title: WGBS_ctrl_rep1


title: CAG-shA5-3

status: Public on Jul 07 2022

type: SRA

city: Hangzhou

first: Yifan

last: Hou

address: No. 79, Qingchun Rd

country: China

institute: Bone Marrow Transplantation Center, The First Affiliated Hospital, School of Medicine, Zhejiang University

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In  this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

molecule: total RNA

organism: Homo sapiens

source_name: human myeloma cell line

growth_protocol: HMCLs cultured in RPMI-1640 supplemented with 10% FBS

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared using NEB Next® Ultra™ RNA Library Prep Kit

treatment_protocol: Ransduced with indicated lentiviruses

tag: cell line

value: CAG

tag: treatment


title: RPMI8226_shA5_3


title: p53Notch1__rep1

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

description: Sample 3

data_processing:
Obtained single-end RNA-seq reads were mapped to the mouse genome assembly, version mm10, with RNA-STAR (Dobin et al., Bioinformatics 2013), with default parameters except for reporting only one hit for multimapping reads ( outFilterMultimapNmax=10, outSAMmultNmax=1) and  filtering reads without evidence in spliced junction table (outFilterType="BySJout").
All subsequent gene expression data analysis was done within the R software (R Foundation for Statistical Computing, Vienna, Austria). Raw reads and mapping quality was assessed by the qQCreport function from the R/Bioconductor software package QuasR (Gaidatzis et al., 2015).
Using RefSeq mRNA coordinates from UCSC (genome.ucsc.edu, downloaded in December 2015) and the qCount function from QuasR package, we quantified gene expression as the number of reads that started within any annotated exon of a gene.
Genome_build: mm10
Supplementary_files_format_and_content: TSV file (tab separated values) with raw counts for Entrez Genes , 1.column is EntrezGeneID, 2. column is length of all exons in nt, 3. and remaining columns contain raw counts

organism: Mus musculus

source_name: Glioma cells from Notch1 -/- tumor

growth_protocol: Mice were euthanized and their brains were isolated.

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Sequencing libraries were generated with the TruSeq Stranded RNA LT kit (Illumina). Sequencing was performed on an Illumina NextSeq 500 according to manufacturer specification.

treatment_protocol: Early stage gliomas were identified by the expression of GFP from the Rosa-CAG::GFP Cre-reporter, micro-dissected, and GFP+ tumor cells purified by FACS.

value: ko

value: wt

tag: rbpj

tag: replicate


title: WGBS_DM_rep1

city: Fukuoka

first: Hiroyuki

last: Sasaki

address: 3-1-1 Maidashi, Higashi-ku

department: Department of Molecular and Structural Biology

country: Japan

institute: Medical Institute of Bioregulation, Kyushu University

library_source: genomic

data_processing:
For ChIP-seq data, paired-end reads were aligned to the mouse genome (mm10) using Bowtie2 with a default setting after removing adaptor sequences and low-quality reads by Trim Galore!. Reads from PCR duplicates were removed by using Samtools ‘markdup’ with an option ‘-r’. To compute normalized enrichment, normalized ChIP read counts were divided by normalized input read counts using deepTools bamCompare with options '--normalizeUsing RPKM'and '--operation ratio'. Spike-in normalization was performed when it is possible.
For CUT&RUN data, paired-end reads were aligned to the mouse genome (mm10) using Bowtie2 with a default setting after removing adaptor sequences and low-quality reads by Trim Galore!. Reads from PCR duplicates were removed by using Samtools ‘markdup’ with an option ‘-r’. Normalized read counts were computed using deepTools bamCoverage with options '--normalizeUsing RPKM'.
For WGBS data,Reads were trimmed to remove low quality bases and adaptor sequences using Trim-Galore! and mapped to the mouse genome (mm10) using Bismark v0.14.5. After confirming reproducibility between replicates, the BAM files were merged using Samtools ‘merge’. CG sites covered by four to 100 reads were considered as informative CG sites, and bins containing more than five informative CG sites were used for downstream analyses by custom Perl scripts. To extract bins in which CG methylation levels are unaffected by Dnmt3a KO in oocytes, we used the following criteria: the difference of CG methylation levels between Dnmt3a KO versus control FGOs <10%, and the CG methylation levels in control FGOs >40%.
For RNA-seq data, the first three bases of the Read 2 derived from the SMART-seq Stranded Adaptor were trimmed prior to mapping using Trim Galore!. After the reads were aligned with Hisat2, reads corresponding to ribosomal RNA were removed by using the BEDTools intersectBed function. FeatureCounts was then used to analyze the gene expression level. The resulting read count data were processed by EdgeR to identify differentially expressed transcripts between two groups. A false discovery rate of <0.05 was used to extract differentially expressed transcripts.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig and text files

molecule: genomic DNA

source_name: Oocyte

growth_protocol: Fully grown oocytes were collected by punching ovaries of female mice at 3-4 weeks of age. For in vitro fertilization, female mice were super-ovulated by the injection of 0.1 ml of CARD HyperOva followed by hCG injection (5 IU) 46–48 h later. Cumulus-oocyte complexes were collected from the oviducts and fertilized with C57BL/6J or JF1 sperm. Zygotes were cultured in EmbryoMax KSOM medium (Merck Millipore) at 37 ºC and 6% CO2. Late 2-cell embryos were harvested at 31-32 h post-fertilization for RNA-seq.

extract_protocol:
For ChIP-seq, MNase-digested chromatin was used. For CUT&RUN, chromatin digested by protein A/protein G-MNase was used. WGBS libraries were constructed using the post-bisulfite adapter tagging method (Miura et al., 2012). A SMART-Seq stranded kit (TAKARA) was used to prepare RNA-seq libraries.
ULI-NChIP-seq protocol was used to prepare ChIP-seq libraries. CUT&RUN libraries were prepared as described before (Ishiuchi et al., Nat. Struct. Mol. Biol. 2021). The PBAT method was used to prepare WGBS libraries as described before (Au et al., Cell Rep. 2019). A SMART-Seq stranded kit (TAKARA) protocol was used to prepare RNA-seq libraries.
ChIP-seq, CUT&RUN, WGBS, and RNA-seq.

treatment_protocol: For ChIP-seq, CUT&RUN, or WGBS, FGOs were collected from mouse ovaries. Pooled FGOs or single late 2-cell embryos were used for RNA-seq.

tag: strain

value: hybrid C57BL/6 / 129


title: H3K27me3_K36M_rep2

tag: antibody


title: P29 single cell TCR of post-Tx HNSCC tumor

city: Boston

first: Shengbao

last: Suo

state: MA

address: 360 Longwood Ave

country: USA

institute: Dana-Farber Cancer Institute

data_processing:
Raw PBMC scRNA-sequencing reads were demultiplexed and aligned to the human reference genome (GRCh38-2020-A from 10x Genomics) for each pooled library using Cell Ranger (v4.0.0). Each pooled library contained multiple patient samples and timepoints; cells from each sample were labelled with distinct Hashtag oligonucleotides (HTO, Cell Hashing). Sequencing files for Gene Expression (measure mRNA level of cells) and Antibody Capture (measure HTO levels of cells) were fed to the “cellranger count” function with the –libraries flag, and the sequences of all HTO used in the library were fed to this function with –feature-ref flag. This generated a digital gene expression matrix, which measured the number of unique molecular identifier (UMI) for each gene and each cell barcode.
The raw gene-by-barcode count matrix was then processed to filter potential empty drops using emptyDrops function from DropletUtils (v1.8.0, R package) (Lun et al., 2019) with the parameters of “lower = 500, ignore = 5”. We initially selected droplets as containing a cell if total UMI counts of this droplet exceed the 99th percentile of the top 10,000 barcodes divided by 10. Finally, only cells with FDR<=0.01 were retained as real cells for the following analysis. The raw HTO-by-barcode matrix was subsequently filtered based on identified real cells.
The filtered HTO-by-barcode matrix for each pooled library was processed using GMM-demux to distinguish singlets from doublets or multiplets based on detection of HTOs with default parameters (Xin et al., 2020). Predicted singlets with a confidence score>=0.8 were defined as true singlet cells. Cell barcodes were then classified and allocated to respective patient samples based on hashtag identities. After processing, the gene-by-barcode count matrix was refined based on these identified singlets and used for the following analyses.
Raw tumor scRNA-sequencing reads were demultiplexed to FASTQ files using Cell Ranger mkfastq (v3.0.0, 10x Genomics), and the Cumulus cellranger-workflow implementation of Cell Ranger count (v4.0.0) on Terra (https://terra.bio/) was used to align reads to the human reference genome (GRCh38-2020-A) and generate a raw counts matrix (Li et al., 2020). Cumulus was used to filter cells from the Cell Ranger raw counts matrix with fewer than 400 UMIs, 200 genes, or greater than 20% of UMIs mapped to mitochondrial genes.
To generate the single-cell V(D)J sequences and annotate each library, we aligned TCR FASTQ reads to human GRCh38 V(D)J reference (v4.0.0 from 10X Genomics, modified to remove TRDD segments) using “cellranger vdj” function from Cell Ranger (v4.0.0). The filtered contig annotations, which contained high-level annotations of each high-confident cellular contig, were further filtered by removing records with ‘raw_consensus_id’ as ‘none’. For blood single-cell V(D)J analysis, the identities of different patient samples in each pooled library were labelled based on demultiplexing of the gene expression matrix.
Assembly: GRCh38
Supplementary files format and content: Each scRNA sequenting sample contains a .h5 file including Gene Expression (tumor and PBMC) and Antibody Capture (PBMC) information. Single cell TCR sequencing data for each sample were saved in a csv file, which is generated by 'cellranger vdj' function and shows the detailed clonotype information. Bulk TCR sequencing data for each sample were provided by Adaptive Biotech and were saved in a tsv file. Hashtag files contain the sequence of each hashtag and the corresponding patient sample information.

source_name: HNSCC tumor

extract_protocol:
Fresh tumor tissue was transferred to a 6 cm tissue culture dish in a small volume of DMEM media and cut into <2 mm pieces with a razor blade. Tissue pieces were centrifuged (400 g for 5 minutes at 4°C for all centrifuge steps) and resuspended in 2-5 mL of a collagenase-containing enzymatic digestion solution (Miltenyi Human Tumor Dissociation Kit #30-095-929), based on the weight of collected tissue, according to manufacturer’s instructions. Biopsies were incubated at 37°C for 20-30 minutes with mixing using a 5-10 mL serological pipet and intermittent gentle vortexing at 2-5-minute intervals. The extent of tumor tissue dissociation was variable and likely dependent on extracellular matrix abundance. The resulting cell suspension was passed through a 70 um nylon mesh filter and washed with an additional 5-10 mL of RPMI media. Filtered tumor cell suspensions were centrifuged and resuspended in 3 mL ACK red blood cell lysis buffer (Gibco #A1049201) for 1 minute at RT, then immediately diluted with 10 mL of PBS (Life Technologies #10437028). Cells were pelleted and resuspended in Zombie NIR (Biolegend) viability dye solution (1:500 in PBS), followed by a 15 minute incubation at RT in the dark. Cells were counted with a hemocytometer, yielding on average 1.3x104 live cells/mg of tumor tissue. Up to 500,000 live cells were then resuspended in 100 uL of FACS wash buffer (FWB; PBS, 2% FBS, 1 mM EDTA) with the addition of the following antibodies: TruStain FcX (Biolegend 422302), CD3-PE/Dazzle (Biolegend 300450), CD45-Pacific Blue (Biolegend 304022), CD66b-PE/Cy7 (Biolegend 305116) and CD15-APC (Biolegend 301908). Cells were incubated on ice for 20 minutes, washed with 1 mL FWB, filtered through 40 um flow-cap strainers, and then resuspended in 500 uL FWB. Cells were sorted using a FACS Aria II or III instrument (BD Biosciences). For most samples, 12-15 x 103 live CD45+CD66b- mononuclear cells (MNC) cells were sorted into T cell media (RPMI + 10% FBS) and immediately transferred to ice. All scRNA-seq was performed using the 10x Genomics 5’ V1 assay and protocols (10x Genomics). CD45+ cells isolated as above were centrifuged and washed with PBS containing 0.05% RNase-free BSA (ThermoFisher Scientific #AM2616), leaving a volume of <32 uL after the final wash. Up to 15,000 cells based on cell sorter count were loaded into a Single Cell Chip A channel, along with reverse transcriptase reagent mixture and 5’ gel beads according to the manufacturer’s protocol.
Libraries were prepared accordingn to 10X Genomics protocols for 5' barcoded GEX and V(D)J TCR (Version 1)

