title: RBM4_3

city: Dalian

first: Wang

last: Yang

address: 9 Lvshun South Rd West Section, Lüshunkou District, Dalian, Liaoning, China

department: Institute of Cancer Stem Cell

institute: Dalian Medical University

description: sample :KYSE150_infected_with_lentivirus pLKO.1-RBM4 sh_96h

data_processing:
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 on containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the down stream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Bowtie v2.0.6 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9.
The mapped reads of each sample were assembled by both Scripture (beta2) (Guttman et al. 2010) and Cufflinks (v2.1.1) (Trapnell et al. 2010) in a reference-based approach. Both methods use spliced reads to determine exons connectivity, but with two different approaches. Scripture uses a statistical segmentation model to distinguish expressed loci from experimental noise and uses spliced reads to assemble expressed segments. It reports all statistically expressed isoforms in a given locus. Cufflinks uses a probabilistic model to simultaneously assemble and quantify the expression level of a minimal set of isoforms that provides a maximum likelihood explanation of the expression data in a given locus (Cabili et al. 2011). Scripture was run with default parameters, Cufflinks was run with ‘min-frags-per-transfrag=0’ and ‘--library-type’, other parameters were set as default.
Cuffdiff (v2.1.1) was used to calculate FPKMs of both lncRNAs and coding genes in each sample (Trapnell, C. et al. 2010). Gene FPKMs were computed by summing the FPKMs of transcripts in each gene group. FPKM means fragments per kilo-base of exon per million fragments mapped, calculated based on the length of the fragments and reads count mapped to this fragment.
Cuffdiff provides statistical routines for determining differential expression in digital transcript or gene expression data using a model based on the negative binomial distribution (Trapnell, C. et al. 2010). Transcripts with an P-adjust <0.05 were assigned as differentially expressed.
Assembly: human NCBI genome build 38
Supplementary files format and content: The gene expression matrix from RNA-seq

growth_protocol: KYSE150 cells were maintained at standard culture conditions (37°C, 5% CO2) in 1640 medium with 10% FBS.

extract_protocol:
RNA was harvested using TRIzol and cleaned using RNAeasy Kit (Qiagen). 5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol:
KYSE150 cells were  infected with lentivirus  pLKO.1-RBM4 sh or with pLKO.1-CTL .
The stable KYSE150 cells were cultured for 4 days.

value: Esophageal squamous cell carcinoma cell

value: RBM4 knockdown

value: infected with lentivirus

tag: time

value: cultured for 4 days


title: RBM4_2

status: Public on Apr 26 2023

type: SRA

country: China

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: 11H_M_520

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq3

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

tag: age

tag: strain


title: 11H_M_521


title: RNA-Seq H9

city: Beijing

first: Yulin

last: Lyu

address: No.5 Yiheyuan Road Haidian District

department: School of Life Sciences

institute: Peking University

data_processing:
Quality control was performed using FastQC.
The raw RNA-seq reads were trimmed using Trimmomatic with parameter ‘ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:7:1:true LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36’ to remove detected adapters.
The clean reads were mapped to human reference genome hg19 using STAR with additional parameter ‘--outSAMtype BAM Unsorted --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical’.
The number of reads mapped to each gene was counted using program featureCounts of Subread package.
Assembly: hg19
Supplementary files format and content: .csv file containing FPKM values of each gene in each sample.

growth_protocol: Human CiPS cells and hES cells were maintained in mTeSR™ Plus Medium on Matrigel coated plates under 21% O2, 5% CO2 at 37 ℃. Human adult adipose derived mesenchymal stromal cells (hADSCs) and human adult skin fibroblasts (hASFs) were cultured in Mesenchymal Stem Cell Growth Medium 2 under 21% O2, 5% CO2 at 37 ℃.

extract_protocol:
Total RNA was isolated using Direct-zol RNA MiniPrep Kit.
RNA sequencing libraries were constructed using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB England BioLabs, E7775). Fragmented and randomly primed 2 x150 bp pairedend libraries were sequenced using Illumina HiSeq X Ten.

treatment_protocol: Human somatic cells were treated with different small molecule combinations during human chemical reprogramming.

value: Human embryonic stem cell


title: hADSCs-1013_H3K4me3_rep2

data_processing:
Quality control was performed using FastQC.
The reads were trimmed using Trimmomatic with parameter ‘ILLUMINACLIP:NexteraPE-PE.fa:2:30:7:1:true LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36’ to remove detected adapters.
The clean reads were mapped to human reference genome hg19 using Bowtie2 with parameter ‘--very-sensitive’.
After converting and sorting the output SAM files to BAM files using Samtools, we removed the duplicated reads and reads with low mapping quality using Picard and Samtools.
The pileup signal intensity for each sample was calculated using MACS2 while peak calling.
Assembly: hg19
Supplementary files format and content: .bw file containing merged signal intensity of each sample
Library strategy: CUT&TAG

extract_protocol:
Approximately 1 x 105 cells of each sample were collected and analyzed with Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme, TD903-02) following the recommended protocol. Briefly, harvest fresh cultures and count 1 x 105 cells for each sample. Then bind cells to Concanavalin A beads at room temperature for 10 min. Next, remove liquid and add primary antibody with ice-cold Antibody Buffer and incubate overnight at 4 oC. The next day, remove liquid and add Guinea Pig Anti-Rabbit Antibody secondary antibody with Dig-Wash Buffer and incubate at room temperature for 1 h. Then, wash sufficiently and bind CUT&Tag pA/G-Tn5 Transposomes at room temperature for 1 h. After gently but throughly wash, tagmentation at 37 ℃ for 1 h and then performed DNA extraction with DNA extraction beads.
For extracted DNA, combinate i7 and i5 Indexed Primer for PCR amplification and perform clean-up for quantification and Illumina sequencing.

value: adult human adipose derived mesenchymal stromal cells

tag: antibody


title: Ctl_2

description: sample :KYSE150_infected_with_lentivirus pLKO.1-CTL_96h

value: WT


title: Ctl_1


title: MM03-ME

city: Nanjing

first: Zhegnxu

last: Sun

address: Guangzhou Road 300

institute: Jiangsu Province Hospital

description: GEXSCOPE

library_source: transcriptomic single cell

data_processing:
Raw reads from scRNA-seq were processed to generate gene expression matrixes using CeleScope (https://github.com/singleron-RD/CeleScope) v1.9.0 pipeline.  Briefly, raw reads were first processed with CeleScope to remove low quality reads with Cutadapt v1.17 to trim poly-A tail and adapter sequences.  Cell barcode and UMI were extracted. Read 1: contains the 24bp GEXSCOPE barcode and the 12bp UMI (bases 25-36). Read 2 contains the cDNA information. After that, we used STAR v2.6.1a  to map reads to the reference genome GRCh38 (ensembl version 92 annotation).  UMI counts and gene counts of each cell were acquired with featureCounts v2.0.1 software, and used to generate expression matrix files for subsequent analysis.
Further processing was done with Seurat v3.1.2 (quality control, dimension-reduction, clustering, differential gene expression analysis).
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: myelomatous effusion

extract_protocol:
After using 40-micron sterile strainers to filter, the ascites sample were then centrifuged at 350× g for 5 min. Then the supernatant was discarded, and the sediment was resuspended in 1ml PBS (HyClone). Afterwards, the GEXSCOPE® red blood cell lysis buﬀer (RCLB, Singleron) was added, and the mixture[Cell: RCLB=1:2 (volume ratio)] was incubated at room temperature for 5-8 min to remove red blood cells
Single-cell suspensiSingle-cell suspensions (200000 cells/mL) with PBS (HyClone) were loaded onto microwell chip using the Singleron Matrix® Single Cell Processing System. Barcoding Beads are subsequently collected from the microwell chip, followed by reverse transcription of the mRNA captured by the Barcoding Beads and to obtain cDNA, and PCR amplification. The amplified cDNA is then fragmented and ligated with sequencing adapters. The scRNA-seq libraries were constructed according to the protocol of the GEXSCOPE® Single Cell RNA Library Kits (Singleron). Individual libraries were diluted to 4 nM, pooled, and sequenced on Illumina novaseq 6000 with 150 bp paired end reads.ons (200000 cells/mL) with PBS (HyClone) were loaded onto microwell chip using the Singleron Matrix® Single Cell Processing System. Barcoding Beads are subsequently collected from the microwell chip, followed by reverse transcription of the mRNA captured by the Barcoding Beads and to obtain cDNA, and PCR amplification. The amplified cDNA is then fragmented and ligated with sequencing adapters. The scRNA-seq libraries were constructed according to the protocol of the GEXSCOPE® Single Cell RNA Library Kits (Singleron). Individual libraries were diluted to 4 nM, pooled, and sequenced on Illumina novaseq 6000 with 150 bp paired end reads.

tag: tissue

value: myelomatous effusion


title: Ctl_3


title: RNA_4_DMOG_podocytes

city: Aachen

first: René

last: Krüger

address: Pauwelsstraße 20

department: Institute for Stem Cell Biology

country: Germany

institute: RWTH Aachen University Medical School

data_processing:
RAW reads were trimmed for Illumina adapter sequences using cutadapt version 1.18 and then aligned to the GRCh38 genome using STAR version 2.6.1c.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: Podocytes cell line (M. Saleem)

growth_protocol: Podocytes were cultured in RPMI medium. Basal medium was supplemented with fetal calf serum 10%, 100 U/ml penicillin and 100 μg/ml streptomycin. Proliferating podocytes were cultured under 33°C, for differentiation subconfluent dishes were transferred to 37°C and cultured for 10 days.

extract_protocol:
RNA was isolated using the peqGold total RNA kit (VWR Peqlab, Erlangen, Germany) according to the manufacturer´s protocol.
Novogene NGS DNA Library Prep Set (Cat No.PT004). Libraries were sequenced on Illumina Novaseq 6000  (Illumina).

treatment_protocol: Sub-confluent cell cultures were exposed to 1 mM dimethyloxalylglycine (DMOG, Cayman) for 16h to induce HIF stabilization.

value: Podocytes cell line (M. Saleem)

value: 16h DMOG


title: RNA_5_hypoxia_podocytes

value: 16h Hypoxia


title: RNA-Seq hCiPSCs-PT5006-1S#

data_processing:
Quality control was performed using FastQC.
The raw RNA-seq reads were trimmed using Trimmomatic with parameter ‘ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:7:1:true LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36’ to remove detected adapters.
The clean reads were mapped to human reference genome hg19 using STAR with additional parameter ‘--outSAMtype BAM Unsorted --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical’.
The number of reads mapped to each gene was counted using program featureCounts of Subread package.
Assembly: hg19
Supplementary files format and content: .xlsx file containing FPKM values of each gene in each sample.

growth_protocol: Human CiPS cells and hES cells (H1) were maintained in mTeSR™ Plus Medium on Matrigel coated plates under 21% O2, 5% CO2 at 37 ℃. Human adult adipose derived mesenchymal stromal cells (hADSCs) and human adult skin fibroblasts (hASFs) were cultured in Mesenchymal Stem Cell Growth Medium 2 under 21% O2, 5% CO2 at 37 ℃.

