title: MDSC, RNA_seq, Nrp1_high, rep2

first: Wen

last: Lei

address: Bioisland

institute: Pediatric Immunity and Healthcare Biomedical Co., Ltd.

description:
gene_count_matrix.csv
Nrp1_pos_M_MDSC_2

data_processing:
Raw data of bulk RNA-seq were processed with trim galor to remove adaptors and filter low-quality reads. Clean reads were aligned to the reference genome (GRCm38) using Hisat2. We quantified gene counts for each sample by using Stringtie and prepDE.py. DEGs between two groups were identified using the R packages DESeq2 and edgeR(absolute log2FoldChange ≥ 1, p value ≤ 0.05). Pathway analysis was performed using Metascape and Gene set enrichment analysis (GSEA) based on Gene Ontology (GO) biological process terms and KEGG pathways.
Raw data of ATAC-seq were processed with Trimmomatic to remove adaptors and filter low-quality reads. Clean reads were mapped on reference genome (GRCm38) using BWA and then subjected to Picard to mark and remove duplicated reads. The peak signals were called by using macs2 and annotated with annotatePeaks.pl. We analyzed differentially accessible regions by using the R packages ChIPseeker and DiffBind. The interpretation of differentially accessible peaks was performed by using bam files as input, and the results are displayed in Integrative Genomics Viewer (IGV).
Assembly: GRCm38
Supplementary files format and content: Bed file for ATAC-seq data with 'Nrp1 high' as the control group.
Supplementary files format and content: Tab-delimited text file containing raw count for each sample for RNA-seq data

source_name: spleen

extract_protocol:
For RNA-seq, a total of 8×104 Nrp1high monocytes or Nrp1low monocytes were sorted from the spleens of C57BL/6J neonatal mice (7-day-old) and lysed in 5 µl 10× lysis buffer. The SMART_x0002_Seq v4 Ultra Low Input RNA Kit (Clontech) was used to prepare the low-input library. Briefly, the lysed RNA was denatured at 72°C for 3 min, and PCR was performed in a mixture of 5× Ultra Low First Strand Buffer, SMART-Seq v4 oligonucleotide, and RNase inhibitor (42°C for 90 min, 70°C for 10 min, and 4°C for hold). PCR Primer II A amplifies cDNA from the SMART sequences introduced by 3′ SMART-Seq CDS Primer II A and the SMART-Seq v4 Oligonucleotide and then purification of amplified cDNA using the Agencourt AMPure XP Kit (Beckman Coulter).  For ATAC-seq, a total of 5×104 Nrp1high monocytes or Nrp1low monocytes were sorted from the spleens 8 of C57BL/6 neonatal mice (7-day-old) and washed once with PBS before they were resuspended by 50 l cold lysis buffer for 10 min on ice. After that, the cell nuclei were resuspended in 50 l of transposition mixture, and the mixture was incubated at 37 °C for 30 min for DNA fragmentation. The DNA fragments were purified with VAHTS DNA Clean Beads.
For RNA-seq, a cDNA library constructed by technology from the pooled RNA was sequenced on the Illumina  platform using a 2×150 bp paired-end sequencing protocol.  For ATAC-seq, libraries were constructed using the TruePrep DNA Library Prep Kit V2 for Illumina (TD501, Vazyme) and the TruePrep Index Kit V2 for Illumina(TD202, Vazyme). Libraries were 2×150 bp paired-end sequenced on a HiSeq X Ten platform (Illumina) with the sequencing read length.

value: spleen

value: myeloid derived suppressor cells (MDSCs)_x0002_

value: wild type


title: MDSC, RNA_seq, Nrp1_high, rep3

status: Public on Apr 12 2024

type: SRA

city: Guangzhou

country: China

description:
gene_count_matrix.csv
Nrp1_pos_M_MDSC_3

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: cell type

tag: genotype


title: Para LB, rep 1 [Barseq3]

city: Palo Alto

first: Benjamin

last: Wang

state: CA

address: 299 Campus Drive

country: USA

institute: Stanford

description:
IT007
barseq3_para9150_processed.csv

library_source: genomic

data_processing:
Data was analyzed using a series of published Rb-Tn-seq scripts from Wetmore et al., 2015 mbio, using the abundance of each barcoded PCR as a proxy for mutant fitness.
Assembly: ASM18873v1 for ST4/74, ASM754v1 for Ty2, ASM2702v1 for D23580, ASM1188v1 for Para9150
Supplementary files format and content: Barseq3_ST474_processed.csv: all log2 fitness values for each gene in ST4/74, relative to time0.
Supplementary files format and content: Barseq3_Ty2_processed.csv: all log2 fitness values for each gene in Ty2, relative to time0.
Supplementary files format and content: Barseq3_Para9150_processed.csv: all log2 fitness values for each gene in Para9150, relative to time0.
Supplementary files format and content: Barseq3_D23580_processed.csv: all log2 fitness values for each gene in D23580, relative to time0.

molecule: genomic DNA

organism: Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150

source_name: ATCC 9150

growth_protocol: Samples were grown to OD~1 in LB, then back-diluted 1:50 into each condition (either LB, ceftriaxone, ciprofloxacin, azithromycin).

extract_protocol:
DNA was extracted using a Qiagen gDNA kit using standard procedures.
Purified gDNA was subjected to a barcoding PCR using Q5 polymerase, with a universal P5 primer and unique P7 for each condition, according to published protocols in Wetmore et al., 2015 mbio. This PCR only captures the barcoded region of each Tn insertion.

treatment_protocol: Each library was grown in stresses (bLB, ceftriaxone, ciprofloxacin, azithromycin) overnight for 16 hours.

value: ATCC 9150

value: Bacterial Tn library

tag: treatment

value: LB


title: Para time 0 replicate 2

description:
time0 is used as reference for other samples
barseq2_Para9150_processed.csv

data_processing:
Data was analyzed using a series of published Rb-Tn-seq scripts from Wetmore et al., 2015 mbio, using the abundance of each barcoded PCR as a proxy for mutant fitness.
Assembly: ASM18873v1 for ST4/74, ASM754v1 for Ty2, ASM2702v1 for D23580, ASM1188v1 for Para9150.
Supplementary files format and content: Barseq2_ST474_processed.csv: all log2 fitness values for each gene in ST4/74, relative to time0.
Supplementary files format and content: Barseq2_Ty2_processed.csv: all log2 fitness values for each gene in Ty2, relative to time0.
Supplementary files format and content: Barseq2_Para9150_processed.csv: all log2 fitness values for each gene in Para9150, relative to time0.
Supplementary files format and content: Barseq2_D23580_processed.csv: all log2 fitness values for each gene in D23580, relative to time0.

growth_protocol: Samples were grown to OD~1 in LB, then back-diluted 1:50 into each condition (either bile stress, iron limitation, osmotic pressure, heat shock).

treatment_protocol: Each library was grown in stresses (bile stress, iron limitation, osmotic pressure, heat shock) overnight for 16 hours.


title: IBD2218_NI

city: Oxford

first: Alison

last: Simmons

address: John Radcliffe Hospital/Headley Way

department: The MRC Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

data_processing:
Illumina bcl2fastq was used to convert raw bcl files to fastq format
Fastq files were processed using 10x Genomics Cellranger software
Genome_build: hg38
Supplementary_files_format_and_content: compressed raw UMI counts matrices from Cellranger outputs for mRNA and antibody libraries.

organism: Homo sapiens

extract_protocol:
Fresh or Frozen colonic biopsies from UC_I, UC_NI, CC_I, CC_NI and HC were digested to yield high viability single cells, which were put through flow-cytometry (FACS) sorting to enrich for CD45+ immune cells, before loading on to the 10X platform for single-cell RNA sequencing
Samples were loaded onto the 10X sc-RNA seq platform, with GEM generation and RNA RT, followed by generation of Gene expression (GEX) libraries, as per protocol CG000183, Rev A

value: Colon

tag: disease

value: Ulcerative colitis

tag: immunotherapy

tag: inflammation

value: Not inflamed

tag: fresh/frozen

value: Fresh

tag: age

tag: gender

value: Male

tag: chemistry

value: 3' chemistry


title: Pool 19 Antibody: Sorted CD3_ADT_Blood_Pool19_Repeat 1

description: Pool 16 (Tissue) paired samples with Pool 19 (Blood) and Pool 22 (Blood)

source_name: T-cells

extract_protocol:
Matched Colonic biopsy (Tissue) and Peripheral Blood (Blood) samples from Healthy controls, patients with inflamed Ulcerative Colitis (UC_I) and Checkpoint inhibitor-induced colitis (CC_I) were defrosted. Tissue was digested to yield high viability single cells, and then tissue and blood were put through flow-cytometry (FACS) sorting to enrich for T cells, before loading on to the 10X platform for single-cell RNA sequencing
Samples were loaded onto the 10X sc-RNA seq platform, with GEM generation and RNA RT, followed by generation of Gene expression (GEX), Antibody tagged oligo (ADT - with CITE-seq proteins and hashing information) and T-cell receptor (TCR) library amplification and indexing, as per protocol CG000208, Rev F

value: Blood

value: T-cells

tag: samples

tag: immunotherapy regimen

value: TIP376(Female), IBD 1464 (Male), TIP489 (Male)

tag: hashtag

value: TIP376 (Hashtag#1), IBD 1464 (Hashtag#2), TIP489 (Hashtag#3)

value: 5' Chemistry


title: GI 6275

data_processing:
Illumina bcl2fastq was used to convert raw bcl files to fastq format
Fastq files were processed using 10x Genomics Spaceranger (version 1.0) software
Genome_build: hg38
Supplementary_files_format_and_content: Spaceranger outputs - raw feature barcode matrix in mtx format, gene list in tab delimited format, spot barcodes in tab delimited format, spatial transcriptomics slide H&E image in jpeg format, spot position to image pixel coordinates.

source_name: Colon tissue

extract_protocol: Adult colonic samples were freshly frozen in OCT blocks and then 4uM sections placed onto an oligo-covered array with subsequent H&E, imaging, sample permeabilization, RNA RT and amplification as per protocol for the 10x visium spatial platform (10x CG000239 Rev D)

value: Checkpoint inhibitor induced colitis

tag: section cut

value: Biopsy

tag: activity

value: Inflamed

value: Dual therapy

value: Female


title: GI3369 (GI 3726)

value: Healthy control


title: Para 42 degrees replicate 1

description:
IT019
barseq2_Para9150_processed.csv

value: ATCC 9150

value: Bacterial Tn library

value: 42 degrees


title: IBD2368_I

value: Colon

value: Ulcerative colitis

value: Fresh


title: BT474, Control, Day 0, rep2

city: Turku

first: Teemu

middle: Daniel

last: Laajala

address: Turun yliopisto

department: Department of Mathematics and Statistics

country: Finland

institute: University of Turku

data_processing:
Reads were called using the manufacturer's bcl2fastq2 base calling software.
Reads were then aligned the reference genome (hg38) using Star version 2.5.2b, with the reference genome along with annotations downloaded from Illumina iGenomes web site.
Reads were then associated with known genes and the number of reads associated with each gene was counted using the subreads-package v1.5.1.
Gene-wise read counts were normalised using the TMM normalization method of the edgeR R/Bioconductor package with log(x+1) transformation for downstream applications.
The data processing pipeline was run using default parameters when possible.
Assembly: hg38
Supplementary files format and content: Tab-separated gene-wise expression (rows) per samples (columns) normalized using TMM.

growth_protocol: BT474 cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using the NucleoSpin RNA purification kit (Macherey‐Nagel). 300 ng of total RNA was used for the construction of sequencing libraries.
TruSeq® Stranded mRNA Sample Preparation, Illumina

treatment_protocol: The cells were treated with 1 uM of lapatinib every 3 days for 9 months

tag: cell line

value: HER2+ breast cancer cell line

value: WT

value: Lapatinib, 1 uM

tag: time

value: Day 0


title: IBD2368_NI

tag: tissue

value: Not inflamed

value: Male

value: 3' chemistry


title: Pool1_PBMC_GEX

description:
Samples in Pool 1, Pool 2 and Pool 3 paired from the same patients
PBMC_S1.zip

source_name: Peripheral blood

extract_protocol:
Matched Cells from biopsies (Tissue) and Peripheral Blood (Blood) were defrosted. Tissue was processed to yield high viability single cells, enriched for Epithelial or Stromal/Immune fractions and then tissue and blood pools were tagged with CITE-seq and hashing antibodies, pooled and loaded on to the 10X platform for single-cell RNA sequencing
Pooled tagged samples were loaded onto the 10X sc-RNA seq platform, with GEM generation and RNA RT, followed by generation of Gene expression (GEX), Antibody tagged oligo (ADT - with CITE-seq proteins and hashing information - '#1' = Hashtag#1 antibody, '#2' = Hashtag#2 antibody, etc) and T-cell receptor (TCR) and B-cell receptor (BCR) library amplification and indexing, as per protocol CG000186 (Rev A). Details of hashing & cite-seq antibodies in methods.