tag: cell marker

value: TCR:ab chains

tag: single cell or bulk

value: Single cell

tag: state

value: Post-Tx

tag: patient diagnosis

value: Head and neck squamous cell Carcinoma (HNSCC)

tag: molecule

value: T cell receptor


title: RPMI8226_shA5_2


title: P28 single cell TCR of post-Tx HNSCC tumor


title: H3K27me3_K36M_rep1


title: p53__rep2

description: Sample 2

source_name: Glioma cells from control tumor


title: RPMI8226_shA5_1


title: P27 single cell TCR of post-Tx HNSCC tumor


title: p53__rep1

description: Sample 1


title: H3K27me3_ctrl_rep2


title: P32 single cell TCR of post-Tx HNSCC tumor


title: RPMI8226_shNC_3

value: shNC


title: H3K27me3_ctrl_rep1


title: P26 single cell TCR of post-Tx HNSCC tumor


title: H3K36me3_K36M_input


title: P32 single cell TCR of pre-Tx HNSCC tumor

value: Pre-Tx


title: H3K36me3_K36M


title: RPMI8226_shNC_2


title: P29 single cell TCR of pre-Tx HNSCC tumor


title: shA5_ip

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw data (raw reads) of fastq format were firstly processed using fastp (version  0.19.11). In this step, clean data (clean reads) were obtained by removing reads  containing adapter, reads containing ploy-N and low-quality reads from raw data
Reference genome and gene model annotation files were downloaded from genome  website directly. Index of the reference genome was built using BWA v0.7.12 and clean  reads were aligned to the reference genome using BWA mem v 0.7.12
After mapping reads to the reference genome, exomePeak R package (version 2.16.0)  was used for the m6A peak identification in each anti-m6A immunoprecipitation group  with the corresponding input samples serving as a control, and q-value threshold of  enrichment of 0.05 was used for all data sets. The m6A-enriched motifs of each group  were identified by HOMER (version 4.9.1).
Genome_build: hg38
Supplementary_files_format_and_content: peak text files

extract_protocol:
total RNA was extracted using Trizol reagent, and poly (A) mRNA was purified from 100 μg total RNA  using a Dynabeads mRNA kit.
immunoprecipitated mRNAs   or Input was used for library construction with NEBNext ultra RNA library prepare kit  for Illumina (New England Biolabs).


title: P27 single cell TCR of pre-Tx HNSCC tumor


title: Perturb-seq Barcodes HTO

city: Cambridge

first: Joshua

last: Levin

address: 75 Ames St

department: Stanley Center

institute: Broad Institute

description: ADT, HTO, and Guide sequencing data from 3' Perturb-seq data

data_processing:
cellranger mkfastq v5.0 was used to generate fastq files for Illumina data
For Ultima and Single End Illumina data, Cutadapt v2.10 was used to remove adapters and qualitfy filter. For 3' data reads without 8 T's from the poly(T) region were discarded. Cutadapt and SeqKit v0.15.0 were used to split these read into 2 pieces for later processing. We removed reads whose cDNA sequence was < 50bp.
seqtk v1.0 was used to downsample the Ultima data to the appropriate level
CellRanger count v5.0 was used to quanifty the number of UMIs per cell in each sample, with CellRanger vdj being used for TCR and BCR data.
CellSNP-lite v1.2.0  and Vireo v0.5.5 were used to identify genotype clusters in the 5' mixture data
Demux-EM v0.1.7  was used to assign cells to hash tag IDs in the Perturb-seq data
Seurat v4.0.0 was used for clustering and downstream analysis
Assembly: hg38
Supplementary files format and content: Most processed data are in MM format, with 3 files per sample: the cell names file, the gene names file, and the MM file with gene by cell UMI count matrix. In addition have h5 files from CellRanger for the Perturb-seq results, including UMI counts from the HTO, ADT, and Guide data. The csv files are for TCR and BCR data produeced by CellRanger vdj.

source_name: A375 cell line

growth_protocol: Perturb-seq only: Perturbed cells selection with puromycin, details see manuscript

extract_protocol: 10x Chromium Next GEM single cell 3' (v3.1) and 5' (v2) gene expression assays

treatment_protocol: Perturb-seq only: Selected perturb-seq cells treated with recombinant IFNγ, details see manuscript

tag: 10x technology

tag: sample type

value: Cell Line


title: Perturb-seq Barcodes ADT


title: H3K36me3_ctrl_input


title: NeuN-Low mouse brain nuclei

city: Athens

first: Robert

middle: J

last: Schmitz

state: GA

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

data_processing:
library strategy: TAB–seq
Data were mapped to the Mus musculus GRCm38 reference genome
TAB-seq analysis were performed as described in Yu, M.; Hon, G.C.; Szulwach, K.E.; Song, C.X.; Zhang, L.; Kim, A.; Li, X.K.; Dai, Q.; Shen, Y.; Park, B.; Min, J.H.; Jin, P.*; Ren, B.*; He, C.* Base-Resolution Analysis of 5-Hydroxymethylcytosine in the Mammalian Genome. Cell. 2012, 149, 1368-1380.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab delimited text file
Column1: chromosome
Column2: cytosine position
Column3: strand
Column4: CNN (N = A, T, C, G)
Column5: methylated cytosines in this site
Column6: totally detected cytosines in this site

source_name: genomic DNA

growth_protocol: Mouse brain nuclei are isolated and sorted into NeuN-High, NeuN-Low and NeuN_Neg subpopulation based on NeuN staining using fluorescence-activated nuclear sorting.

extract_protocol: Genomic DNA (gDNA) was purified from NeuN-High, NeuN-Low and NeuN-Neg mouse brain nuclei using DNeasy kit (Qiagen, Frederick, MD, USA #69504), according to the manufacturer’s instructions. TAB-seq libraries were constructed according to Yu, M.; Hon, G.C.; Szulwach, K.E.; Song, C.X.; Zhang, L.; Kim, A.; Li, X.K.; Dai, Q.; Shen, Y.; Park, B.; Min, J.H.; Jin, P.*; Ren, B.*; He, C.* Base-Resolution Analysis of 5-Hydroxymethylcytosine in the Mammalian Genome. Cell. 2012, 149, 1368-1380.

tag: tissue

value: brain

tag: nuclei subpopulation

value: NeuN-Low


title: NeuN-High mouse brain nuclei

value: NeuN-High


title: NeuN_Neg mouse brain nuclei


title: shA5_input


title: H3K36me3_ctrl


title: shNC_input


title: P31 scRNA-seq of post-Tx HNSCC tumor

value: total RNA


title: RPMI8226_shNC_1


title: Perturb-seq Illumina

description: 3' Perturb-seq data, sequenced with Illumina


title: P32 scRNA-seq of post-Tx HNSCC tumor


title: Trophoblast cells, HS131

city: Beijing

first: Xiangxiang

last: Jiang

state: Beijing

address: 1 Beichen West Road, Chaoyang District

institute: Institute of Zoology, Chinese Academy of Sciences

data_processing:
The paired-end reads Smart-seq2 data was processed using the standard pipeline of Drop-seq_tools-2.0.0 (http://mccarrolllab.com/dropseq/) with modifications.
For read2, bases 1 to 8 were tagged with cell-barcode “XC,”and bases 9 to 16 were tagged with UMI “XM”.
Read1 was trimmed at the 5' end to remove adaptor and TSO sequence, and the 3' end was trimmed to remove poly(A) sequences of length 6 or more and then aligned to hg38 genome reference using STAR aligner.
Gene expression matrix for each cell was then generated with DigitalExpression command.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

source_name: Blastocyst

growth_protocol: Donated human embryos (at the cleavage or blastocyst stage) were thawed and cultured in 8-well chambers to day 13.

extract_protocol:
Single cells were isolated from embryos at embryonic days 8, 9, 10, 11, 12, and 13, incubated with TrypLE Express reagent for 10-15 min at 37°C, and dissociated into single cells. Single cells were randomly picked with a mouth pipette in 0.1% BSA and then transferred to 2.5 μl lysis buffer. The cells were transferred into a 0.2 mL PCR tube (Eppendorf) containing cell lysis buffer and kept at −80°C for library preparation.
The linearized RNA molecules were releasein a thermocycler at 72 °C for 3 min at first. Then, transfer the reactions immediately on ice. Add 2.85 µl RT mixture into every reaction with component as SuperScript II reverse transcriptase, RNase Inhibitor, 5× Superscript II first-strand buffer, dithiothreitol (DTT), betaine, MgCl2, and template switch oligo (TSO) primer. Spin down the 5.4 µl samples in the thermocycler at 25 °C for 5 min, 42 °C for 60 min, 50 °C for 30 min, and then 70 °C for 10 min, 4 °C hold. Prepare 7.5 µl PCR mixture (6.25 μL 2× KAPA HiFi HotStart ReadyMix, ISPCR oligo, and 3′ Anchored oligo) to add in every tube reaction, and amplify samples for 19 cycles. Pool together samples with different barcodes (up to 96 barcodes) and purify DNA. Then prepare the second round of amplification with bio-tinylated index primer and ISPCR oligo for an additional five cycles. Subsequently, purify the biotinylated cDNAs further with 0.8× Ampure XP beads and elute cDNA in 50 µl EB. Next, shear the cDNAs into approximately 300-bp fragments with sonicator.Enrich the cDNA fragments  by Dynabeads® MyOneTM Streptavi- din C1. Libraries were prepared with KAPA Hyper Prep Kits. Use the NEB U-shaped adapter for ligation. Finally, amplify the adapter-ligated fragments using an Illumina QP2 primer and a short universal primer for 9 cycles.
Single Cell RNA-Seq

tag: Stage

value: Day 13

tag: growth condition

value: in vitro culture

tag: cell type

value: trophoblast cells


title: Trophoblast cells, HS132


title: 786-O_DPF3a_ATAC-seq

city: Shenzhen

first: Huanhuan

last: Cui

state: Guangdong

address: Southern University of Science and Technology, No.1088, Xueyuan Avenue, Xili Street, Nanshan District

department: Department of Biology

data_processing:
ATAC-seq reads were trimmed for adaptor sequence using fastp, and then aligned to the hg38 genome assembly using bowtie2 version 2.3.4.3 with the parameters -p 12 -X 2000
The reads that were uniquely mapped with MAPQ over 30 were retained for further analysis, and duplicates were removed by sambamba-0.7.0.
Peaks were called using MACS2 version 2.2.6 with the parameters -g hs --keep-dup all -q 0.05 --slocal 10000 --nomodel --nolambda -B --SPMR. Peaks with strong signals (peak score > 50) were retained for further analysis.
Genome_build: hg38
Supplementary_files_format_and_content: peak text files

source_name: 786-O cells

extract_protocol:
Samples were washed and then lysed in 50 μL of lysis buffer (10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40, 0.1% Tween-20, and 0.01% digitonin) for 3 min on ice. Immediately after lysis, samples were then incubated with the Tn5 transposase and tagmentation buffer at 37°C for 30 min (Vazyme Biotech, TD501)
PCR was then performed to amplify the library for 12 cycles using the following PCR conditions: 72°C for 3 min; 98°C for 30 s followed by thermocycling at 98°C for 15 s, 60°C for 30 s and 72°C for 40s, and finally 5 min at 72°C. After the PCR reaction, libraries were purified with 1.2 ×DNA clean beads (Vazyme Biotech, N411)

tag: cell line

value: renal cell carcinoma (RCC) cell line

tag: genotype/variation

value: DPF3a overexpression


title: Trophoblast cells, HS133


title: 786-O_empty vector_ATAC-seq

institute: Southern University of Science and Technology

value: empty vector contrl


title: shNC_ip

tag: treatment


title: H3K36me2_K36M_rep2

tag: strain

value: hybrid C57BL/6 / 129


title: H3K36me2_K36M_rep1_input


title: P25 single cell TCR of post-Tx HNSCC tumor

value: TCR:ab chains

value: Single cell

value: Post-Tx


title: H3K36me2_K36M_rep1

tag: antibody


title: P30 scRNA-seq of post-Tx HNSCC tumor

tag: cell marker

value: Head and neck squamous cell Carcinoma (HNSCC)


