title: SE3P5CT2

city: Skolkovo

first: Ekaterina

last: Khrameeva

state: Moscow region

address: Novaya St., 100

country: Russia

institute: Skolkovo Institute of Science and Technology

data_processing:
Sequencing reads were mapped to a concatenation of human and mouse reference genomes, and then uniquely mapped reads were separated into human and mouse reads using a pipeline NeatSeq-Flow.
The obtained read counts per gene were further processed using the edgeR package. Low-covered genes were filtered out, read counts were normalized, and differentially expressed genes were found using the default parameters.
Genome_build: GRCh38.p12 for human and GRCm38.p6 for mouse
Supplementary_files_format_and_content: Tab-delimited text files include non-normalized read count values for each sample. One file for human reads and one file for mouse reads. Gene annotation version: oct2018.archive.ensembl.org

source_name: PDX

growth_protocol: All experiments were conducted using 6–8-week-old Nod. Scid mice (Envigo-NOD.CB17-Prkdcscid/NCrHsd). Forming the PDX model, patient-derived tumor tissue samples were implanted subcutaneously in the dorsal flanks of the mice. The tumor take rate varies from 1 to 6 months. PDXs have been maintained by passing the tumors in mice from the first generation to subsequent generations. Upon successful tumor engraftment, the tumors were expanded and re-transplanted into Nod. Scid mice for the drug efficacy experiments. For each PDX, 3mm3 pieces of tumors were implanted. Each group contained 3-6 mice harboring two tumors (n = 6-12).

extract_protocol:
Three tumors from each group (vehicle and cetuximab, a total of 6 samples for each PDX) were subjected to sequencing. Tumors were obtained from different mice within the group. RNA was extracted using the RNeasy mini kit (Qiagen) according to the manufacturer’s instructions.
After quality control of Bioanalyzer (RIN>7), RNAseq libraries were prepared using the TruSeq RNA Sample Preparation kit (Illumina) according to the manufacturer’s protocol. Briefly, 1ug of total RNA was fragmented, followed by reverse transcription and second-strand cDNA synthesis. The DS-cDNA was subjected to end repair, a base addition, adapter ligation, and PCR amplification to create libraries. Qubit and Bioanalyzer were evaluated. Sequencing libraries were constructed with barcodes to allow multiplexing of 6 samples in one lane. Libraries, ready to run, were sent to the g-INCPM institute at the Weizmann Institute of Science for sequencing. On average, 400 million paired-end (75 bp) reads were sequenced per run on an Illumina NextSeq 500 HO instrument.

treatment_protocol: When tumor volume reached 70 to 120 mm3, the animals were randomly divided into two arms treated either with vehicle or cetuximab. In all experiments, tumor measurement was performed with a digital caliper, and tumor volumes were determined with the formula: length × width2 × (π/6). All animal experiments were carried out under the Institutional Animal Care and Use Committee (IACUC) of Ben-Gurion University of the Negev (BGU’s IACUC) according to specified protocols aimed to ensure animal welfare and to reduce suffering. The animal ethical clearance protocol numbers used for this study are IL-80-12-2015 and IL-29-05-2018. The EGFR inhibitor, Cetuximab (Erbitux, Merck), was kindly provided by Soroka Medical Center. The drug was diluted with sterile PBS (1x) for a working concentration of 10 mg/kg for in vivo and 12.5 μg/mL for in vitro experiments. Cetuximab was given in vivo by intraperitoneal injection (i.p.) every five days. The SMAD3 inhibitor, SIS3 (APExBIO), was dissolved in 0.5% DMSO and then with corn oil for a final working concentration of 5mg/kg. SIS3 was given in vivo by i.p. every day. Recombinant mouse TGF-beta1 (BioLegend) was used for the in vitro experiments in a 10ng/ml working concentration.

value: HNC patient-derived xenografts (PDXs)

tag: patient

tag: treatment

value: Vehicle


title: g7

status: Public on Mar 23 2020

type: SRA

city: Hangzhou

first: Liang

last: Li

state: Zhejiang

address: number 866 of Yuhangtang road, West Lake Dist

department: College of Life Sciences

country: China

institute: Zhejiang University

library_source: transcriptomic

data_processing:
the raw reads were filtered by removing reads containing adapter, poly-N (reads with a ratio greater than 5%), and low quality reads (Q < 30). The reference genome (GRCh38.p12) was downloaded from the genome website (ftp://ftp.ensembl.org/pub/release-87/) and its index was built using Hisat2-Build(v2.0.5), and paired-end clean reads were aligned to the reference genome using TopHat (v2.1.1).
The quantitative analysis of gene expression was completed by Cufflinks (v2.2.1)21 based on RPKM which was calculated by Cuffdiff (v1.3.0).
Significant DEGs were identified by adjusting to a P value < 0.05 and an absolute value of log (fold change) > 1 using Cuffdiff (v2.2.1).
Cluster analysis was performed on differentially expressed genes using Euclidean Distance and Pheatmap.
GO enrichment analysis of differentially expressed genes was implemented with Perl module (GO: TermFinder) with a threshold for significance set at P < 0.05. R functions (phyper and q value) were used to test for the statistical enrichment of the differentially expressed genes in the KEGG pathways, corrected to P < 0.05.
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: osteogenesis for 7 days under normal ground condition