value: 5' chemistry

value: PBMC

tag: sample

value: TIP278 (N/A), IBD3947 (N/A), GI4059 (Dual Therapy), PRISE1 (Dual Therapy)

tag: mixed gender


title: MDSC, RNA_seq, Nrp1_high, rep1

description:
gene_count_matrix.csv
Nrp1_pos_M_MDSC_1

value: spleen

tag: cell type

value: myeloid derived suppressor cells (MDSCs)_x0002_

tag: genotype

value: wild type


title: Para naCl replicate 1

description:
IT015
barseq2_Para9150_processed.csv

value: ATCC 9150

value: Bacterial Tn library

tag: treatment

value: 0.4 M NaCl


title: MDSC, RNA_seq, Nrp1_low, rep3

description:
gene_count_matrix.csv
Nrp1_neg_M_MDSC_3


title: para iron replicate 1

description:
IT011
barseq2_Para9150_processed.csv

value: 0.2 mM 2-2' bipyridyl


title: Pool 16 Antibody: Sorted CD3_ADT_Tissue_Pool16

value: Colon

value: T-cells

value: TIP376(Female), IBD 1464 (Male), TIP489 (Male)

value: TIP376 (Hashtag#1), IBD 1464 (Hashtag#2), TIP489 (Hashtag#3)

value: 5' Chemistry


title: IBD3552_I

tag: disease

value: Ulcerative colitis

tag: immunotherapy

tag: inflammation

value: Inflamed

tag: fresh/frozen

value: Fresh

value: Female


title: Pool 13 Antibody: Sorted CD3_ADT_Blood_Pool10_Repeat 2

description: Pool 4 (Tissue) paired samples with Pool 10 (Blood) and Pool 13 (Blood)

value: Blood

tag: samples

value: PRISE14 (Dual Therapy), 6929 (N/A), 6286 (N/A)

tag: age

value: PRISE14 (Hashtag#3), 6929 (Hashtag#4), 6286 (Hashtag#5)

tag: chemistry


title: MDSC, RNA_seq, Nrp1_low, rep2

description:
gene_count_matrix.csv
Nrp1_neg_M_MDSC_2

value: spleen

value: myeloid derived suppressor cells (MDSCs)_x0002_

value: wild type


title: Para bile replicate 1

description:
IT007
barseq2_Para9150_processed.csv

value: ATCC 9150

value: Bacterial Tn library

value: 4% bile


title: IBD3552_NI

value: Colon

value: Not inflamed

tag: gender

value: 3' chemistry


title: Para time 0 replicate 1


title: MDSC, RNA_seq, Nrp1_low, rep1

description:
gene_count_matrix.csv
Nrp1_neg_M_MDSC_1


title: Pool 10 Antibody: Sorted CD3_ADT_Blood_Pool10_Repeat 1

value: T-cells

tag: immunotherapy regimen

tag: hashtag

value: 5' Chemistry


title: IBD3736_I

value: Ulcerative colitis

value: Inflamed

value: Male


title: Para M9 glucose rep 2

description:
IT039
Barseq1_Para9150_processed.csv

data_processing:
Data was analyzed using a series of published Rb-Tn-seq scripts from Wetmore et al., 2015 mbio, using the abundance of each barcoded PCR as a proxy for mutant fitness.
Assembly: ASM18873v1 for ST4/74, ASM754v1 for Ty2, ASM2702v1 for D23580, ASM1188v1 for Para9150
Supplementary files format and content: Barseq1_ST474_processed.csv: all log2 fitness values for each gene in ST4/74, relative to time0
Supplementary files format and content: Barseq1_Ty2_processed.csv: all log2 fitness values for each gene in Ty2, relative to time0
Supplementary files format and content: Barseq1_Para9150_processed.csv: all log2 fitness values for each gene in Para9150, relative to time0
Supplementary files format and content: Barseq1_D23580_processed.csv: all log2 fitness values for each gene in D23580, relative to time0

growth_protocol: Samples were grown to OD~1 in LB, then back-diluted 1:50 into each condition (either NonSPI2, InSPI2, inSPI2-Mg, or M9 glucose)

extract_protocol:
DNA was extracted using a Qiagen gDNA kit using standard procedures
purified gDNA was subjected to a barcoding PCR using Q5 polymerase, with a universal P5 primer and unique P7 for each condition, according to published protocols in Wetmore et al., 2015 mbio. This PCR only captures the barcoded region of each Tn insertion.

treatment_protocol: Each library was grown in a different minimal media (NonSPI2, InSPI2, InSPI2-MG, M9 glucose) overnight for 16 hours

value: M9 glu


title: MDSC, ATAC, Nrp1_low, rep5

description:
H_vs_L_deseq2_sig_annotate.bed
L3_1


title: Pool 7 Antibody: Sorted CD3_ADT_Blood_Pool7

description: Pool 1 (Tissue) paired samples with Pool 7 (Blood)

value: Blood

value: 6274 (Monotherapy), 6275 (Dual therapy), 4980 (N/A)


title: Pool 1 Antibody: Sorted CD3_ADT_Tissue_Pool1


title: IBD3736NI

value: Fresh


title: MDSC, ATAC, Nrp1_low, rep3

description:
H_vs_L_deseq2_sig_annotate.bed
L1_1

value: spleen

value: myeloid derived suppressor cells (MDSCs)_x0002_


title: Pool 19 TCR: Sorted CD3_TCR_Blood_Pool19_Repeat 1

value: TIP376(Female), IBD 1464 (Male), TIP489 (Male)

value: TIP376 (Hashtag#1), IBD 1464 (Hashtag#2), TIP489 (Hashtag#3)


title: Para InSPI2, rep 2

description:
IT031
Barseq1_Para9150_processed.csv

value: ATCC 9150

value: Bacterial Tn library


title: Pool 22: Sorted CD3_GEX_Blood_Pool19_Repeat 2


title: MDSC, ATAC, Nrp1_low, rep4

description:
H_vs_L_deseq2_sig_annotate.bed
L2_1

value: wild type


title: Pool 22 TCR: Sorted CD3_TCR_Blood_Pool19_Repeat 2


title: Pool 4 Antibody: Sorted CD3_ADT_Tissue_Pool4

value: Colon

value: PRISE14 (Dual Therapy), 6929 (N/A), 6286 (N/A)

value: PRISE14 (Hashtag#3), 6929 (Hashtag#4), 6286 (Hashtag#5)


title: MDSC, ATAC, Nrp1_high, rep5

description:
H_vs_L_deseq2_sig_annotate.bed
H3_1


title: Para LB time 0, rep 2

description:
time0 is used as reference for other samples
Barseq1_Para9150_processed.csv


title: Pool 19: Sorted CD3_GEX_Blood_Pool19_Repeat 1

value: T-cells

value: 5' Chemistry


title: Pool 13 TCR: Sorted CD3_TCR_Blood_Pool10_Repeat 2


title: Pool 16 TCR: Sorted CD3_TCR_Tissue_Pool16


title: Pool 16: Sorted CD3_GEX_Tissue_Pool16


title: Para M9 glucose rep 1

description:
IT019
Barseq1_Para9150_processed.csv


title: Para NonSPI2, rep 2

description:
IT027
Barseq1_Para9150_processed.csv


title: MDSC, ATAC, Nrp1_high, rep3

description:
H_vs_L_deseq2_sig_annotate.bed
H1_1


title: Pool 10 TCR: Sorted CD3_TCR_Blood_Pool10_Repeat 1


title: Pool 7 TCR: Sorted CD3_TCR_Blood_Pool7


title: Pool 10: Sorted CD3_GEX_Blood_Pool10_Repeat 1


title: Para inSPI2Mg rep 1

description:
IT015
Barseq1_Para9150_processed.csv


title: Pool 13: Sorted CD3_GEX_Blood_Pool10_Repeat 2


title: Para inSPI2Mg rep 2

description:
IT035
Barseq1_Para9150_processed.csv


title: MDSC, ATAC, Nrp1_low, rep1

description:
H_vs_L_deseq2_sig_annotate.bed
4-L1_FKDL220007840-1a_1


title: MDSC, ATAC, Nrp1_low, rep2

description:
H_vs_L_deseq2_sig_annotate.bed
5-L2_FKDL220007841-1a_1


title: Para InSPI2, rep 1

description:
IT011
Barseq1_Para9150_processed.csv


title: Pool 4 TCR: Sorted CD3_TCR_Tissue_Pool4


title: MDSC, ATAC, Nrp1_high, rep2

description:
H_vs_L_deseq2_sig_annotate.bed
2-H2_FKDL220007838-1a_1


title: Pool 7: Sorted CD3_GEX_Blood_Pool7


title: MDSC, ATAC, Nrp1_high, rep4

description:
H_vs_L_deseq2_sig_annotate.bed
H2_1


title: Pool 1 TCR: Sorted CD3_TCR_Tissue_Pool1


title: Para NonSPI2, rep 1

description:
IT007
Barseq1_Para9150_processed.csv


title: Pool 4: Sorted CD3_GEX_Tissue_Pool4


title: MDSC, ATAC, Nrp1_high, rep1

description:
H_vs_L_deseq2_sig_annotate.bed
1-H1_FKDL220007837-1a_1


title: Para time 0, rep 1


title: Pool 1: Sorted CD3_GEX_Tissue_Pool1


title: pituitary, patient 81

status: Public on Apr 11 2024

city: Saint-Petersburg

first: Elena

last: Nerubenko

address: Akkuratova 2

country: Russia

institute: Almazov National Medical Research Center

data_processing:
GENCODE GRCh38.primary_assembly (v41) and STAR alignment (v2.6.1a). Mapped reads were count with the featureCounts program (v1.6.2). Annotations for transcripts with AnnotationDb library after merging the gene's isoforms transcripts by median. Top genes filtering using mean in rows >1.
Assembly: hg38
Supplementary files format and content: Tab-separated values file includes counts for each sample

source_name: pituitary tumor ACTH-secreting

extract_protocol:
Were used Trizol (Thermo Scientific) method RNA extraction from tissue (after surgery snap-frozen in liquid nitrogen and  stored at -80C).
TruSeq Stranded mRNA kit

value: pituitary tumor ACTH-secreting

value: USP8 mutated


title: pituitary, patient 144

value: USP8 WT


title: pituitary, patient 117


title: pituitary, patient 120


title: pituitary, patient 29, rep2


title: pituitary, patient 126


title: pituitary, patient 87


title: pituitary, patient 135


title: pituitary, patient 77


title: pituitary, patient 150


title: pituitary, patient 65


title: pituitary, patient 112


title: pituitary, patient 29, rep1


title: pituitary, patient 61


title: Negative Control siRNA TGFbeta rep6

city: Kuopio

first: Tiit

last: Örd

address: Neulaniementie 2

institute: A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland

data_processing:
Fastq generation was done on-instrument using DRAGEN BCL Convert v3.10.12.
Sequencing reads were processed using the nf-core RNA-Seq pipeline (version 3.12.0; https://nf-co.re/rnaseq/3.12.0) with default settings (STAR aligner and salmon quantification) using the hg38 genome with Ensembl release 98 transcript definitions.
Assembly: hg38
Supplementary files format and content: raw count matrix

source_name: coronary artery smooth muscle cell

growth_protocol: Cells were cultured in M231 medium (Gibco, M231500) supplemented with SMGS (Gibco, S00725).

extract_protocol:
Total RNA was extracted using the Monarch Total RNA Miniprep Kit (NEB, cat no T2010) following the manufacturer's instructions.
RNA-Seq libraries were generated using the QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen) following the manufacturer's instructions. Libraries were indexed with the i5 6 nt Dual Indexing Add-on Kit (Lexogen) to obtain unique dual indexing. For each sample, 80-200 ng of total RNA was used for library preparation.

treatment_protocol:
siRNA transfection was done using Oligofectamine (Invitrogen, 12252011) following the manufacturer's standard protocol. Cells were grown in 12-well plate wells until they reached 70-80% confluency. Transfection was done in Opti-MEM medium (Gibco, 31985054). Treatments were started 16h after transfection.
Lentivirus expressing human FRZB (or the corresponding empty control virus) was obtained from VectorBuilder. The cells were transduced at a Multiplicity of Infection (MOI) of 2. Transduced cells were selected for 5-6 days using Blasticidin S HCL (Fisher Scientific, 15383671) at a concentration of 6 µg/ml.
For experimental treatments, the cells were first serum-starved (M231 medium with 0.5% FBS) for 8h. Subsequently, the medium was replaced with starvation media containing human recombinant TGFbeta (10 ng/ml; Sino Biologicals 158-10804-HNAC-20) or Cholesterol (70 µg/ml; Sigma-Aldrich C4951), as indicated, or with starvation medium (no treatment control). Cells were lysed for RNA isolation after 48h.