title: p300_ChIP-seq_rep2

data_processing:
ChIP-seq reads were trimmed for adaptor sequence using cutadapt, and then aligned to the hg38 genome assembly using bowtie2 version 2.3.5.1 with the default parameters
The reads that were uniquely mapped with MAPQ over 30 were retained for further analysis, and duplicates were removed by Picard tools.
Peaks were called using MACS2 version 2.2.5 with the parameters -g hs. Peaks with strong signals (peak score > 50) were retained for further analysis.
Bigwig files were generated using deepTools 3.5.0 (bamCoverage -bs 10 --normalize RPKM -p 16)
Genome_build: hg38
Supplementary_files_format_and_content: peak text files, bigwig files

extract_protocol:
The ChIP assay was performed according to the standard protocol provided by SimpleChIP Plus Sonication Chromatin IP Kit (CST)
Libraries were prepared using standard protocol provided by VAHTSTM Universal DNA Library Prep Kit for Illumina® V3 (Vazyme)

tag: chip antibody


title: P29 scRNA-seq of post-Tx HNSCC tumor

tag: single cell or bulk

tag: state


title: P27 scRNA-seq of post-Tx HNSCC tumor

tag: patient diagnosis

tag: molecule


title: Trophoblast cells, HS122

value: Day 12


title: H3K36me2_K36M_rep2_input


title: p300_ChIP-seq_rep1


title: SMAD4_ChIP-seq_rep2

value: SMAD4 (Santa Cruz, sc7966)


title: P28 scRNA-seq of post-Tx HNSCC tumor


title: H3K36me2_ctrl_rep2_input


title: H3K36me2_ctrl_rep2


title: Trophoblast cells, HS121


title: Trophoblast cells, HS112

value: Day 11


title: P26 scRNA-seq of post-Tx HNSCC tumor


title: H3K36me2_ctrl_rep1


title: Trophoblast cells, HS111


title: SMAD4_ChIP-seq_rep1


title: CD45_P53_R2

data_processing:
Single-cell sequencing FASTQ files were processed using Kallisto (v0.46.0) and BUStools (v0.39.3) for sample demultiplexing, barcode processing, pseudo-alignment to mouse transcriptome (Ensembl release 97) and UMI counting.
UMI counts were extracted and filtered using the dropletUtils Bioconductor package (version 1.8.0). Filtering for high-quality cells was done using the cells library sizes, the number of detected genes and the percentage of reads mapping to mitochondrial genes. The package SingleR (v1.2.4) was used for reference-based annot ation of the cells using the Immunological Genome Project (ImmGen) mouse microarray dataset as reference.  The UMI counts matrix for these genes and cells is provided in file UMIsMatrix.txt.gz.
Further quality controls and analyses were performed using the scran (v1.14.5) and scatter (v1.14.5) Bioconductor packages, mostly following the steps of the simpleSingleCell  Bioconductor (v3.10) workflow.
R1: Cell barcode (positions 1:16) + UMI (position 17:28)
R2:Biological read (cDNA)
Genome_build: mm10
Supplementary_files_format_and_content: TSV file (tab separated values) with UMI counts for ensembl release 97 gene models; columns correspond to: 1. ENSEMBL ID, 2. and remaining columns contain UMI counts for each cell; column headers include the cell barcode sequence and the sample ID

source_name: CD45+ immune cells from control tumor

extract_protocol:
Only CD45+ cells (FACS purified) were used for single-cell RNA seqeuncing.
Sorted cell suspensions from each mouse were loaded into a single well of a 10× Genomics Chromium Single Cell Controller.
Single-cell capture and cDNA and library preparation were performed with a Single Cell 3’ v3 Reagent Kit (10× Genomics) according to manufacturer’s instructions.

value: ko

tag: rbpj

value: wt

tag: replicate


title: Trophoblast cells, HS105

value: Day 10


title: SNIP1_ChIP-seq_rep1

value: SNIP1 (Abclonal, A16747)


title: Trophoblast cells, HS123

value: in vitro culture


title: P24 scRNA-seq of post-Tx HNSCC tumor

value: total RNA


title: Trophoblast cells, HS103

value: trophoblast cells


title: P23 scRNA-seq of post-Tx HNSCC tumor


title: HA-DPF3a_ChIP-seq_rep2

value: renal cell carcinoma (RCC) cell line

value: HA (Sigma, H6908)


title: P22 scRNA-seq of post-Tx HNSCC tumor


title: H3K36me2_ctrl_rep1_input


title: CD45_P53_R1


title: CD45_WT_R2

source_name: CD45+ immune cells from healthy brain


title: Trophoblast cells, HS102


title: CD45_P53RBPJ_R1

source_name: CD45+ immune cells from Rbpj-/- tumor


title: 786-O_shSNIP1_RNA-seq_rep1

description: processed data file: sh_RNA_Scr_SNIP1.count

data_processing:
The RNA-seq reads were trimmed for adaptor sequence using cutadapt, then mapped to hg38 reference genome by HISAT2 version 2.1.0 with the default parameters.
Read counts were generated using featureCounts version 2.0.1 with parameters -T 8 -t exon -g gene_id --extraAttributes gene_name.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
Total RNA of cultured cells was isolated using RNA Isolator Total RNA Extraction Reagent (Vazyme) followed by isopropanol precipitation according to standard protocols.
Libraries were prepared using standard protocol provided by VAHTS Stranded mRNA-seq Library Prep Kit (Vazyme).

value: SNIP1 shRNA knockdown


title: Trophoblast cells, HS101


title: P21 scRNA-seq of post-Tx HNSCC tumor


title: Trophoblast cells, HS093

value: Day 9


title: SNIP1_ChIP-seq_rep2


title: P20 scRNA-seq of post-Tx HNSCC tumor

value: Single cell


title: P25 scRNA-seq of post-Tx HNSCC tumor

value: Post-Tx


title: 786-O_shSNIP1_RNA-seq_rep2


title: CD45_WT_R1


title: Trophoblast cells, HS104


title: P19 scRNA-seq of post-Tx HNSCC tumor

value: Head and neck squamous cell Carcinoma (HNSCC)


title: 786-O_shScr_RNA-seq_rep2

value: scrambled control


title: Langerhans islets of NZO mice with carbohydrates

city: Nuthetal

first: Pascal

last: Gottmann

address: Arthur-Scheunert-Allee 114-116

country: Germany

institute: Deutsches Institut für Ernährungsforschung

description:
NZO_plus_CH
Single cell gene expression of NZO+CH mice in pancreatic islets.

data_processing:
cellRanger 3.02
Samtools Version: 1.9 (using htslib 1.9)
Scanpy 1.4.4
Scran (version 1.16)
Scanorama (version 1.4)
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.h5ad
Supplementary_files_format_and_content: *tar: Tar archives include barcodes.tsv, features.tsv, and matrix.mtx files.

source_name: Langerhans islets

extract_protocol:
For single-cell RNA-seq, a pool of 100 islets from 3 mice per condition was dissociated using TrypLE Express (Gibco, Carlsbad, USA) for 12 min at 37 °C. Cells were then washed with PBS containing 2% FCS, filtered through a 40 µm Flowmi Cell Strainer (Bel-Art, Wayne, USA) and diluted to a final concentration of 1,000 cells/µL in PBS containing 2% FCS.
The cell suspension was immediately used for single-cell RNA-seq library preparation using the Chromium Single Cell 3ʹ Reagent Kit v3 (10X Genomics, PN-1000075, Pleasanton, USA) according to the manufacturer’s instructions.
Chromium Single Cell

value: New Zealand Obese (NZO/HIBomDife)

value: Pancreatic islets

value: Carbohydrate-enriched diet

tag: gender

value: male

tag: age

value: 18 weeks


title: CD45_P53RBPJ_R2

value: ko


title: Langerhans islets of NZO mice without carbohydrates

description:
NZO_minus_CH
Single cell gene expression of NZO-CH mice in pancreatic islets.

value: Carbohydrate-free diet


title: HA-DPF3a_ChIP-seq_rep1


title: Trophoblast cells, HS092

tag: Stage

tag: growth condition

value: in vitro culture


title: 786-O_DPF3a_RNA-seq_rep2

description: processed data file: DPF3_RNA_seq.count

tag: cell line

tag: cell type

value: DPF3a overexpression


title: P18 scRNA-seq of post-Tx HNSCC tumor

value: total RNA


title: 786-O_shScr_RNA-seq_rep1

value: renal cell carcinoma (RCC) cell line

tag: genotype/variation


title: P16 scRNA-seq of post-Tx HNSCC tumor


title: Trophoblast cells, HS091

value: trophoblast cells


title: Langerhans islets of OB mice with carbohydrates

description:
OB_plus_CH
Single cell gene expression of OB+CH mice in pancreatic islets.

tag: strain

value: B6.V-Lep ob/ob (OB)

tag: treatment


title: Trophoblast cells, HS083

value: Day 8


title: 786-O_DPF3a_RNA-seq_rep1

description: processed data file: DPF3_RNA_seq.count


title: Trophoblast cells, HS082


title: P14 scRNA-seq of post-Tx HNSCC tumor

tag: cell marker

value: Single cell

value: Post-Tx


title: P15 scRNA-seq of post-Tx HNSCC tumor

value: Head and neck squamous cell Carcinoma (HNSCC)


title: Langerhans islets of OB mice without carbohydrates

description:
OB_minus_CH
Single cell gene expression of OB-CH mice in pancreatic islets.


title: P13 scRNA-seq of post-Tx HNSCC tumor

extract_protocol:
Fresh tumor tissue was transferred to a 6 cm tissue culture dish in a small volume of DMEM media and cut into <2 mm pieces with a razor blade. Tissue pieces were centrifuged (400 g for 5 minutes at 4°C for all centrifuge steps) and resuspended in 2-5 mL of a collagenase-containing enzymatic digestion solution (Miltenyi Human Tumor Dissociation Kit #30-095-929), based on the weight of collected tissue, according to manufacturer’s instructions. Biopsies were incubated at 37°C for 20-30 minutes with mixing using a 5-10 mL serological pipet and intermittent gentle vortexing at 2-5-minute intervals. The resulting cell suspension was passed through a 70 m nylon mesh filter and washed with an additional 5-10 mL of RPMI media.Tumor-infiltrating immune cells were isolated with anti-CD45 magnetic beads. Following filtering of dissociated tumor suspension, cells were centrifuged and then resuspended in 80 mL of MACS buffer (0.5% FBS, 2 mM EDTA in PBS). Human CD45 MicroBeads (20 mL, Miltenyi) were mixed with cells, and then incubated at 4°C for 15 minutes per manufacturer’s protocol. After washing with MACS buffer, beads were applied to a MS magnetic column (Miltenyi) placed in a magnetic MACS separator and washed with 3x500 mL of MACS buffer. To elute cells, the column was removed from the magnet and flushed with 1 mL of MACS buffer. CD45+ cells isolated as above were centrifuged and washed with PBS containing 0.05% RNase-free BSA (ThermoFisher Scientific #AM2616). Up to 15,000 cells based on cell sorter count were loaded into a Single Cell Chip A channel, along with reverse transcriptase reagent mixture and 5’ gel beads according to the manufacturer’s protocol.
Libraries were prepared accordingn to 10X Genomics protocols for 5' barcoded GEX and V(D)J TCR (Version 1)


title: Trophoblast cells, HS081


title: 786-O_empty vector_RNA-seq_rep1

description: processed data file: DPF3_RNA_seq.count

source_name: 786-O_empty vector_RNA-seq

value: empty vector control


title: P32 scRNA-seq of pre-Tx HNSCC tumor

value: Pre-Tx


title: Nerve-derived schwann cells Patient 3

city: Calgary

first: Jeff

last: Biernaskie

state: Alberta

address: 3330 Hospital Drive NW

department: Comparative Biology and Experimental Medicine

country: Canada

institute: University of Calgary

description: 6000 cells loaded

data_processing:
All raw FASTQs reads were aligned to the human referene genome GRCh38 (primary assembly) using the STAR algorithm and quantified through the 10X Genomics cellranger v3.0.0 single cell pipeline, with default and recommended parameter. Only mapped reads were used for normalization before aggregating cells. Since we aggregated libraries constructed with different 10X chemistry versions, cellranger aggr’s batch correction algorithm was used to correct for systematic variability in gene expression profiles due to different versions of the 10X chemistry. The resulting gene-barcode matrix was imported into Seurat (v3 ) R toolkit for quality control, cross-patient integration, and all downstream analysis. All functions were run with default or recommended parameters, unless specified otherwise. Low quality cells (<300 genes/cell and <20 cells/gene) were excluded from the overall experiment. Gene expression was log normalized to a scale factor of 10,000. To begin unsupervised clustering of cells, a selection of highly variable genes was obtained and used to calculate up to 50 principle components. Significance of principle components was determined using JackStraw analysis and by creating a PCElbowPlot. PCs 1 to 25 were used to run and plot a tSNE plot for all cells.
Genome_build: Homo_sapiens : GRCh38
Supplementary_files_format_and_content: Filtered gene - barcode matrix output from CellRanger

molecule: polyA RNA

source_name: Nerve-derived schwann cells Patient 3

growth_protocol: Skin tissue was washed and epithelium removed by incubating with dispase (5 mg/ml) for 1.5 hr at 37 °C. Nerve sample was washed and fascicles pulled out from Sciatic nerve. Then both samples went through identical steps which were then cut into small cubes and incubated with DMEM with 10% fetal bovine serum (FBS), forskolin (Fsk, 5 µM), neuregulin (NRG, 50 ng/ml) and plasmocin (0.02%) for 2 weeks. At the end of 2 weeks, tissue explants were digested overnight at 37 °C with enzymatic cocktail containing dispase (1.25 U/ml) and collagenase IV (0.125%). The cell suspension was filtered through 40 µm filter and seeded onto poly-D-lysine and laminin coated cell culture dish, supplemented with DMEM with 2% FBS, Fsk (5 µM) and NRG (50 ng/ml). After 1 week, SCs were enriched using immunopanning against primate specific p75 antibody and fibroblasts from skin selected against human specific Thy-1 antibody. Purified cells were expanded in DMEM with 2% FBS, Fsk (5 µM) and NRG (50 ng/ml).

