to 15pM and spiked with 25% of the Illumina PhiX control DNA prior to loading the sequencer
Amplicon libraries were prepared for sequencing using standard Illumina protocols

tag: disease status

value: nonIBD

tag: biopsy location

value: ileum

tag: inflammation status

value: NI

tag: institution

value: UNC

tag: sequence batch


title: 240_ileum_NI


title: 219_ileum_NI


title: 300_ileum_NI


title: 316_ileum_NI


title: 160_ileum_NI


title: A2-SAG1

description: SAG SSCs from Plate 1

tag: strain

tag: age

tag: genotype


title: 136_ileum_NI


title: Sample180

tag: gender

value: Female

value: Crohn's Disease

value: Ileum


title: NRAS_INK4A_LN

city: Leuven

first: Florian

last: Rambow

address: Herestraat 49 box 912

country: Belgium

institute: VIB

description: methanol fixed cells

data_processing:
CellRanger
Gene expression of murine single cells was analyzed using the SEURAT pipeline (Satija et al., Cell, 2015). As QC metrics, valid cells had to express at least 400 genes, nUMI>200 and percentage of mitochondrial genes <20%. This resulted in 6567 valid cells with a median library complexity of 1098 genes/cell for further downstream analysis. After scaling and linear dimension reduction, 15 significant principle components (PC) were identified.
Genome_build: mm10

source_name: melanoma infiltrated lymph node

extract_protocol:
Axillary lymph node was isolated from Tyr::NRASQ61K;Ink4a−/− mouse after spontaneous development of melanoma. Tissue was dissected into small pieces and digested using collagenase I & IV (5mg/ml each, Sigma Aldrich) for 20 minutes at 37oC followed by 0.05% Trypsin-EDTA (ThermoFisher Scientific) for 5 minutes at RT. Single cells were separated from remaining tissue using 40 μm Falcon Cell Strainers (Corning) and resuspended in 0.01% BSA. Then, cells were fixed in ice-cold methanol for 15 minutes. Cells were washed with PBS and resuspended in PBS containing 0.01% BSA.
We loaded ~8,700 methanol-fixed cells into one channel of the Chromium system using the 3’ v2 single cell reagent kit (10X Genomics). Following capture and lysis, we synthesized cDNA and amplified for 12 cycles. The amplified cDNA was used to construct Illumina sequencing libraries that were each sequenced on an Illumina NovaSeq6000 system.

value: Lymph node

tag: tumor

value: melanoma


title: 117_ileum_NI


title: Sample179

tag: age at diagnosis

tag: ancestry

value: African American


title: 94_colon_NI

value: colon


title: ALKKRAS_3_sorted

city: Zurich

first: giancarlo

last: russo

state: Schweiz

address: winterthurerstrasse 190

department: Functional Genomics Center Zurich

country: Switzerland

institute: ETH/University of Zurich

data_processing:
bcl2Fastq v2.19 software used for demultiplexing + basecalling.
reads trimmed with trimmomatic, options: ILLUMINACLIP:adapters.fa:1:20:7:5:true AVGQUAL:10 MINLEN:20
reads mapped with STAR  v2.5.4b, options: --sjdbOverhang 150 --twopassMode None --runThreadN 8 --outFilterType BySJout --outFilterMatchNmin 30 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.05 --outMultimapperOrder Random --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMultimapNmax 50 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --chimScoreMin 15 --chimScoreSeparation 10 --outSAMstrandField intronMotif --outSAMattributes All --outStd BAM_Unsorted --outSAMtype BAM Unsorted
count: FeatureCounts (Bioconductor), options: allowMultiOverlap = true; countPrimaryAlignmentsOnly= true; minFeatureOverlap=10; minMapQuality= 10 ; keepMultiHits=true
differential expression analysis: EdgeR, options: normMethod = TMM; backgroundExpression =10; testMethod = glm; deTest =QL
Genome_build: Mus musculus, Ensembl, GRCm38.p5
Supplementary_files_format_and_content: tad-delimited, raw counts

source_name: Ear cSCC tumor cells

extract_protocol:
Ear skin or ear tumors were dissected and prepared for FACS as described. Subsequently, total RNA from sorted cells was extracted using RNeasy Micro Kit (Quiagen, 74004).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: C57BL/6 mixed 129/SV


