title: GBM_36, Control

city: Brno

first: Katerina

last: Amruz Cerna

state: Czech Republic

address: Kamenice 3

department: Department of Histology and Embryology

country: Czech Republic

institute: Faculty of Medicine, Masaryk University

data_processing:
The quality of raw reads with removed UMIs was verified using FastQC v0.11.9 and the potential contamination was screened by FastQ_Screen v0.11.1.
The “TATA” spacer, low-quality reads, and adaptor sequences were removed using TrimmomaticSE v0.36 with parameters “HEADCROP:4 ILLUMINACLIP: Lexogen_quantseq.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36”.
Ribosomal and mitochondrial reads were removed using sortmerna v2.1b.
BAM files with alignment were created with STAR v2.7.0f.
The count tables were generated using the script htseq-count v0.11.4 with annotation version GRCh38.87 and parameter “-m union”. ENSEMBL-IDs were used as identifiers of transcripts.
The counted data were analyzed using R-package DESeq2 v1.34.0.
Assembly: GRCh38
Supplementary files format and content: dds_not-normalized_all.csv contains raw counts with genes in rows and samples in columns.
Supplementary files format and content: dds_normalized_all.csv contains counts normalized by DESeq2 with genes in rows and samples in columns.

growth_protocol:
With a few modifications, the generation of COs followed the protocol described in (Camp et al., 2015; Lancaster and Knoblich, 2014).
U87-GFP and dTomato cell lines were grown on cell culture dishes in DMEM/F12 (Dulbecco’s Modified Eagle Medium) with 10% FBS, 1% Glutamax, 1% non-essential amino acids, and 0.5% Penicillin/Streptomycin and passaged using TrypLE (all from Thermo Fisher Scientific).
To generate spheroids, cells were detached using TrypLE, counted, and seeded at the density of 2000 cells/well in poly-HEMA treated non-adherent V-shaped 96 well plate.
The plate was centrifuged at 200g/2 min to facilitate spheroid formation. Fluorescently labeled U87 spheroids were used for GLICO model experiments after 24 hours.

extract_protocol:
RNA was isolated with RNABlue (TopBio, R013) without Dnase I pretreatment. 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using QuantSeq 3'mRNA-Seq Library Prep FWD for Illumina (Lexogen, 015.96) with i5 6 nt Unique Dual Indexing Add-on Kit (Lexogen, 047.96) and UMI Second Stranded Synthesis Module for QuantSeq FWD (Illumina, Read 1; 081.96).

treatment_protocol:
For setting up a GLICO model without ECM protein scaffolds, we used poly-HEMA treated non-adherent 12 well plates with CODM with vitamin A. A single U87-GFP spheroid was placed on the bottom edge of each well. Subsequently, a single CO was positioned on the top of the spheroid.
One side of the 12 well plate was then placed on top of a 6 cm culture dish resulting in an inclined plane. This inclination ensured the attachment of the glioblastoma spheroid and the CO.
The GLICO was allowed to form for 24 hours in the inclined plate. Subsequently, the plate was kept in the incubator without shaking, and half of the volume of the medium was changed carefully every two days, making sure not to separate the GLICO apart.
After 4 days, the plate was moved to an orbital shaker and cultured for 40 days for NGS analysis.

tag: cell line

value: glioblastoma cell

value: control spheroid


title: GBM_34, Control

status: Public on Feb 22 2023

type: SRA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell type

tag: treatment


title: scRNAseq-mm-Wt-HL-E115-Rep1-L20666

city: Berlin

first: Giulia

last: Cova

address: 63-73 Ihnestrasse

country: Germany

institute: Max Planck Institute

description:
scRNAseq-matrix-counts.mtx.gz
scRNAseq-genes_ids.tsv.gz
scRNAseq-cellmetadata.tsv.gz
scRNAseq-barcodes.tsv.gz

library_source: transcriptomic single cell

data_processing:
The Cell Ranger pipeline v.3 (10x Genomics lnc.) was used for each scRNA-seq sample in order to de-multiplex the raw base call files, to generate the fastq files, and to perform the alignment against a custom mouse reference genome mm9 to create the unique molecular identifier (UMI) count matrix.
Only cells with more than 2000 detected genes and less than 10% of mitochondrial UMI counts were considered for further analysis.
We used scrublet (https://doi.org/10.1016/j.cels.2018.11.005) to identify potential duplets in our dataset. We filtered out cells with a scrublet score higher than 0.2.
Each sample dataset was normalized independently using the SCT method (10.1186/s13059-019-1874-1) implemented in Seurat3 (10.1038/nbt.4096) R package and then integrated the datasets using the Seurat3 IntegrateData function and considering the top 2000 most variable genes.
The first 20 Principal Components of this joint dataset were calculated and used for UMAP projection and cell clustering. To delimitate the major hindlimb bud cell types, we used the Louvain algorithm implemented in the Seurat3 function FindClusters and the expression of well-known marker genes for the limb-comprising cell types. For the AER cluster, we used the marker gene Fgf8. Differential gene expression between the WT and the Dup cells was estimated by modelling the gene expression as a function of the genotype across cells. We fitted a quasi-Poisson distribution to calculate the effect of the Dup genotype on the gene expression distribution of each gene using the monocle3 strategy. We tested that such effect was not equal to 0. We use this condition association effect to rank the genes and identified the pathways associated with the top 200 genes using the Enrichr tool from the Maayan lab50. Finally, we confirmed that the top perturbed genes associated to the muscle pathways are more frequently expressed in the Dup AER cells.
Assembly: mm10

organism: Mus musculus

source_name: Hindlimb

extract_protocol:
The cell concentration was determined using an automated cell counter (Bio-Rad) and cells were subjected to single-cell RNA-sequencing (10x Genomic, ChromiumTM Single Cell 3’ v2; one reaction per time point and per strain has been used) aiming for a target cell recovery of up to 10,000 sequenced cells per sequencing library (time point and strain). Single-cell libraries were generated according to the manufacturer’s instructions with the following conditions: 8 PCR cycles were ran during cDNA amplification and 12 PCR cycles were ran during library generation/sample indexing to increase library complexity. Libraries were sequenced with a minimum of 230 million paired end reads.
scRNA-seq 10X Genomics

treatment_protocol: Limbs from E11.5 mouse embryos were dissected in 1xPBS. A single-cell suspension was obtained by incubating the tissue for 10 min at 37 °C in 200 µL Gibco trypsin-EDTA 0.05% (Thermo Fisher Scientific) and 20 µL 5% BSA (Sigma-Aldrich). Digestion was then blocked by adding 400 µL of BSA 5%. Cells were then resuspended by pipetting and filtered using a 0.40 µm cell strainer (Falcon). Cells were washed once with 0.04% BSA with a centrifugation step performed for 5 min at 1200 r.p.m then resuspended in 0.04% BSA.

tag: tissue

value: Hindlimb

tag: genotype

value: Wild Type

tag: embryonic stage

tag: strain


title: scRNAseq-mm-Inv1-HL-E115-Rep1-L27833

description:
scRNAseq_HL_G4_Inv_mm_features.tsv.gz
scRNAseq_HL_G4_Inv_mm_mm_counts.mtx.gz
scRNAseq_HL_G4_Inv_mm_mm_barcodes.tsv.gz

value: Mutant_Homozygous inversion

value: G4 ESC


title: GBM_32, Control


title: scRNAseq-mm-G4-HL-E115-Rep1-L27831


title: scRNAseq-mm-Inv1-FL-E115-Rep1-L27832

description:
scRNAseq_FL_G4_Inv_mm_features.tsv.gz
scRNAseq_FL_G4_Inv_mm_counts.mtx.gz
scRNAseq_FL_G4_Inv_mm_barcodes.tsv.gz

source_name: Forelimb

value: Forelimb


title: CD69- Trh_cells_ Lung_cGVHD

city: Duarte

first: wei

last: chen

state: CA

address: 1500 E Duarte Rd

department: Cancer Biology-BRI

country: USA

institute: City of Hope National Medical Center

data_processing:
Reads were aligned to mouse TRA and TRB reference (NG_007044.1 and NG_006980.1) using miXCR v2.1 with default settings.
Clone assembly and extraction were also done using miXCR v2.1 with default settings
Assembly: mouse mm10
Supplementary files format and content: text delimited text files containing the TRA and TRB clones
Library strategy: TCR-CDR3 sequencing

source_name: cGVHD

extract_protocol:
mRNAs from Tfh cells were extracted with “Qiagen miRNeasy Micro Kit”.
TCR-CDR3 libraries were prepared using Takara Smarter Mouse TCR a/b Profiling kit following manufacturer's recommendations

value: CD4+T cells subsets

value: Lung


title: GBM_29, GLICO model

source_name: U-87 GFP+ sorted

value: glioblastoma cell (GFP+ sorted)

value: cerebral organoid co-culture


title: GBM_33, GLICO model


title: ST45CD8posPD1neg

city: Adelaide

first: Katie

last: Williams

state: South Australia

address: Sturt Rd, Bedford park

country: Australia

institute: Flinders University

data_processing:
For high-dimensional RNA-seq, R (version 3.5.1) and edgeR library (PMID: 19910308) was applied to analyse the sequencing data.
Features were considered differentially expressed if they satisfied a 2-fold-change and 0.05 adjusted p value cut-off unless otherwise specified. The Benjamini-Hochberg method was used to calculate p-values adjusted for multiple hypotheses.
Gene enrichment analysis was performed with Ingenuity pathway analysis (IPA) software (Qiagen, Hilden, Germany).
Gene set variation analysis (GSVA) was performed in R using the “GSVA” package (PMID: 23323831). The enrichment scores were calculated using the magnitude difference between the largest positive and negative random walk deviations. Paired student t-testing were used to compare enrichment scores between groups.
Assembly: Raw sequence data in FASTQ format were assessed for quality (FastQC, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and ribosomal RNA content (sortmeRNA, http://bioinfo.lifl.fr/RNA/sortmerna/).
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Synovial tissue

extract_protocol:
Total RNA was extracted and processed for library construction by Cofactor Genomics (St. Louis, MO). Total RNA was extracted from cell pellets using the protocol for Arcturus PicoPure™ RNA Isolation Kit (Thermo Fisher, Waltham, MA). Total RNA was reverse-transcribed using an Oligo(dT) primer, and limited cDNA amplification was performed using the SMARTer® Ultra® Low Input RNA Kit for Sequencing – v4 (Takara Bio USA, Inc., Mountain View, CA).
The resulting full-length cDNA was fragmented and tagged, followed by limited PCR enrichment to generate the final cDNA sequencing library (Nextera® XT DNA Library Prep, Illumina, San Diego, CA).
Libraries were sequenced as single-end 75 base reads on a NextSeq500 (Illumina, San Diego, CA) following the manufacturer’s protocols.