value: coronary artery smooth muscle cell

tag: gene perturbation

value: Negative Control siRNA

value: TGFbeta

tag: replicate


title: Negative Control siRNA TGFbeta rep4


title: Negative Control siRNA TGFbeta rep5


title: Negative Control siRNA Cholesterol rep6

value: Cholesterol


title: Negative Control siRNA Cholesterol rep5


title: Negative Control siRNA No treatment rep5

value: No treatment


title: Negative Control siRNA Cholesterol rep4


title: ALCAM siRNA TGFbeta rep6

value: ALCAM siRNA


title: pituitary, patient 139

tag: tissue


title: ALCAM siRNA Cholesterol rep6


title: Negative Control siRNA No treatment rep4


title: ALCAM siRNA TGFbeta rep5


title: ALCAM siRNA TGFbeta rep4


title: ALCAM siRNA Cholesterol rep5


title: pituitary, patient 73


title: ALCAM siRNA No treatment rep5


title: Negative Control siRNA TGFbeta rep1


title: ALCAM siRNA No treatment rep4


title: Negative Control siRNA TGFbeta rep3


title: Negative Control siRNA TGFbeta rep2


title: ALCAM siRNA Cholesterol rep4


title: Negative Control siRNA No treatment rep2


title: Negative Control siRNA Cholesterol rep3


title: Negative Control siRNA No treatment rep1


title: Negative Control siRNA Cholesterol rep1


title: Negative Control siRNA Cholesterol rep2


title: ALCAM siRNA TGFbeta rep3


title: ALCAM siRNA TGFbeta rep2


title: ALCAM siRNA TGFbeta rep1


title: ALCAM siRNA No treatment rep2


title: ALCAM siRNA No treatment rep1


title: FRZB lentiviral overexpression TGFbeta rep3

value: FRZB lentiviral overexpression


title: FRZB lentiviral overexpression TGFbeta rep4


title: ALCAM siRNA Cholesterol rep3


title: ALCAM siRNA Cholesterol rep2


title: FRZB lentiviral overexpression Cholesterol rep4


title: FRZB lentiviral overexpression No treatment rep1


title: FRZB lentiviral overexpression No treatment rep3


title: FRZB lentiviral overexpression Cholesterol rep3


title: control lentivirus TGFbeta rep1

value: control lentivirus


title: FRZB lentiviral overexpression Cholesterol rep2


title: FRZB lentiviral overexpression Cholesterol rep1


title: control lentivirus TGFbeta rep2


title: control lentivirus No treatment rep4


title: FRZB lentiviral overexpression No treatment rep2


title: FRZB lentiviral overexpression TGFbeta rep2


title: control lentivirus No treatment rep2


title: control lentivirus TGFbeta rep3


title: control lentivirus No treatment rep3


title: control lentivirus Cholesterol rep2


title: control lentivirus Cholesterol rep4


title: FRZB lentiviral overexpression No treatment rep4


title: FRZB lentiviral overexpression TGFbeta rep1


title: control lentivirus TGFbeta rep4


title: control lentivirus No treatment rep1


title: control lentivirus Cholesterol rep3


title: control lentivirus Cholesterol rep1


title: MaSC - scMultiome - KO - Rep1 - ATAC

city: Rochester

first: Alexandre

last: Gaspar-Maia

state: MN

address: 200 First street SW

institute: Mayo Clinic

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using TrimGalore v0.6.4 (Cutadapt v3.1)
Reads were then aligned to hg19 (mm9 for DF) whole genome using bowtie2 v2.3.3.1, alignment files were sorted and indexed using samtools v1.9, duplicate removal done using Picard v2.9.0
deepTools bamCoverage v3.5.0 was used to convert bam to bigWig
macs2 v2.2.7.1 was used to call peaks (to convert bam to bed)
scATAC-seq reads were processed using 10x Genomics Cell Ranger ATAC v2.0.0; scMultiome reads were processed using 10x Genomics Cell Ranger ARC v2.0.0; Downstream analysis was done using Seurat and Signac.
Assembly: hg19 (mm9 for DF; hg38 and mm10 for single-cell data)
Supplementary files format and content: bigWig (as produced by deepTools bamCoverage)
Supplementary files format and content: bed (as produced by macs2)
Library strategy: scMultiome

source_name: Mammary stem cells

growth_protocol: Normal Human Melanocytes (NHM) were cultures in Dermal Cell Basal Medium (ATCC) with the addition of 5 µg/mL Insulin, 50 µg/mL Ascorbic Acid, 6 mM L-Glutamine, 1.0 µM Epinephrine, 1.5 mM Calcium Chloride, Peptide Growth Factor and M8 Supplement. MCF-7, DFs and MDA-MB-231L cells were grown in DMEM (Gibco) with 4.5 g/L D-glucose, 110 mg/L sodium pyruvate, 10% FBS and 1% Penicillin/Streptomycin (Hyclone). HMEC cells were grown in complete Mammary Epithelial Cell Growth Media.

extract_protocol:
DNA for ATAC-seq  was prepared from 20,000 cells following the OMNI-ATAC procedures from Corces et al. (Nature Methods 2017) and Buenrostro et al. (Curr Protoc Mol Biol 2016), with modifications, using the Nextera kit (Illumina).  The cells were lysed for 3 minutes on ice and transposed for 30 minutes at 37C.  DNA was cleaned-up using procedures of a DNA extraction column.
The DNA libraries were prepared with 5-9 cycles of PCR amplification with the NEB High Fidelity Master Mix (New England Biolabs).  Clean up was done using the Zymo DNA Clean and Concentrator kit (Zymo Research) and followed with AMPure XP (Beckman Coulter) bead cleanup to remove primer dimers and under-digested chromatin.
Approximately 500,000 DFs were used for total RNA extraction using RNeasy Mini Kit (Qiagen). RNA quality control was performed using Agilent RNA 6000 Nano Kit and all samples had RNA Integrity Number higher than 9.8. Total RNA (1.5 μg) was used for poly(A) mRNA selection using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB) according to the manufacturer’s protocol
Directional, strand-specific RNA libraries were prepared using NEXTflex Rapid Directional RNA-seq Kit (Bioo Scientific) according to the manufacturer’s protocol. Quality of libraries was analyzed using an Agilent bioanalyzer. Barcoded libraries were multiplexed and subjected to 80 bp single-end sequencing
Approximately 100,000 viable cells  were subjected to Tn5 transposase before proceeding to single cell partitioning into gel beads in emulsion and barcoding following established 10X Genomics protocols. Target cell recovery was ~8000 cells per sample
libraries were constructed following established 10X Genomics protocols and sequenced on HiSeq 4000 (Illumina) before demultiplexing,alignment to the reference genome, and post-alignment quality control
Organoids from mammary stem cells were digested with 0.05% trypsin. Cells were then used for nuclei isolation procedure according to 10X genomics specification
Approximately 5000 nuclei per sample were subjected to transposase assays before proceeding to single cell partitioning into gel beads in emulsion, barcoding, pre-amplification, ATAC library construction, cDNA followed by GEX library construction. ATAC and GEX libraries were sequenced separately on an HiSeq 4000 (Illumina) before demultiplexing, alignment to the reference genome, and post-alignment quality control

treatment_protocol: MCF7 cells were treated with estradiol (E2) treatment MCF-7 cells were grown for 5 days in modified DMEM without phenol-red (Hyclone) with 4.5 g/L D-glucose, 4.0 L-glutamine, 10% charcoal-dextran–stripped FBS, 1% Penicillin/Streptomycin and 1nM of 17-β-estradiol or EtOH.

tag: cell line

value: Mammary stem cells

value: mH2A1 and mH2A2 double knockout


title: MaSC - scMultiome - KO - Rep2 - GEX

molecule: nuclear RNA


title: MaSC - scMultiome - KO - Rep2 - ATAC


title: MaSC - scMultiome - KO - Rep1 - GEX


title: 2 DL sy Adi D4 (44)_(SNOWBALLs520824F)

type: RNA

city: Dummerstorf

first: Siriluck

last: Ponsuksili

address: Wilhelm-stahl-allee 2

country: Germany

institute: FBN

description: SMSCs derived from porcine synovial membrane

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 42 C on Affymetrix Porcine Snowball Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Scanning using the GeneChip scanner 3000 were performed according to Affymetrix protocols

data_processing: Data were analysed with Affymetrix GCOS 1.1.1 software using global scaling to a target signal of 500.

label: biotin

organism: Sus scrofa

source_name: mesenchymal stem cells

label_protocol: biotin-labeled cRNAs were prepared according to the standard Affymetrix protocol from 500 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA was isolated using TRI Reagent (Sigma, Taufkirchen, Germany) according to the manufacturer’s protocol. After DNaseI treatment the RNA was cleaned up using the RNeasy Kit (Qiagen, Hilden, Germany).

tag: breed

value: German Landrace

value: fibrous synovium

tag: cell type

value: Adipocyte at day 4


title: 2 DL sy KA D14 (59)_(SNOWBALLs520824F)

value: control un-differentiaed cells at day 14


title: 2 DL fp KA D14 (61)_(SNOWBALLs520824F)

value: adipose synovium


title: 2 DL sy KA D4 (43)_(SNOWBALLs520824F)

value: control un-differentiaed cells at day 4


title: 2 DL fp KA D4 (45)_(SNOWBALLs520824F)


title: 2 DL fp Adi D1 (38)_(SNOWBALLs520824F)

value: Adipocyte at day 1


title: 2 DL sy Adi D7 (52)_(SNOWBALLs520824F)

value: Adipocyte at day 7


title: MaSC - scMultiome - WT - Rep2 - ATAC

tag: genotype

value: wild type


title: 2 AS sy KA D7 (55)_(SNOWBALLs520824F)

value: Angeln Saddleback

value: control un-differentiaed cells at day 7


title: 2 DL sy Adi D1 (36)_(SNOWBALLs520824F)


title: 2 DL fp Adi D14 (62)_(SNOWBALLs520824F)

value: Adipocyte at day 14


title: 2 DL fp KA D1 (37)_(SNOWBALLs520824F)

value: control un-differentiaed cells at day 1


title: 2 DL sy D0_(SNOWBALLs520824F)

value: control un-differentiaed cells at day0


title: 2 AS sy KA D4 (47)_(SNOWBALLs520824F)


title: 2 DL fp Adi D4 (46)_(SNOWBALLs520824F)


title: 2 AS sy KA D1 (39)_(SNOWBALLs520824F)


title: MaSC - scMultiome - WT - Rep1 - ATAC


title: 2 AS sy KA D14 (63)_(SNOWBALLs520824F)


title: 2 AS sy D0_(SNOWBALLs520824F)


title: 2 DL fp KA D7 (53)_(SNOWBALLs520824F)


title: 2 DL fp D0_(SNOWBALLs520824F)


title: 2 DL sy KA D1 (35)_(SNOWBALLs520824F)


title: 2 DL sy Adi D14 (60)_(SNOWBALLs520824F)


title: 2 DL sy KA D7 (51)_(SNOWBALLs520824F)


title: MaSC - scMultiome - WT - Rep2 - GEX


title: 2 DL fp Adi D7 (54)_(SNOWBALLs520824F)


title: 2 AS sy Adi D14 (64)_(SNOWBALLs520824F)


title: MaSC - scMultiome - WT - Rep1 - GEX


title: Normoxia_2, replicate 2, snRNAseq

city: Seattle

first: Hemalatha

last: Bhagavan

state: WA

address: 1900 9th Ave

department: Center for Integrative Brain Research

institute: Seattle Childrens Hospital

library_source: transcriptomic single cell

data_processing:
Expression matrices were generated using 10x Genomics Cell Ranger v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Expression matrix files were analyzed using Seurat v4.0 package for R. The matrix files were individually processed using standard Seurat preprocessing cutoffs. SoupX and DoubletFinder were used to find and remove ambient RNA contamination and doublets, respectively. We further removed nuclei with a nFeature count below 1500 and percent mitochondria above 2.0. Data were normalized using sctransform (SCT) with the method glmGamPoi and included the proportion of mitochondrial reads as a variable to regress
Assembly: mm10-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Pons-Medulla

growth_protocol: WT C57BL6/J mice were subjected to timed mating, selected for males, weaned at PND21 and group housed with littermates.

extract_protocol:
Single nuclei suspensions were prepared using the 10x Genomics protocol (CG000366) with the following modifications: 1) Tween 20 was excluded from the working wash buffer. 2) The lysis buffer was modified by increasing the Nonident-P40 Substitute (Sigma, 74385) final concentration to 0.5% and included Tween-20 (0.1%) as recommended by the manufacturer’s protocol. Frozen tissues were mechanically dissociated in sterile 1.5 ml microcentrifuge tubes, using a 1.5 ml pellet pestle in 1X lysis buffer and incubated in the same solution in total for 10 minutes to lyse cellular plasma membranes, releasing free nuclei. The suspension was then centrifuged at 500 rcf for 5 minutes at 4°C. The resulting nuclear pellets were washed and resuspended in wash buffer. The suspension was passed through a 70-micron filter (pluriStrainer Mini 43-10070-40). To stain nuclei, 2 μM Hoechst dye (Abcam ab228550) was added, and incubated for 10 minutes at 4°C. After incubation, nuclei were centrifuged at 500 rcf for 5 minutes and washed with 1x wash buffer. Finally, nuclei suspension was filtered through a 40-micron filter (pluriStrainer Mini 43-10040-40) and directly used for fluorescence-activated nuclei sorting (FANS) using the BD FACSAria™ III Cell Sorter to enrich single nuclei and remove debris.
Single cell Gene Expression Library was prepared according to Chromium Single Cell Gene Expression 3v3.1 kit (10x Genomics). In Brief, single cells, reverse transcription (RT) reagents, Gel Beads containing barcoded oligonucleotides, and oil were loaded on a Chromium controller (10x Genomics) to generate single cell GEMS (Gel Beads-In-Emulsions) where full length cDNA was synthesized and barcoded for each single cell. Subsequently the GEMS are broken and cDNA from each single cell are pooled. Following cleanup using Dynabeads MyOne Silane Beads, cDNA is amplified by PCR. The amplified product is fragmented to optimal size before end-repair, A-tailing, and adaptor ligation. Final library was generated by amplification
snRNA-Seq

treatment_protocol: C57BL6/J male mice were exposed to CIH or maintained at room air from the PND22 to PND43. The CIH group was subjected to intermittent episodes of hypoxia. Firstly, nitrogen (N2) was continuously injected into the chamber for 60 seconds, reducing the percentage of inspired oxygen (O2) within the chamber to a range of 4.5 to 5%. Subsequently, compressed air was injected for up to 5 minutes to restore the percentage of O2 to 21% before the initiation of a new hypoxia cycle. This protocol was repeated 80 times per day over 8 hours for 21 days. Mice were euthanized and the brainstem was frozen. Single nuclei suspensions were prepared for each of two groups: CIH and Normoxia.