growth_protocol: The SM-31 random position machine (RPM) was used to simulate microgravity conditions. It was operated in random modes of speed (1 -10 r/min) inside a CO2 incubator (5% CO2, 37°C and 100% humidity). After the cells of 3rd passage reached 60-70% confluency, the medium was replaced with osteogenic medium18 (L-Dulbecco’s modified Eagle’s medium (DMEM; Life Technologies) supplemented with 10% FBS, 50 μg/mL L-ascorbic acid (Sigma, Shanghai, China), 10 mM β-glycerophosphate (Sigma), 0.1 μM dexamethasone (Sigma), 100 U/mL penicillin, and 100 μg/mL streptomycin.

extract_protocol:
RNA from cells was extracted using Trizol reagent (Sigma). All RNA samples were detected and analyzed in Vazyme Biotech Co. (Nanjing, China). Briefly, RNA purity was detected by NanoDrop® spectrophotometer (Thermo Fisher, MA, USA), concentration measured using Qubit® RNA Assay Kit in Qubit® 3.0 Fluorometer (Life Technologies, CA, USA), and the integrity assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
The sequencing libraries were generated using the VAHTS mRNA-seq v2 Library Prep Kit for Illumina® (Vazyme, NR601) following manufacturer’s instructions and sequenced on an Illumina Hiseq X Ten platform using 150 bp paired-end module.

treatment_protocol: The flasks were fixed on a cell culture vessel for RPM exposure. Cells grown in NG condition were also filled with osteogenic medium and were statically placed in the same CO2 incubator. The medium was changed twice a week. Cells induced for 0, 2, 7, and 14 days were used to study the effects of simulated microgravity

tag: cell type

value: human bone marrow mesenchymal stem cells

tag: passages

tag: differentiation status

value: osteogenic differentiation day 7

tag: gravity status

value: normal ground gravity

tag: tissue

value: bone


title: SE3P5Cet4

molecule: polyA RNA

organism: Mus musculus

value: Cetuximab


title: SE3P5CT0


title: E12.5-WT-rep2 [RNA-seq]

city: New Orleans

first: Linyan

last: Wang

state: LA

address: 6400 freret street

country: USA

institute: Tulane University

data_processing:
Sequencing reads were mapped to a reference mouse genome (GRCm38/mm10) with  HISAT2 (default parameters)
Gene expression was counted using featureCounts
DEGs were further processed with DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: tabular file including DEGs; GeneID, Base mean, log2(FC), StdErr, Wald-Stats, P-value, P-adj data columns

extract_protocol:
the anterior palatal  mesenchyme from E12.5 Wnt1Cre;Meis2f/f and wildtype embryos was  collected after the removal of the palatal  epithelium using Dispase II (Sigma). Three  biological replicates from each group and  genotype were collected for analyses. Total RNA  was isolated using RNeasy Micro Plus Kit  (Qiagen).
The reverse transcription and amplification of RNA were done and followed by library preparation with TruSeq RNA Sample Preparation Kit v2 (Illumina).

tag: strain background

tag: development stage

tag: genotype/variation

value: Wildtype

tag: tissue/cell type

value: anterior palate mesenchyme


title: E12.5-Wnt1Cre;Meis2f/f-rep3 [ATAC-seq]

library_source: genomic

data_processing:
After  removal of the adaptor sequences, truncated reads  were mapped to GRCm38/mm10 reference  genomes with bowtie 2
The bamCoverage was used to generate a bigwig file, which is visible on the Integrative Genomics Viewer
Peaks from each group were respectively identified on a pool of triplicates using MACS2 callpeak
DiffBind was used to identify sites that exhibit differential accessibility between control and Meis2 mutant groups
Genome_build: mm10
Supplementary_files_format_and_content: bigwig file including peaks