value: Synovial tissue

tag: patient id

tag: cell type cd4

tag: cell type cd8

value: pos

tag: pd-1 expression

value: neg

tag: timepoint

value: BL

tag: disease status

value: irAE


title: GBM_31, GLICO model


title: ST45CD4posPD1pos


title: ST45CD4posPD1neg


title: SF45CD4posPD1neg

source_name: Synovial fluid

value: Synovial fluid


title: SF42CD8posPD1pos

value: RA


title: ST42CD4posPD1pos


title: scRNAseq-mm-G4-FL-E115-Rep1-L27830


title: scRNAseq-mm-Dup-HL-E115-Rep1-L20667

value: Mutant_Homozygous duplication


title: SF42CD8posPD1neg


title: SF42CD4posPD1pos


title: SF42CD4posPD1neg


title: CD69- Trh_cells_Liver_cGVHD

value: Liver


title: Tfh2-Spleen_No_GVHD

source_name: No GVHD

value: Spleen


title: RASTCD8posPD1pos


title: RASTCD8posPD1neg


title: RASTCD4posPD1pos


title: RASFCD8posPD1neg


title: RASFCD8posPD1pos


title: RASFCD4posPD1pos


title: RAPBMCCD8posPD1neg

source_name: Peripheral blood

value: Peripheral blood


title: RAPBMCCD8posPD1pos


title: RAPBMCCD4posPD1pos


title: HCPBMCCD8posPD1pos

value: HC


title: HCPBMCCD8posPD1neg


title: HCPBMCCD4posPD1neg


title: AP4817PBMCCD8posPD1neg


title: RAPBMCCD4posPD1neg


title: AP4817PBMCCD8posPD1pos


title: HCPBMCCD4posPD1pos


title: AP4817PBMCCD4posPD1neg


title: AP4817PBMCCD4posPD1pos


title: AP20PBMCCD8posPD1neg


title: AP20PBMCCD4posPD1pos


title: AP1618PBMCCD8posPD1pos


title: AP1618PBMCCD8posPD1neg


title: AP1518PBMCCD8posPD1pos


title: AP1618PBMCCD4posPD1neg


title: AP20PBMCCD4posPD1neg


title: AP1518PBMCCD4posPD1pos


title: AP1618PBMCCD4posPD1pos


title: AP1518PBMCCD8posPD1neg


title: AP0218PBMCCD8posPD1neg


title: AP1518PBMCCD4posPD1neg


title: AP0218PBMCCD8posPD1pos


title: RASTCD4posPD1neg


title: RASFCD4posPD1neg


title: 42PBMCCD8posPD1pos


title: AP0218PBMCCD4posPD1neg


title: 42PBMCCD8posPD1neg


title: 42PBMCCD4posPD1neg


title: EVWF048_39_15_HSC_P2_H4

city: Oxford

first: Claus

last: Nerlov

address: John Radcliffe Hospital, University of Oxford

department: MRC Molecular Haematology Unit

country: United Kingdom

institute: Weatheral Institute of Molecular Medicine

data_processing:
Short reads (51 bp) from RNA sequencing of mouse HSCs were mapped using Tophat to the mouse genome (mm10) with a supplied set of RefSeq gene model as the input. The mapping parameters ‘-g 1’ was used to allow one alignment to the reference for a given read.
RNAseq: Cells with <500.000 mapped reads with per cent of mapping to the mitochondrial chromosome>10% and<1,000 detected genes were excluded from further analysis. A total of 458 HSCs fulfilled these criteria.
Genome_build: mm10
Supplementary_files_format_and_content: Raw count matrices were generated by featureCounts software and reads per kilobase of transcript per million mapped reads (RPKM) expression values were calculated using a custom R script.

source_name: Bone marrow

extract_protocol:
Single cells from bone marrow were index sorted by FACS
Illumina sequencing libraries were constructed using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Clontech) according to manufacturer's protocol.

tag: phenotype

value: PEM HSC


title: EVWF048_39_15_HSC_P2_H10


title: EVWF048_39_15_HSC_P2_F2


title: EVWF048_39_15_HSC_P2_D9


title: EVWF048_39_15_HSC_P2_E9


title: miRNA F. nucleatum 1

city: Chengdu

first: Keyi

last: Zhang

address: No. 14, section 3, Renmin South Road

country: China

institute: West China Hospital of Stomatology, Sichuan University

data_processing:
Library quality was assessed on the Agilent Bioanalyzer 2100 system and sequenced on the Illumina hiseQ2000/2500 platform.Library quality was assessed on the Agilent Bioanalyzer 2100 system and sequenced on the Illumina hiseQ2000/2500 platform.
For miRNA reads, alignment was performed with Bowtie. Meantime, miREvo and miRDeep2 was used to find novel miRNA with default parameters.
All miRNAs were counted and normalized with TPM, and the correlation analysis of gene expression among samples was conducted.
The aberrantly-expressed miRNAs between experimental and control groups were analyzed by DESeq2.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM values for each Sample ...

source_name: aorta

growth_protocol: Twenty-six 6-week-old C57/BL6 ApoE-/- mice were raised in a specific pathogen-free controlled animal laboratory under 12-h dark/light photophase and fed adaptively for 1 week. After that, 0.2mg/L trimethoprim and 1.0mg/L sulfa were added to the drinking water for 1 week, and the bilateral first molars were rubbed with chlorhexidine mouthwash.

extract_protocol:
The experimental procedures were performed in accordance with the standard test procedures provided by Illumina. 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). The RNA integrity was assessed by Agilent 2100 with RIN number >7.0.
Small RNA sequencing libraries were prepared using TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, USA).

treatment_protocol: In the F.nucleatum group, 0.1ml F.nucleatum suspension was applied to the first molar in the mouth to establish the periodontitis model every alternate day for 12 weeks, while the control group was given 0.5ml 2%CMC.