value: human chemically induced pluripotent stem cells


title: RNA-Seq hCiPSCs-38040-2S#


title: 11H_M_518


title: RNA-Seq hCiPSCs-1013-2S#


title: RNA_2_ctrl_podocytes

value: control


title: RNA-Seq hCiPSCs-3595-1S#


title: RNA-Seq hCiPSCs-1009-1S#


title: 11H_M_519


title: 11H_M_517


title: 11H_M_516


title: RNA-Seq hCiPSCs-0618-8S#


title: RNA_6_hypoxia_podocytes


title: 11H_M_514


title: IL-2 cultured NK cells

city: West Allis

first: Ao

last: Mei

state: Wisconsin

address: 9442 West Maple Ct

institute: Medical College of Wisconsin

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Peripheral blood

extract_protocol:
Natural killer cells are sorted from human PBMC as Lin-CD7+ population. Sorted cells are washed with ice-cold FACS buffer (PBS+10%FBS) and counted to be loaded into 10X Chromium machine.
scRNA libraries were prepared following the user guide of 10X Chromium Single Cell 3' Reagent Kits v3

value: Peripheral blood

tag: donor

value: healthy

value: Natural Killer cells

value: IL-2 treated NK cells


title: RNA-Seq hCiPSCs-0618-1S#


title: RNA-Seq hCiPSCs-0605A-1S#


title: 11H_M_513


title: ChIP_6_H3K27ac_DMOG_podocytes

data_processing:
RAW reads were trimmed for Illumina adapter sequences using cutadapt version 1.18 and then aligned to the GRCh38 genome using  BWA-mem version 0.7.17-r1188.
Reads were sorted using samtools v.1.8.
Reads aligned to mtDNA, low quality reads (MAPQ <30), ENCODE blacklisted regions and duplicates were removed using samtools version 1.8 and Picard version 2.25.2.
Bigwig files were generated using deeptools bamCoverage version 3.5.0, command –normalizeUsing RPGC --binsize 1.
Assembly: GRCh38
Supplementary files format and content: bigWig

source_name: Podocytes

extract_protocol:
ChIP was performed using ChIP-IT high sensitivity kit (Active Motif, Carlsbad, CA, USA). For immunoprecipitations, 20 μg of chromatin and 3-6 μl of antibodies was used.
Novogene NGS DNA Library Prep Set (Cat No.PT004)

value: Podocytes


title: RNA-Seq hCiPSCs-0605-5S#


title: RBM4_1

value: Esophageal squamous cell carcinoma cell

value: RBM4 knockdown


title: ChIP_5_HIF_1b_DMOG_podocytes


title: RNA-Seq hCiPSCs-0605-1S#


title: RNA-Seq hASFs-38040

value: human adult skin fibroblasts


title: ChIP_4_HIF_2a_DMOG_podocytes


title: 11H_M_512


title: 11H_M_447


title: RNA-Seq hASFs-0605


title: RNA-Seq hADSCs-1013


title: RNA_3_DMOG_podocytes


title: RNA-Seq hADSCs-PT5006


title: RNA-Seq hADSCs-1009


title: 11H_M_446


title: ChIP_2_Input_DMOG_podocytes


title: 11H_M_445


title: ChIP_3_HIF_1a_DMOG_podocytes


title: RNA-Seq hADSCs-0809


title: RNA-Seq hCiPSCs-0809-1S#


title: RNA_1_ctrl_podocytes


title: 11H_M_444


title: RNA-Seq hADSCs-0618


title: ATAC_4_DMOG_podocytes

data_processing:
RAW reads were trimmed for Illumina adapter sequences using cutadapt version 1.18 and aligned to the GRCh38 genome using Bowtie2 version 2.3.4.1.
Reads aligned to mtDNA, low quality reads (MAPQ <30), ENCODE blacklisted regions and duplicates were removed using samtools version 1.8 and Picard version 2.25.2.
Bigwig files were generated using deeptools bamCoverage version 3.5.0, command –normalizeUsing RPGC --binsize 1.
Assembly: GRCh38
Supplementary files format and content: bigWig

extract_protocol:
The Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) was performed according to the Omni-ATAC protocol published by Corces et al. (Corces, M., Trevino, A., Hamilton, E. et al. An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat Methods 14, 959–962 (2017). https://doi.org/10.1038/nmeth.4396). In short, libraries were prepared using the Illumina Tagment DNA TDE1 Enzyme and Buffer Kit (Illumina, San Diego, CA, USA) and purified using the DNA Clean and Concentrator-5 Kit (Zymo Research, Freiburg, Germany) according to the manufacturer’s protocol. Following purification, library fragments were amplified by using the NEB Next® High-Fidelity 2X PCR Master Mix (New England Biolabs, Ipswich, UK) and custom-made indexed Nextera PCR primers (Sigma Aldrich, St. Louis, MO, USA). Libraries were amplified for a total of 8 – 12 cycles. Library clean-up and double-sided size selection was performed using AMPure XP beads (Beckman Coulter GmbH, Krefeld, Germany) according to the manufacturer’s recommendations.
ATAC-seq library preparation was carried out using the Omni-ATAC protocol. Libraries were sequenced on Illumina Novaseq 6000 platforms following the manufacturer's protocols.


title: ChIP_1_H3K27ac_ctrl_podocytes


title: ATAC_3_DMOG_podocytes


title: RNA-Seq H1

value: Human embryonic stem cell


title: RNA-Seq hADSCs-0605

value: adult human adipose derived mesenchymal stromal cells


title: hCiPSCs-38040-2S#

data_processing:
The human reference genome hg19 and lambda genome were transformed into fully bisulfite-converted forward (C>T) and reverse (G>A conversion of the forward strand) versions using the script bismark_genome_preparation. Sequence reads were similarly transformed and mapped to prepared genomes using Bowtie2 with parameters set by Bismark.
The alignments to the same position in the genome from the Bismark mapping output were removed using the script deduplicate_bismark.
The methylation information of every single C were extracted using the script bismark_methylation_extractor with parameter ‘-p --no_overlap --ignore 5 --ignore_r2 5 --zero_based --CX --buffer_size 50%’. In this way we got the number of reads that supported methylation and the number of reads covering every CpG site, non-CpG sites were not considered in later analysis.
Assembly: hg19
Supplementary files format and content: .bw file containing CpG methylation signal intensity of each sample

growth_protocol: Human CiPS cells were maintained in mTeSR™ Plus Medium on Matrigel coated plates under 21% O2, 5% CO2 at 37 ℃. Human adult adipose derived mesenchymal stromal cells (hADSCs) were cultured in Mesenchymal Stem Cell Growth Medium 2 under 21% O2, 5% CO2 at 37 ℃.

extract_protocol:
Genomic DNA was extracted using EasyPure Genomic DNA Kit (TransGen, EE101-11). DNA were denatured and bisulfite converted using EZ DNA Methylation-GoldTM Kit (Zymo Research, D5005).
Recovered bisulfite-converted DNAs were constructed into sequencing libraries using Accel-NGS Methyl-Seq DNA Library Kit (Swift, 30024) following the manufacturer’s instructions and each libraries were sequenced 90G raw data by using Illumina HiSeq X Ten.


title: 11H_M_443


title: hCiPSCs-1013-2S#


title: hCiPSCs-0618-8S#


title: ATAC_2_ctrl_podocytes


title: 11H_M_442


title: 11H_M_441


title: RNA-Seq hASFs-3595


title: hADSCs-1013


title: hCiPSCs-0618-1S#


title: 11H_M_440


title: LR21K17DX149

city: Urumqi

first: Zhang

middle: Qing

last: hua

state: Xinjiang

address: Liudao Bay Street

institute: The Second Affiliated Hospital of Xinjiang Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: liver

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: hepatocarcinoma tissue

value: single

value: NO

tag: bclc

value: B

tag: Sex

value: male


title: 11H_M_439


title: 11H_M_438


title: MC38, Saline, rep3, scRNAseq

city: Cambridge

first: Yuzhou

middle: Evelyn

last: Tong

state: MA

address: 77 Massachusetts Ave

institute: Massachusetts Institute of Technology

description: Seq-Well

data_processing:
bcl2fastq2.20.0.422 was used to generat .fastq files from .bcl files.
Cell barcode and UMI tagging of transcript reads was performed using DropSeqTools v2.3 (Macosko et al., 2015)
Assembly: mm10
Supplementary files format and content: Digital gene expression file

molecule: polyA RNA

source_name: MC38 tumor

extract_protocol:
Mouse MC38 tumor samples were digested utilizing the Tumor Dissociation kit (Miltenyi Biotech) 24h post administration. Cells were then stained with CD45 microbeads and CD45+ and CD45- cells were separated using MACS Separator. CD45+ and CD45- single cells for each mouse were loaded in a ratio of 9:1 onto Seq-Well arrays
Single-cell suspensions were loaded onto Seq-Well arrays and processed as according to Gierahn et al., Nature Methods (2017).

value: MC38 tumor

value: Saline was injected

tag: time post_drug


title: MC38, Saline, rep2, scRNAseq

description: Seq-Well


title: MC38, Medium BPD, rep2, scRNAseq

description: Seq-Well

value: R848 bottlebrush prodrugs was injected


title: MC38, Free R848, rep3, scRNAseq

description: Seq-Well

value: Free R848 was injected


title: MC38, Saline, rep1, scRNAseq

description: Seq-Well


title: MC38, Medium BPD, rep1, scRNAseq

description: Seq-Well


title: LR21K17DX148

value: multiple

value: A


title: MC38, Free R848, rep2, scRNAseq

description: Seq-Well


title: 11H_M_437


title: MC38, Free R848, rep1, scRNAseq

description: Seq-Well


title: 11H_M_436


title: LR21K17DX146


title: LR21K17DX147


title: M272

city: Zurich

first: Csaba

last: Földy

state: Zurich

address: Winterthurerstrasse 190

department: Brain Research Institute

country: Switzerland

institute: University of Zurich

data_processing:
Illumina RTA v1.12 was used for base calling, and Illumina bc12fastq v2.20 for demultiplexing and fastq file generation
Sequenced reads were pre-processed using Trimmomatic and Flexbar. Reads were aligned to GRCm38 genome using STAR aligner with parameters trimLeft=10, minTailQuality=15, minAverageQuality=20, and minReadLength=30 to gt gene counts (Data-count.tsv).
Aligned reads were converted to gene counts using featureCounts. Outputs for different cells were merged into a single file using custom Python code
Ensembl names were converted to gene names using Ensembl's Mus_musculus.GRC38.86.gtf file (gene_counts.tsv)
Reads were normalized using scran, and normalized values are stored in normalized_gene_counts.tsv
Assembly: GRCm38
Supplementary files format and content: Note here all of the processed data files. All of them are in tab-separated file format, with genes labeled by gene-names. Data-no_QC-counts.tsv contain raw counts for all cells from a single dataset. Data-counts.tsv contain raw counts for all cells from a single dataset that pass QC. Data-normed.tsv contain normalized (tpm for kallisto alignment) counts for all cells from a single dataset that pass QC.

source_name: Dentate gyrus granule cell

extract_protocol:
single cell cytosol extraction via patch pipette
Nextera XT

value: kainic acid

value: EGFP- cells

tag: quality control

value: Failed


title: M270


title: LR21K17DX145


title: M269

description:
Data-no_QC-counts.tsv
Data-counts.tsv
Data-normed.tsv

value: Passed


title: M268


title: 11H_M_434


title: M267


title: M266

value: EGFP+ cells


title: ATAC_1_ctrl_podocytes

value: Podocytes

value: Podocytes cell line (M. Saleem)