value: Pons-Medulla

value: Brainstem cell classes

value: WT

tag: treatment

value: Normoxia-Room air


title: Normoxia_3, replicate 3, snRNAseq


title: 2 AS sy Adi D1 (40)_(SNOWBALLs520824F)

value: fibrous synovium


title: 2 AS sy Adi D7(56)_(SNOWBALLs520824F)


title: Normoxia_1, replicate 1, snRNAseq


title: 2 AS sy Adi D4 (48)_(SNOWBALLs520824F)

value: Adipocyte at day 4


title: 2 AS fp KA D14 (65)_(SNOWBALLs520824F)

value: control un-differentiaed cells at day 14


title: CIH_2, replicate 2, snRNAseq

value: Chronic Intermittent Hypoxia


title: CIH_3, replicate 3, snRNAseq


title: CIH_1, replicate 1, snRNAseq


title: mouse testis

city: Qingdao

first: JunLin

last: Song

address: Changcheng Road

institute: JunLin Song

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cel Ranger software v2.1.1(https://support 10xgenomics. com/single-cel-gene-expression/software/pipelines/latestwhat- is-cel-range)
Raw count matrices generated by Cell Ranger were imported to Seurat 4.3.0 and filtered for only high-quality cells. Briefly, we removed cells with less than 200 detected genes and genes detected in 3 or fewer cells. Gene expression values were log normalized and scaled before further downstream analyses. Cell clustering and UMAP analysis were performed based on the statistically significant principal components. Marker genes of each cell cluster were determined by Log Fold Change threshold above 0.25 using the default Wilcoxon rank-sum test. After identification of cell clusters, raw count matrices of data subsets were imported to Monocle and only expressed genes above threshold (0.1) were used for analyses. Differentially expressed genes or significantly variable genes among cells were identified by Monocle and used for ordering cells in pseudotime. Only genes with a dispersion ratio above 0.1 were used for training the pseudotime trajectories. To generate the pseudotime heatmaps, DEGs (Differentially Expressed Genes) among cell clusters in pseudotime with qval <0.1 were included and clustered hierarchically based on their expression trends.
Assembly: 10mm
Supplementary files format and content: Tab-separated  values files and matrix files

source_name: mouse testis

extract_protocol:
The mice and pigs’ testis were cut into pieces. The mice and pigs’ epididymis were collected and divided into epididymis caput, epididymis corpus and epididymis cauda. Cut the fresh tissue into pieces, transfer to the 0.2% collagenase IV and DNAse I digestion solution, and incubate at 37°C for 15 min.
Self-designed using MGI C4 droplet generation device, through efficient mRNA capture magnetic beads and droplet recognition microbeads and single-cell RNA library preparation kit The single-cell (nuclear) suspension can be quickly prepared into the library corresponding to the sequencing platform. The DNBelab C library contains cDNA Library, which are derived from MRNA-capturing magnetic beads and droplet recognition microbeads, respectively.

value: mouse testis


title: mouse epididymis corpus

source_name: mouse epididymis corpus

value: mouse epididymis corpus


title: mouse epididymis caput

source_name: mouse epididymis caput

value: mouse epididymis caput


title: Nup358 knock-out, replicate 2, scRNA-seq

city: La Jolla

first: Maximiliano

middle: A

last: D'Angelo

address: 10901 North Torrey Pines Road

department: Cell and Molecular Biology of Cancer Program, NCI-Designated Cancer Center

institute: Sanford Burnham Prebys Medical Discovery Institute

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: 10x Genomics Cellranger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

source_name: Bone marrow

extract_protocol:
Bone marrow cells were stained for flow cytometry with Lin antibody cocktail and with antibodies against Sca1 and cKit. Before sorting, cells were resuspended in HBSS, 1% BSA, 20 mM HEPES pH 7.2. Live Lin-Sca1+cKit+ cells were sorted at 4°C on a BD FACSAria II Cell Sorter (BD Biosciences) with a 70-μm nozzle into DMEM without glucose, glutamine, sodium pyruvate, phenol red and supplemented with 10% FBS. Purity was verified after each sort and was found to be >99%.
Sorted LSK cells were loaded into a Chromium Next GEM Chip and processed with the Chromium Controller (10x Genomics) according to the manufacturer’s instructions for single cell barcoding. Libraries were prepared using Chromium Next GEM Single Cell 3' Reagent Kits v3.1 (10x Genomics) and were sequenced to an average depth of about 50,000 reads per cell.

value: Bone marrow

value: LSK

value: Nup358 KO


title: Nup358 knock-out, replicate 1, scRNA-seq


title: mouse epididymis cauda

source_name: mouse epididymis cauda

value: mouse epididymis cauda


title: Nup358 wild-type, replicate 2, scRNA-seq

value: wild-type


title: 2 AS fp KA D4 (49)_(SNOWBALLs520824F)

value: Angeln Saddleback

value: adipose synovium

value: control un-differentiaed cells at day 4


title: Nup358 wild-type, replicate 1, scRNA-seq


title: MCF-7 - scATAC-seq - KO - Rep2

library_source: genomic single cell

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using TrimGalore v0.6.4 (Cutadapt v3.1)
Reads were then aligned to hg19 (mm9 for DF) whole genome using bowtie2 v2.3.3.1, alignment files were sorted and indexed using samtools v1.9, duplicate removal done using Picard v2.9.0
deepTools bamCoverage v3.5.0 was used to convert bam to bigWig
macs2 v2.2.7.1 was used to call peaks (to convert bam to bed)
scATAC-seq reads were processed using 10x Genomics Cell Ranger ATAC v2.0.0; scMultiome reads were processed using 10x Genomics Cell Ranger ARC v2.0.0; Downstream analysis was done using Seurat and Signac.
Assembly: hg19 (mm9 for DF; hg38 and mm10 for single-cell data)
Supplementary files format and content: bigWig (as produced by deepTools bamCoverage)
Supplementary files format and content: bed (as produced by macs2)

value: macroH2A2 knockout

tag: ectopic expression

value: over-expressed GFP-H2A


title: MCF-7 - scATAC-seq - KO - Rep1


title: MCF-7 - scATAC-seq - WT - Rep1

value: wild type


title: MCF-7 - scATAC-seq - WT - Rep2


title: 2 AS fp KA D1 (41)_(SNOWBALLs520824F)

value: control un-differentiaed cells at day 1


title: 1 DL sy Adi D14 (28)_(SNOWBALLs520824F)

value: German Landrace

value: fibrous synovium

value: Adipocyte at day 14


title: 1 DL sy KA D4 (11)_(SNOWBALLs520824F)


title: Human Mammary Epithelial Cells - ATAC

source_name: Human Mammary Epithelial Cells

value: Human Mammary Epithelial Cells


title: 1 DL sy D0_(SNOWBALLs520824F)

value: control un-differentiaed cells at day0


title: 2 AS fp Adi D14 (66)_(SNOWBALLs520824F)


title: 2 AS fp Adi D4 (50)_(SNOWBALLs520824F)

value: Adipocyte at day 4


title: 2 AS fp D0_(SNOWBALLs520824F)


title: 2 AS fp KA D7 (57)_(SNOWBALLs520824F)

value: control un-differentiaed cells at day 7


title: GFP input  ChIP, replicate2

city: Toronto

first: Jack

last: Greenblatt

state: Ontario

address: 160 College St

department: Donnelly Center

country: Canada

institute: University of Toronto

description:
none
GFP_RPRD1B_merged_at_TTS_7.pdf

data_processing:
Illumina adaptor sequences were removed from the 3’ ends of 51-nt reads, and the remaining reads were mapped to the human genome hg19 using Bowtie 2 with default settings.
After removal of duplicate reads, peaks were called jointly on immunoprecipitated and input samples with MACS2 (version 2.1.2)
ChIP-seq signal intensity (log2(ratio-over-input)) in transcription termination site (TTS) region (from 100 bp upstream of TTS to 2000 bp downstream of TTS) and transcription start site (TSS) (or promoter region) (from 1000 bp upstream of TSS to 300 bp downstream of TSS) of 11340 actively expressed genes (FPKM > 1) in HEK293 cells was analyzed and plotted using R package ‘GenomicPlot’.
Assembly: hg19
Supplementary files format and content: Processed files are in BED format containing broad and narrow peaks
Supplementary files format and content: Processed files are in PDF format depicting POLII ChIPseq signals around transcription termination sites (TTS) under various treatment conditions

growth_protocol: Cell cultures were maintained in Dulbecco's modified Eagle's medium (DMEM) (Wisent Bioproducts catalogue number 319-005-CL) supplemented with 10% FBS (Wisent Bioproducts catalogue number 080-705), sodium pyruvate, non-essential amino acids, and penicillin/streptomycin.

extract_protocol:
Lysates were treated with Turbo DNase (Thermo Fisher Scientiﬁc) and RNase I (Thermo Fisher Scientiﬁc) diluted 1/250 in PBS for 5 minutes at 37°C to digest genomic DNA and partially digest RNA to short fragments of an optimal size range. RNA-protein complexes were puriﬁed using 100 mL of protein G Dynabeads (Thermo Fisher Scientiﬁc) and 10ug antibody, with 2% (20ul) of the total lysate retained for use as a size-matched input (SMI) control. SMI samples were processed as previously described (Van Nostrand et al., 2016). Following stringent high salt washes, the immunoprecipitated RNA was 3′ end dephosphorylated and ligated to a pre-adenylated adaptor at the 3′ end, as described previously. After extensive additional washes and buffer exchange, the immunoprecipitated RNA was 5′ end-labeled using ATP [γ-32P]. The puriﬁed protein-RNA complexes and SMI control samples were separated with SDS-PAGE and transferred to nitrocellulose membrane. Protein was digested using proteinase K, the RNA was puriﬁed using phenol/chloroform. miCLIP procedure was performed as decribed. Total RNA was extracted from HEK293 cells using TRIzol as per manufacturer's protocol. RNA was treated with DNase I to eliminate any contaminating genomic DNA. We used 12 μg of total RNA for miCLIP-seq. 2 μL of RNA Fragmentation Reagents was added to the RNA suspended in 20 μL of sterile water. The mixture was incubated in a heat block at 75°C for exactly 12 minutes. 2.2 μL of stop solution was added to stop the reaction. The fragmented RNA was incubated with 10 μg of m6A antibody for 2 hours at 4°C. RNA-antibody complexes were UV crosslinked twice with 0.15 J/cm2 at 254 nm in a Stratalinker 1800.  Protein G Dynabeads (100 μL) were added, and the samples were rotated for 2 hours at 4°C. Remaining steps, including dephosphorylation, adapter ligation, SDS-PAGE, and RNA-extraction are similar to the iCLIP procecure.
RNAP II was immunoprecipitated from the lysate with 5 µg of RNAP II (N20) antibody (Santa Cruz, catalogue number sc-899, catalogue number F3014) followed by crosslink reversal at 65oC for overnight and DNA precipitation by using QIAEX II Gel Extraction Kit (Qiagene, catalogue number 20051).
Libraries were sequenced on an Illumina HiSeq 2500 to a depth of 20 million 51-nucleotide single end reads.

treatment_protocol: HEK293 cells were crosslinked with 1% formaldehyde (Sigma catalogue number F8775) for 10 minute, harvested in lysis buffer (50 mM Tris-Cl pH 8.1, 10 mM EDTA, 1% SDS, 1 mM Phenylmethylsulfonyl fluoride (PMSF, Sigma, catalogue number P-7626), 10 µg/ ml aprotinin (Sigma, catalogue number A-1153), and 10 µg/ ml leupeptin (Sigma, catalogue number L-2884)) and sonicated by using Branson Sonifier 450 (USA, Danbury, CT) with the setting of Time: hold, Dutycycle: 30%, Output control: 3, 25 pulse each time for 7 time.

value: human embryonic kidney cells (HEK293)

value: GFP integrated

value: GFP was expressed in an HEK293 cell line engineered with the Flp-in system under the control of doxycycline, and expression was induced for 96 hours with 1 µg/ml doxycycline.

tag: chip antibody


title: 2 AS fp Adi D7 (58)_(SNOWBALLs520824F)

value: Angeln Saddleback

value: Adipocyte at day 7


title: 1 DL sy KA D1 (3)_(SNOWBALLs520824F)


title: 1 DL sy Adi D7 (20)_(SNOWBALLs520824F)


title: 1 DL sy Adi D1 (4)_(SNOWBALLs520824F)

value: Adipocyte at day 1


title: 1 DL sy KA D14 (27)_(SNOWBALLs520824F)

value: control un-differentiaed cells at day 14


title: 1 DL sy KA D7 (19)_(SNOWBALLs520824F)


title: 2 AS fp Adi D1 (42)_(SNOWBALLs520824F)

value: adipose synovium


title: 1 DL fp KA D7 (21)_(SNOWBALLs520824F)


title: ChIP-seq of GFP-RPRD1B, replicate 2

description:
RPRD1B_GFP_peaks.broadPeak.bed
RPRD1B_GFP_peaks.narrowPeak.bed
GFP_RPRD1B_merged_at_TTS_7.pdf

value: GFP-RPRD1B integrated

value: GFP tagged RPRD1B was expressed in an HEK293 cell line engineered with the Flp-in system under the control of doxycycline, and expression was induced for 96 hours with 1 µg/ml doxycycline.