value: aorta

value: F. nucleatum-infected


title: miRNA F. nucleatum 3


title: miRNA Control 3

value: non-infected


title: miRNA F. nucleatum 2


title: miRNA Control 1


title: EVWF048_39_15_HSC_P2_A6


title: EVWF048_39_15_HSC_P1_G1


title: EVWF048_39_15_HSC_P2_A1


title: EVWF048_39_15_HSC_P2_C2


title: EVWF048_39_15_HSC_P1_G10


title: EVWF048_39_15_HSC_P2_F10


title: EVWF048_39_15_HSC_P2_D5


title: EVWF048_39_15_HSC_P1_F1


title: EVWF048_39_15_HSC_P1_E2


title: EVWF048_39_15_HSC_P1_E4


title: EVWF048_39_15_HSC_P1_E7


title: EVWF048_39_15_HSC_P1_D1


title: EVWF048_39_15_HSC_P1_E1


title: EVWF048_39_15_HSC_P1_C3


title: 42PBMCCD4posPD1pos


title: miRNA Control 2


title: EVWF048_39_15_HSC_P1_C1


title: EVWF048_39_15_HSC_P1_B4


title: EVWF048_39_15_HSC_P1_B1


title: EVWF048_39_15_HSC_P2_A4


title: EVWF047_36_24_HSC_P2_H7

value: PLT HSC


title: EVWF048_39_15_HSC_P1_A2


title: EVWF047_36_24_HSC_P2_H10


title: EVWF047_36_24_HSC_P2_G9


title: EVWF047_36_24_HSC_P2_G12


title: EVWF047_36_24_HSC_P2_G7


title: EVWF047_36_24_HSC_P2_G10


title: EVWF047_36_24_HSC_P2_F8


title: EVWF047_36_24_HSC_P2_F11


title: EVWF047_36_24_HSC_P2_F12


title: EVWF047_36_24_HSC_P2_E9


title: EVWF047_36_24_HSC_P2_F7


title: EVWF048_39_15_HSC_P1_C4


title: EVWF047_36_24_HSC_P2_F9


title: EVWF047_36_24_HSC_P2_E7


title: EVWF047_36_24_HSC_P2_D8


title: EVWF047_36_24_HSC_P2_E8


title: EVWF047_36_24_HSC_P2_D9


title: EVWF047_36_24_HSC_P2_E11


title: EVWF047_36_24_HSC_P2_D7


title: EVWF047_36_24_HSC_P2_D11


title: EVWF047_36_24_HSC_P2_E10


title: EVWF047_36_24_HSC_P2_D12


title: EVWF047_36_24_HSC_P2_D10


title: EVWF047_36_24_HSC_P2_C9


title: EVWF047_36_24_HSC_P2_C8


title: EVWF047_36_24_HSC_P2_C12


title: EVWF047_36_24_HSC_P2_C7


title: EVWF047_36_24_HSC_P2_G8


title: EVWF047_36_24_HSC_P2_C11


title: EVWF047_36_24_HSC_P2_C10


title: EVWF047_36_24_HSC_P2_B7


title: EVWF047_36_24_HSC_P2_B8


title: EVWF047_36_24_HSC_P2_F10


title: EVWF047_36_24_HSC_P2_B11


title: EVWF047_36_24_HSC_P2_B10


title: EVWF047_36_24_HSC_P2_B12


title: EVWF047_36_24_HSC_P2_A8


title: EVWF047_36_24_HSC_P2_A11


title: EVWF047_36_24_HSC_P2_A7


title: EVWF047_36_24_HSC_P2_A10


title: EVWF047_36_24_HSC_P2_A12


title: EVWF047_36_24_HSC_P1_G6


title: EVWF047_36_24_HSC_P1_H5


title: EVWF047_36_24_HSC_P1_G5


title: EVWF047_36_24_HSC_P1_G4


title: EVWF047_36_24_HSC_P1_F5


title: EVWF047_36_24_HSC_P1_H6


title: EVWF047_36_24_HSC_P1_F6


title: EVWF047_36_24_HSC_P1_G2


title: EVWF047_36_24_HSC_P1_F3


title: EVWF047_36_24_HSC_P1_G1


title: EVWF047_36_24_HSC_P1_E6


title: EVWF047_36_24_HSC_P1_E3


title: EVWF047_36_24_HSC_P1_E5


title: EVWF047_36_24_HSC_P1_E2


title: EVWF047_36_24_HSC_P1_E4


title: EVWF047_36_24_HSC_P1_E1


title: EVWF047_36_24_HSC_P2_A9


title: EVWF047_36_24_HSC_P1_D5


title: EVWF047_36_24_HSC_P1_D6


title: EVWF047_36_24_HSC_P1_D4


title: EVWF047_36_24_HSC_P1_D3


title: EVWF047_36_24_HSC_P1_C6


title: EVWF047_36_24_HSC_P1_C5


title: EVWF047_36_24_HSC_P1_D2


title: EVWF047_36_24_HSC_P1_D1


title: EVWF047_36_24_HSC_P1_B5


title: EVWF047_36_24_HSC_P1_F2


title: EVWF047_36_24_HSC_P1_C3


title: EVWF047_36_24_HSC_P1_B4


title: EVWF047_36_24_HSC_P1_F1


title: EVWF047_36_24_HSC_P1_C4


title: EVWF047_36_24_HSC_P1_C1


title: EVWF047_36_24_HSC_P1_B2


title: EVWF047_36_24_HSC_P1_B3


title: EVWF047_36_24_HSC_P1_F4


title: EVWF047_36_24_HSC_P1_C2


title: EVWF047_36_24_HSC_P1_B6


title: EVWF047_36_24_HSC_P1_B1


title: EVWF047_36_24_HSC_P1_A6


title: EVWF047_36_24_HSC_P1_A5


title: EVWF047_36_24_HSC_P1_A3


title: EVWF047_36_24_HSC_P1_A4


title: EVWF047_36_24_HSC_P1_A1


title: EVWF047_36_24_HSC_P1_A2


title: Evwf044_35_13_HSC_P2_H9


title: Evwf044_35_13_HSC_P2_H8


title: Evwf044_35_13_HSC_P2_H11


title: Evwf044_35_13_HSC_P2_H7


title: Evwf044_35_13_HSC_P2_H10


title: Evwf044_35_13_HSC_P2_G12


title: Evwf044_35_13_HSC_P2_G10


title: Evwf044_35_13_HSC_P2_G11


title: Evwf044_35_13_HSC_P2_F9


title: Evwf044_35_13_HSC_P2_F8


title: Evwf044_35_13_HSC_P2_G7


title: Evwf044_35_13_HSC_P2_E9


title: Evwf044_35_13_HSC_P2_F11


title: Evwf044_35_13_HSC_P2_E8


title: Evwf044_35_13_HSC_P2_E12


title: Evwf044_35_13_HSC_P2_F10


title: Evwf044_35_13_HSC_P2_E10


title: Evwf044_35_13_HSC_P2_D8


title: Evwf044_35_13_HSC_P2_D9


title: Evwf044_35_13_HSC_P2_F12


title: Evwf044_35_13_HSC_P2_F7


title: Evwf044_35_13_HSC_P2_D7


title: Evwf044_35_13_HSC_P2_E11


title: Evwf044_35_13_HSC_P2_D12


title: Evwf044_35_13_HSC_P2_D10


title: Evwf044_35_13_HSC_P2_C9


title: Evwf044_35_13_HSC_P2_D11


title: Evwf044_35_13_HSC_P2_C11


title: Evwf044_35_13_HSC_P2_C10


title: Evwf044_35_13_HSC_P2_C8


title: Evwf044_35_13_HSC_P2_C7


title: Evwf044_35_13_HSC_P2_G9


title: Evwf044_35_13_HSC_P2_G8


title: Evwf044_35_13_HSC_P2_C12


title: Evwf044_35_13_HSC_P2_E7


title: Evwf044_35_13_HSC_P2_B12


title: Evwf044_35_13_HSC_P2_B8


title: Evwf044_35_13_HSC_P2_B7


title: Evwf044_35_13_HSC_P2_A9


title: Evwf044_35_13_HSC_P2_B11


title: Evwf044_35_13_HSC_P2_A8


title: Evwf044_35_13_HSC_P2_A7


title: Evwf044_35_13_HSC_P2_A11


title: Evwf044_35_13_HSC_P2_A10


title: Evwf044_35_13_HSC_P2_A12


title: Evwf044_35_13_HSC_P1_H4


title: Evwf044_35_13_HSC_P1_H5


title: Evwf044_35_13_HSC_P1_H2


title: Evwf044_35_13_HSC_P1_H6


title: Evwf044_35_13_HSC_P1_H1


title: Evwf044_35_13_HSC_P1_G6


title: Evwf044_35_13_HSC_P1_G3


title: Evwf044_35_13_HSC_P1_G1


title: Evwf044_35_13_HSC_P1_F5


title: Evwf044_35_13_HSC_P1_F4


title: Evwf044_35_13_HSC_P1_F2


title: Evwf044_35_13_HSC_P2_B9


title: Evwf044_35_13_HSC_P1_F3


title: Evwf044_35_13_HSC_P1_F1


title: Evwf044_35_13_HSC_P1_G2


title: Evwf044_35_13_HSC_P1_E6


title: Evwf044_35_13_HSC_P1_E2


title: Evwf044_35_13_HSC_P1_H3


title: Evwf044_35_13_HSC_P1_E3


title: Evwf044_35_13_HSC_P1_D5


title: Evwf044_35_13_HSC_P1_E1


title: Evwf044_35_13_HSC_P1_D4


title: Evwf044_35_13_HSC_P1_D6


title: Evwf044_35_13_HSC_P1_D3


title: Evwf044_35_13_HSC_P1_D2


title: Evwf044_35_13_HSC_P1_D1


title: Evwf044_35_13_HSC_P1_G5


title: Evwf044_35_13_HSC_P1_G4


title: Evwf044_35_13_HSC_P1_C5


title: Evwf044_35_13_HSC_P1_C3


title: Evwf044_35_13_HSC_P1_F6


title: Evwf044_35_13_HSC_P1_C4


title: Evwf044_35_13_HSC_P1_C2


title: Evwf044_35_13_HSC_P1_C1


title: Evwf044_35_13_HSC_P1_B6


title: Evwf044_35_13_HSC_P1_B4


title: Evwf044_35_13_HSC_P1_B5


title: Evwf044_35_13_HSC_P1_B3


title: Evwf044_35_13_HSC_P1_B2


title: Evwf044_35_13_HSC_P1_B1


title: Evwf044_35_13_HSC_P1_A6


title: Evwf044_35_13_HSC_P1_A5


title: Evwf044_35_13_HSC_P1_E5


title: Evwf044_35_13_HSC_P1_A4


title: Evwf044_35_13_HSC_P1_A3


title: Evwf038_27_29_HSC_P2_H9


title: Evwf044_35_13_HSC_P1_A2


title: Evwf044_35_13_HSC_P1_A1


title: Evwf038_27_29_HSC_P2_H12


title: Evwf038_27_29_HSC_P2_H7


title: Evwf038_27_29_HSC_P2_H8


title: Evwf038_27_29_HSC_P2_H11


title: Evwf038_27_29_HSC_P2_G12


title: Evwf038_27_29_HSC_P2_G9


title: Evwf038_27_29_HSC_P2_G10


title: Evwf038_27_29_HSC_P2_G11


title: Evwf044_35_13_HSC_P1_C6


title: Evwf038_27_29_HSC_P2_H10


title: Evwf038_27_29_HSC_P2_G8


title: Evwf038_27_29_HSC_P2_F8


title: Evwf038_27_29_HSC_P2_F7


title: Evwf038_27_29_HSC_P2_F12


title: Evwf038_27_29_HSC_P2_F9


title: Evwf038_27_29_HSC_P2_E8


title: Evwf038_27_29_HSC_P2_E9


title: Evwf038_27_29_HSC_P2_F11


title: Evwf038_27_29_HSC_P2_E12


title: Evwf038_27_29_HSC_P2_E11


title: Evwf038_27_29_HSC_P2_D9


title: Evwf038_27_29_HSC_P2_E10


title: Evwf038_27_29_HSC_P2_D8


title: Evwf038_27_29_HSC_P2_D7


title: Evwf038_27_29_HSC_P2_D11


title: Evwf038_27_29_HSC_P2_D12


title: Evwf038_27_29_HSC_P2_A12


title: Evwf038_27_29_HSC_P2_C10


title: Evwf038_27_29_HSC_P2_A9


title: Evwf038_27_29_HSC_P2_C11


title: Evwf038_27_29_HSC_P2_B11


title: Evwf038_27_29_HSC_P2_E7


title: Evwf038_27_29_HSC_P2_C7


title: Evwf038_27_29_HSC_P2_B8


title: Evwf038_27_29_HSC_P2_C9


title: Evwf038_27_29_HSC_P2_C8


title: Evwf038_27_29_HSC_P1_H6


title: Evwf038_27_29_HSC_P2_B10


title: Evwf038_27_29_HSC_P2_B12


title: Evwf038_27_29_HSC_P2_F10


title: Evwf038_27_29_HSC_P1_H4


title: Evwf038_27_29_HSC_P1_H2


title: Evwf038_27_29_HSC_P2_B9


title: Evwf038_27_29_HSC_P2_C12


title: Evwf038_27_29_HSC_P2_A7


title: Evwf038_27_29_HSC_P2_D10


title: Evwf038_27_29_HSC_P2_B7


title: Evwf038_27_29_HSC_P2_A11


title: Evwf038_27_29_HSC_P2_A10


title: Evwf038_27_29_HSC_P1_H5