value: control


title: 11H_M_433


title: LR21K17DX150

value: hepatocarcinoma tissue

value: NO


title: M265


title: 11H_M_432


title: M262

value: saline


title: M261


title: M264


title: LR21K17DX143

value: single

value: YES

value: C

value: male


title: M263


title: 11H_M_431


title: M260


title: LR21K17DX141

value: multiple

value: B

value: female


title: LR21K17DX140


title: 11H_M_430


title: M259

value: EGFP- cells


title: M271

value: kainic acid


title: 11H_M_429


title: M258

value: Passed


title: M257


title: LR21K17DX139


title: M256


title: 11H_M_435


title: M255


title: 11H_M_428


title: LR21K17DX138


title: LR21K17DX144


title: M253


title: 11H_M_427


title: M254


title: LR21K17DX137

value: A


title: M252

value: EGFP+ cells


title: LR21K17DX142


title: 11H_M_426


title: LR21K17DX136


title: M249


title: 11H_M_425


title: LR21K17DX135


title: 11H_M_424


title: 11H_M_423


title: M247


title: LR21K17DX133


title: M246


title: LR21K17DX132


title: LR21K17DX134


title: M243


title: M245

value: Failed


title: 11H_M_422


title: M242


title: 11H_M_421


title: M241


title: M237


title: M238


title: LR21K17DX130


title: 11H_M_420


title: M235


title: 11H_M_419


title: M234


title: M250


title: LR21K17DX129


title: M233


title: 11H_M_418


title: M251


title: LR21K17DX128


title: M232


title: M231


title: M248


title: M230


title: LR21K17DX127


title: M244


title: 11H_M_417


title: M229


title: M227


title: 11H_M_416


title: 11H_M_415


title: M226


title: LR21K17DX131


title: LR21K17DX125


title: M225


title: LR21K17DX124


title: 11H_M_414


title: M224


title: 11H_M_413


title: M222


title: M223


title: M221


title: M220


title: LR21K17DX122


title: LR21K17DX123


title: M219


title: 11H_M_411


title: M218


title: M217


title: 11H_M_410


title: M216


title: M213


title: LR21K17DX126


title: 11H_M_409


title: 11H_M_408


title: M228


title: M214


title: LR21K17DX120


title: LR21K17DX119


title: M215


title: 11H_M_407


title: M211


title: LR21K17DX118


title: M210


title: LR21K17DX117


title: M208


title: M212


title: 11H_M_406


title: M206


title: M207


title: LR21K17DX116


title: 11H_M_412


title: LR21K17DX115


title: 11H_M_405


title: M203


title: 11H_M_403


title: M202


title: M201


title: LR21K17DX113


title: LR21K17DX114


title: 11H_M_402


title: M204


title: M48


title: M47


title: M205


title: M46


title: LR21K17DX121


title: M45


title: 11H_M_400


title: LR21K17DX111


title: 11H_M_401


title: LR21K17DX110


title: M209


title: M44


title: LR21K17DX109


title: 11H_M_399


title: M40


title: M41


title: M39


title: LR21K17DX112


title: 11H_M_398


title: M42


title: LR21K17DX108


title: 11H_M_404


title: M38


title: M37


title: 11H_M_397


title: LR21K17DX107


title: 11H_M_396


title: LR21K17DX106


title: M35


title: M36


title: 11H_M_395


title: M33


title: M32


title: LR21K17DX105


title: M31


title: 11H_M_394


title: M29


title: M30


title: M28


title: LR21K17DX104


title: 11H_M_393


title: M27


title: 11H_M_392


title: LR21K17DX103


title: M26


title: LR21K17DX101


title: LR21K17DX102


title: M25


title: 11H_M_390


title: M24


title: LR21K17DX100


title: 11H_M_388


title: M19


title: LR21K17DX99


title: M20


title: 11H_M_387


title: LR21K17DX98


title: 11H_M_386


title: M17


title: M16


title: M15


title: LR21K17DX97


title: M14


title: LR21K17DX96


title: 11H_M_385


title: M12


title: 11H_M_384


title: LR21K17DX95


title: M11


title: M10


title: 11H_M_255


title: M13


title: LR21K17DX94


title: M23


title: M9


title: 11H_M_254


title: M22


title: M8


title: M21


title: LR21K17DX93


title: M7_1


title: M6_1


title: 11H_M_253


title: M18


title: 11H_M_252


title: M5_1


title: LR21K17DX91


title: 11H_M_251


title: M2


title: M3_1


title: 11H_M_250


title: M4_1


title: 11H_M_249


title: LR21K17DX88


title: dSLAM-seq MCMV 72hpi B

city: Wuerzburg

first: Florian

last: Erhard

address: Versbacher Straße 7

institute: Institute of Virology and Immunobiology, University of Wuerzburg

data_processing:
library strategy: dSLAM-seq
3' sequencing adapter sequence were removed from the 76 nt long reads using Trimmomatic 0.39
Bowtie2 2.3.0 was used to align all reads to ribosomal rRNA and Mycoplasma. Reads mapped to ribosomal rRNA and Mycoplasma were discarded.
STAR 2.5.3a was used to align the remaining reads to the mouse genome, Ensembl transcripts (v90), the MCMV genome (KY348373), and the MCMV transcripts (KY348373).
The total number of unique sequences was taken as the conservative fragment count.
Mapped reads were further processed by iTiSS 1.3 to identify transcription start sites.
Assembly: GRCm38, KY348373
Supplementary files format and content: Tab separated file showing the read count of each transcription start sites. The processed file / iTiSS output is decribed in detasils here: https://github.com/erhard-lab/iTiSS#results

source_name: NIH-3T3 Murine embryonic fibroblasts

growth_protocol: NIH-3T3 cells were cultured in DMEM supplements with 10% NCS and Pen-Strep, 100 IU/mL and 100µg/mL, respectively. Cells at passage 6 were infected at 80% confluency 24h after the last split.

extract_protocol:
Cells were lyzed using Trizol and total cellular RNA was isolated. RNA was subject to alkylation using Iodoacetamide to mediate U to C conversions to distinguish newly synthesized RNA followed by RNA purification following the SLAM-seq protocol (Herzog et al., Nature commun. 2017).
Sequencing libraries were prepared using the dRNA-seq library preparation as described in Whisnant A.W. et al, Nat. Commun (2020)

treatment_protocol: Cells were infected for 30 min with Smith strain MCMV at an MOI with centrifugal enhancement at 800g/30mins, followed by PBS wash and media replacement. 4sU treatment was conducted one hour prior to lysis. Phosphonoacetic acid and cycloheximide treatment was conducted at 300µg/mL and 50µg/mL respectively.

value: Immortalized embryonic fibroblasts

tag: time post infection

value: MCMV, 72 h p.i.

tag: infection with

value: MCMV

tag: replicate

value: Replicate 2

tag: molecule subtype

value: 5' RNA ends (selective)


title: LR21K17DX89

value: hepatocarcinoma tissue

value: single

value: NO


title: dSLAM-seq MCMV 24hpi PAA

description: PAA

tag: cell type

value: MCMV, 24 h p.i.


title: dSLAM-seq MCMV 48hpi B

value: MCMV, 48 h p.i.


title: 11H_M_248


title: 11H_M_389


title: dSLAM-seq MCMV 72hpi A

value: Replicate 1


title: dSLAM-seq MCMV 4hpi CYC

description: CYC

value: MCMV, 4 h p.i.


title: LR21K17DX87

value: multiple

value: female


title: dSLAM-seq MCMV 48hpi A


title: LR21K17DX86

value: YES

value: C

value: male


title: dSLAM-seq MCMV 36hpi B

value: Immortalized embryonic fibroblasts

value: MCMV, 36 h p.i.


title: dSLAM-seq MCMV 36hpi A

value: MCMV


title: 11H_M_246


title: LR21K17DX92


title: LR21K17DX85

value: A


title: 11H_M_247


title: dSLAM-seq MCMV 24hpi B

value: Replicate 2

value: 5' RNA ends (selective)


title: 11H_M_245


title: dSLAM-seq MCMV 18hpi B

value: MCMV, 18 h p.i.


title: dSLAM-seq MCMV 24hpi A


title: LR21K17DX90

value: hepatocarcinoma tissue

value: single


title: dSLAM-seq MCMV 18hpi A


title: dSLAM-seq MCMV 12hpi B

value: MCMV, 12 h p.i.


title: M1

value: kainic acid

value: EGFP+ cells

value: Passed


title: LR21K17DX83

value: NO


title: dSLAM-seq MCMV 12hpi A

value: Replicate 1


title: LR21K17DX82


title: 11H_M_243


title: dSLAM-seq MCMV 6hpi B

value: MCMV, 6 h p.i.


title: dSLAM-seq MCMV 6hpi A


title: dSLAM-seq MCMV 4hpi B

value: MCMV, 4 h p.i.


title: 11H_M_242


title: dSLAM-seq MCMV 4hpi A

value: Immortalized embryonic fibroblasts


title: LR21K17DX81

value: male


title: LR21K17DX80

value: female


title: dSLAM-seq MCMV 1hpi B

value: MCMV, 1 h p.i.

value: MCMV


title: 11H_M_240


title: dSLAM-seq MCMV 2hpi B

value: MCMV, 2 h p.i.

value: Replicate 2

value: 5' RNA ends (selective)


title: LR21K17DX78

value: hepatocarcinoma tissue

value: single

value: A


title: dSLAM-seq MCMV 1hpi A


title: dSLAM-seq MCMV 2hpi A


title: dSLAM-seq mock B

value: Mock


title: 11H_M_239


title: dSLAM-seq mock A


title: LR21K17DX84


title: LR21K17DX77


title: 11mpi,27-May-2009,V12,GEX,biol rep 1

first: Collin

last: Joyce

state: California

address: 10550 N Torrey Pines Rd

institute: The Scripps Research Institute

description: 10x Genomics

data_processing:
BaseCall files were subsequently used to generate library-specific FASTQ files with cellranger mkfastq (v7.0.0) prior to running cellranger count (v7.0.0) with the GRCh38 (release 92) reference to produce cell barcode-gene expression matrices using default settings.
Assembly: GRCh38
Supplementary files format and content: Cellranger count output barcodes.tsv.gz, matrix.mtx.gz and features.tsv.gz files

source_name: Blood

extract_protocol:
Memory B cells separated from approximately 1x106 PBMCs by selective depletion (Switched memory B cell isolation kit; Miltenyi Biotec) were loaded according to the 10X Genomics manufacturer’s protocol for 5’-gene expression to attain 10,000 sequenced cells per well.
Gene expression libraries were prepared according to 10x genomics manufacturer’s protocol.

value: Blood

value: Memory B Cell


title: 11H_M_244


title: 9mpi,11-Mar-2009,V9,GEX,biol rep 5

description: 10x Genomics


title: 9mpi,11-Mar-2009,V9,GEX,biol rep 4

description: 10x Genomics


title: 11H_M_236


title: LR21K17DX75

value: NO


title: 11H_M_235


title: 11H_M_237


title: LR21K17DX74


title: 9mpi,11-Mar-2009,V9,GEX,biol rep 1

description: 10x Genomics


title: 9mpi,11-Mar-2009,V9,GEX,biol rep 3

description: 10x Genomics


title: 9mpi,11-Mar-2009,V9,GEX,biol rep 2

description: 10x Genomics


title: 11H_M_241


title: 11H_M_234


title: LR21K17DX73

value: multiple

value: B


title: MDA-MB-231 siCSRP2 rep 3

city: Strassen

first: Tony

last: KAOMA

address: 1 A-B Rue Thomas Edison

department: Quantitative Biology Unit

country: Luxembourg

institute: Luxembourg Institute of Health

description: 65 hours post transfection

data_processing:
Genome assembly version used was Homo_sapiens GRCh38 with  annotation version of Homo_sapiens.GRCh38.93.gtf
alignement has been done with star_2.5.3a tool version
Counting was made with star using  quantMode GeneCounts
Assembly: hg38 (GRCh38)

source_name: Breast; Mammary gland

growth_protocol: MDA-MB-231 cells were cultured in complete DMEM medium in a standard tissue culture incubator (21% O2, 5% CO2, 37° C)

extract_protocol:
Total RNA was extracted using RNeasy Mini kit (Qiagen)
RNA libraries were prepared for sequencing using TruSeq standard mRNA library Prep assay Illumina

treatment_protocol: MDA-MB-231 cells were plated in 6 well pate, transfected in either non targeting siRNA or with CRP2 targeting siRNA, samples werw harvested 65 hours after transfection

tag: cell line

value: Human epithelial cells

value: Breast; Mammary gland

tag: disease

value: adenocarcinoma

value: CSRP2 targeting siRNA


title: MDA-MB-231 siCSRP2 rep 2

description: 65 hours post transfection

tag: treatment


title: MDA-MB-231 siCSRP2 rep 1

description: 65 hours post transfection


title: 11H_M_233

tag: brain region

tag: age


title: LR21K17DX79

value: male


title: MDA-MB-231 siCTR rep 3

description: 65 hours post transfection

value: non targeting siRNA


title: LR21K17DX72


title: MDA-MB-231 siCTR rep 2

description: 65 hours post transfection


title: MDA-MB-231 siCTR rep 1

description: 65 hours post transfection


title: 11H_M_232

tag: strain


title: 11H_M_238


title: 11mpi,27-May-2009,V12,Non_Mem_GEX,biol rep 1

description: 10x Genomics

tag: tissue

value: PBMC


title: LR21K17DX71


title: M2 (MBNL2(-/-))_3

city: Corbeil-Essonnes

first: MARGOT

last: JARRIGE

address: 28, Rue Henri Desbruères

country: France

institute: I-Stem/INSERM U861

description: CRISPR MBNL2(-/-)

data_processing:
The quality control of the sequencing data was evaluated using FastQC ( v0.11.2)
The reads were trimmed using Prinseq (v0.20.4)(--trim-right 20) and filtered by average quality score (--trim-qual 20) and cutadapt ( v1.16)
Reads were mapped EnsEMBL GRCh37.87 human reference using rna-STAR (v2.7.3)
Reads below a mapping score of 10 or multi-mapped were filtered using samtools (v0.1.19)
The gene expression level in each sample was quantified with HTSeq-count (v0.8.0)
Genome_build: GRCh37.87
Supplementary_files_format_and_content: raw reads counts (no normalization)

source_name: hiPSC-derived motorneurones

growth_protocol: hiPSCs were dissociated with StemPro Accutase Cell Dissociation Reagent (ThermoFisher®) and suspended at 1,5 million cells per 25cm2 flask in differentiation medium N2B27 (DMEM F-12, Neurobasal medium, N2 and B27 supplement without A Vitamin, Penicillin/Streptomycin; ThermoFisher®) supplemented with different combinatory cytokines every two days: SB-431542 (Tocris®), LDN 193189 (Stemgent®), CHIR 99021 (Stemgent®), Y-27632 (StemCell®), Retinoïc Acid (RA, Sigma®), Smoothened Agonist (SAG, Enzo Life®), BDNF (Miltenyi biotec®), GDNF (Miltenyi biotec®), DAPT (Sigma®). Embryoid bodies were maintained for 10 days, then after dissociated and plated at 75 000 cells per cm2 in differentiation medium as mentioned with only BDNF, GDNF, RA, SAG, DAPT and Y-27631. From day 14, cells were maintained in differentiation medium supplemented with BDNF, GDNF and DAPT until day 25. This protocol referred to Maury et al., 2015.