value: Anti-GFP, Invitrogen, G10362. Rabbit monoclonal


title: hESC-11_control

city: Beijing

first: Jiansen

last: Lu

address: No. 5 Yiheyuan Road, Haidian District

department: Biomedical Pioneering Innovation Center (BIOPIC)

institute: Peking University

description: Control group of CLEVER-seq

data_processing:
All the de-multiplexed fastq reads were stripped to remove the low-quality bases and artificial sequences, including MALBAC primer and illumina adaptor sequences using trim galore (version: 0.3.3). The remaining cleaned reads were then aligned to the mm9 mouse and hg19 human reference genome using the Bismark tool (version: 0.23.0)  with the default parameters (Krueger and Andrews, 2011). Duplicated reads were removed using samtools (version: 1.9) (Li et al., 2009).
bigwig files were generated using the 'bamcoverage' module of deeptools (version 3.5.5).
Assembly: mm9 mouse
Supplementary files format and content: bigwig files contains the genome coverage

extract_protocol:
Single mouse/human embryonic stem cells, gametes and early embryos were picked into the lysis buffer (20 mMTris, 2 mM EDTA, 20 mMKCl, and 0.3% TritonX-100) using a mouth pipette. Genomic DNAs were released after treatment with proteinase (QIAGEN) at 50°C for 3 h. To label the 5fC adequately, 150 mM malononitrile (J&K) was added directly to the single cell lysate, which was allowed to react at 37°C for 20 h with continuously shaking in a thermomixer (Eppendorf, 850 r.p.m.). For the control group, same volume of H2O was used instead of malononitrile. To obtain the whole genome 5fC profiles from the single cells, MALBAC technique was applied to amplify the malononitrile-labeled genomic DNAs with minor modifications(Zong et al., 2012). Briefly, 11 rounds of quasi-linear pre-amplification and 15 cycles of exponential amplification were performed to obtain sufficient DNA for library construction.
Sequencing libraries were constructed under the instruction of NEBNext Ultra DNA Library Prep Kit for Illumina (NEB), and the final libraries were amplified using the DeepVent DNA polymerase (3’-5’ exo-, NEB).

value: hESC

value: Control group using H2O without malononitrile


title: 1 DL fp KA D14 (29)_(SNOWBALLs520824F)

value: German Landrace


title: hESC-12_control

description: Control group of CLEVER-seq


title: 1 DL fp KA D4 (13)_(SNOWBALLs520824F)

value: control un-differentiaed cells at day 4


title: ChIP-seq of GFP-RPRD1B, replicate 1


title: 1 DL sy Adi D4 (12)_(SNOWBALLs520824F)

value: fibrous synovium

value: Adipocyte at day 4


title: GFP input  ChIP, replicate1

description:
none
GFP_RPRD1B_merged_at_TTS_7.pdf

value: human embryonic kidney cells (HEK293)


title: ChIP-seq of GFP, replicate 2

description:
GFP_N20_peaks.broadPeak.bed
GFP_N20_peaks.narrowPeak.bed
GFP_RPRD1B_merged_at_TTS_7.pdf

value: GFP integrated


title: Scramble input  ChIP, replicate 2

description:
none
CRI_RPRD1B_merged_at_TTS_7.pdf

value: WT


title: ChIP-seq of GFP, replicate 1

value: GFP was expressed in an HEK293 cell line engineered with the Flp-in system under the control of doxycycline, and expression was induced for 96 hours with 1 µg/ml doxycycline.


title: Scramble input  ChIP, replicate 1

description:
none
CRI_RPRD1B_merged_at_TTS_7.pdf


title: 1 DL fp KA D1 (5)_(SNOWBALLs520824F)

value: control un-differentiaed cells at day 1


title: 1 DL fp D0_(SNOWBALLs520824F)

value: control un-differentiaed cells at day0


title: ChIP-seq of RPRD1B knockout, replicate 1

description:
RPRD1B_Cri_peaks.broadPeak.bed
RPRD1B_Cri_peaks.narrowPeak.bed
CRI_RPRD1B_merged_at_TTS_7.pdf

value: RPRD1B knockout

value: POLR2A N20,Santa Cruz, polyclonal antibody catalogue number sc-899


title: ChIP-seq of Scramble knockout, replicate 1

description:
CriScramble_0_N20_peaks.broadPeak.bed
CriScramble_0_N20_peaks.narrowPeak.bed
CRI_RPRD1B_merged_at_TTS_7.pdf


title: ChIP-seq of Scramble knockout, replicate 2


title: 1 DL fp Adi D14 (30)_(SNOWBALLs520824F)

value: adipose synovium

value: Adipocyte at day 14


title: CCND2.PAS.Sorted.replicate 4

data_processing:
Sequence reads are preprocessed by trimming staggers from the 5’end and anchors from the 3’end using an in-house perl script. Sequence reads that do not contain staggers and/or anchors are discarded.
The preprocessed sequences are then aligned to the TKOv3 gRNA library (containing 70,948 gRNAs targeting 18,053 protein coding genes (4 gRNAs/gene)) using Bowtie v1.1.2 (parameters -v2 -m1 -p4 --sam-nohead). The number of reads that is aligned to each gRNA in TKOv3 in each sample is counted using an in-house perl script. The R package DESeq2 is used to determine genes that show significantly different read counts between sorted and unsorted populations grown in parallel. Genes that have less than 4 guides are excluded from analysis .
To account for the difference in sequencing depth, the read counts of each guide are scaled by a factor, which equals to sum of reads for a guide across all genes, divided by the geometric mean of sums of all guides.
Statistical p-values are adjusted using Benjamini and Hochberg method for multi-testing correction
Assembly: hg19
Supplementary files format and content: tab-delimited text files contain guide count for each gene with up to 4 guides
Supplementary files format and content: tab-delimited text files contain output of DESeq2 analysis

extract_protocol:
Genomic DNA from unsorted and sorted (mCherry/GFP ratio increased) cells extracted by using Wizard Genomic DNA Purification Kit, and gDNA was PCR amplified.
Sequencing libraries were prepared from total of 50 µg (approximately 100-fold coverage of the TKOv3 library) of the extracted genomic DNA in two PCR steps. For the first PCR, a total of 14 PCR reactions were carried out with each containing 3.5 µg (a total of 50 µg) of genomic DNA in 50 μl reaction with 2× NEBNext Ultra II Q5 Master Mix (NEB, catalogue number M0544L) to amplify the gRNA inserts using the forward primer v2.1.F1 GAGGGCCTATTTCCCATGATTC, and reverse primer v2.1.R1 GTTGCGAAAAAGAACGTTCACGG. For the second PCR, the gRNA was amplified using 5 μl of the pooled first PCR products as a template in a 50 μl reaction with NEBNext Ultra II Q5 Master Mix by using the primers harboring Illumina TruSeq adapters i5 (with staggered sequences) and i7 barcodes.
The resulting libraries were sequenced on an Illumina HiSeq2500 to a depth of 10 to 20 millions, using single-read sequencing and completed with standard primers for dual indexing with HiSeq SBS Kit v4 reagents. The first 21 cycles of sequencing were dark cycles, or base additions without imaging. The actual 36-base read begins after the dark cycles and contains 2 index reads, in which i7 is read first, followed by the i5 sequences.

treatment_protocol: HEK293 cells were infected with pooled lentiviral genome-wide TKOv3 gRNA library at a MOI of 0.3 along with 4 µg/ml of polybrene.

value: Lentivirus


title: CCND2.PAS.Sorted.replicate 3


title: CCND2.PAS.Sorted.replicate 1


title: 1 DL fp Adi D4 (14)_(SNOWBALLs520824F)


title: 1 AS sy KA D4 (15)_(SNOWBALLs520824F)

value: Angeln Saddleback


title: 1 AS sy KA D7 (23)_(SNOWBALLs520824F)

value: control un-differentiaed cells at day 7


title: 1 AS sy D0_(SNOWBALLs520824F)


title: 1 AS sy Adi D4 (16)_(SNOWBALLs520824F)


title: ChIP-seq of RPRD1B knockout, replicate 2


title: CCND2.PAS.Unsorted.replicate 4


title: 1 AS fp KA D14 (33)_(SNOWBALLs520824F)

value: control un-differentiaed cells at day 14


title: CCND2.PAS.Unsorted.replicate 3


title: CCND2.PAS.Unsorted.replicate 2


title: 1 DL fp Adi D7 (22)_(SNOWBALLs520824F)

value: German Landrace

value: Adipocyte at day 7


title: 1 AS sy KA D14 (31)_(SNOWBALLs520824F)

value: fibrous synovium


title: 1 AS sy KA D1 (7)_(SNOWBALLs520824F)


title: 1 AS sy Adi D7 (24)_(SNOWBALLs520824F)


title: CCND2.PAS.Sorted.replicate 2

value: human embryonic kidney cells (HEK293)


title: CPEB2.PAS.Sorted.replicate 3


title: 1 AS sy Adi D1 (8)_(SNOWBALLs520824F)

value: Adipocyte at day 1


title: 1 AS sy Adi D14 (32)_(SNOWBALLs520824F)


title: 1 DL fp Adi D1 (6)_(SNOWBALLs520824F)


title: CPEB2.PAS.Sorted.replicate 1

value: WT


title: CPEB2.PAS.Sorted.replicate 2


title: 1 AS fp D0_(SNOWBALLs520824F)


title: 1 AS fp KA D1 (9)_(SNOWBALLs520824F)


title: 1 AS fp KA D4 (17)_(SNOWBALLs520824F)

value: control un-differentiaed cells at day 4


title: 1 AS fp KA D7 (25)_(SNOWBALLs520824F)


title: 1 AS fp Adi D4 (18)_(SNOWBALLs520824F)

value: Adipocyte at day 4


title: CPEB2.PAS.Unsorted. replicate 4


title: nMA-INA6 / F2, Removed by Centrifugation F2 (WPSC) (biol rep 5)

city: Würzburg

first: Regina

last: Ebert

address: Friedrich-Bergius-Ring 15

department: Department of Musculoskeletal Tissue Regeneration

institute: Universität Würzburg

description:
75 cycles ~400 M reads
DE.F1vsF2_annotated_200902.xlsx
DE.F2vsF3_annotated_200902.xlsx
DE.F1vsF2F3_annotated_200902.xlsx
DE.F2vsF1F3_annotated_200902.xlsx
DE.F3vsF1F2_annotated_200902.xlsx
nMA-INA6 / F2 (biol rep 5)

data_processing:
FASTQ files were merged to the respective sample. The quality of FASTQ files was assessed with FastQC tool, and a joint report was created with MultiQC tool.
Fastq files were aligned with STAR to the GRCh38 reference genome build. Quality and alignment statistics of final BAM files were assessed with samtools stats, and a joint report with FastQC reports by MultiQC was generated.
Raw read counts were generated with HTSeq with the union method. HTSeq runs internally in STAR. Differential gene expression analysis was done with edgeR in R 3.6.3, according to the edgeR manual.
Counts were merged and genes with zero counts in all samples were removed (number of genes: 36380).
The whole count table was annotated with R Bioconductor (Gentleman, n.d.) human annotation data package org.Hs.eg.db.
A DGEList Element was created with the raw counts, gene information, i.e. Ensembl GeneIDs, HUGO Symbol, Genename, and ENTREZ GeneIDs and a sample grouping meta data table.
Counts were filtered to keep only those genes which have at least 1 read per million in at least 2 samples (number of genes: 14136). Afterwards normalization factors were recalculated.
A design matrix was created with grouping factor by treatment condition (group=F1, F2, F3, which are abbreviations for CM-INA6, nMA-INA6, MA-INA6, respectively)
Dispersion was estimated, the resulting coefficient of biological variation (BCV) is 0.135, i.e. BCV expression values vary up and down by 13.5% between samples.
A generalized linear (glmQLFit function) model was fitted and pairwise comparisons were made, top significant differential expressed genes were written to a table
Assembly: GRCh38
Supplementary files format and content: Excel sheets of differential gene expression (aggregated biol. replicates) of pairwise comparisons between F1, F2, F3 (e.g. F1vsF2) and comparisons between individual samples and other two aggregated samples (e.g. F1vsF2F3). Columns include gene, ENSEMBL ID, log2 foldchange expression (logFC), p-value, CPM, etc.