title: Evwf038_27_29_HSC_P1_H3


title: Evwf038_27_29_HSC_P2_A8


title: Evwf038_27_29_HSC_P1_G6


title: Evwf038_27_29_HSC_P1_H1


title: Evwf038_27_29_HSC_P1_F4


title: Evwf038_27_29_HSC_P1_F6


title: Evwf038_27_29_HSC_P1_F5


title: Evwf038_27_29_HSC_P1_E5


title: Evwf038_27_29_HSC_P1_E4


title: Evwf038_27_29_HSC_P1_F3


title: Evwf038_27_29_HSC_P1_E3


title: Evwf038_27_29_HSC_P1_E6


title: Evwf038_27_29_HSC_P1_E2


title: Evwf038_27_29_HSC_P1_G3


title: Evwf038_27_29_HSC_P1_E1


title: Evwf038_27_29_HSC_P1_F1


title: Evwf038_27_29_HSC_P1_D2


title: Evwf038_27_29_HSC_P1_D5


title: Evwf038_27_29_HSC_P1_D1


title: Evwf038_27_29_HSC_P1_G1


title: Evwf038_27_29_HSC_P1_D6


title: Evwf038_27_29_HSC_P1_C6


title: Evwf038_27_29_HSC_P1_C5


title: Evwf038_27_29_HSC_P1_C4


title: Evwf038_27_29_HSC_P1_C3


title: Evwf038_27_29_HSC_P1_C2


title: Evwf038_27_29_HSC_P1_G5


title: Evwf038_27_29_HSC_P1_B5


title: Evwf038_27_29_HSC_P1_C1


title: Evwf038_27_29_HSC_P1_B4


title: Evwf038_27_29_HSC_P1_G2


title: Evwf038_27_29_HSC_P1_F2


title: Evwf038_27_29_HSC_P1_B1


title: Evwf038_27_29_HSC_P1_B2


title: Evwf038_27_29_HSC_P1_D3


title: Evwf038_27_29_HSC_P1_A6


title: Evwf038_27_29_HSC_P1_B3


title: Evwf038_27_29_HSC_P1_A1


title: Evwf038_27_29_HSC_P1_A4


title: Evwf038_27_29_HSC_P1_A3


title: Evwf037_27_9_HSC_P2_H8

value: MUL HSC


title: Evwf038_27_29_HSC_P1_A2


title: Evwf037_27_9_HSC_P2_H11


title: Evwf037_27_9_HSC_P2_G9


title: Evwf037_27_9_HSC_P2_G8


title: Evwf037_27_9_HSC_P2_G12


title: Evwf037_27_9_HSC_P2_G7


title: Evwf037_27_9_HSC_P2_G10


title: Evwf037_27_9_HSC_P2_F9


title: Evwf037_27_9_HSC_P2_F12


title: Evwf037_27_9_HSC_P2_G11


title: Evwf037_27_9_HSC_P2_F8


title: Evwf037_27_9_HSC_P2_F11


title: Evwf037_27_9_HSC_P2_E9


title: Evwf037_27_9_HSC_P2_E8


title: Evwf037_27_9_HSC_P2_F10


title: Evwf037_27_9_HSC_P2_E7


title: Evwf037_27_9_HSC_P2_E12


title: Evwf038_27_29_HSC_P1_A5


title: Evwf037_27_9_HSC_P2_E10


title: Evwf037_27_9_HSC_P2_E11


title: Evwf037_27_9_HSC_P2_D9


title: Evwf037_27_9_HSC_P2_D7


title: Evwf037_27_9_HSC_P2_D12


title: Evwf037_27_9_HSC_P2_H10


title: Evwf037_27_9_HSC_P2_D10


title: Evwf037_27_9_HSC_P2_D11


title: Evwf037_27_9_HSC_P2_C8


title: Evwf037_27_9_HSC_P2_C7


title: Evwf037_27_9_HSC_P2_C10


title: Evwf037_27_9_HSC_P2_C11


title: Evwf037_27_9_HSC_P2_B9


title: Evwf037_27_9_HSC_P2_B


title: Evwf037_27_9_HSC_P2_B10


title: Evwf037_27_9_HSC_P2_A9


title: Evwf037_27_9_HSC_P2_A10


title: Evwf037_27_9_HSC_P2_B8


title: Evwf037_27_9_HSC_P2_A12


title: Evwf037_27_9_HSC_P2_A11


title: Evwf037_27_9_HSC_P1_H5


title: Evwf037_27_9_HSC_P1_H6


title: Evwf037_27_9_HSC_P1_G6


title: Evwf037_27_9_HSC_P1_G5


title: Evwf037_27_9_HSC_P1_H2


title: Evwf037_27_9_HSC_P2_C9


title: Evwf037_27_9_HSC_P1_G3


title: Evwf037_27_9_HSC_P1_G4


title: Evwf037_27_9_HSC_P2_C12


title: Evwf037_27_9_HSC_P1_F3


title: Evwf037_27_9_HSC_P1_G2


title: Evwf037_27_9_HSC_P1_F4


title: Evwf037_27_9_HSC_P1_F5


title: Evwf037_27_9_HSC_P1_G1


title: Evwf037_27_9_HSC_P1_F6


title: Evwf037_27_9_HSC_P1_F1


title: Evwf037_27_9_HSC_P1_F2


title: Evwf037_27_9_HSC_P2_H9


title: Evwf037_27_9_HSC_P1_E6


title: Evwf037_27_9_HSC_P1_E3


title: Evwf037_27_9_HSC_P1_E4


title: Evwf037_27_9_HSC_P1_E5


title: Evwf037_27_9_HSC_P1_H4


title: Evwf037_27_9_HSC_P1_D5


title: Evwf037_27_9_HSC_P1_D6


title: Evwf037_27_9_HSC_P1_D1


title: Evwf037_27_9_HSC_P1_D4


title: Evwf037_27_9_HSC_P1_D3


title: Evwf037_27_9_HSC_P1_D2


title: Evwf037_27_9_HSC_P1_C6


title: Evwf037_27_9_HSC_P1_C4


title: Evwf037_27_9_HSC_P1_C5


title: Evwf037_27_9_HSC_P1_C2


title: Evwf037_27_9_HSC_P1_C1


title: Evwf037_27_9_HSC_P1_B5


title: Evwf037_27_9_HSC_P1_B1


title: Evwf037_27_9_HSC_P1_B2


title: Evwf037_27_9_HSC_P1_B4


title: Evwf037_27_9_HSC_P1_A6


title: Evwf037_27_9_HSC_P1_A5


title: Evwf037_27_9_HSC_P1_B6


title: Evwf037_27_9_HSC_P1_A4


title: Evwf037_27_9_HSC_P1_A3


title: Evwf037_27_9_HSC_P1_A1


title: Evwf037_27_9_HSC_P1_E2


title: Evwf037_27_9_HSC_P1_A2


title: Evwf037_27_9_HSC_P1_E1


title: Evwf037_26_17_HSC_P2_H9


title: Evwf037_26_17_HSC_P2_H8


title: Evwf037_26_17_HSC_P2_H10


title: Evwf037_26_17_HSC_P2_G8


title: Evwf037_26_17_HSC_P2_F9


title: Evwf037_26_17_HSC_P2_G10


title: Evwf037_26_17_HSC_P2_F8


title: Evwf037_26_17_HSC_P2_F11


title: Evwf037_26_17_HSC_P2_F7


title: Evwf037_27_9_HSC_P1_B3


title: Evwf037_26_17_HSC_P2_F10


title: Evwf037_26_17_HSC_P2_E8


title: Evwf037_26_17_HSC_P2_E9


title: Evwf037_26_17_HSC_P2_E7


title: Evwf037_26_17_HSC_P2_E10


title: Evwf037_26_17_HSC_P2_D7


title: Evwf037_26_17_HSC_P2_D8


title: Evwf037_26_17_HSC_P2_D12


title: Evwf037_26_17_HSC_P2_C9


title: Evwf037_26_17_HSC_P2_C8


title: Evwf037_26_17_HSC_P2_C12


title: Evwf037_26_17_HSC_P2_B8


title: Evwf037_26_17_HSC_P1_H6


title: Evwf037_26_17_HSC_P2_B9


title: Evwf037_26_17_HSC_P2_A10


title: Evwf037_26_17_HSC_P1_H3


title: Evwf037_26_17_HSC_P1_H4


title: Evwf037_26_17_HSC_P2_B7


title: Evwf037_26_17_HSC_P2_B10


title: Evwf037_26_17_HSC_P2_A12


title: Evwf037_26_17_HSC_P2_C7


title: Evwf037_26_17_HSC_P2_C11


title: Evwf037_26_17_HSC_P1_H1


title: Evwf037_26_17_HSC_P1_H2


title: Evwf037_26_17_HSC_P2_B11


title: Evwf037_26_17_HSC_P2_G11


title: Evwf037_26_17_HSC_P1_G6


title: Evwf037_26_17_HSC_P1_H5


title: Evwf037_26_17_HSC_P2_C10


title: Evwf037_26_17_HSC_P2_A11


title: Evwf037_26_17_HSC_P1_G1


title: Evwf037_26_17_HSC_P1_G2


title: Evwf037_26_17_HSC_P1_G3


title: Evwf037_26_17_HSC_P1_G5


title: Evwf037_26_17_HSC_P1_F5


title: Evwf037_26_17_HSC_P2_E11


title: Evwf038_27_29_HSC_P1_D4


title: Evwf037_26_17_HSC_P1_F6


title: Evwf037_26_17_HSC_P2_D10


title: Evwf037_26_17_HSC_P2_D11


title: Evwf037_26_17_HSC_P1_F3


title: Evwf037_26_17_HSC_P1_F1


title: Evwf037_26_17_HSC_P1_E4


title: Evwf037_26_17_HSC_P1_F4


title: Evwf037_26_17_HSC_P1_D5


title: Evwf037_26_17_HSC_P1_E5


title: Evwf037_26_17_HSC_P1_C6


title: Evwf037_26_17_HSC_P1_F2


title: Evwf037_26_17_HSC_P1_D4


title: Evwf037_26_17_HSC_P1_E6


title: Evwf037_26_17_HSC_P1_B5


title: Evwf037_26_17_HSC_P1_B6


title: Evwf037_26_17_HSC_P1_D2


title: Evwf037_26_17_HSC_P1_A5


title: Evwf037_26_17_HSC_P1_A2


title: Evwf037_26_17_HSC_P1_B2


title: Evwf037_26_17_HSC_P1_E3


title: Evwf037_26_17_HSC_P1_D3


title: Evwf037_26_17_HSC_P1_E2


title: Evwf037_26_17_HSC_P1_A6


title: Evwf037_26_17_HSC_P1_E1


title: Evwf037_26_17_HSC_P1_A4


title: Evwf037_26_17_HSC_P1_C3


title: Evwf037_26_17_HSC_P1_B4


title: Evwf037_26_17_HSC_P1_A3


title: Evwf037_26_17_HSC_P1_C5


title: Evwf037_26_17_HSC_P1_C2


title: Evwf037_26_17_HSC_P1_A1


title: Evwf037_26_17_HSC_P1_D1


title: Evwf037_26_17_HSC_P1_C4


title: smRNA_P9T

city: Shanghai

first: Xi

last: Chen

address: 8th Panshan Road

institute: Second Military Medical University

description: P13, recurrent

data_processing:
The reads with low quality, 5’ primer contaminants, and poly (A) were removed. Also, the reads without 3’adapter and insert tag, the reads shorter than 15 nt or longer than 41 nt were filtered. Adapters of reads were removed by cutadapt package. Quality of clean reads were inspected by fastqc.
Read pairs were mapped by BWA with parameters -n 1 -o 0 -e 0 -l 8 -k 0. All reads mapped to human genome were collected. If two ends of a read pair could be both mapped and their edit distance was less than 5 bp, then they were merged into one fragment whose overlap bases were determined by maximal Phred scores. These fragments were also filtered according to their lengths by the same standard mentioned above. By this procedure, pair-end reads were merged and mapped by BWA with same parameter again. HTSeq was applied to count the read numbers of mature miRNAs in miRBase v22.
Genome_build: hg38
Supplementary_files_format_and_content: miRNA_count_data.txt.gz

source_name: tumor

extract_protocol:
Total RNA was extracted using mirVana miRNA Isolation Kit (Ambion, Austin, TX) according to the manufacturer’s protocol. Quantitation of total RNA was carried out using the Nanodrop 2000 (Thermo Fisher, 5Waltham, MA). RNA integrity was assessed by Agilent 2100 Bioanalyzer (Agilent Technology, Santa Clara, CA).
Total RNA of each sample was used for the small RNA library construction using TruSeq Small RNA Sample Prep Kits (Cat. No. RS-200-0012, Illumina, San Diego, CA) following the manufacturer’s recommendations.