molecule: genomic DNA

extract_protocol:
The GFP-positive anterior palatal shelves  were isolated from E12.5  Wnt1Cre;Meis2f/+;R26RmTmG and  Wnt1Cre;Meis2f/f;R26RmTmG embryos. Samples  were subjected to digestion by a cocktail of 0.02%  collagenase I, II and IV in HBSS for 30min,  followed by Accutase solution (Sigma) treatment  for 5 min at 37℃. After stop of the digestion with  culture medium containing 10% fetal bovine  serum (FBS), cells were washed with PBS  containing 3% FBS and then filtered through a 70-  μm filter. Suspended cells were sorted by  Fluorescence-activated Cell Sorting (FACS) on a  BD FACS Aria Fusion cell sorter (Becton-  Dickinson).
Around 50,000 single GFP-positive  cells from each group were obtained and were  subjected promptly to generation of ATAC-seq  library with the Nextera DNA Library Preparation Kit

tag: genotype

value: Palate mesenchyme cells


title: SE20P2CT5


title: WTX_REF, 10x genomics (cell type mix)

city: Barcelona

first: Lars

last: Velten

address: C. Dr. Aiguader 88, P05

department: Bioinformatics and Genomics

country: Spain

institute: CRG

description: 10x genomics of a mix of cell types

data_processing:
Genome_build: Mus  Genome_build: Mus culus mm10
Conversion of paired end fastq files to unaligned bam; Picard Tools FastqToSam (v. 2.18.14)
Extraction of UMI observations using the Drop-seq tools workflow (v. 1.13; http://mccarrolllab.org/dropseq/) with STAR (v. 2.5.3a) for read alignment.
Filtering for chimeric reads and UMI count extraction using an approach adapted from Dixit et al. (python v. 3.6.6 ; https://www.biorxiv.org/content/10.1101/093237v1.full)
Extraction of perturbation status for each cell based on a cutoff on detected vector molecule counts (R v. 3.5.1).
Supplementary_files_format_and_content: Count tables (.counts.csv) and binary tables specifyng perturbation status (.pertStatus.csv)

source_name: 1:1:1 Mix of 3T3 cells, Embryonic Stem Cells and Neutrophils (all from mouse)

growth_protocol: NIH 3T3 cells were cultivated in DMEM (Thermo, 41965039) supplemented with 10 % FBS and P/S. Mouse embryonic stem cells  were cultivated under FCS/LIF conditions as described (Deliu et al., Nat Neurosco 21, 1717-27).

extract_protocol:
Cells were collected using centrifugation and subjectd to single-cell RNAseq using 10X Genomics. For neutrophils, femurs, tibiae, hips and spines were dissected and cleaned from surrounding tissue. Bones were crushed in cell suspension medium and dissociated cells were filtered, red blood cell lysis was performed and single viable cells were isolated using forward/sideward scatter and DAPI dye exclusion, and CD11b+/Ly6G+ neutrophils were isolated.
TAP-seq, 10x genomics based
Libraries were prepared according to DropSeq protocol (Macosko Cell 2015) or 10X Genomics single-cell RNAseq v2 (Chromium 3' Reagent Kits v2 User Guide Rev C "CG00052") for whole transcriptome or TAP-seq protocol for targeted transcriptome readouts.

tag: cell line

tag: strain

tag: targeting panel

tag: perturbations


title: WTX_REF, 10x genomics (lung mesenchyme)

description: 10x genomics of lung mesenchymal cells

source_name: Lung mesenchyme

extract_protocol:
Lungs were perfused with cold PBS and instilled with collagenase I. Lungs were removed while trachea was clamped. The lungs were cleaned from non-respiratory tissue and minced. Following depletion of erythrocytes, mesenchymal cells were sorted as Dapi–/Epcam–/CD45–/CD31–/Pdgfra+/Sca1–/Npnt+
TAP-seq, 10x genomics based
Libraries were prepared according to DropSeq protocol (Macosko Cell 2015) or 10X Genomics single-cell RNAseq v2 (Chromium 3' Reagent Kits v2 User Guide Rev C "CG00052") for whole transcriptome or TAP-seq protocol for targeted transcriptome readouts.

value: Lung mesenchyme

value: Mouse Celltype Mix panel


title: E12.5-WT-rep1 [RNA-seq]


title: TAP_DEEP, panel 3 (cell type mix)

description: The basic TAP-Seq protocol was performed with indicated target gene panel.

value: 1:1:1 Mix of 3T3 cells, Embryonic Stem Cells and Neutrophils (all from mouse)


title: SE3P5CT1


title: TAP_DEEP, panel 3 (lung cells)


title: SE20P2Cet2


title: SE20P2Cet3


title: SE20P2Cet1


title: SE20P2CT6


title: SE3P5Cet5


title: SE20P2CT4


title: E12.5-WT-rep2 [ATAC-seq]


title: SE18P6CT3


title: SE18P6CT1


title: dentate gyrus: Tg2

city: New York

first: Caghan

last: Kizil

state: NY

institute: Columbia University Irving Medical Center

description: 10X Chromium, single-cell sequencing

data_processing:
Sequencing was performed by 10X Chromium according to the manufacturer’s protocol (Zheng et al., 2016). Read alignment and read counts were done by Cell Ranger 2.1.0.
Genome_build: mm10.e87
Supplementary_files_format_and_content: data files are tab-delimited files with gene names in rows and cell tags in columns.