molecule: polyA RNA

source_name: Blood

extract_protocol:
NucleoSpin RNA II Purification Kit (Macherey-Nagel) according to manual for total RNA yield of 300 - 1000 ng in max 50 µl
TruSeq RNA-seq after Oligo-dT enrichment according to manual

tag: Sex

value: Male

tag: age at_sampling

value: Blood

tag: disease

value: Multiple Myeloma

value: Plasma Cell

tag: sample group

value: 24 h Co-Culture with primary human mesenchymal stem cells

tag: antibody

value: anti-CD45 MACS purified

tag: subpopulation


title: MA-INA6 / F3, Remaining after Centrifugation F3 (WPSC) (biol rep 5)

description:
75 cycles ~400 M reads
DE.F2vsF3_annotated_200902.xlsx
DE.F1vsF3_annotated_200902.xls
DE.F1vsF2F3_annotated_200902.xlsx
DE.F2vsF1F3_annotated_200902.xlsx
DE.F3vsF1F2_annotated_200902.xlsx
MA-INA6 / F3 (biol rep 5)


title: CPEB2.PAS.Unsorted. replicate 3

value: Lentivirus


title: CM-INA6 / F1, hMSC-conditioned Medium F1 (WPSC Control) (biol rep 5)

description:
75 cycles ~400 M reads
DE.F1vsF2_annotated_200902.xlsx
DE.F1vsF3_annotated_200902.xls
DE.F1vsF2F3_annotated_200902.xlsx
DE.F2vsF1F3_annotated_200902.xlsx
DE.F3vsF1F2_annotated_200902.xlsx
CM-INA6 / F1 (biol rep 5)


title: 1 AS fp Adi D14 (34)_(SNOWBALLs520824F)

value: Angeln Saddleback

value: adipose synovium

value: Adipocyte at day 14


title: CPEB2.PAS.Sorted.replicate 4


title: CPEB2.PAS.Unsorted. replicate 2


title: CM-INA6 / F1, hMSC-conditioned Medium F1 (WPSC Control) (biol rep 4)

description:
75 cycles ~400 M reads
DE.F1vsF2_annotated_200902.xlsx
DE.F1vsF3_annotated_200902.xls
DE.F1vsF2F3_annotated_200902.xlsx
DE.F2vsF1F3_annotated_200902.xlsx
DE.F3vsF1F2_annotated_200902.xlsx
CM-INA6 / F1 (biol rep 4)


title: CCND2.PAS.Unsorted.replicate 1


title: CM-INA6 / F1, hMSC-conditioned Medium F1 (WPSC Control) (biol rep 3)

description:
75 cycles ~400 M reads
DE.F1vsF2_annotated_200902.xlsx
DE.F1vsF3_annotated_200902.xls
DE.F1vsF2F3_annotated_200902.xlsx
DE.F2vsF1F3_annotated_200902.xlsx
DE.F3vsF1F2_annotated_200902.xlsx
CM-INA6 / F1 (biol rep 3)


title: G452, 110-119 μm, replicate 2, scRNAseq

city: Celbridge

first: Lais

last: Barbosa Latorraca

state: Kildare

address: UCD Lyons Farm

department: Agriculture and Food Science

country: Ireland

institute: University College Dublin

data_processing:
Trim Galore (version 0.6.6) was used to trim raw sequence reads by removing adapter contamination and poor-quality reads with less than 20 Phred score. Only reads with a minimum 20 bp sequence length after trimming were retained for further processing. The data was mapped to the ARS-UCD 1.2 bovine genome using Hista2. Raw counts were quantified using SeqMonk software (version 11.0.10; Babraham Institute; https://www.bioinformatics.babraham.ac.uk/projects/seqmonk/).
Assembly: ARS-UCD 1.2
Supplementary files format and content: Tab-Delimited Text file containing raw read counts for each sample.

organism: Bos taurus

source_name: Oocyte

extract_protocol:
PCR tubes containing single oocyte samples snap-frozen in PBS + RLT-Plus Buffer at the collection day were transported in dry ice to the Babraham Institute, UK. Oocyte lysates were thawed and transferred to a 96-well plate and incubated with Dynabeads (MyOne Streptavidin C1, Life Technologies) annealed to Smart-seq2 oligo-dTs to capture polyadenylated mRNA. The remaining lysate containing the DNA was transferred to a new 96 well-plate for a subsequent bisulphite conversion analysis. The beads containing the mRNA were diluted in reverse transcription master mix using SuperScript™ II Reverse Transcriptase (Invitrogen) and reverse transcription was performed to produce cDNA.
cDNA was amplified using KAPA HiFi HotStart ReadyMix (Roche), purified with Ampure XP beads with a 1:0.9 ratio, and eluted into 20 μL of water. Amplified cDNA was quantified using a High Sensitivity DNA Assay chip (Agilent Technologies), and libraries were prepared using the Nextera XT Kit (Illumina) with ~300 pg of cDNA in two different replicates. A total of 179 oocytes were sequenced on the NextSeq500 HighOutput 150 bp Single End (replicate 1) and 75 bp Single End (replicate 2) with a sequence depth of ~2 million reads.

value: Oocyte

tag: experimental group

tag: diameter (um)


title: H261, >120 μm, replicate 2, scRNAseq


title: H221, >120 μm, replicate 2, scRNAseq


title: H433, >120 μm, replicate 2, scRNAseq


title: nMA-INA6 / F2, Removed by Centrifugation F2 (WPSC) (biol rep 3)

description:
75 cycles ~400 M reads
DE.F1vsF2_annotated_200902.xlsx
DE.F2vsF3_annotated_200902.xlsx
DE.F1vsF2F3_annotated_200902.xlsx
DE.F2vsF1F3_annotated_200902.xlsx
DE.F3vsF1F2_annotated_200902.xlsx
nMA-INA6 / F2 (biol rep 3)


title: MA-INA6 / F3, Remaining after Centrifugation F3 (WPSC) (biol rep 2)

description:
75 cycles ~400 M reads
DE.F2vsF3_annotated_200902.xlsx
DE.F1vsF3_annotated_200902.xls
DE.F1vsF2F3_annotated_200902.xlsx
DE.F2vsF1F3_annotated_200902.xlsx
DE.F3vsF1F2_annotated_200902.xlsx
MA-INA6 / F3 (biol rep 2)


title: G446, 110-119 μm, replicate 2, scRNAseq


title: CM-INA6 / F1, hMSC-conditioned Medium F1 (WPSC Control) (biol rep 2)

description:
75 cycles ~400 M reads
DE.F1vsF2_annotated_200902.xlsx
DE.F1vsF3_annotated_200902.xls
DE.F1vsF2F3_annotated_200902.xlsx
DE.F2vsF1F3_annotated_200902.xlsx
DE.F3vsF1F2_annotated_200902.xlsx
CM-INA6 / F1 (biol rep 2)


title: MA-INA6 / F3, Remaining after Centrifugation F3 (WPSC) (biol rep 4)

description:
75 cycles ~400 M reads
DE.F2vsF3_annotated_200902.xlsx
DE.F1vsF3_annotated_200902.xls
DE.F1vsF2F3_annotated_200902.xlsx
DE.F2vsF1F3_annotated_200902.xlsx
DE.F3vsF1F2_annotated_200902.xlsx
MA-INA6 / F3 (biol rep 4)


title: CPEB2.PAS.Unsorted. replicate 1


title: MA-INA6 / F3, Remaining after Centrifugation F3 (WPSC) (biol rep 1)

description:
75 cycles ~400 M reads
DE.F2vsF3_annotated_200902.xlsx
DE.F1vsF3_annotated_200902.xls
DE.F1vsF2F3_annotated_200902.xlsx
DE.F2vsF1F3_annotated_200902.xlsx
DE.F3vsF1F2_annotated_200902.xlsx
MA-INA6 / F3 (biol rep 1)


title: G445, 110-119 μm, replicate 2, scRNAseq


title: nMA-INA6 / F2, Removed by Centrifugation F2 (WPSC) (biol rep 1)

description:
75 cycles ~400 M reads
DE.F1vsF2_annotated_200902.xlsx
DE.F2vsF3_annotated_200902.xlsx
DE.F1vsF2F3_annotated_200902.xlsx
DE.F2vsF1F3_annotated_200902.xlsx
DE.F3vsF1F2_annotated_200902.xlsx
nMA-INA6 / F2 (biol rep 1)


title: G229, 110-119 μm, replicate 2, scRNAseq


title: G443, 110-119 μm, replicate 2, scRNAseq


title: 1 AS fp Adi D1 (10)_(SNOWBALLs520824F)


title: nMA-INA6 / F2, Removed by Centrifugation F2 (WPSC) (biol rep 4)

description:
75 cycles ~400 M reads
DE.F1vsF2_annotated_200902.xlsx
DE.F2vsF3_annotated_200902.xlsx
DE.F1vsF2F3_annotated_200902.xlsx
DE.F2vsF1F3_annotated_200902.xlsx
DE.F3vsF1F2_annotated_200902.xlsx
nMA-INA6 / F2 (biol rep 4)


title: G219, 110-119 μm, replicate 2, scRNAseq


title: F51, 100-109 μm, replicate 2, scRNAseq


title: PDAC organoids from patient 37

city: Chikusa-ku, Nagoya, Aichi

first: Kazuya

last: Ichihara

address: Furo-cho

country: Japan

institute: Nagoya University

data_processing:
Reads were mapped on hg19 reference genome using STAR version 2.7.3a and quantified using featureCounts version 1.6.4.
Assembly: hg19
Supplementary files format and content: comma-delimited text files include read counts for each Sample

source_name: Pancreas

extract_protocol:
Total RNA was extracted from the cultured PDO using ISOGEN reagent (NIPPON GENE, Tokyo, Japan) according to the manufacturer’s recommended protocol.
500 ng of total RNA were ribosomal RNA-depleted using NEBNext rRNA Depletion Kit (New England Biolabs, Ipswich, MA, USA), and converted to Illumina sequencing library using NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs).

value: Pancreas

value: PDAC organoids


title: PDAC organoids from patient 50


title: PDAC original sample from patient 50

value: PDAC original sample


title: F448, 100-109 μm, replicate 2, scRNAseq


title: F470, 100-109 μm, replicate 2, scRNAseq


title: F456, 100-109 μm, replicate 2, scRNAseq


title: PDAC organoids from patient 23


title: PDAC original sample from patient 37


title: F482, 100-109 μm, replicate 2, scRNAseq


title: MA-INA6 / F3, Remaining after Centrifugation F3 (WPSC) (biol rep 3)

description:
75 cycles ~400 M reads
DE.F2vsF3_annotated_200902.xlsx
DE.F1vsF3_annotated_200902.xls
DE.F1vsF2F3_annotated_200902.xlsx
DE.F2vsF1F3_annotated_200902.xlsx
DE.F3vsF1F2_annotated_200902.xlsx
MA-INA6 / F3 (biol rep 3)

value: WT


title: G451, 110-119 μm, replicate 2, scRNAseq


title: nMA-INA6 / F2, Removed by Centrifugation F2 (WPSC) (biol rep 2)

description:
75 cycles ~400 M reads
DE.F1vsF2_annotated_200902.xlsx
DE.F2vsF3_annotated_200902.xlsx
DE.F1vsF2F3_annotated_200902.xlsx
DE.F2vsF1F3_annotated_200902.xlsx
DE.F3vsF1F2_annotated_200902.xlsx
nMA-INA6 / F2 (biol rep 2)


title: H213, >120 μm, replicate 2, scRNAseq


title: F450, 100-109 μm, replicate 2, scRNAseq


title: PDAC organoids from patient 54


title: CM-INA6 / F1, hMSC-conditioned Medium F1 (WPSC Control) (biol rep 1)

description:
75 cycles ~400 M reads
DE.F1vsF2_annotated_200902.xlsx
DE.F1vsF3_annotated_200902.xls
DE.F1vsF2F3_annotated_200902.xlsx
DE.F2vsF1F3_annotated_200902.xlsx
DE.F3vsF1F2_annotated_200902.xlsx
CM-INA6 / F1 (biol rep 1)


title: F343, 100-109 μm, replicate 2, scRNAseq


title: PDAC organoids from patient 53


title: PDAC organoids from patient 47


title: F240, 100-109 μm, replicate 2, scRNAseq


title: E484, 90-99 μm, replicate 2, scRNAseq


title: PDAC organoids from patient 46


title: PDAC original sample from patient 23


title: E481, 90-99 μm, replicate 2, scRNAseq


title: E410, 90-99 μm, replicate 2, scRNAseq


title: PDAC organoids from patient 31


title: PDAC organoids from patient 25


title: E363, 90-99 μm, replicate 2, scRNAseq


title: PDAC organoids from patient 35


title: E358, 90-99 μm, replicate 2, scRNAseq


title: PDAC organoids from patient 13


title: E345, 90-99 μm, replicate 2, scRNAseq


title: E319, 90-99 μm, replicate 2, scRNAseq


title: scRNA-seq_E981 iExo-Myc#1 treated mouse

city: Houston

first: Kalluri

last: Lab

state: Texas

address: 1901 East Rd

institute: UT MD Anderson Cancer Center

data_processing:
Using the DroNc-seq alignment pipeline that takes into account both intronic and exonic reads, we obtained the gene expression profiles for individual nuclei in the form of digital gene expression (DGE) matrix for each sample.
We collected ~5000 nuclei for each sample, with 200-400 genes detected per nucleus, depending on the quality of the sample and sequencing depth. There were a total of 40,000 unique Gencode v.27 identifiers or transcript fragments detected across all samples.
Assembly: hg38
Library strategy: DroNc-seq

source_name: U87 tumor xenograft

extract_protocol:
Nuclei from frozen tumor were isolated from ~40 mg of both iExo-Myc and iExo-Sca tissue samples using the EZ Prep buffer (Sigma). Nuclei and custom-made barcode (BC) beads (ChemGenes) were loaded at a concentration of 300,000 nuclei/ml in NSB and 350,000 beads/ml in lysis buffer respectively in separate 3 ml syringes. A 75-micron microfluidic device fabricated in-house was used to run the DroNc-Seq experiments at 1.5, 1.5 and 12 ml/hr flow-rated for the nuclei, BC beads and carrier oil channels respectively, with approximately 22 minutes per collection.
Following collection, drops were broken, and uniquely barcoded cDNA was generated from the barcoded polyT-mRNA hybrids using reverse transcription. These barcoded cDNA attached to the polymer beads called STAMPs, and washed several times in TE buffer containing tween and SDS, and then treated with exonuclease I enzyme (Sigma) to digest and remove any barcodes that did not have a cDNA attached to it. The number of recovered beads or STAMPS were counted. Approximately 20 wells in a PCR plate at 5000 beads per well, and amplified through 15 cycles of PCR. Supernatant from each well were pooled and cleaned with 0.6x SPRI beads. Purified cDNA product was quantified using a Qubit DNA assay kit and 450-650 pg of each sample was used as input for Nextera library preparation reactions (12 cycles). Tagmented libraries were quantified on Agilent BioAnalyzer High sensitivity chip before sequencing.