extract_protocol:
Dissociation from cell culture dish and resuspension in BSA 1%/HBSS
Libraries were prepared according to 10X Genomics ChromiumTM Single Cell 3’ Reagent Guidelines v2  for Patient 1 and v3 for Patients 2 and 3 Chemistry as per the manufacturer’s protocol. In brief, single cells were sorted into 1% BSA–PBS and partitioned into Gel Bead-In-EMulsions (GEMs) using 10xTM GemCodeTM Technology. This process lysed cells and enabled barcoded reverse transcription of RNA, generating full-length cDNA from poly-adenylated mRNA. DynaBeads® MyOneTM Silane magnetic beads were used to remove leftover biochemical reagents, then cDNA was amplified by PCR over 10 cycles. Quality control size gating was used to select cDNA amplicon size prior to library construction. Read 1 primer sequences were added to cDNA during GEM incubation. P5 primers, P7 primers, i7 sample index, and Read 2 primer sequences were added during library construction. Quality control and cDNA quantification was performed using Agilent High Sensitivity DNA Kit. Sequencing was performed first using Illumina MiSeq SR50 to approximate the number of recovered cells in each sample.

value: Nerve-derived schwann cells

tag: library preparation

value: 10X Genomics Single Cell RNAseq v3


title: Nerve-derived schwann cells Patient 1

description: 10,000 cells loaded; Recovered: 7137 cells

data_processing:
All raw FASTQs reads were aligned to the human referene genome GRCh38 (primary assembly) using the STAR algorithm and quantified through the 10X Genomics cellranger v3.0.0 single cell pipeline, with default and recommended parameter. Only mapped reads were used for normalization before aggregating cells. The resulting gene-barcode matrix was imported into Seurat (v2.1.0 ) R toolkit for quality control and all downstream analysis. All functions were run with default or recommended parameters, unless specified otherwise. Low quality cells (<300 genes/cell and <20 cells/gene) were excluded from the overall experiment. Gene expression was log normalized to a scale factor of 10,000. To begin unsupervised clustering of cells, a selection of highly variable genes was obtained and used to calculate up to 50 principle components. Significance of principle components was determined using JackStraw analysis and by creating a PCElbowPlot. PCs 1 to 25 were used to run and plot a tSNE plot for all cells.
Genome_build: Homo_sapiens : GRCh38
Supplementary_files_format_and_content: Filtered gene - barcode matrix output from CellRanger

source_name: Nerve-derived schwann cells

extract_protocol:
Dissociation from cell culture dish and resuspension in BSA 1%/HBSS
Libraries were prepared according to 10X Genomics ChromiumTM Single Cell 3’ Reagent Guidelines v2 Chemistry as per the manufacturer’s protocol. In brief, single cells were sorted into 1% BSA–PBS and partitioned into Gel Bead-In-EMulsions (GEMs) using 10xTM GemCodeTM Technology. This process lysed cells and enabled barcoded reverse transcription of RNA, generating full-length cDNA from poly-adenylated mRNA. DynaBeads® MyOneTM Silane magnetic beads were used to remove leftover biochemical reagents, then cDNA was amplified by PCR over 10 cycles. Quality control size gating was used to select cDNA amplicon size prior to library construction. Read 1 primer sequences were added to cDNA during GEM incubation. P5 primers, P7 primers, i7 sample index, and Read 2 primer sequences were added during library construction. Quality control and cDNA quantification was performed using Agilent High Sensitivity DNA Kit. Sequencing was performed first using Illumina MiSeq SR50 to approximate the number of recovered cells in each sample.

tag: tissue

value: 10X Genomics Single Cell RNAseq v2


title: P29 scRNA-seq of pre-Tx HNSCC tumor

tag: single cell or bulk

tag: state


title: Skin-derived schwann cells Patient 1

description: 10,000 cells loaded; Recovered: 7123 cells

source_name: Skin-derived schwann cells

value: Skin-derived schwann cells


title: Skin-derived fibroblasts Patient 1

description: 10,000 cells loaded; Recovered: 9585 cells

source_name: Skin-derived fibroblasts

value: Skin-derived fibroblasts


title: P27 scRNA-seq of pre-Tx HNSCC tumor

tag: patient diagnosis

tag: molecule


title: Skin-derived fibroblasts Patient 3

description: 6000 cells loaded

source_name: Skin-derived fibroblasts Patient 3


title: P24 scRNA-seq of pre-Tx HNSCC tumor


title: Skin-derived schwann cells Patient 2

description: 6000 cells loaded

source_name: Skin-derived schwann cells Patient 2


title: SNVT223

city: Illkirch

first: Stephane

middle: D

last: VINCENT

address: 1 rue Laurent Fries

department: Development and Stem Cells

country: France

institute: IGBMC

data_processing:
Image analysis and base calling were performed using RTA 2.7.7 and bcl2fastq 2.20.0.422.
preprocessing CUTADAPT 1.10 to remove adpatators, low-quality seqeunces and reads shorter than 40 nt
elimination of rRNA sequences
STAR 2.5.3 alignment on a hybrid genome composed of mm10 and ASM294v3 (S. pombe, spike in)
htseq-count 0.6.1p1 quantification using “union” mode and Ensembl 93 annotations for mouse and Ensembl Fungi 41 annotations for S. pombe
Differential gene expression analysis was performed using DESeq2 1.16.1 using the spike-in counts for the size factors
Assembly: mm10, ASM294v3 for the spike-in
Supplementary files format and content: DESeq2_betaprior_mES_LIF_20220331.txt (Differential gene expression text file)
Supplementary files format and content: sp_counts_22022.tsv (htseq file for the spike-in S pombe reads in tabular format)
Supplementary files format and content: mm10_counts_22022.tsv (htseq file for the murine reads in tabular format)

source_name: ES cells

extract_protocol: P2722 : Total RNA-Seq libraries were generated from 50 ng of nascent RNA using TruSeq Stranded Total RNA Library Prep Gold kit and TruSeq RNA Single Indexes kits A and B (Illumina, San Diego, USA), according to manufacturer's instructions but omitting the ribodepletion step. Briefly, nascent RNA were purified on RNA Clean XP beads and fragmented into small pieces using divalent cations at 94oC for 1 minutes. Cleaved RNA fragments were then copied into first strand cDNA using reverse transcriptase and random primers followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. Strand specificity was achieved by replacing dTTP with dUTP during second strand synthesis. The double stranded cDNA fragments were blunted using T4 DNA polymerase, Klenow DNA polymerase and T4 PNK. A single 'A' nucleotide was added to the 3' ends of the blunt DNA fragments using a Klenow fragment (3' to 5'exo minus) enzyme. The cDNA fragments were ligated to double stranded adapters using T4 DNA Ligase. The ligated products were enriched by PCR amplification (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 10 cycles; 5 min at 72oC). Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.

treatment_protocol:
The nascent RNA has been metabolically labeled with 4-SU, purified and fragmented by sonication.(do not expect nice rRNA bands...).
We used S pombe 4SU-labelled RNA as spike.

value: ES cells

tag: genotype

value: Supt3 KO


title: SNVT222


title: 786-O_empty vector_RNA-seq_rep2

description: processed data file: DPF3_RNA_seq.count

value: empty vector Ccontrol


title: Nerve-derived schwann cells Patient 2

description: 6000 cells loaded

source_name: Nerve-derived schwann cells Patient 2


title: P23 scRNA-seq of pre-Tx HNSCC tumor

source_name: HNSCC tumor

value: total RNA


title: SNVT221

value: Supt3 WT


title: P18 scRNA-seq of pre-Tx HNSCC tumor


title: Skin-derived fibroblasts Patient 2

description: 6000 cells loaded

source_name: Skin-derived fibroblasts Patient 2


title: SNVT220


title: OEPs, ATAC

status: Public on Jul 06 2022

city: London

first: Andrea

last: Streit

address: Guys Hospital, Great Maze Pond

department: Centre for Craniofacial & Regenerative Biology

country: United Kingdom

institute: Kings College London

data_processing:
Data was processed and aligned using the NF-core ATACseq v1.2.0 pipeline (doi: 10.5281/zenodo.2634132).
Reads were trimmed using Trim Galore! Reads were aligned using BWA. Alignments merged using Picard. Narrow peaks were called using MACS2 with an effective genome size of 1.05e9.
Genome_build: galgal6
Supplementary_files_format_and_content: ATAC_R1.mLb.clN_peaks.narrowPeak

organism: Gallus gallus

source_name: otic epibranchial progenitors (OEPs)

growth_protocol: Embryos were grown in ovo at 38°C until reaching the desired stage.

extract_protocol:
30 pieces of OEP tissue were manually dissected and processed for ATACseq.
Libraries were prepared following standard protocols using Nextera Sample low input kit (Illumina, 15028212).

value: OEPs

value: somite stage 8-9


title: Skin-derived schwann cells Patient 3

description: 6000 cells loaded

source_name: Skin-derived schwann cells Patient 3


title: T-2

city: Shanghai

first: Haodong

last: Lin

address: Haining Road100, Shanghai, People’s Republic of China

department: Orthopedic Surgery

institute: Shanghai General Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200080, China

data_processing:
Illumina data collection software used for basecalling.
NGS (Next Generation Sequencing) technology uses high-throughput sequencer illumina Hiseq 2500 to sequence cDNA. The original image file obtained first, and then through base recognition and error filtering, finally get the original sequencing fragments that can be used for analysis, we call it Reads, and the result is stored in fastq format, which includes the base composition information of the sequence and its corresponding Sequence quality information, pair-end sequencing (pair-end) will be divided into two Reads files
In transcriptome sequencing, we can estimate the level of gene expression by the number of reads mapped to the gene region, but the number of reads is not only proportional to the gene expression level, but also related to the length of the gene itself and the amount of sequencing data. In order to make the gene expression levels of different genes and different samples comparable, the reads were converted into FPKM (Fragments Per Kilobase of exon model per Million mapped reads) to standardize the gene expression levels
We first use Stringtie (version: 1.3.0) to count the number of Fragments of each gene after Hisat2 comparison, and then use TMM (trimmed mean of M values) method to normalize, and finally Use the perl script to calculate the FPKM value of each gene.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: FPKM and counts values for each Sample

organism: Rattus norvegicus

source_name: Injured sciatic nerve tissue

extract_protocol:
Total RNA was extracted using miRNeasy Mini Kit (Cat#217004, Qiagen)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea, CA,USA)and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Sprague Dawley

value: Injured sciatic nerve tissue


title: T-1


title: C-3

source_name: Normal sciatic nerve tissue

value: Normal sciatic nerve tissue


title: C-2


title: C-1


title: RNA-seq, synovial fibroblasts isolated from Ets1-ΔFib mice (6-Ets1ΔFib)

city: Tokyo

first: Hiroshi

last: Takayanagi

address: 7-3-1, Hongo, Bunkyo-ku, Tokyo

department: Department of Immunology

institute: The University of Tokyo

description: Synovial fibroblasts (CD45-CD31-CD146-PDPN+) sorted from ankle joints of Ets1-ΔFib mice (STIA)

data_processing:
Complementary DNA was synthesized and amplified using SMART-seq v.4 Ultra Low Input RNA Kit for Sequencing (Clontech Laboratories), then subjected to Ion Proton sequencer (Thermo Fisher Scientific) and further processed using CLC genomics Workbench v.12
Assembly: mm10
Supplementary files format and content: counts.csv

source_name: Synovial fibroblasts of Ets1-ΔFib mice

extract_protocol:
Fresh synovial tissue was dissociated in type II collagenase solution (Worthington, 4 mg/mL) at 37 °C for 1 hour with frequent shaking. After the first 30-min incubation, cell suspensions were carefully homogenized by a series of 18G, 21G and 25G needles until the cell suspension passed through the needles smoothly. After digestion, cells were collected by centrifugation and the cell pellet was then treated with ACK buffer (Sigma) to lyse the red blood cells, and then filtered using 100-μm cell strainers to remove the tissue debris to get the single-cell suspensions. Synovial fibroblasts (CD45-CD31-CD146-PDPN+) of the ankle joints were sorted from the inflammed synovium and subjected to RNA-seq
Complementary DNA was synthesized and amplified using SMART-seq v.4 Ultra Low Input RNA Kit for Sequencing (Clontech Laboratories), then subjected to Ion Proton sequencer (Thermo Fisher Scientific).