source_name: dentate gyrus

extract_protocol:
The DGs from WT and APP/PS1 mice were dissected in ice cold PBS with Pen/Strep and the cell dissociation was done using Neural Tissue Dissociation Kit (P) (Miltenyi Biotech) as described (Bhattarai et al., 2016). Cells were next FACS sorted using Propodium Iodide Cell viability dye. Single cell analyses were performed as described (Cosacak et al., 2019). Sequencing was performed by 10X Chromium according to the manufacturer’s protocol (Zheng et al., 2016).
10X Chromium

treatment_protocol: No treatment done. WT and Transgenic APP/PS1 mouse dentate gyrus cells used for single-cell sequencing.

value: dentate gyrus

tag: source

value: transcriptomic

tag: selection

value: cDNA


title: SE18P6Cet1

tag: patient

tag: treatment


title: SE18P6CT0


title: dentate gyrus: Tg1

description: 10X Chromium, single-cell sequencing


title: dentate gyrus: Ctl2

description: 10X Chromium, single-cell sequencing

value: wilt type


title: dentate gyrus: Ctl1

description: 10X Chromium, single-cell sequencing


title: TAP_CT, c-Kit+ bone marrow, sample 2

description: TAP-seq was performed for cells from bone marrow, using a target gene panel designed to distinguish cell types and differentiation stages

data_processing:
Mus Musculus mm10
Conversion of paired end fastq files to unaligned bam; Picard Tools FastqToSam (v. 2.18.14)
Extraction of UMI observations using the Drop-seq tools workflow (v. 1.13; http://mccarrolllab.org/dropseq/) with STAR (v. 2.5.3a) for read alignment.
Filtering for chimeric reads and UMI count extraction using an approach adapted from Dixit et al. (python v. 3.6.6 ; https://www.biorxiv.org/content/10.1101/093237v1.full)
Extraction of perturbation status for each cell based on a cutoff on detected vector molecule counts (R v. 3.5.1).
Supplementary_files_format_and_content: Count tables (.counts.csv) and binary tables specifyng perturbation status (.pertStatus.csv)

source_name: c-Kit+ Bone marrow

extract_protocol:
Fresh bone marrow cells were isolated by crushing mouse bones in media supplemented with FCS and the supernatant was collected. Cells were stained with fluorescently labelled antibodies against lineage markers (CD4, CD8, CD11b, B220, Gr1, Ter119) and c-Kit. A DNA dye was used to exclude debris. Single DNA+c-Kit+ cells were sorted into PBS-2%FCS.
TAP-seq, 10x genomics based
Libraries were prepared according to DropSeq protocol (Macosko Cell 2015) or 10X Genomics single-cell RNAseq v2 (Chromium 3' Reagent Kits v2 User Guide Rev C "CG00052") for whole transcriptome or TAP-seq protocol for targeted transcriptome readouts.

tag: cell type

value: c-Kit+ Bone marrow

value: Bone marrow


title: TAP_CT, c-Kit+ bone marrow, sample 1


title: TAP_CT, total bone marrow, sample 1

source_name: Total Bone marrow

extract_protocol:
Fresh bone marrow cells were isolated by crushing mouse bones in media supplemented with FCS and the supernatant was collected. Cells were stained with fluorescently labelled antibodies against lineage markers (CD4, CD8, CD11b, B220, Gr1, Ter119) and c-Kit. A DNA dye was used to exclude debris. Single DNA+ cells were sorted into PBS-2%FCS.
TAP-seq, 10x genomics based
Libraries were prepared according to DropSeq protocol (Macosko Cell 2015) or 10X Genomics single-cell RNAseq v2 (Chromium 3' Reagent Kits v2 User Guide Rev C "CG00052") for whole transcriptome or TAP-seq protocol for targeted transcriptome readouts.