value: tumor


title: smRNA_P7T

description: P11, recurrent


title: smRNA_P9N

description: P13, recurrent

source_name: Adjacent tissue

value: Adjacent tissue


title: smRNA_P8N

description: P12, recurrent


title: smRNA_P7N

description: P11, recurrent


title: smRNA_P6T

description: P10, recurrent


title: CiADC cells, Day6, rep2

city: Guangxi

first: ben

last: huang

address: NO.100. DAXUE EAST RD, Nanning

institute: School of Animal Science and Technology, Guangxi University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by fastp (version 0.18.0).
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome(Bos taurus：9913) using HISAT(2.2.4) with “-rna-strandness RF” and other parameters set as a default.
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach. For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated to quantify its expression abundance and variations, using RSEM software.
Supplementary files format and content: fpkms and counts

organism: Bos taurus

source_name: CiAD cell

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

extract_protocol:
Total RNA was extracted from the treated BearF cells with F from day 0 , day 3 and day 6 using TRIzol Reagent according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara).
RNA libraries for RNA-seq were prepared using Ribo-Zero TM Magnetic Kit (Epicentre, Madison, WI, USA) following manufacturer's protocols.

treatment_protocol: BearFs were seeded into 60-mm dish at 80% confluence. After 24 hours, Cells were treated for 6 days with induction medium (N2B27+VBR: 500ug/mL VPA, 1μM TTNPB, 10μM RepSox) and subsequently transferred to adipocyte maintenance medium (DMEM/F12 contain Insulin, Rosiglitazone). The medium was changed every two days.

value: CiAD cell

value: induced adipocytes

value: WT

value: reprogramming

tag: time

value: Day 6


title: CiADC cells, Day3, rep1

value: Day 3


title: CiADC cells, Day6, rep1


title: smRNA_P8T

description: P12, recurrent


title: CiADC cells, Day3, rep3


title: CiADC cells, Day3, rep2


title: Bovine fibroblasts, Control, Day0, rep1

source_name: BearF cell

value: BearF cell

value: fibroblasts

value: Day 0


title: Bovine fibroblasts, Control, Day0, rep3


title: Bovine fibroblasts, Control, Day0, rep2


title: smRNA_P4T

description: P12, primary


title: smRNA_P5T

description: P13, primary


title: smRNA_P5N

description: P13, primary


title: smRNA_P2N

description: P10, primary


title: smRNA_P4N

description: P12, primary


title: smRNA_P2T

description: P10, primary


title: smRNA_P3N

description: P11, primary


title: CiADC cells, Day6, rep3


title: zebrafish early embryos, WGA treated, 5 hpf, dome-like stage

city: Beijing

first: Weimin

last: Shen

address: Tsinghuayuan park

institute: School of life science, Tsinghua University

description: library name is same with column name of each sample in processed data file

data_processing:
BGISEQ-500 platform was used for base-calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence on trimmomatic software v0.36 with paramwters ILLUMINACLIP:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:50, then mapped to GRCz11 whole genome using Bowtie2 v2.2.5 with parameters -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using software RSEM v1.2.8 from Langmead, B. et al., Nat. Methods, 2012, and Li, B. & Dewey, C. N., BMC Bioinformatics, 2011.
Assembly: GRCz11
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

molecule: polyA RNA

organism: Danio rerio

source_name: whole mount embryo

extract_protocol:
total RNAs were extracted from dechorionated whole embryos with RNeasy Mini Kit (Qiagen)
RNA libraries were prepared for sequencing using standard protocols

treatment_protocol: 1 nl WGA of 0.65 ng/nl dissolved in nuclease free water was microinjected into yolk of embryos at 1-cell stage.

value: whole mount embryo

value: early embryo

value: embryonic cell

value: wildtype

value: 0.65 ng WGA injected at 1-cell stage


title: zebrafish early embryos, WGA treated, 4.3 hpf


title: smRNA_P1T


title: smRNA_P1N


title: zebrafish early embryos, wildtype, 4.3 hpf, dome stage


title: smRNA_P6N

description: P10, recurrent


title: smRNA_P13RT


title: smRNA_P3T

description: P11, primary


title: smRNA_P11PT


title: smRNA_P12RT


title: smRNA_P10RT


title: smRNA_P11RT


title: smRNA_P13PN


title: smRNA_P11RN


title: smRNA_P12RN


title: smRNA_P13PT


title: smRNA_P12PT


title: smRNA_P11PN


title: smRNA_P10RN


title: smRNA_P12PN


title: smRNA_P10PN


title: Old3_373_S373

library_source: genomic single cell

data_processing:
ATAC-seq: Raw reads were trimmed using TrimGalore! software and inspected using FastQC
ATAC-seq: Trimmed reads were aligned to the mouse genome (NCBI37 assembly (mm9)) using Bowtie2 software, the resulting SAM files were converted to BAM files using SAMtools
ATAC-seq: Duplicate reads were removed using Picard tools
ATAC-seq: Mitochondrial reads removal and read shift were performed using ATACseqQC R package.
Assembly: NCBI37 (mm9)
Supplementary files format and content: Count matrix of reads mapped in chomatin regions open in HSC clones generated by single cell transplantations. Row names indicate the genomic coordinates of open chromatins.

molecule: genomic DNA

extract_protocol:
Bone marrow cells were sorted by FACS
Illumina sequencing libraries were constructed according to a plate-based single cell ATACseq protocol

value: Old-HSC


title: Old3_374_S374


title: Old3_378_S378


title: Old3_384_S384


title: Old3_379_S379


title: Old3_377_S377


title: Old3_375_S375


title: Old3_381_S381


title: Old3_380_S380


title: smRNA_P13RN


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title: Old3_363_S363


title: Old3_366_S366


title: Old3_383_S383


title: Old3_372_S372


title: Old3_359_S359


title: Old3_356_S356


title: smRNA_P10PT

value: tumor


title: Old3_364_S364


title: Old3_355_S355


title: Old3_368_S368


title: Old3_361_S361


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title: zebrafish early embryos, MZnup133, 4.5 hpf

data_processing:
Raw RNA-seq data were first processed by Trim Galore! with default parameters to trim the adaptor-containing and low-quality reads
The filtered reads were mapped to zebrafish GRCz11 reference genome with STAR v2.5.3a_modified (Dobin et al., 2013) with the following parameters:–outSAMstrandField intronMotif–outSAMattributes All–outSAMunmapped Within–outSAMattrIHstart 0–outWigStrand Stranded-outFilterMultimapNmax 20–twopassMode Basic.
The gene expression level was normalized to fragments per kilobase of exon per million mapped fragments (FPKM) by Cufflinks v2.2.1 (Trapnell  et al., 2012).
Assembly: GRCz11
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

value: nup133 knockout

tag: developmental stage

value: 4.5 hpf


title: zebrafish early embryos, wildtype, 4.5 hpf_control for Tgnup133 and MZnup133


title: zebrafish early embryos, Tgnup133, 4.5 hpf

value: nup133 transgenic overexpression


title: zebrafish early embryos, Melys, 4.5 hpf

value: elys knockout


title: zebrafish early embryos, wildtype, 4.5 hpf_control for Melys


title: Old2_205_S205


title: zebrafish early embryos, Melys, 4 hpf

value: 4 hpf


title: zebrafish early embryos, MZnup133, 4 hpf


title: zebrafish early embryos, wildtype, 4 hpf_control for Melys


title: zebrafish early embryos, Tgnup133, 4 hpf


title: Old2_202_S202


title: Old2_203_S203


title: Old2_204_S204


title: Old2_216_S216


title: Old2_201_S201


title: zebrafish early embryos, wildtype, 4 hpf_control for Tgnup133 and MZnup133


title: Old2_199_S199


title: Old2_209_S209


title: Old2_200_S200


title: zebrafish early embryos, Melys, 3 hpf

value: 3 hpf


title: Old2_198_S198


title: Old2_210_S210


title: zebrafish early embryos, MZnup133, 3 hpf


title: Old2_197_S197


title: zebrafish early embryos, Tgnup133, 3 hpf


title: zebrafish early embryos, wildtype, 3 hpf_control for Melys


title: Old2_196_S196


title: Old2_207_S207


title: zebrafish early embryos, wildtype, 3 hpf_control for Tgnup133 and MZnup133


title: Old2_195_S195


title: Old2_194_S194


title: Old2_193_S193


title: 2-Mut

city: Piscataway

first: Kelvin

middle: Y.

last: Kwan

state: NJ

address: 604 Allison Rd.

department: Cell Biology & Neuroscience

institute: Rutgers University

description: 10X scRNAseq from shox2 mutant zebrafish

data_processing:
10X Genomics cellRanger pipeline
scanpy pipeline
Genome_build: ENSEMBL GRCz11, release 98
Supplementary_files_format_and_content: cellRanger features.tsv, barcodes.tsv and matrix.tsv files

source_name: developing inner ear and surrounding tissue

growth_protocol: Zebrafish embryos were obtained by natural spawning of sexually mature adults. Embryos were collected and kept in 60µg/ml of Instant Ocean Sea Salt solution supplemented with methylene blue at 28.5oC

extract_protocol:
Sorted embryos were dechorionated with 1mg/ml pronase E and 1X HBSS and rinsed two twice with de-yolking solution (0.03mM MS-222 and 1X DMEM, high glucose and 1X B27), The embryos yolk was mechanically dissociated by gently pipetting the embryos in the de-yolking solution. Embryos were rinsed three times in de-yolking solution before micro dissecting the region of the otic vesicle and associated neurons with 0.33mm fine needles53. The isolated otic region was transferred with a fire-polished glass pipette in a 0.5ml Lo-bind tube coated with 10%BSA in 1X PBS90. Dissected tissue was kept on ice in de-yolking solution until cell dissociation. Tissue was washed with 1X HBSS, incubated at room temperature with 200µl of FACSmax (Gelantis) supplemented with 1 mg/ml of activated papain (Worthington) for 5 minutes and mechanically dissociated with 10%BSA/1XPBS coated tips 90. The dissociated cells were centrifuged at 300g for 5 minutes at 4°C. The dissociation solution was removed, and cells were washed twice with 1% BSA/1XPBS. Cells were counted using the Moxi Z automated cell counter (Orflo) using the Type S cassettes before the final spin. Cells were resuspended at 1200 cells/µl in 0.05%BSA/ 1X PBS and placed on ice.
Single-cell cDNA libraries were generated using the Chromium Next GEM Single Cell 3′ GEM, Library & Gel Bead Kit v3 (10X Genomics) as suggested by manufacturer.