title: A10-SAG1

description: PF SSCs from Plate 2

data_processing:
RNA-Seq alignment to the reference was performed using STAR v2.5.3a using default conditions as described in Dobin et al., Bioinformatics, 2013.
Gene counts were tabulated from STAR v2.5.3a by mapping against mouse mm9 reference and used as input to Seurat. The counts coincide with those produced by htseq-count with default parameters.
The R package Seurat v2.3.0 was used for QC, analysis, and exploration of single-cell RNA-Seq data using R v3.4.4.
Genes expressed in at least 3 cells and cells with at least 200 expressed genes were retained for further analysis. Gene expression measurements for each cell were normalized by their total expression, scaled by 10,000, and log-transformed. Following normalization, genes that varied between single cells were identified.
PCA was performed on genes to output a set of genes that most strongly defined a set of principal components. Seurat’s graph-based clustering approach was used to cluster the cells. Seurat was further used to perform tSNE clustering which placed cells with similar local neighborhoods in high-dimensional space together in low-dimensional space. Positive and negative markers in each cluster were identified by comparing genes in cells of one cluster against genes in all other cells. Only genes that were detected in at least 25% of cells in either of the two populations were tested. Violin plots were used to visualize expression of top markers in each cluster. Finally, a heatmap of the top 20 marker genes across all cells in the 4 clusters was plotted.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include gene count values for each Sample.

extract_protocol:
Total single cell RNA profiles of SSCs isolated post-natal day 3 posterior frontal (PF), sagittal (SAG), coronal (COR) sutures and the growth plate (GP) of the tibial long bone from CD-1, wild-type mice were purified using Qiagen MiRNeasy Kit (Cat #217084) following the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina single cell RNA seq protocols.

tag: tissue

value: post natal day 3


title: Sample178

tag: diagnosis

value: Control


title: B1-SAG1

description: SAG SSCs from Plate 1

value: wild type

tag: cell type

value: Skeletal Stem Cell


title: A11-SAG1

description: SAG SSCs from Plate 1

value: Suture complex:bone/mesenchyme


title: 87_colon_NI

value: nonIBD


title: ALKKRAS_2_sorted


title: ALKKRAS_1_sorted


title: G8-PF2

description: PF SSCs from Plate 2

source_name: Cranial Posterior Frontal Suture


title: 78_colon_NI


title: A6-SAG1

description: SAG SSCs from Plate 1


title: Sample177

value: Male


title: Sample176


title: Sample181


title: ALK_4_sorted


title: 49_colon_NI

value: NI


title: G7-PF2

description: PF SSCs from Plate 2


title: G6-PF2

description: PF SSCs from Plate 2


title: Sample174


title: Sample175


title: ALK_1_sorted


title: B10-SAG1

description: SAG SSCs from Plate 1


title: G5-PF2

description: PF SSCs from Plate 2


title: 35_colon_NI

value: UNC


title: ALK_2_sorted


title: 42_colon_NI


title: Sample173


title: Sample172


title: Sample171

value: Ulcerative Colitis


title: WT_4_sorted

source_name: Ear skin Keratinocytes


title: 32_colon_NI


title: G4-PF2

description: PF SSCs from Plate 2


title: G3-PF2

description: PF SSCs from Plate 2


title: G2-PF2

description: PF SSCs from Plate 2


title: WT_1_sorted


title: Sample170

value: Female

value: Crohn's Disease


title: G1-PF2

description: PF SSCs from Plate 2


title: 236_colon_NI


title: 30_colon_NI


title: Sample169

value: Ileum


title: F9-PF2

description: PF SSCs from Plate 2


title: Sphere-2

city: Chengdu

first: Zhonghan

last: Li

state: Sichuan

address: 29 Wangjiang Road

department: College of Life Sciences

institute: Sichuan University

data_processing:
Quanlity filtering using fastp (version 0.20.0) with default parameters.
Mapping to GRCm38 using HISAT2 (version 2.1.0) with default parameters.
The expression level of each gene was quantified guided by reference annotation (Mus musculus, GRCm38.91) using FeatureCounts (v1.6.0) with parameters of "-t gene -g gene_name".
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited file include reads counts of all genes in each sample.

source_name: cultured primary dental papilla cells in 3D environment for 8 days

growth_protocol: Monolayer cells were cultured in EpiCM basal medium supplemented with 2% fetal bovine serum(Cat#No.0010, StemCellTechnologies, USA), 1% cell growth supplement (EpiCGS, Cat#No.4152, StemCellTechnologies, USA) and 1% penicillin/streptomycin solution (Cat#No.0503, StemCellTechnologies, USA) for 14days.Primary Spheres were obtained by seeding DPCs at passage 2 onto 6-well Ultra low attachment plates (Cat#3471, Corning, USA) at a density of 1*104 cells/cm2 in basal EpiCM medium supplemented with methylcellulose(MC, Cat#M03134, StemCellTechnologies, USA) for 8days.