extract_protocol:
Total RNAs were isolated using the RNAeasy Mini extraction kit (Qiagen®) according to the manufacture’s protocol.
Illumina® Stranded mRNA Prep,
PolyA capture, fragmentation , retrotrancription and amplification

value: replicate 3

tag: genotype

value: CRISPR MBNL2(-/-)


title: M2 (MBNL2(-/-))_2

description: CRISPR MBNL2(-/-)

value: replicate 2


title: 11H_M_231

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq3


title: LR21K17DX70

value: hepatocarcinoma tissue

value: single

tag: bclc

value: A


title: LR21K17DX76

tag: Sex


title: 11H_M_229


title: M2 (MBNL2(-/-))_1

description: CRISPR MBNL2(-/-)

value: replicate 1


title: DM1_2

description: DM1 cell line


title: DM1_3

description: DM1 cell line


title: LR21K17DX69

value: NO


title: DKO_3

description: CRISPR MBNL1(-/-); MBNL2(-/-) (DKO)

value: CRISPR MBNL1(-/-); MBNL2(-/-) (DKO)


title: 11H_M_228


title: WT_3

description: WT cell line

value: WT


title: LR21K17DX65


title: DKO_1

description: CRISPR MBNL1(-/-); MBNL2(-/-) (DKO)


title: 11H_M_230


title: LR21K17DX67

value: B


title: 11H_M_225


title: LR21K17DX64


title: V5, TSGFP, PD, rep2

city: Vienna

first: Andreas

last: Lackner

address: Schwarzspanierstrasse 17

department: Center for Anatomy and Cell Biology

country: Austria

institute: Medical University of Vienna

data_processing:
read trimming: CUTADAPT (2.8)
alignment: bowtie 2 (2.3.5.1)
alignment processing: samtools (1.10)
peak calling: MACS2 (2.2.7.1)
idr_filtering: ChIPpeakAnno (3.26.4)
Genome_build: mm10
Supplementary_files_format_and_content: bigwig, bed/peaksets

source_name: mouse trophoblast stem cells (mTSCs)

growth_protocol: Mouse TS cells were grown in a standard TS medium (RPMI 1640 supplemented with 20% fetal calf serum, 2mM L-Glutamine, 2mM sodium pyruvate and 100mM 2-mercaptoethanol) containing 70% mouse embryonic fibroblast -conditioned medium and 100 ng ml-1 Fgf2 and 1 µg ml-1 heparin. Cells were split every third day using trypsin.

extract_protocol:
ChIPseq libraries were generated with 5-10ng DNA using the NEBNext Ultra II DNA library preparation master mix (New England Biolabs, E7645) according to the manufacturer’s instructions.
RNAseq. RNA was extracted using RNeasy mini kit (Qiagen) and treated with DNaseI (Qiagen).
RNA-seq (Quantseq)

treatment_protocol: For differentiation, TSCs were exposed to 3 µM PD0325901 (Tocris) in full TSC media for 24h

value: mouse trophoblast stem cells (mTSCs)

tag: differentiation state

value: 24h differentiation with PD (PD)

tag: modification

tag: parental cell line

tag: chip antibody

value: anti-V5 Agarose Affinity Gel (Sigma-Aldrich/ A7345)


title: LR21K17DX63

value: male


title: DM1_1

description: DM1 cell line

tag: replicate


title: 11H_M_224

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.


title: WT_2

description: WT cell line


title: LR21K17DX66


title: 11H_M_227


title: Erf, V5PD, rep2

description:
BIGWIGS.tar: Erf_V5_V5PD_101602_129469_GL.bw
IDR_FILTERED.tar:  Erf_CoV5_WT_PD_IDR_CPA.bed


title: 11H_M_226


title: V5, TSGFP, PD, rep1


title: 11H_M_223


title: OVA_RNA

city: Zhenjiang

first: Xiaowei

last: Xu

address: No.438, Jiefang Road, Jingkou District, Zhenjiang City, Jiangsu Province

institute: Jiangsu University

data_processing:
Illumina bcl2fastq 2.0 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using HISAT2
Transcript abundance values were obtained from gene-level count matrices were generated by StringTie
Gene counts were normalized using geometric mean (GEO) in DESeq2 package and log2 transformed. Removal of unwanted variation (RUV) was used to remove batch effects and genes with no counts in over 50% of the samples were removed.
Differential gene expression by limma voom was performed on normalized gene counts, using batch effects and the first two PCAs of aligning and sequencing as covariates.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes gene abundance for each sample

source_name: lung

growth_protocol: The mice were housed at 25°C and fed standard rodent chow and tap water.

extract_protocol:
Total RNA was extracted from each tissue sample using the Trizol method.
After incubation of RNA with a biotin-modified probe, the probe was captured by a streptavidin magnetic bead to eliminate rRNA. The obtained samples were purified by AMPure XP magnetic beads, and then buffer composed of elution, fragmented, and random primers was added and the samples were incubated at 94°C. Thermal fracture led to fragments distributed between 100 and 300 bp. Using first-strand synthesis buffer and Invitrogen SuperScript IV reverse transcriptase, this fragmented RNA was used as a template to synthesize the first-strand cDNA. Actinomycin D was added to the first-strand synthesis buffer to prevent the reverse transcription of DNA templates and to ensure the reverse transcription specificity of RNA templates. After that, the double-stranded synthesis premix system was added to the synthesized first-strand cDNA, and the product was purified by Agencourt AMpure XP magnetic beads. From this reaction we obtained purified double-stranded cDNA and then added a 3' end plus "A" buffer reaction system to this system. Finally, ligation buffer and a double-stranded sequencing linker was added to the library; we used T4 DNA ligase to attach the Illumina sequencing linker to the DNA library. The library was purified using the Agencourt SPRI select Nucleic Acid Fragment Screening kit.

treatment_protocol: In all two groups, the Six-week-old female BALB/c mice were sensitized on day 0, 7, and 14 with 40 μg OVA (Sigma, Poole, UK) and 2 mg 10% aluminum hydroxide (Sigma) in PBS by In review. This is a provisional file, not the final typeset article intraperitoneal injection. Then, the sensitized mice were challenged with aerosol OVA (5%) in a plastic chamber (30 × 20 × 15 cm) from days 21 to 55. Mice from Hypo-EVs group were treated with Hypo-EVs (40 μg suspended in 0.5 mL PBS) by inhaling. After four times treatment (day 26, 33, 40 and 47), the mice were sacrificed on day 55. Then the lungs of mice in OVA and Hypo-EVs groups were taken.

value: BALB/c

value: lung

value: female

value: 14 weeks old

tag: group

value: OVA

tag: sample type

value: extracellular vesicles (EVs)


title: Erf, V5PD, rep1

tag: cell type


title: DKO_2

description: CRISPR MBNL1(-/-); MBNL2(-/-) (DKO)

value: replicate 2


title: LR21K17DX68

value: hepatocarcinoma tissue

value: single

value: A


title: 11H_M_222


title: LR21K17DX61

value: multiple

value: NO


title: Ncor1, ErfRescue, 29, SR

description:
BIGWIGS.tar: Ncor1_ErfRescue_SR_128697_128699.bw
IDR_FILTERED.tar:  Ncor1_ErfRescue_SR_IDR_CPA.bed

value: self-renewal (SR)

value: anti-Ncor1 (Abcam/ab3482)


title: Ncor1, ErfRescue, 2, PD

description:
BIGWIGS.tar: Ncor1_ErfRescue_PD_128698_128700.bw
IDR_FILTERED.tar:  Ncor1_ErfRescue_PD_IDR_CPA.bed

value: mouse trophoblast stem cells (mTSCs)

value: 24h differentiation with PD (PD)


title: Ncor1, ErfRescue, 29, PD


title: 11H_M_221


title: LR21K17DX60

value: YES

value: C

value: male


title: Ncor1, ErfRescue, 2, SR


title: Hypo-EVs_RNA

value: BALB/c

value: lung

value: female

value: Hypo-EVs


title: WT_1

description: WT cell line

value: replicate 1

value: WT


title: Ncor1, ErfKO, 29, SR

description:
BIGWIGS.tar: Ncor1_ErfKO_SR_128693_128695.bw
IDR_FILTERED.tar:  Ncor1_ErfKO_SR_IDR_CPA.bed

value: ErfKO


title: LR21K17DX59

value: hepatocarcinoma tissue

value: single


title: 11H_M_220


title: Ncor1, ErfKO, 2, PD

description:
BIGWIGS.tar: Ncor1_ErfKO_PD_128694_128696.bw
IDR_FILTERED.tar:  Ncor1_ErfKO_PD_IDR_CPA.bed


title: Ncor1, ErfKO, 2, SR


title: Ncor1, V5PD8

description:
BIGWIGS.tar: Ncor1_V5PD_128691_128692.bw
IDR_FILTERED.tar:  Ncor1_WT_PD_IDR_CPA.bed


title: 11H_M_219


title: LR21K17DX57

value: NO

value: B


title: 11H_M_218


title: Ncor1, V5PD7

value: anti-Ncor1 (Abcam/ab3482)


title: Ncor1, V5SR8

description:
BIGWIGS.tar: Ncor1_V5SR_128689_128690.bw
IDR_FILTERED.tar:  Ncor1_WT_SR_IDR_CPA.bed

value: mouse trophoblast stem cells (mTSCs)

value: self-renewal (SR)


title: LR21K17DX58


title: Ncor1, V5SR7


title: LR21K17DX56

value: multiple

value: A


title: 11H_M_217


title: 11H_M_216


title: LR21K17DX62


title: Ncor2, ErfRescue, 29, SR

description:
BIGWIGS.tar: Ncor2_ErfRescue_SR_128685_128687.bw
IDR_FILTERED.tar:  Ncor2_ErfRescue_SR_IDR_CPA.bed

value: anti-Ncor2 (Abcam/ ab5802)


title: Ncor2, ErfRescue, 2, PD

description:
BIGWIGS.tar: Ncor2_ErfRescue_PD_128686_128688.bw
IDR_FILTERED.tar:  Ncor2_ErfRescue_PD_IDR_CPA.bed

value: 24h differentiation with PD (PD)


title: 11H_M_215


title: LR21K17DX54

value: YES

value: C

value: male


title: Ncor2, ErfRescue, 2, SR


title: Ncor2, ErfKO, 29, PD

description:
BIGWIGS.tar: Ncor2_ErfKO_PD_128682_128684.bw
IDR_FILTERED.tar:  Ncor2_ErfKO_PD_IDR_CPA.bed


title: Ncor2, ErfKO, 29, SR

description:
BIGWIGS.tar: Ncor2_ErfKO_SR_128681_128683.bw
IDR_FILTERED.tar:  Ncor2_ErfKO_SR_IDR_CPA.bed


title: 11H_M_214


title: 11H_M_213


title: Ncor2, ErfKO, 2, SR


title: Ncor1, ErfKO, 29, PD


title: LR21K17DX53


title: LR21K17DX52


title: Ncor2, ErfKO, 2, PD


title: Ncor2, V5PD7

description:
BIGWIGS.tar: Ncor2_V5PD_128679_128680.bw
IDR_FILTERED.tar:  Ncor2_WT_PD_IDR_CPA.bed


title: LR21K17DX51


title: Fkh2_R2

city: Los Angeles

first: Remo

last: Rohs

address: 1050 Childs Way

department: Quantitative and Computational Biology

institute: University of Southern California

description:
processed data file:
Fkh2_core_ddG.tsv
Fkh2_edge_ddG.tsv

data_processing:
library strategy: SELEX-seq
Fixed adapters are trimmed using cutadapt v2.10, leaving only bases of the 16 bp variable region (Test Samples: cutadapt -g ^CGC -a CCTGGAATTCTCGGGTGCCAAGGAACTCCAG$ -O 10 -n 2 --discard-untrimmed --max-n 0 -m 16 -M 16; Production Samples: cutadapt -g ^CAG -a TCCGTATCGCTCCTCCAATG$ -O 10 -n 2 --discard-untrimmed --max-n 0 -m 16 -M 16)
Unexpected runs of cytidine were present in the Fhl1 samples, reads with runs of at least 7 cytidines were removed
The relative enrichment of various length k-mers are calculated using the same process as the SELEX package on bioconductor, the square root of the enrichment is provided for R2 samples
Supplementary files format and content:
tsv files that can be easily viewed in excel or a text editor of your choice
folders of tsv files are archived and compressed into tar.gz format

organism: synthetic construct

source_name: bound fragments from in vitro library

extract_protocol:
The protein of interest was incubated with the randomized library and run on a non-denaturing polyacrylamide gel at 4 ⁰C. Bound fragments were excised and purified using phenol:chloroform:isoamyl extraction. An aliquot was then used for an additional round of selection and extraction. Illumina adapters and barcodes and were then added to the selected libraries usng 4 cycle PCR, and samples were sent for sequencing.
A hand-mixed library containing a 16 bp randomized region was ordered from IDT with standard desalting. The library was made double stranded using the Klenow reaction.