treatment_protocol: No treatment, embryos of different genotypes used

value: ~22 hpf embryos

value: inner ear and surrounding tissue


title: 3-Het

description: 10X scRNAseq from shox2 heterozygote zebrafish


title: Old2_192_S192


title: 1-WT

description: 10X scRNAseq from shox2 wild-type zebrafish


title: Old2_191_S191


title: Old2_190_S190


title: Old2_189_S189


title: Old2_187_S187


title: Old2_188_S188


title: Old2_186_S186


title: Old2_185_S185


title: 7507867070_R04C01

type: genomic

city: Rochester

first: Ellen

middle: L

last: Goode

state: MN

address: 200 First Street SW

department: Quantitative Health Sciences

institute: Mayo Clinic

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing:
Data were normalized separately for the two platforms. For Illumina Infinium Methylation EPIC, a Functional normalization was performed using the 'minfi' R/Bioconductor package. For Illumina InfiniumHumanMethylation 450 BeadChip, each batch was individually adjusted for plate effect, as follows: fit a linear model to the logit-transformed methylation values for each CpG locus and included a fixed effect term for plate; the logit-transformed locus means were then added back onto the unstandardized residuals derived from these models, before back transforming values on the logit-scale to a 0 to 1 scale. The batches were merged together and adjusted for batch effect using the same linear model approach.
Normalized Average Beta

source_name: Fresh Frozen Tumor

label_protocol: Standard Illumina Protocol

extract_protocol: Standard Illumina Protocol

tag: gender

value: Female

tag: histology

value: Serous

tag: grade

value: High

tag: participationsite

tag: batch


title: 7507867081_R04C02


title: Old2_184_S184

tag: cell type


title: 7507875067_R06C02


title: 7507875077_R05C02


title: 7507875077_R05C01


title: 7507867075_R02C01


title: 7507875059_R06C01


title: 7507875077_R04C01


title: Old2_182_S182


title: Old2_183_S183


title: 7507875077_R01C01


title: Old2_181_S181


title: 7507875059_R04C02


title: Old2_180_S180


title: 7507867072_R03C02


title: 7507875048_R01C02


title: Old2_179_S179


title: 7507875095_R02C01


title: Old2_177_S177


title: Old2_178_S178


title: 7507867080_R05C01


title: Old2_176_S176


title: 7507875067_R05C01


title: 7507875095_R05C02


title: 7507867068_R05C02


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title: Old2_174_S174


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title: Old1_237_S141


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title: Old1_234_S138


title: C-D4-exp13-input_S95

city: Chicago

first: Sarah

middle: J

last: Sun

state: Illinois

address: 900 E 57th Street

institute: University of Chicago

library_source: genomic

data_processing:
mm10
read alignment; bowtie2
filter; samtools view; -q 20
sort; samtools sort
remove duplicates; picard MarkDuplicates; REMOVE_DUPLICATES = TRUE
call peaks; macs2 callpeak; -q 0.05, --keep-dup all
generate count matrix; featureCounts
processed_data: text file, raw counts matrix of reads overlapping each peak for each sample

extract_protocol:
fixation/sonication
Diagenode MicroPlex Library Preparation kit (v3)

tag: cell line

value: macrophage

tag: genotype

value: WT

tag: primary treatment

tag: secondary treatment


title: B-D4-exp13-input_S96

value: beta glucan


title: Old1_232_S136

tag: strain


title: B-D2-exp13-input_S94


title: 5771461025_R01C02


title: Old1_244_S148


title: C-D2-exp13-input_S93


title: C-D6-exp12-input_S91


title: Old1_231_S135


title: Old1_230_S134


title: Old1_229_S133


title: Old1_228_S132


title: B-D4-exp12-input_S90


title: Old1_238_S142


title: Old1_224_S128


title: Old1_225_S129


title: C-D4-exp12-input_S89


title: Old1_223_S127


title: C-D2-exp12-input_S87


title: B-D2-exp12-input_S88


title: C-D4-exp11-input_S85


title: Old1_222_S126


title: B-D4-exp11-input_S86


title: B-D2-exp11-input_S84


title: Old1_233_S137


title: Old1_220_S124


title: Old1_221_S125


title: C-D2-exp11-input_S83


title: B-D14-exp8-input_S82


title: Old1_218_S122


title: C-D14-exp8-input_S81


title: Old1_217_S121


title: Old1_216_S120


title: B-D12-exp8-input_S80


title: B-D6-exp12-input_S92


title: C-D12-exp8-input_S79


title: B-D10-exp8-input_S78


title: Old1_215_S119


title: Old1_214_S118


title: C-D10-exp8-input_S77


title: B-D8-exp8-input_S76


title: Old1_209_S113


title: Old1_212_S116


title: B-D6-exp8-input_S74


title: C-D8-exp8-input_S75


title: Old1_208_S112


title: B-D6-exp13-input_S184


title: C-D6-exp8-input_S73


title: Old1_211_S115


title: Old1_205_S109


title: B-D14-exp10-input_S182


title: Old1_207_S111


title: C-D6-exp13-input_S183


title: Old1_219_S123


title: C-D14-exp10-input_S181


title: Old1_203_S107


title: Old1_204_S108


title: Old1_202_S106


title: Old1_201_S105


title: B-D10-exp10-input_S178


title: C-D12-exp10-input_S179


title: B-D12-exp10-input_S180


title: C-D10-exp10-input_S177


title: Old1_200_S104


title: B-D8-exp10-input_S176


title: Old1_199_S103


title: Old1_213_S117


title: C-D8-exp10-input_S175


title: Old1_196_S100


title: Old1_195_S99


title: C-D6-exp10-input_S173


title: B-D14-exp9-input_S172


title: Old1_193_S97


title: 5765301041_R04C01


title: Old1_192_S288


title: Old1_191_S287


title: C-D12-exp9-input_S169


title: C-D14-exp9-input_S171


title: B-D12-exp9-input_S170


title: B-D10-exp9-input_S168


title: Old1_187_S283


title: Old1_190_S286


title: C-D10-exp9-input_S167


title: Old1_186_S282


title: Old1_185_S281


title: Old1_184_S280


title: C-D8-exp9-input_S165


title: B-D8-exp9-input_S166


title: Old1_198_S102


title: Old1_181_S277


title: Old1_183_S279


title: C-D6-exp9-input_S163


title: B-D6-exp13-H3K4me3_S162

extract_protocol:
fixation/sonication/immunoprecipitation
Diagenode MicroPlex Library Preparation kit (v3)