extract_protocol:
Cells were collecteded by centrifugation  and RNA was harvested using Trizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

value: dental papilla

tag: growth

value: in 3D environment


title: Sphere-1


title: Sample168

value: African American


title: WT_5_sorted

value: C57BL/6 mixed 129/SV


title: F7-PF2

description: PF SSCs from Plate 2

value: post natal day 3


title: 22_colon_NI

value: colon


title: Sample167


title: monolayer cells-3

source_name: cultured primary dental papilla cells in plate for 8 days

value: in plate


title: monolayer cells-2


title: Sample166

value: Control


title: 151_colon_NI


title: F5-PF2

description: PF SSCs from Plate 2

value: Suture complex:bone/mesenchyme

value: wild type

value: Skeletal Stem Cell


title: F3-PF2

description: PF SSCs from Plate 2


title: Sample165


title: 131_colon_NI

value: nonIBD

value: NI


title: Sphere-3


title: Sample164


title: DPC primary cells-3

source_name: Primary dental papilla cells


title: monolayer cells-1


title: F12-PF2

description: PF SSCs from Plate 2


title: F11-PF2

description: PF SSCs from Plate 2


title: 130_colon_NI

value: UNC


title: Sample162

value: Male

value: Ulcerative Colitis


title: 23_colon_NI


title: DPC primary cells-1


title: Sample163

value: Female

value: Crohn's Disease

value: Ileum


title: F6-PF2

description: PF SSCs from Plate 2


title: F10-PF2

description: PF SSCs from Plate 2


title: 183_colon_NI


title: Sample160

value: African American


title: 2498_ileum_NI

description:
intestinal bacteria 16S rRNA
WashU_abundance_genera.txt
WashU_abundance_species.txt

value: CD

value: ileum

value: WashU


title: F1-PF2

description: PF SSCs from Plate 2

value: post natal day 3


title: E9-PF2

description: PF SSCs from Plate 2


title: Sample161


title: 573_ileum_NI


title: Sample159

value: Control


title: SEB+Vehicle3

city: Columbia

first: Mitzi

last: Nagarkatti

state: SC

address: 6439 Garners Ferry Rd

department: PMI

institute: University of South Carolina School of Medicine

hyb_protocol: Labeled samples were hybridized to miRNA 4.0 chips overnight (16h, 48°C, 60 RPM) then washed and stained on an Affymetrix GCS 3000 system Fluidics station using the FS450_0002 protocol.

scan_protocol: Chips were scanned on a Affymetrix GCS 3000 system scanner.

data_processing:
Affymetrix Expression Console Version 1.4.1.46 was used for quality control, data summarization, and normalization. The processing algorithm used was RMA-DABG. Affymetrix Transcriptome Analysis Console Version 3.1.0.5 was used to perform differential expression analyses. MicroRNAs were considered differentially expressed between the two groups if linear fold change was greater than ±2 and the ANOVA p-value was less than 0.05
RMA

source_name: MNCs

label_protocol: 500ng total RNA was used as starting material for labeling according to the Affymetrix FlashTag Biotin HSR RNA Labeling Kit manufacturer protocol.

growth_protocol: Acute lung injury was induced in 6-8 week old mice by exposing mice to SEB dual dose model. Mice were treated daily for three days with vehicle or 10mg/kg each (i.p.) of THC starting on immediately after SEB exposure

extract_protocol: Total RNA was isolated with Qiagen miRNeasy micro kit.

treatment_protocol: lung infiltrating mononuclear cells were isolated by ficol gradient separation.

value: 6-8 weeks


title: SEB+Vehicle2


title: Sample158


title: DPC primary cells-2

value: dental papilla


title: 3187_ileum_NI


title: 1748_ileum_NI


title: E8-PF2

city: Stanford

first: Natalina

last: Quarto

institute: Stanford University School of Medicine

description: PF SSCs from Plate 2

value: Suture complex:bone/mesenchyme

value: wild type

value: Skeletal Stem Cell


title: Sample157


title: SEB+Vehicle1


title: 3175_ileum_NI

value: NI


title: E3-PF2

description: PF SSCs from Plate 2


title: 877_ileum_NI


title: 2943_ileum_NI


title: Sample156

value: Male


title: SEB+THC3


title: E2-PF2

description: PF SSCs from Plate 2


title: 80_ileum_NI


title: Sample155


title: 2075_3_XLSB_32_days

city: Baltimore

first: Carlo

last: Colantuoni

institute: Johns Hopkins Univ. School of Medicine

data_processing:
After sequencing run the Illumina Real Time Analysis (RTA) module was used to perform image analysis, base calling, and the BCL Converter (bcl2fastq v2.17.1.14) were followed to generate FASTQ files which contain the sequence reads.
Read-level Q/C was performed by FastQC (v0.11.5). Pair-end reads of cDNA sequences are aligned back to the human genome (UCSC hg19 from Illumina iGenome) by the spliced read mapper TopHat (v2.0.9) with default option with “--mate-innder-dist 160” and “--library-type fr-firststrand” parameters based on known transcripts of Ensembl Build GRCh37.75.
To achieve gene-level expression profile, the properly paired and mapped reads are achieved by “samtools sort –n” option, and these reads are counted by htseq-count v0.9.1 (with intersection-strict mode and stranded option) according to gene annotation (Ensembl Build GRCh37.75) and RPKM is calculated.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each sample

source_name: human iPSC

growth_protocol: Monolayer culture of hPSC in feeder-free condition was done following the previously established protocol (Chen et al., 2012).  The hPSCs were dissociated to single cells with accutase (A11105, Life Technologies), plated at a density of 1 X 105 cells/cm2 in a Matrigel (354277, BD)-coated plate and cultured with mTeSR1 (05850, Stem Cell Technology). Cells were plated in medium containing 5 μM Y27632, ROCK inhibitor (Y0503, Sigma-Aldrich) to increase cell survival upon dissociation. ROCK inhibitor was removed from the medium at 24 hours after plating and cells were cultured for another 4 days before next passage.