treatment_protocol: 8-week-old mice were treated with 150 μL pooled K/BxN serum on day 0, day 2 and day 9 intraperitoneally, and sacrificed on day 16 for RNA-seq analysis.

value: Arthritic synovium

value: synovial fibroblasts

tag: disease state

value: serum transfer-induced arthritis (STIA)


title: KMS11 normo MP

type: RNA

city: Akita

first: Sho

last: Ikeda

address: Hondo 1-1-1

department: Hematology

institute: Akita univ.

hyb_protocol: As materials and methods for DNA mycroarray protocol version 6.7 (Agilent).

scan_protocol: Agilent G2600A SureScan Microarray Scanner System.

data_processing: GeneSpring (Agilent), computed normalized signal intencity with 75%tile normalization.

source_name: KMS11 normo MP

growth_protocol: normoxia: 21%O2, hypoxia: 1%O2.

extract_protocol: Total RNA was extracted with Trizol.

treatment_protocol: RPMI1640 plus 10% FCS.

tag: oxygen status

value: normoxia

tag: population

value: MP


title: 8226 hypo SP

source_name: 8226 hypo SP

label_protocol: As materials and methods for DNA mycroarray protocol version 6.7 (Agilent).

value: hypoxia

value: SP


title: KMS11 normo SP

source_name: KMS11 normo SP


title: KMS11 hypo MP

source_name: KMS11 hypo MP


title: RNA-seq, synovial fibroblasts isolated from Ets1-flox mice (5-Ets1flox)

description: Synovial fibroblasts (CD45-CD31-CD146-PDPN+) sorted from ankle joints of Ets1-flox mice (STIA)

source_name: Synovial fibroblasts of Ets1-flox mice


title: RNA-seq, synovial fibroblasts isolated from Ets1-ΔFib mice (3-Ets1ΔFib)


title: KMS11 hypo SP

source_name: KMS11 hypo SP


title: RNA-seq, synovial fibroblasts isolated from Ets1-flox mice (4-Ets1flox)


title: RNA-seq, synovial fibroblasts isolated from Ets1-ΔFib mice (1-Ets1ΔFib)


title: RNA-seq, synovial fibroblasts isolated from Ets1-flox mice (2-Ets1flox)


title: 8226 hypo MP

source_name: 8226 hypo MP


title: T-3


title: 8226 normo MP

source_name: 8226 normo MP


title: Lib4_1_21

city: Lyon

first: Frédéric

last: Flamant

state: France

address: 46 allée d'Italie

department: IGFL

institute: ENSL

data_processing:
fastq-join - Joins two paired-end reads on the overlapping ends (Galaxy Version 1.1.2-806.1)
FASTQ Groomer convert between various FASTQ quality formats (Galaxy Version 1.0.4)
FASTQ to Tabular converter (Galaxy Version 1.1.5)
Counts occurrence with R-script
Supplementary_files_format_and_content: Counts table can be used to compair the frequency of a given T3RE is the input library, transfected cells without T3, and transfected cells with T3.

source_name: Transfected HEK293 human cells

growth_protocol: Cells transfected in serum free medium and supplemented with thyroid hormone when indicated.

extract_protocol:
RNeasy Micro Kit (Qiagen) followed by reverse transcription except for  lib7-1-21 (DNA extraction with Qiagen microkit)
TruSeq Amplicon

treatment_protocol: TransIT-Lt1 transfection reagent (Mirus Corporation Madison WI, USA)

tag: amount of dna transfected

value: 1200ng of DNA transfected

value: With T3


title: Lib7_1_21

tag: cell line

value: Input library

value: No T3


title: Lib3_1_21


title: Lib2_1_21

value: 600ng of DNA transfected


title: _20_HSC6-39465-13171_Ch600

city: Regensburg

first: Christa

last: Buechler

address: Franz Josef Strauss Allee 11

institute: University Hospital Regensburg

description: gene expression

hyb_protocol: GeneChip WT Terminal Labeling and Hybridization / Ambion WT Expression Kit  - Sample processing and Affymetrix microarray hybridization (Human Gene 2.1 ST Array ) were carried out at a genomics core facility: Center of Excellence for Fluorescent Bioanalytics (KFB, University of Regensburg, Germany).

data_processing: Expression Console Software

label: Biotin

source_name: HSC Chemerin 600 ng/ml

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: standard

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Cells were incubated with rising levels of recombinant chemerin for 24 h

tag: cell type

value: HSC


title: _24_HSC7-40375-13326_Ch600

description: gene expression

scan_protocol: Sample processing and Affymetrix microarray hybridization (Human Gene 2.1 ST Array ) were carried out at a genomics core facility: Center of Excellence for Fluorescent Bioanalytics (KFB, University of Regensburg, Germany).


title: _03_PHH-39465-13171_Ch480

description: gene expression

source_name: PHH Chemerin 480 ng/ml

value: PHH


title: Lib1_1_21


title: _06_PHH-39965-13231_Ch360

description: gene expression

source_name: PHH Chemerin 360 ng/ml


title: _21_HSC7-40375-13326_K

description: gene expression

source_name: HSC control 3


title: _23_HSC7-40375-13326_Ch480

description: gene expression

source_name: HSC Chemerin 480 ng/ml


title: _15_HSC1-37205-12511_Ch480

description: gene expression


title: _17_HSC6-39465-13171_K

description: gene expression

source_name: HSC control 2


title: _04_PHH-39465-13171_Ch600

description: gene expression

source_name: PHH Chemerin 600 ng/ml


title: _13_HSC1-37205-12511_K

description: gene expression

source_name: HSC control 1


title: _12_PHH-40375-13316_Ch600

description: gene expression


title: _10_PHH-40375-13316_Ch360

description: gene expression


title: _09_PHH-40375-13316_K

description: gene expression

source_name: PHH control 3


title: _08_PHH-39965-13231_Ch600

description: gene expression


title: _19_HSC6-39465-13171_Ch480

description: gene expression


title: _22_HSC7-40375-13326_Ch360

description: gene expression

source_name: HSC Chemerin 360 ng/ml


title: _05_PHH-39965-13231_K

description: gene expression

source_name: PHH control 2


title: _14_HSC1-37205-12511_Ch360

description: gene expression


title: _16_HSC1-37205-12511_Ch600

description: gene expression


title: 8226 normo SP

source_name: 8226 normo SP


title: _11_PHH-40375-13316_Ch480

description: gene expression


title: _01_PHH-39465-13171_K

description: gene expression

source_name: PHH control 1


title: _18_HSC6-39465-13171_Ch360

description: gene expression


title: _02_PHH-39465-13171_Ch360

description: gene expression


title: _07_PHH-39965-13231_Ch480

description: gene expression


title: mamel134-C [ATAC-Seq]

city: New York

first: Jana

last: Biermann

state: New York

address: 622 W168th Street

institute: Columbia University

data_processing:
Raw sequencing FASTQ files were evaluated for quality and adapter content using FastQC v0.11.9 followed by adapter removal (-a CTGTCTCTTATA -A CTGTCTCTTATA) and quality trimming using cutadapt v3.6 (Martin, 2011) and finally aligned with hisat2 v2.2.1 (Kim et al., 2019) (default, -X 1000) to the human genome (GRCh38). Using samtools the BAM files were sorted, filtered for extra-chromosomal DNA, mitochondrial DNA and for reads overlapping blacklisted regions (Amemiya et al., 2019). Duplicate reads were removed using sambamba v0.6.8 (Tarasov et al., 2015) before downstream analyses. Accessible peaks were identified for each sample using MACS2 (v2.2.7.1, parameters: --nomodel --shift -100 --extsize 200 –broad) (Feng et al., 2012). BigWig files were generated using bamcoverage from deepTools2 (v3.5.1; --normalizeUsing CPM --binSize 25 --smoothLength 100) (Ramírez et al., 2016).
Assembly: GRCh38
Supplementary files format and content: DEseq.normalized.counts.csv: normalized counts
Supplementary files format and content: allpeaks_read.counts.rpkm.threshold.csv: read counts of all peaks
Supplementary files format and content: promoters_read.counts.rpkm.threshold.csv: read counts of all promoters

source_name: Melanoma extracranial metastasis (patient-derived cell line)

growth_protocol: All melanoma cell lines were grown in melanoma growth media (RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum, GlutaMax, 10 mM HEPES, 10 mg/L insulin, 5.5 mg/L transferrin, and 6.7 µg/L sodium, and 55 µM 2-mercaptoethanol (all from Thermo Fisher Scientific)) under adherent conditions at 37 ºC and 5% CO2 in a humidified incubator. For bulk RNA-seq cell lines were cultured as triplicates for 10 days and cell pellets were collected from each cell line at ~80% confluence.

extract_protocol:
DNA was isolated using the Qiagen MiniElute Reaction Cleanup Kit
Libraries were quantified using a 2200 TapeStation system (Agilent) and D5000 tapes. Final libraries were sequenced on a NovaSeq 6000 with S4 flow cell with 2x150 bp paired-end sequencing.

tag: metastatic site

value: ECM

tag: patient id

tag: sequencing technique

value: ATAC-seq

tag: rna-seq available

value: yes

tag: scrna-seq available

value: no

tag: tcr-seq available


title: mamel134-B [ATAC-Seq]


title: HKC treated with TGF-β1 - duplicate #2

city: Chicago

first: Vidhi

last: Dalal

state: Illinois

address: 225 East Chicago Ave, Box 37

institute: Lurie Children's Hospital

data_processing:
Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Indexes of the reference genome was built using STAR and paired-end clean reads were aligned to the reference genome using STAR (v2.5).
STAR used the method of Maximal Mappable Prefix(MMP) which can generate a precise mapping result for junction reads.
HTSeq v0.6.1 was used to count the read numbers mapped of each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis between the two conditions (two biological replicates per condition) was performed using the DESeq2 R package (2_1.6.3).
TFCat and Cosmic database were used to annotate the differential expressed gene.
Assembly: hg38
Supplementary files format and content: matrix table containing fpkm values for each sample

source_name: HKC

growth_protocol: HKC were grown in humidified atmosphere with 5% CO2 at 37C in Dulbecco’s Modified Eagle Medium/F-12 (1:1) with 9% heat-inactivated fetal bovine serum (FBS), 0.9 mM HEPES buffer, 90 units/mL penicillin, 90 µg/mL streptomycin, 225 ng/mL amphotericin B, and 1.8 mM L-glutamine.