value: U87 tumor xenograft

tag: strain

tag: age

value: 6-8 weeks old

value: MSC Exosomes encasing human anti-Myc siRNA#1


title: E305, 90-99 μm, replicate 2, scRNAseq


title: D475, 80-89 μm, replicate 2, scRNAseq


title: scRNA-seq_E972 iExo-Scrc#1 treated mouse

tag: tissue

value: MSC Exosomes encasing scramble-siRNA#1


title: 929E iExo-Scr#2 treated mouse

data_processing:
BCL files were converted to FASTQ using Illumina bcl2fastq/2.20.0 module.
The FASTQ files were  aligned to hg19+mm10 reference genome for PDX samples (mm10 added to remove mouse reads) using STAR (2.6.0b) and followed by mark_duplication (http://broadinstitute.github.io/picard/) to generate bam files.
Assembly: hg19

extract_protocol:
Total RNA was extracted with Trizol (Invitrogen) and cleaned up using a RNeasy extraction kit (Qiagen). RNA concentration was measured by NanoDrop, and RNA quality was assessed using Bioanalyzer RNA 6000 Nano assay (Agilent). RNA quality was assessed using Bioanalyzer RNA 6000 Nano assay. Samples with a RNA integrity number score ≥7.2 were submitted for sequencing to the MD Anderson Cancer Center Sequencing and ncRNA core using Illumnia Next Seq 500 was used for the sequencing.
Library construction and Illumina-ready sequencing library generation were prepared by following the manufacturer’s guidelines. cDNA concentration was estimated using High Sensitivity dsDNA Qubit kit and quantified using HS DNA Bioanalyzer. Following capture and lysis, cDNA was synthesized and amplified to construct Illumina sequencing libraries and sequenced with Illumina Nextseq 500.

tag: cell line

value: MSC Exosomes encasing scramble-siRNA#2

tag: time

value: At euthanasia


title: scRNA-seq_E990 iExo-Myc#1 treated mouse

tag: cell type


title: 925E iExo-Scr#2 treated mouse

tag: genotype

tag: treatment


title: E324, 90-99 μm, replicate 2, scRNAseq


title: D400, 80-89 μm, replicate 2, scRNAseq


title: D364, 80-89 μm, replicate 2, scRNAseq


title: 924E iExo-Scr#2 treated mouse


title: scRNA-seq_E968 iExo-Scrc#1 treated mouse


title: D359, 80-89 μm, replicate 2, scRNAseq


title: D357, 80-89 μm, replicate 2, scRNAseq


title: 921E iExo-Myc#2 treated mouse

value: MSC Exosomes encasing human anti-Myc siRNA#2


title: D356, 80-89 μm, replicate 2, scRNAseq


title: 922E iExo-Scr#2 treated mouse


title: D323, 80-89 μm, replicate 2, scRNAseq


title: 735E iExo-Myc#2 treated mouse


title: D318, 80-89 μm, replicate 2, scRNAseq


title: C473, 70-79 μm, replicate 2, scRNAseq


title: 731E iExo-Myc#2 treated mouse


title: control group 2

city: Jinan

first: Guiping

address: 202 Gongye North Road, Licheng District, Jinan City, Shandong Province

institute: Shandong Academy of Agricultural Sciences

data_processing:
A cDNA library constructed by the pooled RNA was sequenced run with Illumina NovaseqTM 6000 sequence platform.Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads.To get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
Fastp and perl scripts in house were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases.
De novo assembly of the transcriptome was performed with Trinity 2.4.0. Trinity groups transcripts into clusters based on shared sequence content. Such a transcript cluster is very loosely referred to as a 'gene'. The longest transcript in the cluster was chosen as the 'gene' sequence (aka Unigene). All assembled Unigenes were aligned against the non-redundant (Nr) protein database (http://www.ncbi.nlm.nih.gov/), Gene ontology (GO) (http://www.geneontology.org), SwissProt (http://www.expasy.ch/sprot/), Kyoto Encyclopedia of Genes and Genomes (KEGG) (http://www.kegg.jp/kegg/) and eggNOG (http://eggnogdb.embl.de/) databases using DIAMOND with a threshold of Evalue<0.00001.
Salmon was used to perform expression level for Unigenes by calculating TPM. The differentially expressed Unigenes were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with statistical significance (p value < 0.05) by R package edgeR.
Assembly: De novo assembly of the transcriptome was performed with Trinity 2.4.0.
Supplementary files format and content: gene_expression.xlsx

organism: Osmia excavata

source_name: Osmia excavata Alfken

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA).  1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) following manufacturer's protocols.

value: Osmia excavata Alfken

value: control


title: 728E iExo-Myc#2 treated mouse


title: 799E iExo-Myc#2 treated mouse


title: C471, 70-79 μm, replicate 2, scRNAseq


title: control group3


title: C467, 70-79 μm, replicate 2, scRNAseq


title: E991 iExo-Scr#1 treated mouse

value: At euthanisa


title: control group 1


title: E985 iExo-Scr#1 treated mouse


title: E974 iExo-Scr#1 treated mouse


title: C431, 70-79 μm, replicate 2, scRNAseq


title: decocooning group2

value: Water immersion


title: Vasculogenic Mimicry Control, 48 hours, replicate 4

city: Santiago

first: Gareth

last: Owen

state: Region Metropolitana

address: Avenida Libertador Bernardo O'Higgins 340

department: Department of Physiology

country: Chile

institute: Pontificia Universidad Catolica De Chile

data_processing:
Data was processed by BGI Genomics following their protocol. In brief, firstly, the reads mapped to rRNAs were removed and got the rawdata, then the low quality reads were filtered (more than 20% of the bases qualities are lower than 10), reads with adaptors and reads with unknown bases (N bases more than 5%) to get the clean reads. Then those clean reads were mapped onto reference genome (hg38), followed with novel gene prediction, SNP & INDEL calling and gene splicing detection. Finally, DEGs (differentially expressed genes) were identified between samples and clustering analysis and functional annotations were done.
Assembly: hg38
Supplementary files format and content: Spreadsheet file includes FPKM gene data for each sample
Supplementary files format and content: Spreadsheet file includes FPKM transcript data for each sample

growth_protocol: HEY-A8 cells were maintened in DMEM/F-12 media, supplemented with 10% fetal bovine serum and 1% antibiotics, in a humidified space with 5% CO2 at 37°C.

extract_protocol:
RNA was obtained at different timepoints of Vasculogenic Mimicry formation (2, 8, 24 and 48 hours) using TriZol (Invitrogen) and the following the manufacturers protocol. Samples were sent to BGI Genomics for the RNA-seq analysis.
RNA libraries were constructed by BGI Genomics following their protocol. In brief, the first step in the workflow involves purifying the poly-A containing mRNA molecules using poly-T oligoattached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter. The products are then purified and enriched with PCR amplification. We then quantified the PCR yield by Qubit and pooled samples together to make a single strand DNA circle (ssDNA circle), which gave the final library.

treatment_protocol: Vasculogenic Mimicry formation was induced by seeding HEY-A8 cells on top of Matrigel for 1 hour, and then adding RPMI1640 media, supplemented with 15% fetal bovine serum and 1% antibiotics, in a humidified space with 5% CO2 at 37°C. For control experiment, Matrigel was denatured using dry-heat at 65°C for 10 minutes. After that the protocol is the same as the treatment.

value: High-Grade Serous Ovarian Cancer

value: Denatured Matrigel (no Vasculogenic Mimicry)


title: Vasculogenic Mimicry Control, 48 hours, replicate 3


title: C407, 70-79 μm, replicate 2, scRNAseq

value: Oocyte


title: Vasculogenic Mimicry Treatment, 48 hours, replicate 3

value: Natured Matrigel (Vasculogenic Mimicry)


title: Vasculogenic Mimicry Treatment, 48 hours, replicate 2


title: C387, 70-79 μm, replicate 2, scRNAseq


title: E990 iExo-Myc#1 treated mouse


title: Vasculogenic Mimicry Control, 48 hours, replicate 2


title: decocooning group3

last: Wang


title: Vasculogenic Mimicry Treatment, 48 hours, replicate 1


title: C347, 70-79 μm, replicate 2, scRNAseq


title: Vasculogenic Mimicry Control, 48 hours, replicate 1


title: E983 iExo-Myc#1 treated mouse


title: C327, 70-79 μm, replicate 2, scRNAseq


title: Vasculogenic Mimicry Treatment, 24 hours, replicate 4


title: E961 iExo-Myc#1 treated mouse


title: decocooning group1


title: Vasculogenic Mimicry Control, 24 hours, replicate 4


title: Vasculogenic Mimicry Treatment, 48 hours, replicate 4


title: Vasculogenic Mimicry Treatment, 24 hours, replicate 3


title: B465, 60-69 μm, replicate 2, scRNAseq


title: Vasculogenic Mimicry Control, 24 hours, replicate 2


title: Vasculogenic Mimicry Control, 24 hours, replicate 3


title: Vasculogenic Mimicry Treatment, 24 hours, replicate 1


title: B464, 60-69 μm, replicate 2, scRNAseq


title: E962 iExo-Scr#1 treated mouse


title: MLL-AF9_pool2

city: Montreal

first: Brian

last: Wilhelm

state: Quebec

address: 2950 Chem. de Polytechnique

department: Institut de recherche en immunologie et en cancérologie

institute: Université de Montréal

data_processing:
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 32, based on Ensembl 98) using STAR version 2.7.1a
Gene expressions were obtained both as readcount directly from STAR as well as computed using RSEM in order to obtain normalized gene and transcript level expression, in TPM values, for these stranded RNA libraries
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: blood

growth_protocol: Cells used for RNA-seq were not grown in culture. After prepartion of cells in medai at standard density, samples were immediately collected for RNA-seq.

extract_protocol:
Total RNA from transduced cells (~1x10^5) was isolated using TRIzol LS as recommended by the manufacturer (Invitrogen) and then further purified using RNeasy columns (Qiagen). Libraries were subjected to standard Illumina sequencing protocols.
standard Illumina Truseq RNA-seq protocol followed

treatment_protocol: Cells were isoalted and placed into media supplemented with FLT3L (100ng/ml), SCF (100ng/ml), IL-3 (20ng/ml), IL-6 (20ng/ml), SR1 (500nM) and UM171 (35nM) at a denisty of 0.5x10^6 cells/mL prioro to collection in Trizol.

value: Untreated

value: Model-secondary

tag: fab

tag: fusion


title: Vasculogenic Mimicry Treatment, 24 hours, replicate 2


title: MLL-AF9_pool1


title: Vasculogenic Mimicry Control, 24 hours, replicate 1


title: CD34_pool3

value: Cord blood


title: Vasculogenic Mimicry Treatment, 8 hours, replicate 4


title: Vasculogenic Mimicry Control, 8 hours, replicate 4


title: Vasculogenic Mimicry Treatment, 8 hours, replicate 3


title: PDX-B3

value: Patient - PDX


title: B440, 60-69 μm, replicate 2, scRNAseq


title: B438, 60-69 μm, replicate 2, scRNAseq


title: Vasculogenic Mimicry Control, 8 hours, replicate 3


title: PDX-B1


title: Vasculogenic Mimicry Control, 8 hours, replicate 2


title: Vasculogenic Mimicry Treatment, 8 hours, replicate 1


title: B432, 60-69 μm, replicate 2, scRNAseq


title: CD34BW


title: B430, 60-69 μm, replicate 2, scRNAseq


title: Vasculogenic Mimicry Control, 8 hours, replicate 1


title: B472, 60-69 μm, replicate 2, scRNAseq


title: CD34-pool-Connie


title: Vasculogenic Mimicry Control, 2 hours, replicate 4


title: Vasculogenic Mimicry Treatment, 2 hours, replicate 3


title: Vasculogenic Mimicry Treatment, 2 hours, replicate 2


title: B409, 60-69 μm, replicate 2, scRNAseq


title: AF9-CRISPR11990

value: Human model


title: Vasculogenic Mimicry Control, 2 hours, replicate 3


title: A461, <60 μm, replicate 2, scRNAseq


title: Vasculogenic Mimicry Control, 2 hours, replicate 2


title: Vasculogenic Mimicry Treatment, 2 hours, replicate 1


title: AF9-POOL


title: A460, <60 μm, replicate 2, scRNAseq


title: 19H236-NUP98

value: Patient

value: NOS


title: Vasculogenic Mimicry Control, 2 hours, replicate 1


title: 16H110

value: Patient -Primary


title: B16F10 cells, MTyr-OANPs 48 h, rep3

city: shanghai

first: yang

last: chen

address: siping road

institute: tongji university

data_processing:
Basecalls performed using CASAVA version 1.4
Assembly: mm9
Supplementary files format and content: excel files include pfkm values for each sample

source_name: B16F10 cells

growth_protocol: Mouse Melanoma cells (B16F10) were cultured in RPMI 1640 medium (Hyclone; Logan, UT, USA) supplemented with 10% fetal bovine serum (Hyclone; Logan, UT, USA) and 50 IU/mL penicillin-streptomycin, at 37 °C in a water-jacketed incubator containing 5% wt/vol CO2.