extract_protocol:
RNeasy Mini Kit (Qiagen, Ct# 74106)
RNAseq libraries were constructed using Illumina TruSeq Stranded Total RNA RiboZero Gold sample Prep Kit (RS-122-2303) following the manufacturer’s protocol. The concentration of RNA was measured by Qubit (Life Technologies). Quality of RNAseq library was measured by LabChipGX (Caliper) using HT DNA 1K/12K/HiSens Labchip. The final cDNA libraries were sequenced using HiSeq 3000 for high-throughput DNA sequencing.

treatment_protocol: The 6 human iPSC lines (2063-1, -2; 2053-2, -6, 2075-1, -3) were differentiated into forebrain NSCs as previously described (Maroof et al., 2013). NSCs were cultured in N2-B27 medium supplemented with XAV939 (2 μM, Stemgent), LDN193189 (100 nM) and SB431542 (10 μM) (XLSB) for 12 days. mTesR medium was gradually switched to N2-B27 in the first 7 days as following: day0 100% mTesR, day1 75%mTesR + 25% N2-B27, day3 50% mTesR and N2-B27, day5 25% mTesR + 75% N2-B27, day7 100% N2-B27. NSCs were passaged on day 8 in N2 + B27 +XLSB; XLSB was withdrawn on day 12. On day 17, NSCs were passaged over astrocytes or without astrocytes and terminally differentiated in Neurobasal medium (NB) + B27 until day 32.