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (Qiagen) according to manufacturer’s instructions.
Lirabry was constructed for RNA sequencing using the NEBNext Ultra RNA Library Prep Kit for Illumina at Novogene.
RNA sequencing; strategy PE150

treatment_protocol: HKC were treated with either recombinant human TGF-β1 (final concentration of 2.5 ng/mL) or an equivalent volume of vehicle for 72 hours, with replacement of medium and re-treatment after 48 hours.

value: HKC

value: human renal epithelial cells

value: WT

tag: treatment


title: HKC treated with TGF-β1 - duplicate #1


title: HKC treated with vehicle - duplicate #1

value: vehicle


title: 2686-C [ATAC-Seq]


title: HKC treated with vehicle - duplicate #2


title: 5B1-A [ATAC-Seq]

source_name: Melanoma brain metastasis (patient-derived cell line)

value: MBM


title: 4LN-A [ATAC-Seq]


title: 5B1-B [ATAC-Seq]


title: 4LN-B [ATAC-Seq]


title: 273LN-A [ATAC-Seq]


title: 4LN-C [ATAC-Seq]


title: 2686-A [ATAC-Seq]


title: 273LN-C [ATAC-Seq]


title: BI3-C [ATAC-Seq]


title: BI3-B [ATAC-Seq]


title: 273BM-C [ATAC-Seq]


title: 273BM-B [ATAC-Seq]


title: BI3-A [ATAC-Seq]


title: THP-1 cells, methamphetamine-treated, biol rep 2

city: Kunming

first: Deshenyue

last: Kong

address: 1168 West Chunrong Road

institute: Kunming Medical University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp (version 0.19.7) (parameter-fastp -g -q 5 -u 50 -n 15 -l 150)
Trimmed sequence reads were mapped using HISAT2 Software
Gene expression quantification using the featureCounts in subread software
Assembly: http://ftp.ensembl.org/pub/release-99/fasta/homo_sapiens/
Assembly: http://ftp.ensembl.org/pub/release-99/gtf/homo_sapiens/
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Peripheral blood

growth_protocol: Jurkat and THP-1 cells were cultured in RPMI Medium 1640 (Invitrogen) supplemented with 10% fetal bovine serum (Biological Industries). NK-92 cells were cultured in MEMα (PM150422) with 0.2mM Inositol, 0.1mM β-mercaptoethanol (PB180633), 0.02mM Folic Acid, 200U/mL recombinant IL-2, 12.5% HS (164215-100), 12.5% FBS (164210-500), and 1% P/S (PB180120) (Procell, Wuhan, China). Exponentially growing cells, at approximately 60–75% confluence, were counted, and seeded into T25 culture flasks (5.0×105 cells/flask, 25 cm2 growth area) (Corning). The cells were incubated at 37°C in a 5% CO2 humidified incubator.

extract_protocol:
Total RNA was isolated using a Trizol RNA isolation kit (Qiagen). Total amounts and integrity of RNA were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer (5×). First-strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. The remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure was ligated to prepare for hybridization. To select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained.

treatment_protocol: 0 or 250 μM methamphetamine treated for 24 h

tag: tissue

value: Peripheral blood

value: monocyte

value: 250 μM methamphetamine treated for 24 h


title: THP-1 cells, methamphetamine-treated, biol rep 3


title: BI5-A [ATAC-Seq]


title: 273BM-A [ATAC-Seq]


title: BI5-C [ATAC-Seq]


title: BI5-B [ATAC-Seq]


title: mamel134-A [ATAC-Seq]


title: THP-1 cells, methamphetamine-treated, biol rep 1


title: 2686-B [ATAC-Seq]


title: 5B1-C [ATAC-Seq]


title: THP-1 cells, Control, biol rep 3

value: 0 μM methamphetamine treated for 24 h


title: 273LN-B [ATAC-Seq]


title: NK-92 cells, methamphetamine-treated, biol rep 3

value: natural killer cell


title: THP-1 cells, Control, biol rep 1


title: NK-92 cells, Control, biol rep 3


title: NK-92 cells, methamphetamine-treated, biol rep 2


title: NK-92 cells, methamphetamine-treated, biol rep 1


title: NK-92 cells, Control, biol rep 1


title: NK-92 cells, Control, biol rep 2


title: mamel134-C

description: Bulk RNA-seq of patient-derived cell line

data_processing:
FASTQ files were quantified using Kallisto.
Assembly: GRCh38
Supplementary files format and content: patient_cell_lines_RNA-seq_counts.csv
Supplementary files format and content: patient_cell_lines_metadata.csv
Supplementary files format and content: abundance.tsv files (output from Kallisto)

extract_protocol:
Total RNA was extracted from frozen pellets using RNAeasy Plus (Qiagen) with 5e5 cells per column.
RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer's instructions (New England Biolabs). Briefly, mRNAs were initially enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3'ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing libraries were validated on the Agilent TapeStation (Agilent Technologies), and quantified by using Qubit 2.0 Fluorometer (ThermoFisher Scientific) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).

value: RNA-seq

tag: atac-seq available


title: Jurkat cells, methamphetamine-treated, biol rep 3

value: Jurkat

value: T lymphoblast


title: 2686-C

value: ECM


title: Jurkat cells, Control, biol rep 1


title: Jurkat cells, Control, biol rep 2


title: Jurkat cells, methamphetamine-treated, biol rep 1


title: Jurkat cells, methamphetamine-treated, biol rep 2


title: Jurkat cells, Control, biol rep 3


title: 5B1-B


title: 5B1-A


title: mamel134-B


title: 4LN-C


title: 2686-A


title: 2686-B


title: mamel134-A


title: 273BM-B


title: 5B1-C


title: 273BM-C


title: 273BM-A


title: 273LN-B


title: 4LN-A


title: 4LN-B


title: BI5-B


title: 273LN-C


title: BI5-A


title: BI3-B


title: BI5-C


title: THP-1 cells, Control, biol rep 2


title: 273LN-A


title: BI3-A


title: BI3-C


title: H_8

city: Minneapolis

first: Brenda

last: Ogle

state: MN

address: 7-130 Hasselmo Hall 312 Church St. SE

department: Biomedical Engineering

institute: University of Minnesota

data_processing:
base-calling via Illumina Casava 1.8 software
The Sequenced Reads/raw reads often contain low quality reads or reads with adapters, which will affect the analysis quality and reliability.  To avoid this, it's necessary to filter the raw reads and get the clean reads. The procedure of raw reads filtering is as follows:  (1) Remove reads containing adapters;  (2) Remove reads containing N > 10% (N represents base that could not be determined);  (3) Remove low quality reads: The Qscore (Quality value) of over 50% bases of the read is <= 5.
Mapping clean reads to the reference genome or the transcriptome is the basis for the next following analysis. For human and mice, the  species with completed annotation, when only differential expression gene (quantification) analysis is needed, the raw data can map reads to the  transcriptome directly. However, in studies on transcript structural variation, such as alternative splicing, variation, the fusion gene, the alignment  should be carried out at the genomic level. STAR v2.5 software is used to accomplish the mapping. The alignment by STAR precisely and effectively  performs positioning junction reads for RNA sequencing data analysis.
The abundance of transcript reflects the gene expression level directly. In RNA-seq experiment, we estimate gene expression level by the  abundance of transcripts (count of sequencing) that mapped to genome or exon. Reads count is proportional to gene expression level, gene length  and sequencing depth. FPKM (short for the expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced)  is the most common method of estimating gene expression levels, which takes the effects into consideration of both sequencing depth and gene  length on counting of fragments. Differential expression analysis was performed using the DESeq2 R package 2_1.6.3. The resulting p-values were adjusted using Benjamini and Hochberg's approach for controlling the False Disovery Rate (FDR). Genes with an adjusted p-value <0.05 found by DESeq2 were assigned as differentially expressed.
Assembly: hg38
Supplementary files format and content: The input data for differential gene expression analysis is read counts from gene expression level analysis. The differential gene expression  analysis commonly contains three steps:  1) Read counts Normalization;  2) Model dependent p-value estimation;  3) FDR value estimation based on multiple hypothesis testing

source_name: mutant (MYH7 R723C and MYH6 R725C) hiPSC-CMs

growth_protocol: Isogenic control hiPSC-CMs and mutant hiPSC-CMs were obtained via the fully defined direct cardiac differentiation by modulating Wnt/b-catenin signaling. Briefly, hiPSCs were cultured on Matrigel-coated 6-well plates in mTeSR1 medium for 5 days to reach 80-90% confluency. To harvest singularized cells, the culture medium was removed, and the wells were washed one time with sterile DPBS, then added 1 mL of room-temperature Accutase into each well. The plates were transferred into the incubator to allow Accutase to react at 37°C for 8 min. 0.5 mL of mTeSR1 medium was added into each well to stop Accutase reactions. The singularized cells were resuspended in mTeSR1 with 5 μM ROCK inhibitor (Y27632), seeded with the density of 5 x 10^5 cells/well on Matrigel-coated 24-well plates and maintained at 37°C, 5% CO2 incubator for 24 hours. After 24 hours, on Day -1, 1 mL of fresh mTeSR1 medium was added to each well. On Day 0, the start of cardiac differentiation, 1 mL of RPMI/B-27 without insulin (RPMI minus) medium with 8 μM GSK3-β inhibitor (CHIR99021) was added into each well for 24 hours in the 37°C, 5% CO2 incubator to induce mesoderm. On Day 1, CHIR99021 medium was replaced with fresh RPMI/B27 minus medium. On Day 3, 0.5 mL of exhausted medium from each well was collected and mixed 1:1 with fresh RPMI/B27 minus insulin medium. Wnt inhibitor (IWP2) was added into the mixed medium to achieve the concentration of 5 μM. Each well was incubated with IWP2 for 48 hours to induce cardiac differentiation. On Day 5, fresh RPMI/B27 minus insulin was added into each well. On Day 7 and every 3 days thereafter, fresh maintenance medium, RPMI/B-27 medium, was added to each well. Spontaneous twitching was observed on Day 8, and robust spontaneous contraction occurred by Day 12.

extract_protocol:
Total RNA were isolated from undifferentiated and differentiated isogenic control and R723C hiPSCs using the RNeasy kit (Qiagen) according to the manufacturer’s protocol. Briefly, washed the cells once with sterile PBS and lysed in RLT-lysis buffer for specific time points. RNA isolation was performed as per the protocol, followed by on-column DNA digestion to remove any traces of DNA as per the instructions. For cDNA synthesis, 100-1000 ng of total RNA was used and synthesized using the SuperScript IV VILO kit (Thermo Fisher Scientific) according to the manufacturer's protocol. Quantitative PCR (qPCR) was performed using gene-specific oligos and the SYBR-green method.
The total RNA was isolated as described above. For the bulk-RNAseq analysis, 1 μg of total RNA was submitted to Novogene (https://en.novogene.com/) for sequencing and data analysis. At Novogene, cDNA libraries are sequenced using the state-of-the-art Illumina NovaSeq platforms, which utilize a paired-end 150 bp sequencing strategy (short-reads).

value: hiPSC-derived cardiomyocytes

tag: age

value: Day 15 after initiationof cardiac differentiation

value: MYH7/MYH6 mutant


title: G_7

tag: genotype


title: GM12878_RNA_Rep3

city: Nashville

first: Tyler

last: Hansen

state: TN

address: 2215 Garland Ave

department: Biochemistry

institute: Vanderbilt University

description: reporter RNA

data_processing:
Library strategy: ATAC-STARR-seq
Fastqs were trimmed using trimgalore
reads were mapped to the hg38 reference genome index using bowtie2
accessible peaks were called on mapped reads using Genrich, ATAC mode
active and silent regions were called using a custom processed described in the manuscript
Tn5-corrected cut counts signal was generated with the TOBIAS package
Genome_build: hg38
Supplementary_files_format_and_content: .narrowPeak are accessibility peaks
Supplementary_files_format_and_content: .bed files are the active and silent regions
Supplementary_files_format_and_content: .bw file is the cut count signal used in footprinting

source_name: EBV-transformed B cells

growth_protocol: GM12878 cells were routinely cultured in complete media (RPMI 1640, 15% FBS) at a cell density between 2e5 and 10e5 cells/ml.

extract_protocol:
Cells were pelleted and processed using the protocol outlined in the manuscript.
Libraries were assembled using the protocol outlined in the manuscript.

value: EBV-transformed B cells


title: C_3

source_name: isogenic control hiPSC-CMs

value: wild type


title: GM12878_DNA_Rep3

description: plasmid DNA


title: sample2_CT

city: Madison

first: Hasan

last: Khatib

state: Wisconsin

address: 1675 Observatory Dr.