tag: round

tag: protein


title: Ncor2, V5PD6


title: 11H_M_212

tag: brain region


title: Ncor2, V5SR7

description:
BIGWIGS.tar: Ncor2_V5SR_128677_128678.bw
IDR_FILTERED.tar:  Ncor2_WT_SR_IDR_CPA.bed


title: Fkh2_R1


title: PPMP rep2

city: Seoul

first: Jung-Woong

last: Kim

address: 84 Heuksuk-ro Dongjak-ku

department: Life Science

country: South Korea

institute: Chung-Ang University

data_processing:
Illumina Casava software used for basecalling
Sequenced read were trimmed for adaptor sequence, and masked for low-quality sequence using TrimGalore 0.6.6
Alignment to GRCh38.103 whole genome with STAR 2.7a and abuandence estimation with RSEM1.3.3
FPKM calculation result from RSEM isoform.result file and differential gene expression by edgeR 3.38.4, DESeq2 1.36.0
Assembly: GRCh38.103
Supplementary files format and content: txt files include raw counts, normalized counts(FPKM)

extract_protocol:
Total RNA was extracted using Trizol reagent and mRNA was extracted by mRNA pull-down using poly-A tagged bead.
RNA libraries were prepared for sequencing using TruSeq Stranded mRNA library Preparation Kit protocols

tag: cell line

value: breast cancer

value: PPMP

tag: time


title: 11H_M_210

tag: age

tag: strain


title: PPMP rep1

tag: genotype


title: Fkh1_R2

description:
processed data file:
Fkh1_core_ddG.tsv
Fkh1_edge_ddG.tsv


title: Ncor2, V5SR6

value: WT


title: Ncor2, ErfRescue, 29, PD


title: 11H_M_209


title: Fkh1_R1


title: LR21K17DX55

tag: tissue

value: hepatocarcinoma tissue

tag: bclc

tag: Sex

value: female


title: Input, Ncor2, ErfRescue, 29, PD

tag: differentiation state

tag: modification

tag: parental cell line


title: 11H_M_208


title: Vehicle rep1

value: Vehicle


title: Fkh1_Fkh2_R0

source_name: in vitro library


title: Input, Ncor2, ErfRescue, 2, PD

tag: chip antibody


title: Fhl1_R1


title: Fhl1_R2


title: 11H_M_206


title: Input, Ncor2, ErfRescue, 2, SR


title: Sporadic sample 5 (atac-seq)

city: Salzburg

first: Wolfgang

last: Esser-Skala

address: Hellbrunner Strasse 34

institute: University of Salzburg

description:
10x Genomics
barcodes.tsv
filtered_peak_bc_matrix.h5
matrix.mtx
peaks.bed

data_processing:
Raw sequencing data were demultiplexed, aligned to a reference genome (GRCh38), counted using Cell Ranger ATAC v1.0.2 (10x Genomics), and aggregated using Cell Ranger ATAC Aggregator.
Assembly: GRCh38
Supplementary files format and content: bed (called peak locations in browser extensible data format)
Supplementary files format and content: h5 (filtered peak-barcode matrix in HDF5 format)
Supplementary files format and content: json (Cell Ranger summary in JavaScript object notation format)
Supplementary files format and content: mtx (filtered peak-barcode matrix in Matrix Market Exchange format)
Supplementary files format and content: tsv (barcodes in tab-separated value format)

molecule: nuclear RNA

source_name: bone marrow

extract_protocol:
Fresh bone marrow aspirates were collected in heparin or EDTA blood collection tubes at the time of diagnosis. Mononuclear cells were isolated by density gradient centrifugation and cryopreserved in liquid nitrogen.
Mononuclear cells of bone marrow aspirates were thawed and then resuspended in RPMI media containing DNAse I (Roche), followed by a wash with cold 0.1% bovine serum albumin (BSA, Sigma) in phosphate buffered saline (PBS). Cells were then stained with the following antibodies: CD34-APC (BD, clone #581), CD38-BV711 (BD horizon, #HIT2), CD45-APC-Cy7 (BD, #2D1), GD2-FITC (kindly provided by Prof. Handgretinger, University of Tübingen, #ch14:18), L1CAM-PE (Miltenyi,  #REA163) in PBS/BSA 0.1% for 10 min at 4°C. Finally, cells were stained with DAPI (Sigma) for 5 min at 4°C, following which the cells were passed through a 70 μm cell strainer into FACS tubes in PBS/BSA 0.1%. Acquisition and sorting of live cells were performed with FACSAria and the DIVA Software version 8.0 (Becton Dickinson). Sorted single cells were split into halves and were taken forward for scATAC-seq and scRNA-seq processing.   Nuclei isolation from bone marrow single cells was performed according to a 10x Genomics, Inc. protocol (CG000212). Briefly, cells in PBS/BSA 0.1% buffer were centrifuged for 5 min at 4°C, followed by incubation with 0.1x lysis buffer for 3 min on ice. Cells were then washed with cold 1x wash buffer and resuspended in diluted nuclei buffer to generate a nuclei stock concentration corresponding to 10,000 targeted nuclei recovery. Nuclei transposition and downstream library generation were performed using Chromium Single Cell ATAC Reagent Kits User Guide v1.1 (10x Genomics, Inc.) following their recommended protocol. Quality and concentration of libraries were determined using TapeStation (Agilent Technologies) and Qubit Fluorometric Quantification (Thermo Fisher Scientific). Samples were then normalized, pooled together, and sequenced (2x50bp) in NovaSeq (Illumina).

value: bone marrow

tag: diagnosis

value: neuroblastoma

tag: sample id

tag: sample type

value: Sporadic sample


title: Sporadic sample 4 (atac-seq)


title: Input, Ncor2, ErfKO, 29, PD

tag: cell type

value: mouse trophoblast stem cells (mTSCs)

value: ErfKO


title: Hcm1_R2

tag: round

tag: protein


title: 11H_M_205

first: Joseph

last: Ecker

address: 10010 North Torrey Pines Road

institute: HHMI-Salk-Institute

source_name: C57BL/6J Male P56 Mouse Brain

tag: brain region


title: 11H_M_204

tag: age


title: Sporadic sample 3 (atac-seq)


title: Sporadic sample 2 (atac-seq)


title: 11H_M_211

tag: strain


title: 11H_M_203


title: Input, Ncor2, ErfKO, 29, SR

value: self-renewal (SR)


title: Hcm1_Fhl1_R0


title: Sporadic sample 1 (atac-seq)


title: Input, Ncor2, ErfKO, 2, PD


title: Fkh1_R2_test

description:
processed data file:
Fkh1_test_core_ddG.tsv
Fkh1_test_edge_ddG.tsv


title: 11H_M_202


title: Input, Ncor2, ErfKO, 2, SR


title: ATRX-deleted sample 2 (atac-seq)

value: ATRX-deleted sample


title: 11H_M_201


title: Vehicle rep2

tag: cell line

tag: genotype

tag: time


title: ATRX-deleted sample 1 (atac-seq)

tag: tissue


title: Input, Ncor2, ErfRescue, 29, SR

tag: differentiation state


title: 11H_M_207


title: 11H_M_200


title: R0_test


title: MYCN-amplified sample 4 (atac-seq)

value: MYCN-amplified sample


title: Input, Ncor2, V5PD5

value: 24h differentiation with PD (PD)

tag: modification


title: RNA_Macaque_BA23_M1

city: Dallas

first: Genevieve

last: Konopka

state: TX

address: 5323 Harry Hines Blvd.

department: Neuroscience

institute: UT Southwestern Medical Center

description:
All_Species_UMI_Count_Matrix_snRNAseq.mtx
All_Species_UMI_Count_Matrix_MetaData.txt
All_Species_UMI_Count_Matrix_Genes.txt
All_Species_UMI_Count_Matrix_Barcodes.txt
Seurat_Astrocyte_RNA.RDS
Seurat_Excitatory_RNA.RDS
Seurat_Inhibitory_RNA.RDS
Seurat_Microglia_RNA.RDS
Seurat_OPCOli_RNA.RDS

data_processing:
Barcode correction, alignment are performed using cellranger count (Software: 10x Genomics Cell Ranger 3.1.0)
Chimpanzee, macaque reads were mapped to human (CrossMap)
Reads counted per gene (featureCounts) and gene-cell matrix was constructed (umi-tools)
Ambient RNA contamination removed (CellBender)
Low quality cell barcodes, doublets were removed (Refer to supplementary methods)
Genome_build: Human: GRCh38, Chimpanzee: panTro5 (Pan_tro 3.0), Rhesus Macaque: rheMac10 (Mmul_10)
Supplementary_files_format_and_content: processed expression matrix: mtx files, gene and barcode information are in separate files
Supplementary_files_format_and_content: Cell barcode meta data

organism: Macaca mulatta

source_name: Post-mortem brain, Brodmann Area 23

extract_protocol:
Nuclei for snRNA-seq were isolated from human, chimpanzee, and macaque BA23 brain tissue. Debris was removed with a density gradient centrifugation using the Nuclei PURE 2M Sucrose Cushion Solution and Nuclei PURE Sucrose Cushion Buffer from Nuclei PURE Prep Isolation Kit (#NUC201-1KT, Sigma Aldrich).
Droplet-based single-nuclei RNA-seq libraries were prepared using the Chromium Single Cell 3’ v3.1 (1000121, 10x Genomics) according to the manufacturer’s protocol81. Libraries were sequenced using an Illumina NovaSeq 6000.

value: brain

value: Brodmann Area 23

tag: Sex

value: M

tag: molecule subtype

value: nuclear RNA


title: 11H_M_199

city: La Jolla


title: Macaque_BA23_M1

description:
Macaque_Count_Matrix_snATACseq_Barcodes.txt
Macaque_Count_Matrix_snATACseq_Genes.txt
Macaque_Count_Matrix_snATACseq_MetaData.txt
Macaque_Count_Matrix_snATACseq.mtx
Seurat_Astrocyte_ATAC_Macaque.RDS
Seurat_Excitatory_ATAC_Macaque.RDS
Seurat_Inhibitory_ATAC_Macaque.RDS
Seurat_Microglia_ATAC_Macaque.RDS
Seurat_OPCOli_ATAC_Macaque.RDS

data_processing:
Barcode correction, alignment are performed using cellranger count (Software: 10x Genomics Cell Ranger ATAC 1.1.0)
Supplementary_files_format_and_content: Read duplicates were removed (picard MarkDuplicates)
Peak calling (macs2 --nomodel, --keep-dup all, extsize 200, --shift –100 )
Common peak identification across samples and species (Refer to supplementary methods)
Peak-cell matrix generation (custom scripts)
Low quality cell barcodes, doublets were removed (Refer to supplementary methods)
Genome_build: Human: GRCh38, Chimpanzee: panTro5 (Pan_tro 3.0), Rhesus Macaque: rheMac10 (Mmul_10)
Supplementary_files_format_and_content: processed binarized peak-cell matrix: mtx file, peak and barcode information are in separate files
Supplementary_files_format_and_content: Cell barcode meta data

extract_protocol:
Nuclei for snATAC-seq were isolated from human, chimpanzee, and macaque BA23 brain tissue as previously described: https://www.protocols.io/view/isolation-of-nuclei-from-frozen-tissue-for-atac-se-6t8herw
Droplet-based single-nuclei ATAC-seq libraries were prepared using the Chromium Single Cell ATAC Library kit (1000110, 10x Genomics) according to the manufacturer’s protocols. Libraries were sequenced using an Illumina NovaSeq 6000.


title: Hcm1_R1


title: MYCN-amplified sample 2a (atac-seq)

tag: diagnosis


title: MYCN-amplified sample 3 (atac-seq)

tag: sample id


title: 11H_M_197


title: Input, Ncor2, V5SR5

value: WT

tag: parental cell line

tag: chip antibody


title: Input, Ncor2, V5SR6

tag: cell type


title: SABio_Testis-R_EbovAb_NHP14

city: Barcelona

first: luisa

last: santus

address: Plaça d'Eusebi Güell, 1-3

country: Spain

institute: Barcelona Supercomputing Center

data_processing:
We used Hisat v2.1.0 (Kim et al. 2019) to compute assembly indexes and known splice sites and mapped each samples’ reads to the assembly. We run Hisat2 with default parameters, except for rna-strandness, that we set to "FR", as inferred by InferExperiment.py from RSeQCc v3.0.0 (Wang et al. 2012)
We merged the technical replicates with samtools -merge.
We removed duplicates with umi_tools dedup v1.0.0.
We excluded all samples with less than 10M sequenced reads, a mapping rate lower than 0.3 or a genic mapping rate lower than 0.7. We defined the genic mapping rate as the proportion of exonic and intronic reads, as computed by read_distribution.py from RSeQCc v3.0.0 (Wang et al. 2012).
We ran de novo transcriptome assembly separately on each sample with Stringtie v1.3.6 (Pertea et al. 2015), with default parameters except for strand information that was set to "--fr".
Genome_build: Mmul_10 (rheMac10)
Supplementary_files_format_and_content: Stringtie output: de novo transcriptome assembly in gtf format.