tag: subjectid

tag: iPSclinerep

tag: treatmentcondition

tag: daysofneuraldifferentiation


title: 2075_3_XLSB_30_days


title: E11-PF2

description: PF SSCs from Plate 2


title: 520_ileum_NI

tag: disease status

tag: biopsy location

tag: inflammation status

tag: institution


title: E6-PF2

description: PF SSCs from Plate 2

tag: strain

tag: age

tag: genotype


title: 5123_ileum_NI

tag: sequence batch


title: 2075_3_XLSB_17_days


title: Sample153

tag: gender

tag: age at diagnosis

tag: ancestry

value: Ulcerative Colitis


title: 2075_3_XLSB_8_days


title: SEB+THC1

value: Female


title: 2075_1_XLSB_32_days


title: E10-PF2

description: PF SSCs from Plate 2

tag: tissue

tag: cell type


title: D9-PF2

description: PF SSCs from Plate 2


title: Sample151

tag: diagnosis


title: Sample152

value: Crohn's Disease


title: SEB+THC2


title: 3215_ileum_NI


title: 2702_ileum_NI

tag: rutgeerts score


title: 2075_1_XLSB_30_days

tag: subjectid

tag: iPSclinerep

tag: treatmentcondition


title: Sample150

value: Ileum


title: 4416_ileum_NI

tag: disease status

tag: biopsy location


title: Sample149

value: African American


title: 2075_1_XLSB_17_days

tag: daysofneuraldifferentiation


title: D7-PF2

description: PF SSCs from Plate 2

tag: strain


title: E12-PF2

description: PF SSCs from Plate 2

tag: age


title: D6-PF2

description: PF SSCs from Plate 2

tag: genotype


title: 641_ileum_NI

value: CD

tag: inflammation status

tag: institution

tag: sequence batch


title: Sample154

tag: gender

tag: age at diagnosis

tag: ancestry


title: 2378_ileum_NI

value: ileum


title: E1-PF2

description: PF SSCs from Plate 2

tag: tissue

tag: cell type


title: D5-PF2

description: PF SSCs from Plate 2


title: 2075_1_XLSB_8_days

tag: subjectid


title: 2196_ileum_NI

tag: rutgeerts score

value: WashU


title: 2063_2_XLSB_32_days

tag: iPSclinerep

tag: treatmentcondition


title: D4-PF2

description: PF SSCs from Plate 2

value: post natal day 3


title: 1696_ileum_NI

tag: disease status

tag: biopsy location


title: Sample147

tag: diagnosis


title: Sample146


title: D3-PF2

description: PF SSCs from Plate 2

tag: strain

tag: age


title: 2063_2_XLSB_30_days

tag: daysofneuraldifferentiation


title: 621_ileum_NI

tag: inflammation status

tag: institution


title: 2063_2_XLSB_17_days


title: Sample145

tag: gender


title: D2-PF2

description: PF SSCs from Plate 2

tag: genotype


title: 3155_ileum_NI

tag: sequence batch


title: 2063_2_XLSB_8_days


title: 2124_ileum_NI


title: D12-PF2

description: PF SSCs from Plate 2

tag: tissue


title: Sample144

tag: age at diagnosis

tag: ancestry


title: D11-PF2

description: PF SSCs from Plate 2

tag: cell type


title: 2004_ileum_NI

tag: rutgeerts score


title: 2063_1_XLSB_32_days

tag: subjectid

tag: iPSclinerep

tag: treatmentcondition


title: Sample142

tag: diagnosis


title: Sample143


title: D10-PF2

description: PF SSCs from Plate 2

tag: strain


title: Sample148


title: 2063_1_XLSB_30_days


title: Sample141

value: Control


title: 550_ileum_NI

tag: disease status

tag: biopsy location


title: 2063_1_XLSB_17_days

tag: daysofneuraldifferentiation


title: C9-PF2

description: PF SSCs from Plate 2

tag: age


title: Sample140

tag: gender


title: 5243_ileum_NI

tag: inflammation status

tag: institution


title: 4550_ileum_NI

tag: sequence batch


title: C8-PF2

description: PF SSCs from Plate 2

tag: tissue

tag: genotype


title: 2063_1_XLSB_8_days


title: Sample139

tag: age at diagnosis

tag: ancestry


title: C7-PF2

description: PF SSCs from Plate 2

tag: cell type


title: 3875_ileum_NI


title: 2053_6_XLSB_32_days

tag: subjectid

tag: iPSclinerep


title: Sample138

tag: diagnosis


title: Sample137


title: 2053_6_XLSB_17_days

tag: treatmentcondition


title: C3-PF2

description: PF SSCs from Plate 2

tag: strain


title: C2-PF2

description: PF SSCs from Plate 2


title: 3219_ileum_NI

tag: disease status

tag: biopsy location

tag: rutgeerts score


title: C12-PF2

description: PF SSCs from Plate 2

tag: age


title: 2667_ileum_NI

tag: inflammation status


title: Sample136

tag: gender


title: 2053_2_XLSB_32_days

tag: daysofneuraldifferentiation


title: Sample135

tag: tissue


title: C10-PF2

description: PF SSCs from Plate 2

tag: genotype


title: 2053_2_XLSB_30_days


title: Sample134

tag: age at diagnosis


title: B9-PF2

description: PF SSCs from Plate 2


title: 2247_ileum_NI

tag: institution

tag: sequence batch


title: 2003_ileum_NI


title: Sample133

tag: ancestry


title: 2053_6_XLSB_8_days

tag: subjectid

tag: iPSclinerep


title: B8-PF2

description: PF SSCs from Plate 2

tag: cell type


title: 2053_2_XLSB_17_days

tag: treatmentcondition


title: 2053_6_XLSB_30_days


title: 787_ileum_NI

tag: disease status


title: Sample132

tag: diagnosis


title: 2053_2_XLSB_8_days


title: B7-PF2

description: PF SSCs from Plate 2

tag: strain


title: 50_colon_NI

value: nonIBD

tag: biopsy location

value: colon

value: UNC


title: Sample131


title: 2741_ileum_NI

tag: inflammation status

tag: rutgeerts score


title: Sample130

tag: gender


title: 3626_ileum_NI


title: P8.FGF20r

source_name: human embryonic stem cell H9 (WA09)

growth_protocol: H9 hESCs were dissociated to single cells and maintained in feeder-free conditions. Neural differentiation from hESCs was induced using dual SMAD inhibition. hNSCs were expanded and serially passaged every 6 days in 20 ng/ml FGF2.

treatment_protocol: On final passage, hNSCs were exposed to different FGF2 concentrations.