title: C-D6-exp13-H3K4me3_S161


title: Old1_173_S269


title: B-D6-exp10-input_S174


title: Old1_194_S98


title: Old1_174_S270


title: C-D14-exp10-H3K4me3_S159


title: Old1_172_S268


title: B-D14-exp10-H3K4me3_S160


title: Old1_170_S266


title: B-D12-exp10-H3K4me3_S158


title: C-D12-exp10-H3K4me3_S157


title: Old1_167_S263


title: Old1_165_S261


title: C-D10-exp10-H3K4me3_S155


title: B-D8-exp10-H3K4me3_S154


title: Old1_159_S255


title: C-D8-exp10-H3K4me3_S153


title: Old1_161_S257


title: Old1_160_S256


title: B-D6-exp9-input_S164


title: B-D14-exp9-H3K4me3_S150


title: Old1_158_S254


title: Old1_156_S252


title: B-D12-exp9-H3K4me3_S148


title: B-D6-exp10-H3K4me3_S152


title: C-D12-exp9-H3K4me3_S147


title: C-D14-exp9-H3K4me3_S149


title: Old1_157_S253


title: Old1_153_S249


title: B-D10-exp9-H3K4me3_S146


title: Old1_171_S267


title: C-D10-exp9-H3K4me3_S145


title: Old1_154_S250


title: B-D10-exp10-H3K4me3_S156


title: Old1_149_S245


title: Old1_164_S260


title: Old1_150_S246


title: B-D8-exp9-H3K4me3_S144


title: C-D8-exp9-H3K4me3_S143


title: Old1_148_S244


title: C-D6-exp9-H3K4me3_S141


title: B-D6-exp9-H3K4me3_S142


title: C-D6-exp10-H3K4me3_S151


title: Old1_147_S243


title: Old1_143_S239


title: Old1_145_S241


title: B-D6-exp13-H3K27Ac_S140


title: Old1_141_S237


title: Old1_140_S236


title: B-D14-exp10-H3K27Ac_S138


title: Old1_138_S234


title: B-D12-exp10-H3K27Ac_S136


title: C-D12-exp10-H3K27Ac_S135


title: Old1_137_S233


title: Old1_136_S232


title: Old1_152_S248


title: B-D10-exp10-H3K27Ac_S134


title: C-D10-exp10-H3K27Ac_S133


title: Old1_133_S229


title: B-D8-exp10-H3K27Ac_S132


title: Old1_135_S231


title: C-D8-exp10-H3K27Ac_S131


title: B-D6-exp10-H3K27Ac_S130


title: Old1_131_S227


title: Old1_129_S225


title: Old1_128_S224


title: Old1_130_S226


title: Old1_127_S223


title: C-D6-exp13-H3K27Ac_S139


title: C-D14-exp9-H3K27Ac_S127


title: B-D12-exp9-H3K27Ac_S126


title: Old1_124_S220


title: Old1_126_S222


title: C-D14-exp10-H3K27Ac_S137


title: C-D12-exp9-H3K27Ac_S125


title: B-D10-exp9-H3K27Ac_S124


title: Old1_123_S219


title: Old1_121_S217


title: C-D10-exp9-H3K27Ac_S123


title: Old1_118_S214


title: Old1_120_S216


title: Old1_116_S212


title: B-D8-exp9-H3K27Ac_S122


title: B-D6-exp9-H3K27Ac_S120


title: C-D6-exp10-H3K27Ac_S129


title: B-D14-exp9-H3K27Ac_S128


title: Old1_115_S211


title: B-D6-exp13-H3K4me1_S118


title: C-D6-exp13-H3K4me1_S117


title: Old1_114_S210


title: B-D14-exp10-H3K4me1_S116


title: Old1_111_S207


title: Old1_112_S208


title: B-D12-exp10-H3K4me1_S114


title: Old1_113_S209


title: Old1_110_S206


title: C-D14-exp10-H3K4me1_S115


title: B-D10-exp10-H3K4me1_S112


title: C-D12-exp10-H3K4me1_S113


title: Old1_108_S204


title: Old1_106_S202


title: Old1_105_S201


title: B-D8-exp10-H3K4me1_S110


title: C-D8-exp9-H3K27Ac_S121


title: C-D10-exp10-H3K4me1_S111


title: Old1_104_S200


title: C-D8-exp10-H3K4me1_S109


title: C-D6-exp9-H3K27Ac_S119


title: Old1_100_S196


title: B-D6-exp10-H3K4me1_S108


title: Old1_097_S193


title: Old1_099_S195


title: B-D14-exp9-H3K4me1_S106


title: C-D6-exp10-H3K4me1_S107


title: C-D14-exp9-H3K4me1_S105


title: Old1_095_S95


title: Old1_094_S94


title: B-D12-exp9-H3K4me1_S104


title: Old1_093_S93


title: Old1_091_S91


title: C-D12-exp9-H3K4me1_S103


title: Old1_089_S89


title: Old1_090_S90


title: C-D10-exp9-H3K4me1_S101


title: B-D10-exp9-H3K4me1_S102


title: B-D8-exp9-H3K4me1_S100


title: C-D8-exp9-H3K4me1_S99


title: Old1_088_S88


title: Old1_103_S199


title: C-D6-exp9-H3K4me1_S97


title: Old1_085_S85


title: B-D6-exp9-H3K4me1_S98


title: Old1_086_S86


title: Old1_087_S87


title: Old1_080_S80


title: B-D2-exp13-H3K4me3_S70


title: Old1_079_S79


title: Old1_078_S78


title: B-D4-exp13-H3K4me3_S72


title: C-D2-exp13-H3K4me3_S69


title: Old1_077_S77


title: B-D6-exp12-H3K4me3_S68


title: Old1_074_S74


title: C-D6-exp12-H3K4me3_S67


title: Old1_069_S69


title: B-D4-exp12-H3K4me3_S66


title: Old1_066_S66


title: C-D4-exp12-H3K4me3_S65


title: B-D2-exp12-H3K4me3_S64


title: C-D2-exp12-H3K4me3_S63


title: Old1_064_S64


title: B-D4-exp11-H3K4me3_S62


title: Old1_067_S67


title: Old1_065_S65


title: Old1_062_S62


title: Old1_060_S60


title: B-D2-exp11-H3K4me3_S60


title: Old1_056_S56


title: C-D4-exp11-H3K4me3_S61


title: C-D2-exp11-H3K4me3_S59


title: Old1_057_S57


title: Old1_059_S59


title: C-D4-exp13-H3K4me3_S71


title: B-D14-exp8-H3K4me3_S58


title: C-D14-exp8-H3K4me3_S57


title: Old1_055_S55


title: B-D12-exp8-H3K4me3_S56


title: C-D12-exp8-H3K4me3_S55


title: Old1_053_S53


title: Old1_054_S54


title: Old1_052_S52


title: B-D10-exp8-H3K4me3_S54


title: C-D10-exp8-H3K4me3_S53


title: Old1_051_S51


title: B-D8-exp8-H3K4me3_S52


title: Old1_049_S49


title: Old1_050_S50


title: Old1_048_S48


title: B-D4-exp13-H3K27Ac_S48


title: Old1_047_S47


title: C-D6-exp8-H3K4me3_S49


title: Old1_046_S46


title: C-D4-exp13-H3K27Ac_S47


title: Old1_045_S45


title: B-D2-exp13-H3K27Ac_S46


title: C-D6-exp12-H3K27Ac_S43


title: Old1_042_S42


title: Old1_041_S41


title: Old1_040_S40


title: B-D6-exp12-H3K27Ac_S44


title: B-D4-exp12-H3K27Ac_S42


title: Old1_044_S44


title: Old1_043_S43


title: B-D2-exp12-H3K27Ac_S40


title: C-D4-exp12-H3K27Ac_S41


title: Old1_039_S39


title: Old1_038_S38


title: C-D2-exp12-H3K27Ac_S39


title: C-D8-exp8-H3K4me3_S51


title: Old1_037_S37


title: Old1_035_S35


title: B-D4-exp11-H3K27Ac_S38


title: B-D6-exp8-H3K4me3_S50


title: C-D4-exp11-H3K27Ac_S37


title: Old1_034_S34


title: S19

city: Paris

first: Noémie

last: Robil

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

data_processing:
Sequencing, data quality, reads repartition (e.g., for potential ribosomal contamination), and insert size estimation were performed using FastQC, Picard-Tools, Samtools and rseqc
Reads were mapped using STAR_2.4.0
Genome_build: rn6
Supplementary_files_format_and_content: Tab-delimited text file includes deseq2 normalized expression values for each gene and for each sample. Annotations from Rat FAST DB v2018_1_full were also provide.

organism: Rattus norvegicus

source_name: purified neuron+OCM

growth_protocol: Hippocampal neuron cultures were obtained from  hippocampi which were dissected from E18 rat embryo and cultured 17DIV. To obtain purified neuron cultures anti-mitotic agents (FdU, U, 5µM) were added 24h after dissection, and then removed after 36h.

extract_protocol:
The patch electrode was filled with the recording solution including RNase inhibitor (5µl for 1ml). Following electrophysiology recording from an individual neuron, total RNA was extracted by aspirating the cellular contents in the glass electrode tip, and put in a tube containing 3.5 µl of lysis buffer with RNase inhibitor
For mRNAs capture, reverse transcription and amplification, we used the SMART-Seq v4 ultra low input RNA Kit (634894).
Then the full-length cDNA was processed with the Nextera XT DNA Library Preparation Kit from Illumina
The indexed paired-end libraries produced were sequenced by NGS (next-generation sequencing) (Illumina HiSeq platform) - Illumina NextSeq500 2x75bp

treatment_protocol: Oligodendrocyte conditioned medium (OCM) was collected from oligodendrocyte cultures which were obtained from dissociated P2 wistar rat cortices, cultured for 7 to 15 DIV before overnight shaking. OCM was added to purified neurons at DIV3 when indicated.

tag: strain background

value: Wistar

tag: genotype/variation

value: vesicular GABA transporter (VGAT)-venus transgenic

tag: tissue/cell type

value: hippocampal neuron (for all samples)

tag: cell subtype

value: GABAergic neuron

tag: culture period

value: 17 day in vitro for all samples

tag: treatment

value: purified neuron+OCM


title: Old1_033_S33

tag: phenotype

value: Old-HSC


title: Old1_032_S32


title: Old1_031_S31


title: C-D2-exp11-H3K27Ac_S35

tag: timepoint


title: Old1_030_S30


title: C-D2-exp13-H3K27Ac_S45


title: S11

tag: developmental stage


title: Old1_029_S29


title: B-D14-exp8-H3K27Ac_S34


title: S9


title: Old1_026_S26


title: C-D14-exp8-H3K27Ac_S33


title: Old1_028_S28


title: Old1_025_S25


title: S8

source_name: purified neuron + oligodendrocyte conditioned medium (OCM)


title: B-D12-exp8-H3K27Ac_S32


title: Old1_023_S23


title: Old1_022_S22


title: S25

source_name: purified neuron (without glial cells)

value: purified neuron  (without glial cells)


title: Old1_021_S21


title: C-D12-exp8-H3K27Ac_S31


title: Old1_020_S20


title: B-D2-exp11-H3K27Ac_S36


title: B-D10-exp8-H3K27Ac_S30


title: S17


title: Old1_019_S19


title: Old1_018_S18


title: Old1_015_S15


title: B-D8-exp8-H3K27Ac_S28


title: C-D10-exp8-H3K27Ac_S29


title: Old1_027_S27


title: S6

value: purified neuron ( without glial cells)


title: Old1_017_S17


title: P28


title: Old1_013_S13


title: Old1_010_S10


title: C-D8-exp8-H3K27Ac_S27


title: Old1_024_S24


title: Old1_009_S9


title: S21

source_name: neuron cultured with glial cells

value: neuron cultured with glial cells


title: B-D6-exp8-H3K27Ac_S26


title: P3


title: S24


title: Old1_005_S5


title: C-D6-exp8-H3K27Ac_S25


title: Old1_008_S8


title: Old1_004_S4


title: B-D4-exp13-H3K4me1_S24


title: S13


title: Young2-154

value: Young-HSC


title: P1


title: C-D4-exp13-H3K4me1_S23


title: Young2-153


title: Young2-152


title: P2


title: Young2-151


title: ech5


title: Young2-150


title: ech1


title: Young2-149


title: Young2-148


title: C-D2-exp13-H3K4me1_S21


title: Young2-147


title: P36

value: pyramidal neuron


title: B-D6-exp12-H3K4me1_S20


title: Young2-146


title: P34


title: Young2-155


title: Young2-145


title: Young2-144


title: C-D6-exp12-H3K4me1_S19


title: P33


title: Young2-143


title: B-D4-exp12-H3K4me1_S18


title: S27


title: Young2-140


title: C-D4-exp12-H3K4me1_S17


title: Young2-139


title: S3


title: Young2-142


title: B-D2-exp12-H3K4me1_S16


title: Young2-138


title: B-D2-exp13-H3K4me1_S22


title: Young2-136


title: C-D2-exp12-H3K4me1_S15


title: Young2-135


title: Young2-134


title: B-D4-exp11-H3K4me1_S14


title: C-D4-exp11-H3K4me1_S13


title: Young2-132


title: Young2-133


title: Young2-129


title: Young2-130


title: B-D2-exp11-H3K4me1_S12


title: C-D2-exp11-H3K4me1_S11


title: Young2-127


title: Young2-137


title: B-D12-exp8-H3K4me1_S8


title: Young2-124


title: colorectal cancer, nonimmune cells

city: Guangzhou

first: Jie

last: Long

address: No.106 Zhongshan 2nd Road

institute: Guangdong Provincial People's Hospital

data_processing:
For scRNA-seq, the BD Genomics Rhapsody Targeted Analysis pipeline was used to demultiplex cellular barcodes, map reads to the reference genome.
For ST-seq, raw sequencing reads were processed with CellRanger V3 and aligned to human genome
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw UMI counts and metadata for every cells
Supplementary files format and content: H&E staining images for ST-seq tissues

source_name: colorectal and liver tissues

extract_protocol:
For scRNA-seq, freshly resected tumors were rinsed with 1×PBS for three times, cut into small pieces and transferred to 15 mL digestion medium containing collagenase IV (1 mg/mL, C5138, Sigma-Aldrich) in DME/F-12 1:1 (70100300, Biosharp). Tissues were digested for 45 minutes at 37 ℃ under agitation at 120 rpm, afterwards, the samples were filtered using a 150 μm nylon mesh. Following the centrifugation at 450 g for 5 minutes, the supernatants were discarded and the cell pellets were resuspended in 3 mL red blood cell lysis buffer (C3702, Beyotime) at 4 ℃ for 10 minutes. After washing with 1×PBS, the cell pellets were suspended in 1×PBS containing 0.2% bovine serum albumin (4240GR500, BioFroxx) and filtered using a 74 μm nylon mesh. Single cell suspensions were stained with APC/Cy7-CD45 (HI30, BioLegend) and 7-aminoactinomycin D (7-AAD, B226396, BioLegend) for fluorescence-activated cell sorting using BD Aria ⅡI (BD Biosciences). Non-immune cells were sorted as 7-AAD-CD45-, and immune cells as 7-AAD-CD45+. For spatial transcriptome sequencing (ST-seq), The tissues were obtained from patients after resection, fixed by formalin and embedded in the paraffin. 10x FFPE gene expression slide (PN-1000185, 10x Genomics) was used for ST. Slide with 5μm FFPE section was dewaxed with xylene (214736, Sigma-Aldrich) and stained with hematoxylin (51275, Sigma-Aldrich) and eosin (HT110116, Sigma-Aldrich). After visualizing and scanning the whole slide, decrosslinking was performed using the TE buffer (10-0046, GeneMed) to release the RNA. Forward and reverse human transcriptome probes (PN-1000364, 10x Genomics) were used for probe hybridization overnight.
Single-cell library preparation was carried out according to the BD Rhapsody™ Single-Cell Whole transcriptome analysis alpha protocol (https://www.bdbiosciences.com/) and ST library were constructed according to the 10x protocol (CG000407_VisiumSpatialGeneExpressionforFFPE_UserGuide_RevA)