source_name: Testis-R

extract_protocol:
We extracted total RNA (preferentially enriched for long RNA >200 nt) using a hybrid TRIzol/column-based extraction published previously (Barnes KG et al. Clin Inf Dis 2017). Briefly, we added chloroform to TRIzol homogenates, centrifuged to separate the aqueous and organic phases, and transferred the aqueous phase to a new microfuge tube. We added AVL Buffer (QIAamp Viral RNA Mini Kit, QIAgen) and ethanol to the aqueous phase, bound RNA on QIAamp Mini Spin columns by centrifugation, washed the column with Buffers AW1, AW2, and ethanol, and eluted in nuclease-free water. We further treated samples with TURBO DNase (Thermo Fisher Scientific) and purified RNA using RNAClean XP magnetic beads (Beckman Coulter).
We prepared strand-specific RNA-Seq libraries using the TruSeq Stranded mRNA Kit (Illumina) with modifications. Starting from 100–1000 ng total RNA per sample, we performed ribosomal RNA depletion with antisense DNA oligos and RNase H (Matranga CB et al. Genome Biol 2014). During the cleanup of ribo-depleted RNA with RNAClean XP magnetic beads (Beckman Coulter), we eluted ribo-depleted RNA with FPF (Illumina) and fragmented the RNA at 94 °C for 2 min. We then proceeded with the TruSeq Stranded mRNA Kit per manufacturer's protocol, starting from the reverse transcription step. The remainder of the manufacturer's protocol includes dUTP marking of the second strand, end repair and dA-tailing of the cDNA, ligation with Y-shape adaptors, USER digestion of the second strand, and 15 cycles of PCR.

treatment_protocol: Rhesus monkeys between 2–5 years old were challenged with a uniformly lethal dose (2121 PFU) of Ebola virus/H. sapiens-tc/COD/1995/Kikwit-9510621 (GenBank #KU182905.1; Filoviridae: Zaire ebolavirus) administered intramuscularly. 1, 3, 6, and 12 days post-challenge, rhesus monkeys were treated with fully human polyclonal anti-Ebola IgG antibodies produced in transchromatic bovines (SAB-139/V3–V4), irrelevant human IgG control from transchromatic bovines, or saline. Upon reaching pre-determined clinical criteria, each animal was euthanized. Each organ was trimmed to remove excess fat, cut into ~50–250 mg pieces, and homogenized in TRIzol (Thermo Fisher Scientific) to inactivate Ebola virus and lyse cells for RNA extraction. This same animal cohort has already been described previously (Luke T et al. J Infect Dis 2018)

value: Testis-R

tag: day post-infection

tag: treatment

value: Ebola virus IgG immunoglobulins


title: Input, Ncor1, ErfRescue, 29, PD


title: 11H_M_196

tag: brain region

tag: age


title: MYCN-amplified sample 1 (atac-seq)

tag: sample type


title: SABio_Testis-R_EbovAb_NHP13


title: Control sample 5 (atac-seq)

value: ganglioneuroma

value: Control sample


title: SABio_Testis-R_EbovAb_NHP12


title: Input, Ncor1, ErfRescue, 29, SR


title: 11H_M_195

tag: strain


title: Control sample 4 (atac-seq)

value: bone marrow


title: Input, Ncor1, ErfRescue, 2, PD


title: Fkh1_R1_test

tag: round

tag: protein


title: 11H_M_194


title: Control sample 3 (atac-seq)

tag: tissue


title: SABio_Testis_EbovAb_NHP14

source_name: Testis

value: Testis


title: Input, Ncor1, ErfRescue, 2, SR

value: mouse trophoblast stem cells (mTSCs)

tag: differentiation state

tag: modification


title: 11H_M_193


title: SABio_Testis_EbovAb_NHP12

tag: Sex


title: 11H_M_192


title: Control sample 2 (atac-seq)

tag: diagnosis

value: ganglioneuroblastoma


title: Input, Ncor1, ErfKO, 29, PD

value: ErfKO


title: Input, Ncor2, V5PD6


title: Control sample 1 (atac-seq)

tag: sample id


title: Input, Ncor1, ErfKO, 29, SR

value: self-renewal (SR)

tag: parental cell line


title: SABio_Spleen_EbovAb_NHP11

source_name: Spleen

value: Spleen

value: F


title: 11H_M_198


title: 11H_M_127


title: Input, Ncor1, ErfKO, 2, PD

value: 24h differentiation with PD (PD)

tag: chip antibody


title: 11H_M_126


title: SABio_Spleen_EbovAb_NHP10


title: SABio_Spleen_CtrlAb_NHP6

value: Control


title: Sporadic sample 5 (rna-seq)

description: 10x Genomics

data_processing:
Raw sequencing data were demultiplexed, aligned to a reference genome (GRCh38) and counted using Cell Ranger v3.0.2 (10x Genomics).
Assembly: GRCh38
Supplementary files format and content: h5 (count matrix in HDF5 format)
Supplementary files format and content: csv (Cell Ranger summary in comma-separated values format)

extract_protocol:
Fresh bone marrow aspirates were collected in heparin or EDTA blood collection tubes at the time of diagnosis. Mononuclear cells were isolated by density gradient centrifugation and cryopreserved in liquid nitrogen.
Mononuclear cells of bone marrow aspirates were thawed and then resuspended in RPMI media containing DNAse I (Roche), followed by a wash with cold 0.1% bovine serum albumin (BSA, Sigma) in phosphate buffered saline (PBS). Cells were then stained with the following antibodies: CD34-APC (BD, clone #581), CD38-BV711 (BD horizon, #HIT2), CD45-APC-Cy7 (BD, #2D1), GD2-FITC (kindly provided by Prof. Handgretinger, University of Tübingen, #ch14:18), L1CAM-PE (Miltenyi,  #REA163) in PBS/BSA 0.1% for 10 min at 4°C. Finally, cells were stained with DAPI (Sigma) for 5 min at 4°C, following which the cells were passed through a 70 μm cell strainer into FACS tubes in PBS/BSA 0.1%. Acquisition and sorting of live cells were performed with FACSAria and the DIVA Software version 8.0 (Becton Dickinson). Sorted single cells were split into halves and were taken forward for scATAC-seq and scRNA-seq processing.   Bone marrow single cells were taken forward for library generation using the Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10x Genomics, Inc.) following their recommended protocol. In brief, 10,000 cells were used as input for the Gel Beads in-Emulsion (GEM) generation, where cDNA is generated and barcoded, followed by cDNA amplification and library construction. Quality and concentration of libraries were determined using TapeStation (Agilent Technologies) and Qubit Fluorometric Quantification (Thermo Fisher Scientific). Samples were then normalized, pooled together, and sequenced (2x50bp) in NovaSeq (Illumina).

value: neuroblastoma

value: Sporadic sample


title: Sporadic sample 4 (rna-seq)

description: 10x Genomics


title: Input, Ncor1, V5PD5

tag: cell type

value: WT


title: 11H_M_124


title: SABio_Skin_EbovAb_NHP10

source_name: Skin

value: Skin

tag: day post-infection


title: Sporadic sample 2 (rna-seq)

description: 10x Genomics


title: Sporadic sample 3 (rna-seq)

description: 10x Genomics


title: SABio_Skin_EbovAb_NHP11

tag: treatment

value: Ebola virus IgG immunoglobulins


title: 11H_M_125

tag: brain region


title: Input, Ncor1, V5PD4


title: 11H_M_123

tag: age


title: Input, Ncor1, ErfKO, 2, SR


title: SABio_Skin_CtrlAb_NHP6


title: 11H_M_122


title: SABio_Serum_EbovAb_NHP11

source_name: Serum

value: Serum


title: Sporadic sample 1 (rna-seq)

description: 10x Genomics

tag: sample type


title: Input, Ncor1, V5SR5


title: ATRX-deleted sample 2 (rna-seq)

description: 10x Genomics

value: ATRX-deleted sample


title: Input, Ncor1, V5SR4


title: H3K27ac, ErfRescue, 29, PD

description:
BIGWIGS.tar: H3K27ac_ErfRescue_PD_128638_128640.bw
IDR_FILTERED.tar:  H3K27ac_ErfRescue_PD_IDR_CPA.bed

value: Anti-H3K27ac (Diagenode/C15410196)


title: 11H_M_121

tag: strain


title: ATRX-deleted sample 1 (rna-seq)

description: 10x Genomics

value: bone marrow


title: MYCN-amplified sample 4 (rna-seq)

description: 10x Genomics

value: MYCN-amplified sample


title: H3K27ac, ErfRescue, 29, SR

description:
BIGWIGS.tar: H3K27ac_ErfRescue_SR_128637_128639.bw
IDR_FILTERED.tar:  H3K27ac_ErfRescue_SR_IDR_CPA.bed

value: mouse trophoblast stem cells (mTSCs)


title: 11H_M_120


title: SABio_Serum_EbovAb_NHP10


title: SABio_Serum_CtrlAb_NHP6


title: 11H_M_119


title: SABio_Ovary-R_EbovAb_NHP11

source_name: Ovary-R

value: Ovary-R


title: 11H_M_118


title: H3K27ac, ErfRescue, 2, PD


title: MYCN-amplified sample 3 (rna-seq)

description: 10x Genomics


title: MYCN-amplified sample 2a (rna-seq)

description: 10x Genomics


title: SABio_Ovary-R_EbovAb_NHP10


title: 11H_M_117


title: H3K27ac, ErfKO, 29, SR

description:
BIGWIGS.tar: H3K27ac_ErfKO_SR_128633_128635.bw
IDR_FILTERED.tar:  H3K27ac_ErfKO_SR_IDR_CPA.bed

value: self-renewal (SR)

value: ErfKO


title: Control sample 5 (rna-seq)

description: 10x Genomics

value: ganglioneuroma

value: Control sample


title: SABio_Ovary-R_CtrlAb_NHP6

value: F

value: Control


title: H3K27ac, ErfKO, 29, PD

description:
BIGWIGS.tar: H3K27ac_ErfKO_PD_128634_128636.bw
IDR_FILTERED.tar:  H3K27ac_ErfKO_PD_IDR_CPA.bed

value: 24h differentiation with PD (PD)


title: 11H_M_116


title: SABio_Ovary_EbovAb_NHP11

source_name: Ovary

value: Ovary


title: SABio_Oral_EbovAb_NHP11

source_name: Oral

value: Oral


title: Control sample 4 (rna-seq)

description: 10x Genomics


title: MYCN-amplified sample 1 (rna-seq)

description: 10x Genomics

value: neuroblastoma


title: H3K27ac, ErfKO, 2, SR


title: 11H_M_113


title: SABio_Ovary_EbovAb_NHP10

value: Ebola virus IgG immunoglobulins


title: H3K27ac, V5PD3

description:
BIGWIGS.tar: H3K27ac_V5PD_128631_128632.bw
IDR_FILTERED.tar:  H3K27ac_WT_PD_IDR_CPA.bed

value: WT


title: 11H_M_114


title: Control sample 2 (rna-seq)

description: 10x Genomics

value: ganglioneuroblastoma


title: Control sample 3 (rna-seq)

description: 10x Genomics

value: bone marrow


title: H3K27ac, V5PD4

value: Anti-H3K27ac (Diagenode/C15410196)


title: Control sample 1 (rna-seq)

description: 10x Genomics


title: H3K27ac, V5SR4

description:
BIGWIGS.tar: H3K27ac_V5SR_128629_128630.bw
IDR_FILTERED.tar:  H3K27ac_WT_SR_IDR_CPA.bed

value: mouse trophoblast stem cells (mTSCs)


title: H3K27ac, ErfRescue, 2, SR


title: SABio_Oral_CtrlAb_NHP6


title: 11H_M_112


title: 11H_M_111


title: SABio_Lung_EbovAb_NHP11

source_name: Lung

value: Lung


title: 11H_M_115


title: SABio_Lung_CtrlAb_NHP6


title: MYCN-amplified sample 2b (rna-seq)

description: 10x Genomics

value: MYCN-amplified sample


title: SABio_LN-mes_EbovAb_NHP11

source_name: Lymph node-mes

value: Lymph node-mes


title: 11H_M_110


title: SABio_Lung_EbovAb_NHP10


title: H3K27ac, V5SR3

source_name: mouse trophoblast stem cells (mTSCs)