tag: passage

tag: fgf


title: B5-PF2

description: PF SSCs from Plate 2

tag: tissue

value: Suture complex:bone/mesenchyme

tag: age

tag: genotype

value: wild type


title: P5.FGF20r


title: B4-PF2

description: PF SSCs from Plate 2

value: Skeletal Stem Cell


title: 3400_ileum_NI

value: NI

tag: institution

tag: sequence batch


title: P6.FGF20r


title: 2413_ileum_NI


title: B3-PF2

description: PF SSCs from Plate 2


title: B12-PF2

description: PF SSCs from Plate 2


title: 1830_ileum_NI


title: B2-PF2

description: PF SSCs from Plate 2


title: 1833_ileum_NI


title: P2.FGF20r


title: Sample129

value: Male

tag: age at diagnosis

tag: ancestry


title: P4.FGF20r


title: P3.FGF20r


title: Sample125


title: Sample127

value: Female


title: Sample128

value: Crohn's Disease


title: B11-PF2

description: PF SSCs from Plate 2

tag: cell type


title: 897_ileum_NI

tag: disease status


title: B10-PF2

description: PF SSCs from Plate 2


title: Sample126

tag: diagnosis

value: Ulcerative Colitis

value: Ileum


title: P1.FGF0


title: Sample124

value: African American


title: 5021_ileum_NI

value: CD

value: ileum


title: B1-PF2

description: PF SSCs from Plate 2

tag: strain

value: post natal day 3


title: P8.FGF0.1

description: R


title: 2071_ileum_NI

tag: biopsy location

value: WashU


title: 2668_ileum_NI

tag: inflammation status


title: Sample123


title: Sample122

value: Control


title: A9-PF2

description: PF SSCs from Plate 2


title: 5175_ileum_NI

tag: rutgeerts score


title: A8-PF2

description: PF SSCs from Plate 2


title: 334_ileum_NI


title: Sample121

tag: gender


title: P8.FGF20

description: O

tag: passage


title: 1389_ileum_NI


title: A6-PF2

description: PF SSCs from Plate 2


title: Sample120


title: A7-PF2

description: PF SSCs from Plate 2


title: P6.FGF0.1

description: N

tag: fgf


title: P6.FGF1

description: M


title: 780_ileum_NI


title: P6.FGF10

description: L


title: A5-PF2

description: PF SSCs from Plate 2

tag: tissue


title: 388_ileum_NI


title: A4-PF2

description: PF SSCs from Plate 2

tag: age


title: Sample118


title: Sample117


title: 2640_ileum_NI


title: P6.FGF20

description: I


title: 1710_ileum_NI


title: Sample116


title: P8.FGF1

description: Q


title: A3-PF2

description: PF SSCs from Plate 2

tag: genotype


title: A2-PF2

description: PF SSCs from Plate 2


title: P8.FGF10

description: P


title: Sample115


title: 339_ileum_NI

tag: institution


title: A12-PF2

description: PF SSCs from Plate 2


title: Sample119


title: 2591_ileum_NI

tag: sequence batch


title: P4.FGF10

description: F


title: Sample113

tag: age at diagnosis


title: A10-PF2

description: PF SSCs from Plate 2


title: 1643_ileum_NI


title: 1580_ileum_NI


title: P4.FGF20

description: E


title: P3.FGF0.1

description: D


title: 1512_ileum_NI


title: E8-PF1

description: PF SSCs from Plate 1


title: P3.FGF1

description: C


title: Sample112

tag: ancestry


title: P4.FGF0.1

description: H


title: 1276_ileum_NI


title: Sample111


title: P3.FGF10

description: B


title: E4-PF1

description: PF SSCs from Plate 1

tag: cell type


title: Sample109


title: P4.FGF1

description: G


title: 3542_ileum_NI

tag: disease status


title: E2-PF1

description: PF SSCs from Plate 1


title: P3.FGF20

description: A


title: 3288_ileum_NI


title: E1-PF1

description: PF SSCs from Plate 1


title: A1-PF2

description: PF SSCs from Plate 2


title: Sample108

tag: diagnosis


title: 2727_ileum_NI


title: Sample107


title: 3360_ileum_NI


title: E7-PF1

description: PF SSCs from Plate 1

tag: strain


title: Sample106


title: Sample110


title: D9-PF1

description: PF SSCs from Plate 1


title: P2.FGF10


title: 3280_ileum_NI

tag: biopsy location


title: D5-PF1

description: PF SSCs from Plate 1


title: Sample105


title: 3276_ileum_NI

tag: inflammation status


title: Sample114


title: P2.FGF20


title: Sample104


title: D4-PF1

description: PF SSCs from Plate 1


title: 1728_ileum_NI

tag: rutgeerts score


title: Sample103

tag: gender


title: P2.FGF0.1

tag: passage


title: P2.FGF1

tag: fgf


title: D3-PF1

description: PF SSCs from Plate 1

tag: tissue


title: D24G12

city: Taichung

first: Asif

last: Hameed

state: Taichung

address: Kuo Kuang Rd.

department: Soil and Environmental Sciences

country: Taiwan

institute: National Chung Hsing University

data_processing:
cDNA library was sequenced using 150 base pair reads on NextSeq 500 PE2. The sequence quality was analyzed using FastQC v 0.11.5. RNA-seq reads were trimmed using Trimmomatic v 0.35. The reads were mapped using the local alignment with Bowtie2 v 2.1.0 against the RefSeq of CC-SAMT-1T and read counts were obtained using HTSeq-count v 0.5.4p2. The differential expression analysis of the RNA-seq data was performed with package DESEq2 v 1.12.1. The normalized counts were then obtained for each annotated gene. After normalization, the log2 fold change (M) and mean log2 expression (A) were calculated according to the formulae given below. Case, normalized case count+1; Control, normalized control count+1.
Genome_build: NZ_CP007202.1
Supplementary_files_format_and_content: Total No. of files: 5; Type of files: Excel Worksheets (.xls); Contents: 1-1 statistical comparisons of case and control (as specified in file name); File names: L36.1 vs. D36.1 RNAseq.xls, L36.2 vs. D36.2 RNAseq.xls, D24R12 vs. D36 RNAseq.xls, D24G12 vs. D36 RNAseq.xls, D24B12 vs. D36 RNAseq.xls.