department: Animal and Dairy Sciences

institute: University of Wisconsin-Madison

data_processing:
For each sample, FastQC and Trimmomatic were used to generate sequence quality reports, and to trim adapter sequences and low quality reads, respectively. After, trimmed reads were aligned to the human reference genome (NCBI Homo sapiens GRCh38.p13) using STAR (Dobin et al., 2013) with parameters –outSAMmapqUnique 60 --outFilterType BySJout --outSAMstrandField intronMotif --quantMode GeneCounts --twopassMode Basic
Read counts for each gene were estimated using “--quantMode GeneCounts” option in STAR.
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: embryonic kidney (HEK293T) cells

growth_protocol: HEK293T cells were cultured in 24 well plates with  Gibco DMEM/F12 medium (Life Technologies, CA, USA) containing 10% Gibco fetal bovine serum (Life technologies). Cells were incubated at 37°C in a humidified 5% CO2-containing atmosphere

extract_protocol:
Forty-eight hours after transfection, cells were lysed, and every four wells were combined for total RNA extraction using TRIzol.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: HEK293T cells were transfecred with dCas9-p300 and two PRM1 gRNAs targeting the promoter region (ratio 3 (dCas9-p300):1 (two gRNAs))

value: embryonic kidney (HEK293T)

value: control


title: D_4


title: sample4_CT


title: sample4_TR

value: transfected with lipofectamine 2000, 375 ng of dCas9-p300, and 125 ng of an equimolar concentration of each PRM1 gRNA expression vector


title: sample3_TR


title: RhoA_DN 2

city: Halle

first: Robert

last: Eckenstaler

address: Kurt-Mothes-Str. 3

department: Institute of Pharmazie

institute: Martin-Luther-University

description: overexpression of dominant negative RhoA (T19N) replicate 2

data_processing:
Sequencing and data procession were performed by Novogene.
Alignment: to human genome (GRCh38) with HiSat2 (v2.0.5)
Annotations: Ensembl (GRCh38.p13)
Abundance measurements: HTSeq (v0.6.1)
Differential gene expression: DESeq2 software package (v1.20.0)
Genome_build: human genome (GRCh38)
Supplementary_files_format_and_content: tab-delimited text files including FPKM for abundance measurements

source_name: cultured endothelial cells

growth_protocol: HUVECs were cultured in ready-to-use basal endothelial cell medium (EBM-2, Promocell) supplemented with 2% fetal calf serum (FCS), basic fibroblast growth factor (bFGF), VEGF, insulin-like growth factor-1 (IGF-1), epidermal growth factor (EGF), hydrocortisone, ascorbic acid, gentamycin sulfate and amphotericin-B at 37°C in humidified air with 5% CO2.

extract_protocol:
RNA was extracted using TRIZOLTM reagent (Thermo Fisher Scientific) according to manifacturer's instructions.
NEBNext® Ultra ™ RNA Library Prep Kit for Illumina® (New England BioLabs)

treatment_protocol: HUVECs were infected with VSV-G-pseudotyped lentiviral particles derived from pHIV-SFiG-1335 (EGFP) transfer plasmids with a multiplicity of infection (MOI) of 500. For control cells (Ctr.), empty pHIV-SFiG-1335 was transduced. For overexpression of constitutively active (Q63L) and dominant negative (T19N) RhoA, a sequence expressing the respective RhoA mutants was inserted into the pHIV-SFiG-1335 backbone.

value: human umbilical vein endothelial cells (HUVECs)

tag: passages

value: 2 to 7

tag: genotype/variation

value: overexpression of dominant negative RhoA (T19N mutant)


title: sample2_TR


title: RhoA_DN 3

description: overexpression of dominant negative RhoA (T19N) replicate 3


title: RhoA_DN 1

description: overexpression of dominant negative RhoA (T19N) replicate 1


title: sample1_TR


title: GM12878_Plasmid-Library

description: plasmid DNA

source_name: GM12878 Plasmid Library Complexity Check


title: Ctr 1

description: control replicate 1

value: wildtype levels of RhoA


title: GM12878_RNA_Rep1

description: reporter RNA

source_name: GM12878 Reporter RNA Rep1


title: RhoA_CA 3

description: overexpression of constitutively active RhoA (Q63L) replicate 3

value: overexpression of constitutively active RhoA (Q63L mutant)


title: Ctr 3

description: control replicate 3


title: GM12878_DNA_Rep2

description: plasmid DNA

source_name: GM12878 Reisolated Plasmid Rep2


title: RhoA_CA 1

description: overexpression of constitutively active RhoA (Q63L) replicate 1


title: RhoA_CA 2

description: overexpression of constitutively active RhoA (Q63L) replicate 2


title: sample1_CT


title: Ctr 2

description: control replicate 2


title: sample3_CT


title: In vitro haustoria, without Host, biol rep1 [NH1_S6]

city: University Park

first: Michael

last: Axtell

state: PA

address: 280 Mueller Lab

department: Biology

institute: Pennsylvania State University

description: ReadGroup "NH1_S6_R1_001_ca"

data_processing:
3' Adapter trimming used cutadapt version 3.5 with settings -a AGATCGGAAGAGCACACGTCTGAAC --discard-untrimmed -m 15 -j 4
Trimmed fastq reads were aligned to the Cuscuta campestris genome (version 0.32 from Vogel et al. 2018 [doi 10.1038/s41467-018-04344-z]) and analyzed with respect to known interface-induced microRNA loci using ShortStack version 3.8.5. Settings:  ShortStack --genomefile cuscuta_campestris_assembly_r0-32.fasta --locifile ccm-IIM_v2_pre-miRNA.SSLoci.tsv --outdir SS --bowtie_cores 3 --sort_mem 6G --readfile H1_S9_R1_001_ca.fastq H2_S10_R1_001_ca.fastq H3_S11_R1_001_ca.fastq NH1_S6_R1_001_ca.fastq NH2_S7_R1_001_ca.fastq NH3_S8_R1_001_ca.fastq T1_S3_R1_001_ca.fastq T2_S4_R1_001_ca.fastq T3_S5_R1_001_ca.fastq
The Counts.txt file produced by ShortStack was then processed in R to organize the count data and calculate reads per million mapped (RPMM) for each locus.
Assembly: Cuscuta campestris version 0.32 genome assembly, cucam_0.32.assembly.dna.fasta.gz , from https://plabipd.de/project_cuscuta2/start.ep and described in Vogel et al. (2018) [doi 10.1038/s41467-018-04344-z]
Supplementary files format and content: csv file in "tidy" format with one observation per row. An observation is a specific microRNA locus from a specific library. The key variable is column 'RPMM', which shows the reads per million mapped. Column 'ReadGroup' specifies the sample. This is the source file for all figures in the study.

organism: Cuscuta campestris

source_name: In vitro haustoria

growth_protocol: Colonies of Cuscuta campestris were cultivated in a summer greenhouse using both beets and Coleus as hosts. Shoot tips, about 6-8 cm in length were cut with scissors.

extract_protocol:
Total RNA was extracted using bead-beater disruption of tissue coupled with Tri-Reagent (Sigma) per the manufacturer's instructions.
5ul of total RNA, at 100ng/ul, was used for library construction. Small RNA libraries were constructed using a random-splint-ligation protocol, essentially as described by Maguire et al. (2020) [doi 10.1093/nar/gkaa480] except with the inclusion of dual indices. Amplified libraries were cleaned using spin columns, quantified using UV spectrophotometry, and mixed in an equal-mass pool. The pool was size-selected using a BluePippin device set to recover fragments from 150-190bp (corresponding to insert sizes of 12 to 52 nucleotides). The size-selected pool was then sequenced on a NextSeq 2000 instrument using custom oligos and dual indexing.

treatment_protocol: Shoot tip samples were immediately flash-frozen pending total RNA extraction. In vitro hasutoria were induced by placing tips on 3% agarose plates, covered with 8 microscope slides to provide physical pressure. The "with host" samples also had detached Arabidopsis thaliana leaves arrayed on top of the tips with the abaxial leaf surfaces in contact with the Cuscuta tips. Plates were exposed to a far-red LED bulb for 2 hours, followed by a 4 day incubation in darkness. Cuscuta samples with induced haustoria were then removed and flash-frozen pending RNA extraction.

value: In vitro haustoria

value: wild-type (isolate 'Dottie')

value: in vitro haustoria, without host tissue (Arabidopsis thaliana leaves)


title: GM12878_RNA_Rep2

description: reporter RNA

source_name: GM12878 Reporter RNA Rep2


title: In vitro haustoria, without Host, biol rep3 [NH3_S8]

description: ReadGroup "NH3_S8_R1_001_ca"


title: Shoot tips, biol rep2 [T2_S4]

description: ReadGroup "T2_S4_R1_001_ca"

source_name: Shoot tips

value: Shoot tips


title: In vitro haustoria, without Host, biol rep2 [NH2_S7]

description: ReadGroup "NH2_S7_R1_001_ca"


title: In vitro haustoria, with Host, biol rep2 [H2_S10]

description: ReadGroup "H2_S10_R1_001_ca"

value: in vitro haustoria, with host tissue (Arabidopsis thaliana leaves)


title: In vitro haustoria, with Host, biol rep1 [H1_S9]

description: ReadGroup "H1_S9_R1_001_ca"


title: In vitro haustoria, with Host, biol rep3 [H3_S11]

description: ReadGroup "H3_S11_R1_001_ca"


title: Shoot tips, biol rep3 [T3_S5]

description: ReadGroup "T3_S5_R1_001_ca"


title: ss15_262135, scRNAseq

data_processing:
All data was processed using a custom Nextflow pipeline available at https://github.com/alexthiery/otic-reprogramming. All packages and versions are containerised in Docker images called by the pipeline. Full documentation of pipeline parameters and how to reproduce the analysis is available at https://alexthiery.github.io/otic-reprogramming/
Adaptor sequences were trimmed using cutadapt v2.10, aligned using hisat2 v2.2.1, sorted using samtools v1.10, and read counts obtained using htseq v0.12.4.
RNA velocity counts were obtained using Velocyto v0.17.17.
Genome_build: galgal6
Supplementary_files_format_and_content: assayData.csv (raw counts)
phenoData.csv (sample metadata)
gfpData.csv (raw gfp counts)
onefilepercell_ss8-TSS_P2_C10_75_and_others_TVIUH.loom (raw velocyto counts)

source_name: Pax2+ cells

growth_protocol: Chick embryos were electroporated and grown at 38°C until reaching the desired stage.

extract_protocol:
EGFP+ single cells were individually collected by FACS into 96 well plates.
Libraries were prepared following SmartSeq2 NexteraXT indications.
single cell RNA seq

treatment_protocol: Chick embryos were electroporated at head fold stage with pTK-Pax2E1-EGFP plasmids.

value: Pax2+ cells

tag: Stage


title: ss15_268158, scRNAseq


title: ss15_260159, scRNAseq


title: ss15_264111, scRNAseq


title: ss15_269146, scRNAseq


title: ss15_263123, scRNAseq


title: ss15_266182, scRNAseq


title: ss15_265194, scRNAseq


title: ss15_257195, scRNAseq


title: Shoot tips, biol rep1 [T1_S3]

description: ReadGroup "T1_S3_R1_001_ca"