tag: tissue

value: colorectal and liver tissues


title: Young2-126


title: Young2-120


title: C-D12-exp8-H3K4me1_S7


title: Young2-122


title: Young2-123


title: colorectal cancer, immune cells


title: Young2-119


title: Young2-125


title: C-D14-exp8-H3K4me1_S9


title: B-D10-exp8-H3K4me1_S6


title: Young2-117


title: 4Cseq-hg-Patient371-FB-FGF8-Rep2-L21113

data_processing:
Sequencing reads were mapped, normalized and smoothed with pipe4C53 using the reference genome GRCh37 and default settings. All viewpoints were performed in replicates and as quality measure >70% of reads were mapped within a size range of 1Mb and >80% within 100kb around the viewpoint.
Assembly: hg19
Library strategy: 4C-seq

source_name: Skin fibroblasts

extract_protocol:
Skin biopsies were collected from SHFM3 patients and controls by standard procedures. Fibroblasts were cultured in DMEM (Lonza) supplemented with 10% fetal calf serum (Gibco), 1% L-glutamine (Lonza) and 1% penicillin/streptomycin (Lonza).
For 4C-seq libraries fixation and lysis were performed as described for Capture Hi-C. After the first digestion with DpnII (NEB), sticky ends were religated in a 50 ml falcon tube (700 μl 10 ligation buffer (Fermentas), 7 ml H2O, 50 U T4 DNA ligase (Thermo); overnight at 16 °C) and DNA de-cross linked and cleaned as described for the Capture Hi-C. Next, a second digestion (150 μl sample, 50 μl 10× Csp6I buffer (Thermo), 60 U Csp6I (Thermo) 295 μl H2O; overnight at 37 °C) and another re-ligation were performed. For all viewpoints, DNA was purified using a PCR clean up Kit (Qiagen) and 1.6 μg DNA was amplified by PCR (LBX1 Viewpoint: read-primer 5′-TCTATATGCTACCATGATC-3′, secondary-primer 5′-GATGAACTGGAATACCCA-3′; FGF8 Viewpoint: read-primer 5′-AGGGTGCGTTCCAAGATC-3′, secondary-primer 5′-GGTGGCCTGGATGGAAGT-3′; BTRC Viewpoint: read-primer 5′-CAACGCAGCGCCCGGATC-3′, secondary-primer 5′-CTGGGAATGAGGACCTAGGGC-3′). For the library reaction, primers were modified with TruSeq adapters (Illumina): Adapter1 5′-CTACACGACGCTCTTCCGATCT-3′ and Adapter2 5′-CAGAC GTGTGCTCTTCCGATCT-3′. Between 50 and 200 ng were used as input of a single 4C PCR reaction depending on the complexity. The reaction was performed in a 50 μl volume using the Expand Long Template System (Roche) and 29 reaction cycles. After the PCR all reactions were combined and the DNA purified with a PCR clean up Kit (Qiagen).

value: Skin fibroblasts

value: Patient with duplication


title: 4Cseq-hg-Patient371-FB-FGF8-Rep1-L21106


title: Young2-115


title: Young2-118


title: C-D10-exp8-H3K4me1_S5

value: macrophage

value: WT


title: Young2-116


title: Young2-131


title: Young2-113


title: 4Cseq-hg-Patient371-FB-BTRC-Rep1-L21105


title: 4Cseq-hg-Patient371-FB-BTRC-Rep2-L21112


title: Young2-128


title: B-D8-exp8-H3K4me1_S4

value: beta glucan


title: B-D14-exp8-H3K4me1_S10


title: Young2-121


title: 4Cseq-hg-Patient371-FB-LBX1-Rep2-L21111


title: C-D8-exp8-H3K4me1_S3


title: Young2-112


title: Young2-111


title: B-D6-exp8-H3K4me1_S2


title: Young2-108


title: Young2-109


title: Young2-107


title: 4Cseq-hg-Patient371-FB-LBX1-Rep1-L21104


title: Young2-110


title: 4Cseq-hg-Control-FB-FGF8-Rep2-L21110

value: Healthy control


title: C-T0-4

data_processing:
mm10
remove adapter sequences; trimmomatic-0.36; ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
read alignment; STAR; --sjdbOverhang 100
generate count matrix; featureCounts
processed_data: text file, raw counts matrix of reads overlapping each gene for each sample

extract_protocol:
RNA extracted with Qiagen RNeasy kit
Illumina TruSeq


title: 4Cseq-hg-Control-FB-FGF8-Rep1-L21103


title: Young2-105


title: Young2-106


title: 4Cseq-hg-Control-FB-BTRC-Rep2-L21109


title: Young2-114


title: Young2-103


title: Young2-104


title: Young2-102


title: 4Cseq-hg-Control-FB-BTRC-Rep1-L21102


title: Young2-101


title: BG-T0-4


title: Young2-100


title: Young2-99


title: 4Cseq-hg-Control-FB-LBX1-Rep1-L21101


title: C-D6-exp8-H3K4me1_S1


title: Young2-98


title: Young2-96


title: BG-T0-3


title: C2_18h


title: Young2-94


title: Young2-92


title: Young2-97


title: C-T0-3


title: C2_15h


title: Young2-93


title: Mel022-iLN

city: Los Angeles

first: Feiyang

last: Ma

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

data_processing:
The single cell libraries were then sequenced on the Illumina NovaSeq 6000 S4 200 cycle flow cell, generating 28 ́98 reads. A median sequencing depth of 50,000 reads/cell was targeted for each sample.
Raw reads were aligned to the human genome (hg38) and the digital expression matrix was generated using the cellranger count. Reads from individual samples were merged to generate the digital expression matrix using cellranger aggr.
R package Seurat was used to analyze the data.
Assembly: hg38
Supplementary files format and content: expression matrix

source_name: skin

extract_protocol:
Live CD45+HLA-DR+ cells were sorted from processed tumors.
Using the Chromium Single Cell 3′ Reagent Kit v3, single cell suspensions were partitioned into nanoliter droplets, known as gel- bead-in-emulsions (GEMs), to achieve single cell resolution. The cDNA generated within each individual GEM was tagged with a common 16-nt 10 ́ barcode and a 12-nt unique molecular barcode during the reverse transcription reaction. Purified cDNA was amplified in 11 cycles (98° 3 min, (98° 15 sec, 63° 20 sec, 72° 1 min) x 11, 72° 1 min) before being purified using SPRIselect beads. The cDNA concentration was then determined using an Agilent Bioanalyzer. Purified cDNA (10 μL) was used to generate the Illumina library for sequencing. For preparation of samples to be analyzed on the 10 ́ Genomics platform, the Chromium Single Cell 3′ GEM, Library & Gel Bead Kit v3 16 rxns (PN-1000075), Chromium Chip B Single Cell Kit, 48 rxns (PN- 1000073) and Chromium i7 Multiplex Kit (PN-120262) were used.

value: skin

value: CD45+HLA-DR+ cells


title: Mel014-uLN


title: Young2-89


title: BG-T0-2


title: Mel018-uLN


title: Young2-88


title: Mel014-iLN


title: C-T0-2


title: Mel018-iLN


title: Young2-87


title: C2_12h


title: C2_7h


title: Young2-86


title: Mel009-iLN


title: 4Cseq-hg-Control-FB-LBX1-Rep2-L21108


title: Young2-85


title: C2_4h


title: Young2-84


title: Young2-83


title: Mel002-uLN


title: Young2-90


title: Young2-91


title: Young2-82


title: Young2-80


title: C1_18h


title: Young2-81


title: C1_15h


title: SK-N-AS sgCDK8 MEKi rep2

city: Cambridge

first: Gabriela

last: Alexe

state: MA

address: 415 Main St.

department: Computational Biology and Bioinformatics

institute: Broad Institute

data_processing:
Quality control tests for unmapped reads were performed based on the FastQC v.0.11.9 software (Babraham Bioinformatics, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and summarized with multiQC v1.7. The ERCC RNA Spike-In Mix (ThermoFisher Cat. No.: 4456740, https://tools.thermofisher.com/content/sfs/manuals/ERCC92.zip) was used as an external RNA control to estimate the variability in transcriptional performance (Bioconductor erccdashboard).
The spiked human reads were mapped to the hg38/gencode v30 human genome using STAR v2.6.1d  with standard parameters  --outSAMtype BAM SortedByCoordinate --outSAMunmapped None      --outSAMattributes NH HI NM MD AS XS --outReadsUnmapped Fastx --outSAMstrandField intronMotif --quantMode TranscriptomeSAM GeneCounts --quantTranscriptomeBan IndelSoftclipSingleend. Quality control for the mapped reads and for replicate reproducibility were performed using SARTools v1.7.3.
One sample (sgCCNC_MEKI_R1_dropped_lowQC) did not pass the QC tests and it was dropped out from any further analysis.
Gene level reads were summarized by counting the reads that overlapped the hg38/gencode v30 annotated gene exons, by using the featureCounts v1.6.3 method implemented in the Subread v2.0.0 package (http://subread.sourceforge.net).
Gene counts were normalized and used to quantify differential genes between the experimental and control conditions using the DESeq2 v1.32.0 method. Reads were normalized based on DESeq2 scaling factors. Gene expression was estimated based on log2(TPM+1) scores for normalized reads. Pair-wise genome-wide expression scatter dot plots, PCA, hierarchical clustering dendrograms and volcano plots were used to estimate the correlation of the  replicate samples correlation and the transcriptional dynamics across experimental phenotypes (SARTools v1.7.4, and Morpheus visualization platform, https://software.broadinstitute.org/morpheus). Genes with max(log2(TPM+1)) ≥ 1 across all samples were annotated as “expressed”.
Genome_build: hg38/gencode.v30
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with log2(TPM+1) expression scores for every gene and every sample.

source_name: neuroblastoma

growth_protocol: SK-N-AS cells were infected with a single vector containing Cas9 and the indicated sgRNA.  Cells were then selected with puromycin.

extract_protocol:
After four days of treatment, RNA was harvested and purified with the Qiagen RNeasy Plus Mini Kit (Qiagen # 74134).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Nine days after infection, cells were treated with either DMSO or 3 nM trametinib in triplicate.

value: SK-N-AS

tag: infection

value: MEKi


title: Young2-77

source_name: Bone marrow

tag: cell type


title: Young2-78