source_name: CC-SAMT-1T cells incubated under 24 h dakness followed by 12 h green light exposure

growth_protocol: Cells were cultivated in 200 ml full-strength marine broth (BD Difco 2216) taken in a 500-ml conical flask fitted with an air-permeable silicon plug (Silicosen; plug-type) at 25°C for 36 h (100 rpm). One hundred µl of freshly prepared (16 h) cells of CC-SAMT-1T in full-strength marine broth (cultured under darkness) was used as a seed for each treatment. Cells were cultivated under constant full-spectrum light (L36.1 and L36.2) and constant darkness (D36.1 and D36.2; control). For the analysis of photoperiodic spectral impact, 24 h-old cells pre-cultured under darkness were exposed to 12 h of red, green and blue light illuminations (D24R12, D24G12 and D24B12, respectively); a control was maintained under constant darkness (D36).

extract_protocol:
Total RNA was extracted from cell pellet using TRI reagent solution (Ambion) according to manufacturer’s instructions. Ultrapure DEPC water and 1-bromo-3-chloropropane were purchased from Protech and Sigma-Aldrich, respectively. Residual DNA was removed by using TURBO DNase (Ambion) according to the manufacturer’s instructions. The quality and quantity of RNA were assessed using a NanoPhotometer (Implen). DNA-free RNA was subjected to ribosomal RNA depletion using the MicrobeEXPRESS kit (Ambion) according to manufacturer’s instructions.
A complementary DNA (cDNA) library of the messenger RNA was prepared by using TruSeq® Stranded mRNA Sample Preparation kit (Illumina, San Diego, CA) according to the manufacturer’s instructions. The cDNA library was generated after reverse transcription and 15 cycles of PCR using primers analogous to the adapters.

treatment_protocol: Full-spectrum light treatment (L36.1 and L36.2): Cells were cultivated in 500-ml culture flasks under Philips MASTER TL-D De Luxe 18W/965 fluorescent lamps (Striking intensity: 31 µmol photons m–2 s–1) for 36 h. Red, green and blue light treatments (D24R12, D24G12 and D24B12): 24 h-old cells cultivated under constant darkness in 500-ml culture flasks were exposed to red, green and blue lights (Cree XLamp XP-E2) (striking intensity: 37 µmol photons m–2 s–1) for additional 12 h. Dark-incubated controls (D36.1, D36.2 and D36): Darkness was achieved by loosely wrapping the 500-ml culture flasks containing 200 ml culture broth with a black film (Mulch CJ-200) followed by a cover of aluminum foil. Samples designated as D24R12, D24G12 and D24B12 were treated similarly for the initial 24 h to attain darkness.

tag: culture media

value: Marine broth (BD Difco 2216)

tag: incubation time (h)


title: D24B12

source_name: CC-SAMT-1T cells incubated under 24 h dakness followed by 12 h blue light exposure


title: 1654_ileum_NI

tag: institution


title: Sample102

source_name: Crohn's Disease_Ileum


title: 1352_ileum_NI

tag: sequence batch


title: D12-PF1

address: 257 Campus Drive

description: PF SSCs from Plate 1

tag: age

tag: genotype


title: D36

source_name: CC-SAMT-1T cells incubated under 36 h contant darkness


title: D24R12

source_name: CC-SAMT-1T cells incubated under 24 h dakness followed by 12 h red light exposure


title: D8-PF1

description: PF SSCs from Plate 1

tag: cell type


title: Sample101

tag: age at diagnosis

tag: ancestry


title: D11-PF1

description: PF SSCs from Plate 1

tag: strain


title: Sample100

tag: diagnosis


title: L36.2

source_name: CC-SAMT-1T cells incubated under 36 h constant full-spectrum light


title: 5088_ileum_NI

source_name: mucosal biopsy

tag: disease status

tag: biopsy location

tag: inflammation status


title: L36.1


title: Sample099

tag: gender


title: D10-PF1

description: PF SSCs from Plate 1


title: D1-PF1

description: PF SSCs from Plate 1


title: Sample098

source_name: Ulcerative Colitis_Ileum


title: 5062_ileum_NI

tag: rutgeerts score


title: D36.2


title: Sample097

tag: tissue


title: 4523_ileum_NI


title: D36.1

tag: culture media


title: C9-PF1

description: PF SSCs from Plate 1


title: C8-PF1

description: PF SSCs from Plate 1


title: Sample096


title: Sample095


title: 4512_ileum_NI


title: miR-324-3p.1 duplex RNA-seq replicate 2

city: Seoul

first: Haedong

last: Kim

address: 1 Gwanak-ro, Gwanak-gu

department: Biological Sciences

country: South Korea

institute: Seoul National University

description: RNA-seq

data_processing:
Reads were mapped to the human genome (GRCh38) and gene expression levels were quantified using RSEM according to the instructions.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-separated values (tsv) files containing gene names and corresponding TPM-normalized read counts.