extract_protocol:
Total RNA was isolated and purified from B16F10 cells using TRIzol (Invitrogen) according to the manufacture. The concentration of RNA was checked using Qubit (Invitrogen), and the integrity was assessed using Bioanalyzer 2100 (Agilent). 1 μg total RNA was used for poly (A) RNA purification using Dynabeads Oligo (dT) 25-61005 (Thermo Fisher) with two rounds of purification.
the sequencing library was constructed through PCR, with the program set to 3 stages as following: denaturation at 95 °C for 3 min (first stage); denaturation at 98 °C for 15 secs, annealing at 60 °C for 15 secs, and extension at 72 °C for 30 secs (second stage, run 8 cycles); and final extension at 72 °C for 5 min. At last, the sequencing library was sequenced using illumine Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) with the model of 2 × 150 bp paired-end sequencing (PE150).

treatment_protocol: MTyr-OANPs treatment for 48hrs

value: B16F10 cells

value: melanoma cell

value: WT

value: MTyr-OANPs 48h


title: B16F10 cells, MTyr-OANPs 48 h, rep2


title: A439, <60 μm, replicate 2, scRNAseq


title: A459, <60 μm, replicate 2, scRNAseq


title: B16F10 cells, no treatment, rep3

value: no treatment


title: 10H152


title: B16F10 cells, no treatment, rep2


title: A435, <60 μm, replicate 2, scRNAseq


title: B16F10 cells, no treatment, rep1


title: A429, <60 μm, replicate 2, scRNAseq


title: U16-1730


title: RNA seq, KO, male mice-3, 18-22w

city: New Haven

first: Pai

address: 333 cedar

institute: Yale University

data_processing:
Raw RNA Seq fastq files were processed using fastp tool (version 0.20.0)
Cleaned reads were aligned using STAR (version 2.7.9)
Expression quantification for aligned reads was performed using featureCounts (version 2.0.0)
an expression threshold of >6 read counts in at least 20% of samples; genes not meeting this expression threshold were eliminated from downstream analyses
Assembly: mm10
Supplementary files format and content: csv file includes TPM normalized expression values for each sample

source_name: Spleen

extract_protocol:
RNA was harvested using RNA mini kit (Qiangen)
RNA libraries for RNA-seq were prepared using rRNA depletion kit following manufactures protocols

value: Spleen

value: B cell

value: Tlr9 fl/fl CD19 Cre+/- B6


title: RNA seq, KO, male mice-1, 18-22w


title: T21


title: A428, <60 μm, replicate 2, scRNAseq

value: Oocyte


title: NTF

value: Untreated


title: A426, <60 μm, replicate 2, scRNAseq


title: RNA seq, Ctr, male mice-3, 18-22w

value: Tlr9 fl/fl CD19 Cre-/- B6


title: A427, <60 μm, replicate 2, scRNAseq


title: 1 AS fp Adi D7 (26)_(SNOWBALLs520824F)

description: SMSCs derived from porcine synovial membrane

data_processing: Data were analysed with Affymetrix GCOS 1.1.1 software using global scaling to a target signal of 500.

extract_protocol: Total RNA was isolated using TRI Reagent (Sigma, Taufkirchen, Germany) according to the manufacturer’s protocol. After DNaseI treatment the RNA was cleaned up using the RNeasy Kit (Qiagen, Hilden, Germany).

tag: breed

value: Angeln Saddleback

value: adipose synovium

value: Adipocyte at day 7


title: L693

value: Human model-tertiary


title: neurons, excised, scRNA-seq

city: New York

first: Hao

last: Jin

state: New York

address: 3227 Broadway

institute: Columbia University

description: 10 X Genomics

data_processing:
The barcode demultiplexing, alignment and molecular counting were made using Cell Ranger analysis software
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: brain

extract_protocol:
For sample 1, we isolated single cells from the cNST as previously described with the following modifications. Briefly, mice were anaesthetized with isoflurane and transcardially perfused with ice-cold carbogenated (95% O2, 5% CO2) NMDG-HEPES-ACSF (93 mM NMDG, 2.5 mM KCl, 1.2 mM NaH2PO4, 30 mM NaHCO3, 20 mM HEPES, 25 mM glucose, 10 mM MgSO4, 1 mM CaCl2, 1 mM kynurenic-acid Na salt, 5 mM Na-ascorbate, 2 mM Thiourea, 3 mM Na-pyruvate, pH 7.4). The brainstems were rapidly extracted and sliced into 300 μm sections containing the cNST using a vibratome (Leica, #VT-1000S) in ice-cold NMDG-HEPES-ACSF solution with continuous carbogenation. The cNSTs were dissected, pooled (from 5 animals), and digested in Trehalose-HEPES-ACSF (92 mM NaCl, 2.5 mM KCl, 1.25 mM NaH2PO4, 30 mM NaHCO3, 20 mM HEPES, 25 mM glucose, 2 mM MgSO4, 2 mM CaCl2, 1 mM kynurenic-acid Na salt, 2.5 wt/vol trehalose, pH 7.4) containing Papain (20 U ml-1, Worthington, #LK003150) and DNase I (25 U ml-1) at 35oC for approximately one hour. Using Pasteur pipettes with progressively narrowing tip diameters, the tissue was triturated in DNase I-containing (25 U ml-1) Trehalose-HEPES-ACSF solution to form single-cell suspension. The dissociated cells were passed through 40 μm filter and resuspended in Resuspension-ACSF (117 mM NaCl, 2.5 mM KCl, 1.25 mM NaH2PO4, 30 mM NaHCO3, 20 mM HEPES, 25 mM glucose, 1 mM MgSO4, 2 mM CaCl2, 1 mM kynurenic-acid Na salt, 0.05% BSA, pH 7.4).
The resulting cell suspension was processed by the Columbia Genome Core to encapsulate and barcode individual cells using the 10X Genomics Chromium system.
For sample 2, we used TRAP2; Ai9 mice that were TRAP-labeled with tdTomato in response to LPS. Cells from the cNST were isolated as described above. The cell suspension was stained with DRAQ5 (Thermoscientific, #62254) and Calcein Violet (Thermoscientific, #C34858) to label viable cells, prior to FACS. A total of 288 tdTomato+ LPS TRAPped cells and 96 tdTomato- cells were sorted into 96-well plates pre-loaded with cell lysis buffer containing 0.1% TritonX-100, SuperaseIN (Ambion, #AM2694), 1 mM dNTP and 1 μM capture primer (i.e. bar-coding).
cDNA was synthesized using Maxima Reverse Transcriptase (Thermoscientific, #EP0753) according to manufacturer’s instruction. cDNA from all the wells/cells was combined, followed by clean-up using Silane beads (Thermoscientific #37002D). Pooled cDNA was amplified using Kapa HotStart Mix with SMART PCR primer (0.2 μM), and then purified using AMPureXP beads (Beckman Coulter Life Sciences #A63880). 0.6 ng of cDNA was used as input to prepare libraries using Nextera XT kit (Illumina #FC-131-1024).

value: brain


title: L691


title: B16F10 cells, MTyr-OANPs 48 h, rep1


title: RNA seq, KO, male mice-2, 18-22w


title: A416, <60 μm, replicate 2, scRNAseq


title: K5A


title: AF9_mouse

value: Human model-secondary


title: A412, <60 μm, replicate 2, scRNAseq


title: NK cells, rDKK1, 2

city: SAINT LOUIS

first: Seunghyun

last: Lee

state: MO

address: 660 S. Euclid Ave., Box 8228

institute: Washington University in St.Louis

data_processing:
Partek Flow software (Partek Inc., St. Louis, MO) was used for data analysis. Briefly, sequenced reads were aligned with STAR 2.7.8a index (Mus musculus – mm10 assembly, Whole genome index). Raw read counts were obtained by quantitating aligned reads using HTSeq with Ensembl Transcripts release 102 annotation model. Raw read counts were then normalized using counts per million (CPM) and offset of 0.0001 was added to all normalized read counts. Normalized read counts for each mRNA were statistically modeled using Partek Flow’s Gene Specific Analysis (GSA) approach.
Assembly: mm10
Supplementary files format and content: tab-delimited text files includes raw counts for each sample

source_name: sorted cell

extract_protocol:
RNA was isolated from the sorted cells using RNeasy Micro Kit (Qiagen). Total RNA integrity was determined using Agilent Bioanalyzer or 4200 Tapestation. Library preparation was performed with 10ng of total RNA with a Bioanalyzer RIN score greater than 8.0. ds-cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) per manufacturer's protocol. cDNA was fragmented using a Covaris E220 sonicator using peak incident power 18, duty factor 20%, cycles per burst 50 for 120 seconds. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases.
ds-cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) per manufacturer's protocol.

value: sorted cell

value: Primary cells

value: immune cells


title: NK cells, PBS, 2


title: NK cells, PBS, 3


title: NK cells, rDKK1, 3


title: NK cells, PBS, 1


title: PyMT tumor cells, mDKN01, 3

source_name: tumor

value: tumor

value: tumor cells


title: PyMT tumor cells, mDKN01, 2


title: A380, <60 μm, replicate 2, scRNAseq


title: PyMT tumor cells, mDKN01, 1


title: A406, <60 μm, replicate 2, scRNAseq


title: RNA seq, Ctr, male mice-2, 18-22w

value: Spleen


title: RNA seq, Ctr, male mice -1, 18-22w

value: B cell


title: 11193_mouseAF6


title: PyMT tumor cells, IgG, 3


title: A377, <60 μm, replicate 2, scRNAseq


title: PyMT tumor cells, IgG, 2


title: PyMT tumor cells, IgG, 1


title: 19H066

value: Patient -Primary


title: A371, <60 μm, replicate 2, scRNAseq

value: Oocyte


title: A368, <60 μm, replicate 2, scRNAseq


title: NK cells, rDKK1, 1


title: Mammary tumor from Q3738 (R26(RhoC/+);FloxNeoNeuNT;MMTV-CreNLST) mouse [R-21]

first: Sean

last: Egan

address: 686 Bay St.

institute: Hospital for Sick Children

description:
R_vs_N_DifExp_FPKMs_DESeq2
R_vs_N_Filt_DifExp_FPKMs_edgeR

data_processing:
The quality of the data is assessed using FastQC v.0.11.5
Adaptors are trimmed using Trim Galore v. 0.5.0 and the quality of the trimmed reads is re-assessed with FastQC
The trimmed reads are also screened for presence of rRNA and mtRNA sequences using FastQ-Screen v.0.10.0
The raw trimmed reads are aligned to the reference genome using the STAR aligner, v.2.6.0c.
The filtered STAR alignments are processed to extract raw read counts for genes using htseq-count v.0.6.1p2
Assembly: GRCm38.p6, M25 Gencode gene models
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes FPKM values for each sample

source_name: Mammary tumor

extract_protocol:
RNA was isolated from tumors using Qiagen RNeasy Kit (Cat # 74104)
Libraries were prepared using Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus  kit following manufacturer's protocol

value: Mammary tumor


title: Mammary tumor from (R26(RhoC/+);FloxNeoNeuNT;MMTV-CreNLST) mouse [R-18]


title: Mammary tumor from P497_3LB (R26(RhoC/+);FloxNeoNeuNT;MMTV-CreNLST) mouse [R-15]


title: Souris-MLL-AF6-11

value: Untreated


title: Mammary tumor from P497_3L (R26(RhoC/+);FloxNeoNeuNT;MMTV-CreNLST) mouse [R-16]


title: A350, <60 μm, replicate 2, scRNAseq


title: 16H073


title: A329, <60 μm, replicate 2, scRNAseq


title: ML-2

value: cell line-Primary


title: AF6_sample3_mouse


title: Mammary tumor from N9934 (R26(RhoC/+);FloxNeoNeuNT;MMTV-CreNLST) mouse [R-12]


title: AF6_sample1_mouse


title: Mammary tumor from P497_1R (R26(RhoC/+);FloxNeoNeuNT;MMTV-CreNLST) mouse [R-13]


title: Mammary tumor from P497_1L (R26(RhoC/+);FloxNeoNeuNT;MMTV-CreNLST) mouse [R-14]


title: Mammary tumor from N9931 (R26(RhoC/+);FloxNeoNeuNT;MMTV-CreNLST) mouse [R-10]


title: Mammary tumor from N9255_4L (R26(RhoC/+);FloxNeoNeuNT;MMTV-CreNLST) mouse [R-7]


title: Mammary tumor from N9255_3R (R26(RhoC/+);FloxNeoNeuNT;MMTV-CreNLST) mouse [R-6]


title: A282, <60 μm, replicate 2, scRNAseq


title: mEpiSC-12_control

description: Control group of CLEVER-seq

value: mouse epiblast stem cell

value: Control group using H2O without malononitrile


title: 10H111


title: A227, <60 μm, replicate 2, scRNAseq


title: Mammary tumor from N8907 (R26(RhoC/+);FloxNeoNeuNT;MMTV-CreNLST) mouse [R-2]


title: Mammary tumor from N7682 (R26(RhoC/+);FloxNeoNeuNT;MMTV-CreNLST) mouse [R-1]


title: A209, <60 μm, replicate 2, scRNAseq


title: Mammary tumor from P7972 (control) mouse [N-17]

value: FloxNeoNeuNT;MMTV-CreNLST