value: Total Bone marrow


title: HSPC TetO-Tcf15

city: Boston

first: Alejo

middle: E

last: Rodriguez-Fraticelli

state: MA

address: 1 Blackfan Circle

department: Hematology-Oncology

institute: Boston Children's Hospital

description:
inDrop scRNAseq libraries containing: WT (control) and TetO-Tcf15 (experiment)
ARF2019_Sample6_cell_bcs_flat.txt
ARF2019_Sample6_counts_norm.csv.gz
ARF2019_Sample6_genes.txt
ARF2019_Sample6_samp_id_flat.txt
ARF2019_Sample6_selected_cell_groupings.csv
ARF2019_Sample6_selected_custom_colors.csv
ARF2019_Sample6_selected_expr.csv.gz
ARF2019_Sample6_selected_original_cell_indices.txt
inDrop single cell RNA-seq libraries

data_processing:
inDrops single cell RNAseq
BCL2 files were downloaded, and converted into FASTQ files for each of the inDrop sequencing reads (R1: 61 cycles, R2: 8 cycles, R3: 8 cycles, R4: 14 cycles). Then, inDrop FASTQ files were demultiplexed using a custom python pipeline (github.com/indrops/). Libraries used the V3 inDrop primer architecture. Sequencing reads were first merged, sorted, and then written into FASTQ files in which single cell and UMI barcodes for each read are listed in the header. These files are provided as RAW FASTQ files and can be used to continue the indrops.py pipeline from step 3. Single-cell barcodes for each cDNA read were matched against a white-list of all possible inDrop v3 cell barcodes (these sequences can be obtained in github.com/indrops/indrops/blob/master/ref/barcode_lists/). Up to two nucleotide mismatch errors were corrected. Then, reads were aligned to the mm9 mouse referenced transcriptome using Bowtie v1.1.1, and then quantified and processed into counts of UMI-filtered transcripts per gene. These tables are provided as TSV files, and the gene lists as TXT files (processed data files). These TSV files were processed with the SPRING-data_prep pipeline (github/AllonKleinLab/SPRING_dev). Counts matrices were first filtered to exclude cell barcodes associated with low numbers of reads. This determination was made by manually inspecting a weighted histogram of UMI counts for each cell barcode. The distribution of UMI counts was typically bimodal, and we chose a threshold to remove the smallest peak. The normalized UMI-filtered counts matrices for each sample are provided as processed data files (CSV). For clonal annotation (CROPseq sgRNA or LARRY lentiviral barcodes), filtered fastq files obtained after the first step of the indrop.py script were analyzed with the LARRY.py script (github.com/AllonKleinLab/LARRY) to generate intermediate LARRY.fastq.gz files, and then analyzed with the clonal-annotation.ipynb script (github.com/AllonKleinLab/LARRY) to generate LARRY barcode list files (provided as processed data files).
Libraries indexed as in (Zilionis et al. 2017) were sequenced with Illumina NextSeq500. Bcl2Illumina Bcl2fastq v2.0 and first step of the inDrops.py pipeline (github.com/indrops) was used to generate demultiplexed single fastq files containing single cell barcode, UMI and biological read).
Sequenced cDNA reads were mapped to mm9 using bowtie through the inDrop.py pipeline (github.com/indrops)
Single cell matrix files (tsv) were generated from the inDrop.py pipeline (github.com/indrops)
Single cell expression tables were UMI filtered and normalized using the SPRING-data_prep pipeline (github.com/SPRING_dev)
Lentiviral barcodes and sgRNA sequences were obtained from the inDrops fastq files generated after the first step of inDrops.py by running the LARRY.py script and then matching them to the UMI-filtered gene expression tables using the Clonal_annotation.ipynb script (github.com/AllonKleinLab/LARRY)
Genome_build: mm8 and mm9
Supplementary_files_format_and_content: For all samples, counts.tsv files represent unfiltered (cells X genes) gene expression matrices for each individually processed library, the genes.txt files contain the information of genes used for each sample, the counts_norm.csv file contains the normalized/filtered gene expression matrix, samp_id or samp_id_flat.txt contains the sample information for each filtered cell in the matrix, cell_bcs_flat.txt contains the single cell barcode information for each filtered cell in the matrix, and barcode_list.txt contains the lentiviral barcode or sgRNA sequences for each filtered cell. For samples 2 and 3, the projected_clusters.csv  contains the cluster assignment information for each filtered cell in the matrix after projection of onto the clusters of sample 1. For samples 2 and 3, samp_id_flat_for_clonal_annotation.txt and samp_id2.txt are used for LARRY barcode calling. For Sample6, selected_expr.csv.gz is the normalized filtered counts matrix in csv format for a selected subset of the counts_norm matrix, selected_cell_groupings.csv contains the clusters for selected cells in the selected_expr.csv matrix, selected_original_cell_indices contains the cell indices of the counts_norm matrix, and selected_custom_colors.csv contains the binary information assigning cells as TetO-Tcf15/EGFP (1) or wt (0).

source_name: Mouse bone marrow dissociated cells

growth_protocol: C57BL/6J mice were purchased from Jackson Labs (JAX) Mice or bred in-house, and were housed in specific pathogen-free (SPF) conditions under regular diet. All protocols were supervised by the BCH IACUC.