title: ss15_255124, scRNAseq


title: GM12878_DNA_Rep1

description: plasmid DNA

source_name: GM12878 Reisolated Plasmid Rep1


title: ss15_261147, scRNAseq


title: ss15_259171, scRNAseq


title: ss15_258183, scRNAseq


title: ss15_242173, scRNAseq


title: ss15_245137, scRNAseq


title: ss15_246125, scRNAseq


title: ss15_243161, scRNAseq


title: ss15_254136, scRNAseq


title: ss15_256112, scRNAseq


title: ss15_250113, scRNAseq


title: ss15_253148, scRNAseq


title: ss15_240102, scRNAseq


title: ss15_248101, scRNAseq


title: ss15_238126, scRNAseq


title: ss15_236150, scRNAseq


title: ss15_244149, scRNAseq


title: ss15_267170, scRNAseq


title: ss15_229139, scRNAseq


title: ss15_232103, scRNAseq


title: ss15_234174, scRNAseq


title: ss15_228151, scRNAseq


title: ss15_247113, scRNAseq


title: ss15_237138, scRNAseq


title: ss15_233186, scRNAseq


title: ss15_241185, scRNAseq


title: ss15_231115, scRNAseq


title: ss15_221140, scRNAseq


title: ss15_225187, scRNAseq


title: ss15_223116, scRNAseq


title: ss15_230127, scRNAseq


title: ss15_226175, scRNAseq


title: ss15_220152, scRNAseq


title: ss15_227163, scRNAseq


title: ss15_252160, scRNAseq


title: ss15_217188, scRNAseq


title: ss15_218176, scRNAseq


title: ss15_222128, scRNAseq


title: ss15_224104, scRNAseq


title: ss15_216105, scRNAseq


title: ss15_212153, scRNAseq


title: ss15_211165, scRNAseq


title: ss15_235162, scRNAseq


title: ss15_239114, scRNAseq


title: ss15_219164, scRNAseq


title: ss15_214129, scRNAseq


title: ss15_206130, scRNAseq


title: ss15_213141, scRNAseq


title: ss15_205142, scRNAseq


title: ss15_201190, scRNAseq


title: ss15_209189, scRNAseq


title: ss15_207118, scRNAseq


title: ss15_210177, scRNAseq


title: ss15_204154, scRNAseq


title: ss15_208106, scRNAseq


title: ss15_295179, scRNAseq


title: ss15_203166, scRNAseq


title: ss15_296191, scRNAseq


title: ss15_215117, scRNAseq


title: ss15_202178, scRNAseq


title: ss15_296106, scRNAseq


title: ss15_294130, scRNAseq


title: ss15_294167, scRNAseq


title: ss15_293155, scRNAseq


title: ss15_289190, scRNAseq


title: ss15_292154, scRNAseq


title: ss15_293142, scRNAseq


title: ss15_290178, scRNAseq


title: ss15_292143, scRNAseq


title: ss15_289107, scRNAseq


title: ss15_291166, scRNAseq


title: ss15_290119, scRNAseq


title: ss15_288190, scRNAseq


title: ss15_288107, scRNAseq


title: ss15_291131, scRNAseq


title: ss15_287119, scRNAseq


title: ss15_295118, scRNAseq


title: ss15_287178, scRNAseq


title: ss15_283130, scRNAseq


title: ss15_284142, scRNAseq


title: ss15_284155, scRNAseq


title: ss15_285143, scRNAseq


title: ss15_283167, scRNAseq


title: ss15_286166, scRNAseq


title: ss15_281191, scRNAseq


title: ss15_281106, scRNAseq


title: ss15_282179, scRNAseq


title: ss15_280108, scRNAseq


title: ss15_279177, scRNAseq


title: ss15_276141, scRNAseq


title: ss15_275168, scRNAseq


title: ss15_278165, scRNAseq


title: ss15_279120, scRNAseq


title: ss15_278132, scRNAseq


title: ss15_286131, scRNAseq


title: ss15_285154, scRNAseq


title: ss15_273192, scRNAseq


title: ss15_277153, scRNAseq


title: ss15_274180, scRNAseq


title: ss15_275129, scRNAseq


title: ss15_272188, scRNAseq


title: ss15_282118, scRNAseq


title: ss15_273105, scRNAseq


title: ss15_274117, scRNAseq


title: ss15_270164, scRNAseq


title: ss15_271121, scRNAseq


title: ss15_280189, scRNAseq


title: ss15_271176, scRNAseq


title: ss15_269152, scRNAseq


title: ss15_268140, scRNAseq


title: ss15_267169, scRNAseq


title: ss15_268157, scRNAseq


title: ss15_270133, scRNAseq


title: ss15_269145, scRNAseq


title: ss15_276156, scRNAseq


title: ss15_267128, scRNAseq


title: ss15_277144, scRNAseq


title: ss15_266181, scRNAseq


title: ss15_272109, scRNAseq


title: ss15_265193, scRNAseq


title: ss15_266116, scRNAseq


title: ss15_259127, scRNAseq


title: ss15_263122, scRNAseq


title: ss15_262134, scRNAseq


title: ss15_261146, scRNAseq


title: ss15_260139, scRNAseq


title: ss15_264187, scRNAseq


title: ss15_264110, scRNAseq


title: ss15_260158, scRNAseq


title: ss15_257194, scRNAseq


title: ss15_256186, scRNAseq


title: ss15_256111, scRNAseq


title: ss15_265104, scRNAseq


title: ss15_257103, scRNAseq


title: ss15_258115, scRNAseq


title: ss15_261151, scRNAseq


title: ss15_259170, scRNAseq


title: ss15_254135, scRNAseq


title: ss15_255174, scRNAseq


title: ss15_254162, scRNAseq


title: ss15_255123, scRNAseq


title: ss15_263175, scRNAseq


title: ss15_253150, scRNAseq


title: ss15_252159, scRNAseq


title: ss15_262163, scRNAseq


title: ss15_251171, scRNAseq


title: ss15_251126, scRNAseq


title: ss15_248185, scRNAseq


title: ss15_247173, scRNAseq


title: ss15_249195, scRNAseq


title: ss15_247124, scRNAseq


title: ss15_249102, scRNAseq


title: ss15_246161, scRNAseq


title: ss15_250183, scRNAseq


title: ss15_243172, scRNAseq


title: ss15_246136, scRNAseq


title: ss15_242113, scRNAseq


title: ss15_243125, scRNAseq


title: ss15_248112, scRNAseq


title: ss15_245148, scRNAseq


title: ss15_242184, scRNAseq


title: ss15_241196, scRNAseq


title: ss15_244160, scRNAseq


title: ss15_241101, scRNAseq


title: ss15_239184, scRNAseq


title: ss15_244137, scRNAseq


title: ss15_258182, scRNAseq


title: ss15_245149, scRNAseq


title: ss15_239113, scRNAseq


title: ss15_240196, scRNAseq


title: ss15_240101, scRNAseq


title: ss15_252138, scRNAseq


title: ss15_253147, scRNAseq


title: ss15_250114, scRNAseq


title: ss15_238125, scRNAseq


title: ss15_238172, scRNAseq


title: ss15_236149, scRNAseq


title: ss15_236148, scRNAseq


title: ss15_235161, scRNAseq


title: ss15_234173, scRNAseq


title: ss15_237137, scRNAseq


title: ss15_235136, scRNAseq


title: ss15_234124, scRNAseq


title: ss15_233112, scRNAseq


title: ss15_230126, scRNAseq


title: ss15_232102, scRNAseq


title: ss15_231183, scRNAseq


title: ss15_229159, scRNAseq


title: ss15_232195, scRNAseq


title: ss15_228150, scRNAseq


title: ss15_229138, scRNAseq


title: ss15_230171, scRNAseq


title: ss15_227162, scRNAseq


title: ss15_226174, scRNAseq


title: ss15_227135, scRNAseq


title: ss15_231114, scRNAseq


title: ss15_237160, scRNAseq


title: ss15_228147, scRNAseq


title: ss15_225111, scRNAseq


title: ss15_225186, scRNAseq


title: ss15_226123, scRNAseq


title: ss15_224194, scRNAseq


title: ss15_224103, scRNAseq


title: ss15_223115, scRNAseq


title: ss15_233185, scRNAseq


title: ss15_223182, scRNAseq


title: ss15_219163, scRNAseq


title: ss15_220151, scRNAseq


title: ss15_222127, scRNAseq


title: ss15_221139, scRNAseq


title: ss15_221158, scRNAseq


title: ss15_219134, scRNAseq


title: ss15_220146, scRNAseq


title: ss15_222170, scRNAseq


title: ss15_215181, scRNAseq


title: ss15_218175, scRNAseq


title: ss15_217110, scRNAseq


title: ss15_218122, scRNAseq


title: ss15_216104, scRNAseq


title: ss15_217187, scRNAseq


title: ss15_210176, scRNAseq


title: ss15_214169, scRNAseq


title: ss15_211133, scRNAseq


title: ss15_209188, scRNAseq


title: ss15_214128, scRNAseq


title: ss15_209109, scRNAseq


title: ss15_208192, scRNAseq


title: ss15_208105, scRNAseq


title: ss15_207180, scRNAseq


title: ss15_211164, scRNAseq


title: ss15_212145, scRNAseq


title: ss15_212152, scRNAseq


title: ss15_207117, scRNAseq


title: ss15_206129, scRNAseq


title: ss15_213157, scRNAseq


title: ss15_210121, scRNAseq


title: ss15_216193, scRNAseq


title: ss15_215116, scRNAseq


title: ss15_204144, scRNAseq


title: ss15_202120, scRNAseq


title: ss15_203165, scRNAseq


title: ss15_206168, scRNAseq


title: ss15_213140, scRNAseq


title: ss15_201108, scRNAseq


title: ss15_205156, scRNAseq


title: ss15_202177, scRNAseq


title: ss15_205141, scRNAseq


title: ss15_201189, scRNAseq


title: ss15_204153, scRNAseq


title: ss15_203132, scRNAseq


title: ss11_291130, scRNAseq


title: ss11_296190, scRNAseq


title: ss11_290118, scRNAseq


title: ss11_294166, scRNAseq


title: ss11_293154, scRNAseq


title: ss11_285153, scRNAseq


title: ss11_288189, scRNAseq


title: ss11_292142, scRNAseq


title: ss11_283129, scRNAseq


title: ss11_289106, scRNAseq


title: ss11_282117, scRNAseq


title: ss11_284141, scRNAseq


title: ss11_295178, scRNAseq


title: ss11_287177, scRNAseq


title: ss11_286165, scRNAseq


title: ss11_281105, scRNAseq


title: ss11_280188, scRNAseq


title: ss11_270163, scRNAseq


title: ss11_269151, scRNAseq


title: ss11_272187, scRNAseq


title: ss11_276140, scRNAseq


title: ss11_278164, scRNAseq


title: ss11_268139, scRNAseq


title: ss11_279176, scRNAseq


title: ss11_275128, scRNAseq


title: ss11_274116, scRNAseq


title: ss11_273104, scRNAseq


title: ss11_271175, scRNAseq


title: ss11_265103, scRNAseq


title: ss11_266115, scRNAseq


title: ss11_257102, scRNAseq


title: ss11_260138, scRNAseq


title: ss11_261150, scRNAseq


title: ss11_258114, scRNAseq


title: ss11_277152, scRNAseq


title: ss11_267127, scRNAseq


title: ss11_264186, scRNAseq


title: ss11_253149, scRNAseq


title: ss11_259126, scRNAseq


title: ss11_263174, scRNAseq


title: ss11_262162, scRNAseq


title: ss11_256185, scRNAseq


title: ss11_254161, scRNAseq


title: ss11_255173, scRNAseq


title: ss11_244148, scRNAseq


title: ss11_247184, scRNAseq


title: ss11_249101, scRNAseq


title: ss11_251125, scRNAseq


title: ss11_234123, scRNAseq


title: ss11_239183, scRNAseq


title: ss11_248196, scRNAseq


title: ss11_236147, scRNAseq


title: ss11_237159, scRNAseq


title: ss11_232194, scRNAseq


title: ss11_242124, scRNAseq


title: ss11_238171, scRNAseq


title: ss11_230170, scRNAseq


title: ss11_252137, scRNAseq


title: ss11_240195, scRNAseq


title: ss11_235135, scRNAseq


title: ss11_231182, scRNAseq


title: ss11_229158, scRNAseq


title: ss11_228146, scRNAseq


title: ss11_224193, scRNAseq


title: ss11_227134, scRNAseq


title: ss11_226122, scRNAseq


title: ss11_223181, scRNAseq


title: ss11_222169, scRNAseq


title: E16.5_Dlx5/6-CIE; Rosa-Sp9-OE/+_LGE 3

first: Zhenmeiyu

last: Li

address: 138 Yi Xue Yuan Road

institute: Fudan University

data_processing:
Levels of gene expression were reported in fragments per kilobase of exon per million fragments mapped (FPKM).
Significantly differentially expressed genes were defined on the basis of a false detection rate (FDR) < 0.05.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: LGE

extract_protocol:
Total RNA was purified with a Mini RNA isolation kit (Zymo)
according to the manufacturer’s protocol (Illumina TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Mouse).

value: LGE

value: Dlx5/6-CIE; Rosa-Sp9-OE/+


title: ss11_246172, scRNAseq


title: ss11_245160, scRNAseq


title: ss11_243136, scRNAseq


title: ss11_221157, scRNAseq


title: ss11_220145, scRNAseq


title: ss11_219133, scRNAseq


title: E16.5_Dlx5/6-CIE 3


title: ss11_218121, scRNAseq


title: E16.5_Dlx5/6-CIE; Rosa-Sp9-OE/+_LGE 1


title: E16.5_Dlx5/6-CIE 1


title: ss11_217109, scRNAseq


title: E16.5_Dlx5/6-CIE 2


title: ss11_215180, scRNAseq


title: ss11_216192, scRNAseq