value: self-renewal (SR)


title: H3K27ac, ErfKO, 2, PD

value: ErfKO


title: H3K4me3, ErfRescue, 29, PD

description:
BIGWIGS.tar: H3K4me3_ErfRescue_PD_128626_128628.bw
IDR_FILTERED.tar:  H3K4me3_ErfRescue_PD_IDR_CPA.bed

value: anti-H3K4me3 (Diagenode/C15410003)


title: H3K4me3, ErfRescue, 29, SR

description:
BIGWIGS.tar: H3K4me3_ErfRescue_SR_128625_128627.bw
IDR_FILTERED.tar:  H3K4me3_ErfRescue_SR_IDR_CPA.bed


title: 11H_M_109


title: 11H_M_108


title: SABio_LN-mes_EbovAb_NHP10

value: F


title: H3K4me3, ErfKO, 29, SR

description:
BIGWIGS.tar: H3K4me3_ErfKO_128621_128623.bw
IDR_FILTERED.tar:  H3K4me3_ErfKO_SR_IDR_CPA.bed


title: RNA_Human_BA23_H2

value: brain

value: Brodmann Area 23

value: M

tag: molecule subtype

value: nuclear RNA


title: SABio_Oral_EbovAb_NHP10

value: Oral

value: Ebola virus IgG immunoglobulins


title: H3K4me3, ErfRescue, 2, PD

value: 24h differentiation with PD (PD)


title: SABio_LN-mes_CtrlAb_NHP6

value: Control


title: 11H_M_105


title: 11H_M_99


title: SABio_LN-ax-R_EbovAb_NHP11

source_name: Lymph node-ax-R

value: Lymph node-ax-R


title: H3K4me3, ErfRescue, 2, SR

value: mouse trophoblast stem cells (mTSCs)


title: RNA_Human_BA23_H4


title: 11H_M_97


title: SABio_LN-ing_EbovAb_NHP11

source_name: Lymph node-ing

value: Lymph node-ing


title: 11H_M_104


title: SABio_LN-ax-R_EbovAb_NHP10


title: H3K4me3, ErfKO, 29, PD

description:
BIGWIGS.tar: H3K4me3_ErfKO_PD_128622_128624.bw
IDR_FILTERED.tar:  H3K4me3_ErfKO_PD_IDR_CPA.bed


title: SABio_LN-ing_EbovAb_NHP10


title: 11H_M_101


title: 11H_M_100


title: 11H_M_96


title: Human_BA23_H4

description:
Human_Count_Matrix_snATACseq_Barcodes.txt
Human_Count_Matrix_snATACseq_Genes.txt
Human_Count_Matrix_snATACseq_MetaData.txt
Human_Count_Matrix_snATACseq.mtx
Seurat_Astrocyte_ATAC_Human.RDS
Seurat_Excitatory_ATAC_Human.RDS
Seurat_Inhibitory_ATAC_Human.RDS
Seurat_Microglia_ATAC_Human.RDS
Seurat_OPCOli_ATAC_Human.RDS


title: H3K4me3, V5PD2

description:
BIGWIGS.tar: H3K4me3_V5PD_128619_128620.bw
IDR_FILTERED.tar:  H3K4me3_WT_PD_IDR_CPA.bed

value: WT


title: H3K4me3, ErfKO, 2, PD


title: Human_BA23_H3


title: SABio_Liver_EbovAb_NHP11

source_name: Liver

value: Liver


title: 11H_M_107


title: 83-PBMC

city: Madison

first: Aleksandar

middle: K.

last: Stanic

state: WI

address: 202 S. Park St., Meriter Atrium B

department: Obstetrics and Gynecology

institute: University of Wisconsin - Madison

data_processing:
CellRanger v3.1 count and vdj pipelines were applied to fastq files to generate feature matrices.
We enriched the data for high-quality cells according to the following metrics (keeping cells with mean absolute deviation within [-3,3]): fraction of UMIs aligning to mitochondrial transcripts, fraction of housekeeping genes detected, number of RNA or surface features detected, and number of RNA (surface feature) UMIs
We removed cells without VDJ sequencing data or that appeared to be CD4+CD8+/CD4-CD8- based on scatterplots.
Using Seurat v3.0/v4.0, we applied log normalization to RNA and centered-log-ratio (CLR) to surface proteins, performed clustering analysis, and dimensionality reduction.
We manually annotated the clusters based on their marker genes and surface protein expression.
Genome_build: GRCh38 3.0
Supplementary_files_format_and_content: Supplementary files include antibody capture feature reference file (feature_reference.csv), output from CellRanger that was used for downstream analysis (cellrange_output.tar.gz), differential expression analysis results (cluster_marker_and_DE_genes.xlsx), and count data and derived features for high-quality cells in multiple formats (final_processed_data.tar.gz; includes text and Seurat 4.0 RDS). Future users may need to run Seurat::UpdateSeuratObject to update the object for newer versions of Seurat.

source_name: T cells from peripheral blood

growth_protocol: Sequenced cells in this study were isolated from tissues and not grown.

extract_protocol:
T cells from decidua basalis and matched PBMCs were enriched using the Dynabeads® Untouched™ Human T Cells Kit (Invitrogen).    T cell enriched samples were then labeled with Zombie NIR™ Fixable Viability Kit (BioLegend). Subsequently, cells treated with TruStain FcX™ (BioLegend), then labeled with fluorochrome- and TotalSeq™-C oligonucleotide-conjugated antibodies. Samples were then sorted into PBS (Ca++/MG++ free, 1% non-acetylated BSA, 1 mL/mL RNase inhibitor) using the BD FACSAria in a 3 laser (488nm, 561nm, 405nm) configuration, collecting 100,000 live, CD3+ cells. Sorted cells were then processed using the Chromium Next GEM Chip A Single Cell A Chip Kit (10X Genomics).
According to manufacturer's protocol (10X Genomics Chromium, Single Cell Immune Profiling 5' v1.1 chemistry;  10X Genomics V(D)J Single-Cell RNA-Seq pipeline)

treatment_protocol: Matched decidual and PBMC samples were sourced from five term normal elective cesarean sections (>37 wks GA) under the approval of Meriter IRB# 2018-10 protocol (three were retained after data quality control). Decidua basalis tissue was dissected from the maternal surface of the placenta and decidua parietalis tissue was scraped from the fetal membrane. Decidual tissue was mechanically and enzymatically dissociated. PBMCs were isolated from whole blood via density gradient centrifugation. PBMC layer was extracted and washed with PBS, counted, adjusted to an optimal concentration of 4 X106 cells/mL and cryopreserved.

value: T cells

tag: localization

value: PBMC


title: H3K4me3, ErfKO, 2, SR

value: self-renewal (SR)

value: ErfKO

value: anti-H3K4me3 (Diagenode/C15410003)


title: H3K4me3, V5SR2

description:
BIGWIGS.tar: H3K4me3_V5SR_128617_128618.bw
IDR_FILTERED.tar:  H3K4me3_WT_SR_IDR_CPA.bed


title: SABio_LN-ax-R_CtrlAb_NHP6

source_name: Lymph node -ax-R

tag: tissue

value: Lymph node -ax-R

value: F


title: 11H_M_95

source_name: C57BL/6J Male P56 Mouse Brain


title: RNA_Human_BA23_H3

source_name: Post-mortem brain, Brodmann Area 23

value: brain

value: Brodmann Area 23

value: M

value: nuclear RNA


title: 85-PBMC


title: 11H_M_91


title: 81-PBMC


title: SABio_LN-ing_CtrlAb_NHP6

value: Control


title: SABio_Liver_CtrlAb_NHP6


title: H3K4me3, V5SR3

tag: differentiation state


title: 83-Basal

source_name: T cells from decidua basalis

value: Decidua basalis


title: SABio_Liver_EbovAb_NHP10

value: Ebola virus IgG immunoglobulins


title: 11H_M_93


title: 11H_M_90


title: 81-Basal


title: H3K4me3, V5PD3

value: mouse trophoblast stem cells (mTSCs)

value: 24h differentiation with PD (PD)

tag: modification


title: Input, Histone, ErfRescue, 29, SR


title: 11H_M_89


title: Input, Histone, ErfRescue, 2, PD


title: SABio_Kidney_EbovAb_NHP11

source_name: Kidney

value: Kidney

tag: Sex


title: SABio_Kidney_EbovAb_NHP10


title: SABio_Kidney_CtrlAb_NHP6


title: 11H_M_88


title: Input, Histone, ErfRescue, 2, SR


title: 85-Basal

value: T cells


title: 11H_M_85


title: Input, Histone, ErfKO, 29, PD


title: SABio_CSF_EbovAb_NHP11

source_name: Cerebrospinal fluid

value: Cerebrospinal fluid


title: 11H_M_83


title: 11H_M_84


title: Input, Histone, ErfKO, 29, SR

value: self-renewal (SR)


title: Input, Histone, ErfRescue, 29, PD


title: SABio_CSF_EbovAb_NHP10


title: SABio_CSF_CtrlAb_NHP6


title: Input, Histone, ErfKO, 2, PD

value: ErfKO


title: Input, Histone, ErfKO, 2, SR


title: SABio_Brain_EbovAb_NHP9

source_name: Brain

value: Brain


title: 11H_M_80


title: Input, Histone, V5PD2

value: WT


title: Input, Histone, V5PD1


title: 11H_M_81


title: SABio_Brain_EbovAb_NHP14


title: SABio_Brain_EbovAb_NHP11

value: F


title: SABio_Brain_EbovAb_NHP12


title: 11H_M_79


title: Input, Histone, V5SR1


title: 11H_M_78


title: V188_SR3

data_processing:
read trimming: bbduk (38.86)
alignment: STAR (2.7.3a)
alignment processing: samtools (1.10)
read counting: htseq-count (0.11.2)
Genome_build: mm10
Supplementary_files_format_and_content: txt/counts

extract_protocol:
Quantseq libraries were prepared with 250 ng RNA using QuantSEQ 3’ mRNA-Seq Library Prep Kit FWD for Illumina (015.96, Lexogen) according to manufacturer’s recommendations. The libraries were pooled and sequenced with a 50-base-pair single-end protocol on an Illumina HiSeq 2500 sequencer.
RNAseq. RNA was extracted using RNeasy mini kit (Qiagen) and treated with DNaseI (Qiagen).
RNA-seq (Quantseq)

value: shControl

value: TSGFP


title: 11H_M_76


title: SABio_Brain_EbovAb_NHP10


title: 11H_M_82


title: Lung cancer, #19

type: genomic

city: Chiba

first: Kazuhiro

last: DAINO

address: 4-9-1 Anagawa, Inage-ku

country: Japan

institute: National Institutes for Quantum and Radiological Science and Technology

hyb_protocol: Slides were hybridised in 1X Agilent Blocking Agent/Hi-RPM Buffer for 24 hours at 67°C in a rotating hybridization oven, then washed with the Agilent Oligo aCGH Buffer 1 and Buffer 2 in an ozone-depleted hood.

scan_protocol: Scanned on an Agilent microarray scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

source_name: Lung adenocarcinoma of neutron-irradiated mouse

label_protocol: Labeling reactions with cyanine 5-UTP and cyanine 3-UTP were performed according to the Agilent SureTag DNA labeling kit (Agilent Technologies, Santa Clara, CA, USA).

growth_protocol: Mice were housed in autoclaved cages and maintained in a room with a controlled temperature (23 ± 1°C) and humidity (50 ± 5%) under a regular 12-hours light, 12-hours dark cycle. They were fed a standard laboratory animal diet (MBR-1; Funabashi Farm, Tokyo, Japan) and sterilized water ad libitum.

extract_protocol: Genomic DNA was extracted by QIAmp DNA Micro kit (Qiagen).

treatment_protocol: Mice were left untreated or were subjected to whole-body irradiated with gamma-rays, carbon-ions or neutrons at 7 weeks old.