extract_protocol:
EGFP-positive (TetO-Tcf15) and control (wild-type) Kit+ donor Ly5.2+ cells were extracted from bone marrow and encapsulated using inDrop (Zillionis et al. 2017).
InDrop libraries constructed as in (Zilionis et al. 2017).
Whole bone marrow from large bones (except the cranium) was prepared by crushing in 2% FBS-supplemented PBS. Red blood cells were removed by specific cell lysis (RBC lysis). HSC and Kit cells were enriched by magnetic separation using CD117 (cKit) beads from Miltenyi corporation, and further purified by FACS to isolate the SLAM+ LT-HSCs (HSC libraries) and the rest of cKit cells (KIT libraries). After encapsulation with inDrop, libraries were distributed into equal parts of approximately 2000-3000 cells  each.
Library construction protocol was as in Zilionis et al. Nature Protocols 2017.

treatment_protocol:
Donor LT-HSCs were extracted from M2rtTA/M2rtTA mice and labeled with a pLV-EGFP-TRE-mTcf15 lentivirus. Recipient mice were treated with 1 mg/ml Dox in drinking water for 2 months before cell isolation.
Donor mice were euthanized and the entire LT-HSC compartment was isolated and labeled with a lentivirus for over-night. Recipient mice were lethally irradiated (split dose of 550 cGy) and transplanted with the barcoded LT-HSCs. Recipients were allowed to reconstitute the bone marrow for 4 months, before proceeding to euthanasia.

tag: transplant series


title: SE18P6Cet3

value: HNC patient-derived xenografts (PDXs)


title: CROPseq BM rep B - KIT library 15

description:
inDrop scRNAseq library containing donor CROPseq KIT cells pooled from 5 recipients - replicate B  (library 15)
ARF2019_Sample5_barcode_list.txt
ARF2019_Sample5_cell_bcs_flat.txt
ARF2019_Sample5_counts_norm.csv.gz
ARF2019_Sample5_genes.txt
ARF2019_Sample5_samp_id_flat.txt
Simultaneous inDrop single cell RNA-seq libraries and sgRNA-targeted RNA-seq libraries

extract_protocol:
mNeonGreen-positive HSCs and Kit+ donor Ly5.2+ cells were extracted from bone marrow and encapsulated using inDrop (Zillionis et al. 2017).
After RNA amplification, half of the RNA was used to construct whole transcriptome libraries as in (Zilionis et al. 2017) and the other half of the RNA was used to construct sgRNA targeted libraries as in (Wagner et al. 2018).
Whole bone marrow from large bones (except the cranium) was prepared by crushing in 2% FBS-supplemented PBS. Red blood cells were removed by specific cell lysis (RBC lysis). HSC and Kit cells were enriched by magnetic separation using CD117 (cKit) beads from Miltenyi corporation, and further purified by FACS to isolate the SLAM+ LT-HSCs (HSC libraries) and the rest of cKit cells (KIT libraries). After encapsulation with inDrop, libraries were distributed into equal parts of approximately 2000-3000 cells  each.
Library construction protocol was as in Zilionis et al. Nature Protocols 2017.

treatment_protocol:
Donor LT-HSCs were extracted from Dox-inducible Cas9 mice and labeled with a custom designed CROPseq library, expressing an mNeonGreen reporter. Recipient mice were treated with 1 mg/ml Dox in drinking water for 2 months before cell isolation.
Donor mice were euthanized and the entire LT-HSC compartment was isolated and labeled with a lentivirus for over-night. Recipient mice were lethally irradiated (split dose of 550 cGy) and transplanted with the barcoded LT-HSCs. Recipients were allowed to reconstitute the bone marrow for 4 months, before proceeding to euthanasia.


title: CROPseq BM rep B - KIT library 11

description:
inDrop scRNAseq library containing donor CROPseq KIT cells pooled from 5 recipients - replicate B  (library 11)
ARF2019_Sample5_barcode_list.txt
ARF2019_Sample5_cell_bcs_flat.txt
ARF2019_Sample5_counts_norm.csv.gz
ARF2019_Sample5_genes.txt
ARF2019_Sample5_samp_id_flat.txt
Simultaneous inDrop single cell RNA-seq libraries and sgRNA-targeted RNA-seq libraries


title: CROPseq BM rep B - KIT library 7

description:
inDrop scRNAseq library containing donor CROPseq KIT cells pooled from 5 recipients - replicate B  (library 7)
ARF2019_Sample5_barcode_list.txt
ARF2019_Sample5_cell_bcs_flat.txt
ARF2019_Sample5_counts_norm.csv.gz
ARF2019_Sample5_genes.txt
ARF2019_Sample5_samp_id_flat.txt
Simultaneous inDrop single cell RNA-seq libraries and sgRNA-targeted RNA-seq libraries