growth_protocol: A172 cells were grown in DMEM media (Welgene) supplemented with 10% FBS (Welgene).

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen).
A172 cells were transfected with control miRNA or miR-324 duplexes using the Lipofectamine 3000 reagent (Thermo Scientific). Cells were harvested after 1 day of transfection and total RNAs were isolated using TRIzol (Invitrogen). The RNA quality was confirmed using Agilent 2100 Bioanalyzer and DNA nanoball sequencing for transcriptome (oligo dT enrichment; stranded; 100 bp paired-end) was performed on the BGISEQ-500 platform by BGI Tech Solutions (Hong Kong).

tag: cell line

tag: transfected with

value: miR-324-3p.1 duplex


title: C7-PF1

description: PF SSCs from Plate 1

value: Suture complex:bone/mesenchyme


title: miR-324-3p.1 duplex RNA-seq replicate 1

description: RNA-seq


title: 3957_ileum_NI

tag: institution

tag: sequence batch


title: C6-PF1

description: PF SSCs from Plate 1

tag: age

tag: genotype

value: wild type


title: Sample094

tag: age at diagnosis

value: White


title: miR-324-5p duplex RNA-seq replicate 2

description: RNA-seq

value: miR-324-5p duplex


title: Sample093

tag: ancestry


title: C5-PF1

description: PF SSCs from Plate 1

tag: strain

tag: cell type

value: Skeletal Stem Cell


title: 3673_ileum_NI

tag: disease status

value: NI


title: 3571_ileum_NI

tag: biopsy location


title: miR-324-5p duplex RNA-seq replicate 1

description: RNA-seq


title: C4-PF1

description: PF SSCs from Plate 1


title: 1339_ileum_NI

tag: inflammation status


title: Sample091

tag: gender

value: Male

value: Hispanic

tag: diagnosis


title: Sample092

value: Female

value: Ulcerative Colitis

tag: tissue

value: Ileum


title: C12-PF1

description: PF SSCs from Plate 1


title: 4937_ileum_NI

value: CD

value: ileum

tag: rutgeerts score


title: miNC RNA-seq replicate 2

description: RNA-seq

tag: cell line

value: control miRNA


title: 3005_ileum_NI

value: WashU


title: Sample090


title: miNC RNA-seq replicate 1

description: RNA-seq

tag: transfected with


title: C2-PF1

description: PF SSCs from Plate 1

value: post natal day 3


title: C11-PF1

description: PF SSCs from Plate 1


title: JG342 replicate 2

first: Ian

middle: Daniel

last: Ferguson

address: 265 Campus Dr

department: Cancer Biology PhD program

institute: Stanford University

data_processing:
HISAT v2.0.4
Bowtie v2.2.5
RSEM v1.2.12
Supplementary_files_format_and_content: TPM (transcripts per million) values for Samples 1-4 with gene names and NCBI Reference Sequence IDs

growth_protocol: MM.1S cells were grown in RPMI-1640 medium supplemented with 10% FBS, PenStrep, and 2mM glutamine.

extract_protocol:
RNA extraction from flash frozen cell pellets (5e6 cells) was peformed by BGI (Beijing Genomics Institute)
Libraries were constructed by BGI.
BGISEQ-500 platform, RNA QC done with Agilent 2100 Bio analyzer and Agilent RNA 6000 Nano kit

treatment_protocol: Cells were treated with 350nM JG342 or DMSO for 26 hours.

value: multiple myeloma cell line

tag: treatment

value: JG342 at 350nM


title: 2623_ileum_NI

tag: institution

tag: sequence batch


title: Sample089

value: Crohn's Disease


title: DMSO replicate 2

value: DMSO


title: 2333_ileum_NI


title: Sample088

value: White


title: C1-PF1

description: PF SSCs from Plate 1

value: Suture complex:bone/mesenchyme

tag: age

tag: genotype

value: wild type

value: Skeletal Stem Cell


title: JG342 replicate 1


title: Sample087

value: Male

tag: age at diagnosis

tag: ancestry

value: Asian

value: Control


title: 2085_ileum_NI

value: NI


title: 1287_ileum_NI

value: CD


title: B8-PF1

description: PF SSCs from Plate 1

tag: strain

tag: cell type