value: F1 hybrid of B6 and C3H mice

tag: gender

value: Male

value: Lung adenocarcinoma

value: neutron-irradiated

source_name: Normal ear

value: Ear skin


title: Lung cancer, #21


title: Lung cancer, #23


title: 11H_M_75


title: Lung cancer, #18

source_name: Lung adenocarcinoma of carbon-irradiated mouse

value: Female

value: carbon-irradiated


title: Lung cancer, #20


title: Lung cancer, #24


title: SABio_Brain_EbovAb_NHP13

value: M

value: Ebola virus IgG immunoglobulins


title: SABio_Brain_CtrlAb_NHP7

value: Control


title: V188_SR2

value: mouse trophoblast stem cells (mTSCs)

value: self-renewal (SR)


title: SABio_Brain_CtrlAb_NHP6

value: Brain


title: V188_SR1


title: Input, Histone, V5SR2

value: WT


title: 11H_M_73


title: SABio_Brain_CtrlAb_NHP5


title: 11H_M_74


title: 11H_M_72


title: V188_PD3

value: 25h differentiation with PD (PD)


title: V188_PD2

value: 24h differentiation with PD (PD)

value: shControl


title: SABio_Brain_CtrlAb_NHP4


title: 11H_M_71


title: V188_PD1

value: TSGFP


title: Lung cancer, #22

value: F1 hybrid of B6 and C3H mice

value: Male


title: Lung cancer, #17

value: Lung adenocarcinoma


title: Lung cancer, #16

value: Ear skin


title: SABio_Brain_CtrlAb_NHP3


title: V183_SR3


title: 11H_M_69


title: SABio_Adrenal_EbovAb_NHP10

source_name: Adrenal gland

value: Adrenal gland

value: F


title: SABio_Adrenal_CtrlAb_NHP6


title: 11H_M_68


title: V183_SR1


title: 11H_M_67


title: Lung cancer, #15

value: Female

value: carbon-irradiated


title: Lung cancer, #14


title: NCI-H23-R (AMG 510) treated with AMG510 rep2

city: South San Francisco

first: Marc

last: Hafner

address: Building 45-1, 1 DNA Way

department: Oncology Bioinformatics

institute: Genentech

description: NCI-H23-R (AMG 510) treated with AMG510

data_processing:
ATAC-seq reads were analyzed using the ENCODE ATAC-seq pipeline v1.
Reads were trimmed of adapters by cutadapt (version 1.9.1) and mapped to hg38 by Bowtie2 (version 2.2.6). Bam files were converted to tagAlign format, which was then adjusted for Tn5 by shifting +4 bp for positive strand and by −5bp for negative strand. TagAlign files were used to call peaks using MACS2 (version 2.1.0).  Peaks with p<1e-6 were retained for differential analysis.
Bam files were converted to tagAlign format, which was then adjusted for Tn5 by shifting +4 bp for positive strand and by −5bp for negative strand. TagAlign files were used to call peaks using MACS2 (version 2.1.0).  Peaks with p<1e-6 were retained for differential analysis.
TagAlign files were used to call peaks using MACS2 (version 2.1.0).  Peaks with p<1e-6 were retained for differential analysis.
Assembly: Hg38
Supplementary files format and content: bed files containing NarrowPeaks

source_name: Lung

growth_protocol: Cells were growing in RPMI + 10% FBS

extract_protocol:
Cryo-preserved cells were thawed, washed with 1× PBS and counted. About 100,00 cells were then lysed for 5 minutes on ice in 100 µL of Lysis buffer (10 mM Tris, pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40, 0.1% Tween-20 and 0.01% digitonin). 1 ml of wash buffer (10 mM Tris, pH7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20) was then added and the pellets were spun down at 500 g for 10 minutes at 4 °C.
The cell pellets were resuspended in 50 uL of tagmentation buffer (25 µL 2× TD buffer, 16.5 µL PBS, 0.5 µL 10% tween 20, 0.5 µL of 1% Digitonin, 2.5 µL Tn5 transposase and 5 µL H2O). The tubes were incubated at 37 °C for 30 minutes, followed by DNA isolation using the Qiagen MinElute Cleanup Kit (Cat. No. 28206). The DNA was then amplified using NEBNext 2× PCR Master mix (Cat. No. M0541L)

treatment_protocol: Cells were treated with sotorasib or sotorasib + GNE-7883 for 24h then cryo-preserved

value: Lung

tag: cell line

value: Carcinoma Non-Small Cell


title: 11H_M_66


title: 11H_M_70


title: NCI-H23-R (AMG 510) treated with AMG510 rep1

description: NCI-H23-R (AMG 510) treated with AMG510


title: V183_PD3

source_name: mouse trophoblast stem cells (mTSCs)

value: mouse trophoblast stem cells (mTSCs)

tag: parental cell line


title: V183_PD2


title: Lung cancer, #13


title: Lung cancer, #12

source_name: Lung adenocarcinoma of gamma-irradiated mouse

value: gamma-irradiated


title: Lung cancer, #11


title: SABio_Adrenal_EbovAb_NHP11

value: Ebola virus IgG immunoglobulins


title: Lung cancer, #10


title: 11H_M_65


title: NCI-H23 treated with AMG510 rep2

description: NCI-H23 treated with AMG510


title: V183_PD1


title: Lung cancer, #8


title: V183_SR2

value: self-renewal (SR)


title: Lung cancer, #9


title: 11H_M_2876


title: 11H_M_64


title: V182_SR2


title: NCI-H23 treated with AMG510 rep1

description: NCI-H23 treated with AMG510


title: NCI-H23 treated with DMSO rep2

description: NCI-H23 treated with DMSO

value: DMSO


title: Lung cancer, #5

source_name: Lung adenocarcinoma of non-irradiated mouse

value: non-irradiated


title: Lung cancer, #6


title: Lung cancer, #7


title: 11H_M_2875


title: NCI-H23 treated with DMSO rep1

description: NCI-H23 treated with DMSO


title: A-MDL117_v3_81618

city: Montreal

first: David

last: Cheishvili

state: Quebec

address: 3655 Sir William Osler

country: Canada

institute: McGill

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Epic Human Methylation 850K Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Genome Studio software v2011.1

label: Cy3, Cy5

source_name: saliva

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from LBC samples using Qiagen DNeasy Kit according to standard instructions

value: male

value: saliva

tag: disease state

value: normal

tag: individual

value: Control

tag: timepoint (intervention)

value: After

value: 53 years


title: V182_PD3

tag: cell type

value: 25h differentiation with PD (PD)

value: TSGFP


title: Lung cancer, #4

value: F1 hybrid of B6 and C3H mice

value: Male

value: Lung adenocarcinoma

tag: treatment

value: Ear skin


title: B-MDL139_v2_52819

value: Subject

value: Midpoint

tag: age

value: 70 years


title: NCI-H358-R (AMG 510) treated with AMG510 rep2

value: Lung

value: Carcinoma Non-Small Cell


title: 11H_M_2874

tag: brain region


title: V182_PD2

value: mouse trophoblast stem cells (mTSCs)

value: 24h differentiation with PD (PD)


title: 11H_M_2873

tag: strain


title: NCI-H358-R (AMG 510) treated with AMG510 rep1


title: 11H_M_2872


title: Lung cancer, #3

value: Female

value: non-irradiated


title: V182_PD1


title: A-MDL106_v1_32918

value: male

tag: sample type

value: saliva

value: normal

value: Control

value: Before

value: 50 years


title: NCI-H358 treated with AMG510 rep2

description: NCI-H358 treated with AMG510


title: B-MDL126_v3_121018

value: After

value: 62 years


title: V233_SR2

value: self-renewal (SR)

value: shErf

value: TSGFP


title: NCI-H358 treated with AMG510 rep1

description: NCI-H358 treated with AMG510

value: Lung


title: B-MDL128_v3_11719

value: Subject


title: 11H_M_2871


title: V188_SR5

value: mouse trophoblast stem cells (mTSCs)

value: shControl


title: Lung cancer, #2

value: F1 hybrid of B6 and C3H mice

value: Female

value: Lung adenocarcinoma

value: Ear skin


title: 11H_M_2870


title: V188_PD5

value: 24h differentiation with PD (PD)


title: B-MDL132_v2_11419

value: male

value: saliva

value: normal

value: Midpoint

value: 60 years


title: NCI-H358 treated with DMSO rep2

description: NCI-H358 treated with DMSO

value: Carcinoma Non-Small Cell

value: DMSO


title: A-MDL120_v3_91818

value: Control

value: After

value: 61 years


title: V233_SR3

value: mouse trophoblast stem cells (mTSCs)

value: self-renewal (SR)

value: shErf

value: TSGFP


title: 11H_M_2868


title: Lung cancer, #1

value: F1 hybrid of B6 and C3H mice

value: Male

value: Lung adenocarcinoma

value: non-irradiated


title: NCI-H358 treated with DMSO rep1

description: NCI-H358 treated with DMSO

value: Lung


title: SAM24409711, replicate 1, scRNASeq

data_processing:
Read pseudoalignment: kallisto (version 0.46.2)
BUS file processing and gene count matrix creation: bustools (version 0.40.0)
Assembly: GRCh38 / Ensembl 90
Supplementary files format and content: Tab-separated values files and matrix files

growth_protocol: NCI-H358 and NCI-H23 cell lines were barcoded with TraCe-seq barcoding libraries and expanded in culture to establish the starting TraCe-seq cell populations. A fraction of the starting populations were profiled by single cell RNA-sequencing (scRNA-seq) to capture the relative clonal abundance and transcriptional profile of each barcoded clones right before drug treatment. In parallel, the rest of the cells were treated with sotorasib alone or in combination with GNE-7883 until resistant clones emerged under sotorasib single agent treatment. We conducted scRNA-seq profiling to capture acute responses to the treatment at 72h post treatment as well as after resistance has emerged to capture adaptive changes. These time points were chosen to allow us capture the differential transcriptional responses in the resistant versus sensitive clones, and compare the responses to sotorasib single agent versus sotorasib + GNE-7883 combination at individual clone and single cell level.

extract_protocol:
Cultured cells were trypsinized into single cell suspensions in PBS.
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics). Briefly, cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

tag: time point

value: several months


title: B-MDL144_v3_82119

value: male

value: saliva

value: normal

value: Subject

value: 57 years


title: V233_SR1


title: V233_PD3

value: 24h differentiation with PD (PD)


title: 11H_M_2867


title: SAM24409168, replicate 2, scRNASeq

tag: tissue

value: Carcinoma Non-Small Cell

value: DMSO


title: 11H_M_2869


title: A-MDL111_v3_62518

value: Control

value: After

value: 64 years


title: B-MDL104_v2_5118

value: Midpoint

value: 53 years


title: 11H_M_2866


title: SAM24409168, replicate 1, scRNASeq


title: 11H_M_2865


title: V233_PD1

value: mouse trophoblast stem cells (mTSCs)

tag: differentiation state

value: shErf

value: TSGFP


title: V188_SR6

value: self-renewal (SR)

tag: modification

value: shControl


title: B-MDL116_v1_6718

value: male

value: saliva

value: Before

value: 58 years


title: 11H_M_2864


title: SAM24409166, replicate 1, scRNASeq

value: Lung

value: AMG-510 800nm + TEADi 500nm


title: V188_SR4


title: V182_SR1


title: B-MDL144_v1_61719

value: normal

value: Subject

value: 57 years


title: 11H_M_2862


title: V188_PD6

value: 24h differentiation with PD (PD)


title: A-MDL138_v3_62119

value: Control

value: After

value: 50 years


title: SAM24409164, replicate 1, scRNASeq

value: Carcinoma Non-Small Cell


title: V188_PD4

value: mouse trophoblast stem cells (mTSCs)

value: TSGFP


title: A-MDL123_v2_92618

value: Midpoint

value: 66 years


title: SAM24409162, replicate 2, scRNASeq


title: B-MDL131_v1_12518

value: male

value: saliva

value: 56 years


title: WT, SR4

value: self-renewal (SR)

value: WT


title: 11H_M_2860


title: SAM24409162, replicate 1, scRNASeq

value: Lung

value: AMG-510 800nm + TEADi 500nm


title: A-MDL113_v2_61218

value: normal

value: 70 years


title: SAM24409166, replicate 2, scRNASeq


title: B-MDL129_v3_11819

value: Subject


title: WT, SR3


title: SAM24409164, replicate 2, scRNASeq


title: 11H_M_2863


title: WT, SR2


title: B-MDL104_v3_52918

value: After

value: 53 years


title: A-MDL102_v2_42618

value: Control

value: 54 years


title: 11H_M_2858


title: 11H_M_2859


title: 11H_M_2857


title: WT, PD4

value: mouse trophoblast stem cells (mTSCs)

value: 24h differentiation with PD (PD)

value: TSGFP


title: WT, SR1


title: A-MDL113_v3_71118

value: male


title: SAM24409159, replicate 2, scRNASeq

value: Carcinoma Non-Small Cell

value: Baseline

value: Day 0


title: WT, PD3

value: WT


title: 11H_M_2861


title: SAM24409159, replicate 1, scRNASeq

value: Lung


title: A-MDL136_v2_21919

value: saliva

value: Midpoint

value: 58 years


title: WT, PD2


title: 11H_M_2855


title: 11H_M_2854


title: A-MDL134_v1_1919

value: normal

value: Before

value: 65 years


title: SAM24407133, replicate 2, scRNASeq

value: DMSO


title: WT, PD1


title: 11H_M_2853


title: B-MDL124_v3_11218

value: Subject

value: After

value: 54 years


title: SAM24409160, replicate 1, scRNASeq