title: CROPseq BM rep B - KIT library 14

description:
inDrop scRNAseq library containing donor CROPseq KIT cells pooled from 5 recipients - replicate B  (library 14)
ARF2019_Sample5_barcode_list.txt
ARF2019_Sample5_cell_bcs_flat.txt
ARF2019_Sample5_counts_norm.csv.gz
ARF2019_Sample5_genes.txt
ARF2019_Sample5_samp_id_flat.txt
Simultaneous inDrop single cell RNA-seq libraries and sgRNA-targeted RNA-seq libraries


title: CROPseq BM rep B - KIT library 6

description:
inDrop scRNAseq library containing donor CROPseq KIT cells pooled from 5 recipients - replicate B  (library 6)
ARF2019_Sample5_barcode_list.txt
ARF2019_Sample5_cell_bcs_flat.txt
ARF2019_Sample5_counts_norm.csv.gz
ARF2019_Sample5_genes.txt
ARF2019_Sample5_samp_id_flat.txt
Simultaneous inDrop single cell RNA-seq libraries and sgRNA-targeted RNA-seq libraries


title: CROPseq BM rep B - KIT library 10

description:
inDrop scRNAseq library containing donor CROPseq KIT cells pooled from 5 recipients - replicate B  (library 10)
ARF2019_Sample5_barcode_list.txt
ARF2019_Sample5_cell_bcs_flat.txt
ARF2019_Sample5_counts_norm.csv.gz
ARF2019_Sample5_genes.txt
ARF2019_Sample5_samp_id_flat.txt
Simultaneous inDrop single cell RNA-seq libraries and sgRNA-targeted RNA-seq libraries


title: SE18P6Cet2


title: CROPseq BM rep B - KIT library 8

description:
inDrop scRNAseq library containing donor CROPseq KIT cells pooled from 5 recipients - replicate B  (library 8)
ARF2019_Sample5_barcode_list.txt
ARF2019_Sample5_cell_bcs_flat.txt
ARF2019_Sample5_counts_norm.csv.gz
ARF2019_Sample5_genes.txt
ARF2019_Sample5_samp_id_flat.txt
Simultaneous inDrop single cell RNA-seq libraries and sgRNA-targeted RNA-seq libraries


title: CROPseq BM rep B - KIT library 12

description:
inDrop scRNAseq library containing donor CROPseq KIT cells pooled from 5 recipients - replicate B  (library 12)
ARF2019_Sample5_barcode_list.txt
ARF2019_Sample5_cell_bcs_flat.txt
ARF2019_Sample5_counts_norm.csv.gz
ARF2019_Sample5_genes.txt
ARF2019_Sample5_samp_id_flat.txt
Simultaneous inDrop single cell RNA-seq libraries and sgRNA-targeted RNA-seq libraries


title: CROPseq BM rep B - KIT library 13

description:
inDrop scRNAseq library containing donor CROPseq KIT cells pooled from 5 recipients - replicate B  (library 13)
ARF2019_Sample5_barcode_list.txt
ARF2019_Sample5_cell_bcs_flat.txt
ARF2019_Sample5_counts_norm.csv.gz
ARF2019_Sample5_genes.txt
ARF2019_Sample5_samp_id_flat.txt
Simultaneous inDrop single cell RNA-seq libraries and sgRNA-targeted RNA-seq libraries


title: CROPseq BM rep B - KIT library 2

description:
inDrop scRNAseq library containing donor CROPseq KIT cells pooled from 5 recipients - replicate B  (library 2)
ARF2019_Sample5_barcode_list.txt
ARF2019_Sample5_cell_bcs_flat.txt
ARF2019_Sample5_counts_norm.csv.gz
ARF2019_Sample5_genes.txt
ARF2019_Sample5_samp_id_flat.txt
Simultaneous inDrop single cell RNA-seq libraries and sgRNA-targeted RNA-seq libraries


title: CROPseq BM rep B - HSC library 8

description:
inDrop scRNAseq library containing donor CROPseq HSCs pooled from 5 recipients - replicate B  (library 8)
ARF2019_Sample5_barcode_list.txt
ARF2019_Sample5_cell_bcs_flat.txt
ARF2019_Sample5_counts_norm.csv.gz
ARF2019_Sample5_genes.txt
ARF2019_Sample5_samp_id_flat.txt
Simultaneous inDrop single cell RNA-seq libraries and sgRNA-targeted RNA-seq libraries


title: CROPseq BM rep B - KIT library 1

description:
inDrop scRNAseq library containing donor CROPseq KIT cells pooled from 5 recipients - replicate B  (library 1)
ARF2019_Sample5_barcode_list.txt
ARF2019_Sample5_cell_bcs_flat.txt
ARF2019_Sample5_counts_norm.csv.gz
ARF2019_Sample5_genes.txt
ARF2019_Sample5_samp_id_flat.txt
Simultaneous inDrop single cell RNA-seq libraries and sgRNA-targeted RNA-seq libraries


title: CROPseq BM rep B - KIT library 3

description:
inDrop scRNAseq library containing donor CROPseq KIT cells pooled from 5 recipients - replicate B  (library 3)
ARF2019_Sample5_barcode_list.txt
ARF2019_Sample5_cell_bcs_flat.txt
ARF2019_Sample5_counts_norm.csv.gz
ARF2019_Sample5_genes.txt
ARF2019_Sample5_samp_id_flat.txt
Simultaneous inDrop single cell RNA-seq libraries and sgRNA-targeted RNA-seq libraries


title: CROPseq BM rep B - HSC library 7

description:
inDrop scRNAseq library containing donor CROPseq HSCs pooled from 5 recipients - replicate B  (library 7)
ARF2019_Sample5_barcode_list.txt
ARF2019_Sample5_cell_bcs_flat.txt
ARF2019_Sample5_counts_norm.csv.gz
ARF2019_Sample5_genes.txt
ARF2019_Sample5_samp_id_flat.txt
Simultaneous inDrop single cell RNA-seq libraries and sgRNA-targeted RNA-seq libraries


title: CROPseq BM rep B - HSC library 3

description:
inDrop scRNAseq library containing donor CROPseq HSCs pooled from 5 recipients - replicate B  (library 3)
ARF2019_Sample5_barcode_list.txt
ARF2019_Sample5_cell_bcs_flat.txt
ARF2019_Sample5_counts_norm.csv.gz
ARF2019_Sample5_genes.txt
ARF2019_Sample5_samp_id_flat.txt
Simultaneous inDrop single cell RNA-seq libraries and sgRNA-targeted RNA-seq libraries


title: CROPseq BM rep B - HSC library 5

description:
inDrop scRNAseq library containing donor CROPseq HSCs pooled from 5 recipients - replicate B  (library 5)
ARF2019_Sample5_barcode_list.txt
ARF2019_Sample5_cell_bcs_flat.txt
ARF2019_Sample5_counts_norm.csv.gz
ARF2019_Sample5_genes.txt
ARF2019_Sample5_samp_id_flat.txt
Simultaneous inDrop single cell RNA-seq libraries and sgRNA-targeted RNA-seq libraries


title: CROPseq BM rep B - KIT library 5

description:
inDrop scRNAseq library containing donor CROPseq KIT cells pooled from 5 recipients - replicate B  (library 5)
ARF2019_Sample5_barcode_list.txt
ARF2019_Sample5_cell_bcs_flat.txt
ARF2019_Sample5_counts_norm.csv.gz
ARF2019_Sample5_genes.txt
ARF2019_Sample5_samp_id_flat.txt
Simultaneous inDrop single cell RNA-seq libraries and sgRNA-targeted RNA-seq libraries


title: CROPseq BM rep B - HSC library 1

description:
inDrop scRNAseq library containing donor CROPseq HSCs pooled from 5 recipients - replicate B  (library 1)
ARF2019_Sample5_barcode_list.txt
ARF2019_Sample5_cell_bcs_flat.txt
ARF2019_Sample5_counts_norm.csv.gz
ARF2019_Sample5_genes.txt
ARF2019_Sample5_samp_id_flat.txt
Simultaneous inDrop single cell RNA-seq libraries and sgRNA-targeted RNA-seq libraries


title: CROPseq BM rep B - HSC library 4

description:
inDrop scRNAseq library containing donor CROPseq HSCs pooled from 5 recipients - replicate B  (library 4)
ARF2019_Sample5_barcode_list.txt
ARF2019_Sample5_cell_bcs_flat.txt
ARF2019_Sample5_counts_norm.csv.gz
ARF2019_Sample5_genes.txt
ARF2019_Sample5_samp_id_flat.txt
Simultaneous inDrop single cell RNA-seq libraries and sgRNA-targeted RNA-seq libraries


title: CROPseq BM rep B - KIT library 9

description:
inDrop scRNAseq library containing donor CROPseq KIT cells pooled from 5 recipients - replicate B  (library 9)
ARF2019_Sample5_barcode_list.txt
ARF2019_Sample5_cell_bcs_flat.txt
ARF2019_Sample5_counts_norm.csv.gz
ARF2019_Sample5_genes.txt
ARF2019_Sample5_samp_id_flat.txt
Simultaneous inDrop single cell RNA-seq libraries and sgRNA-targeted RNA-seq libraries


title: TAP_CT, total bone marrow, sample 2

description: TAP-seq was performed for cells from bone marrow, using a target gene panel designed to distinguish cell types and differentiation stages


title: CROPseq BM rep B - KIT library 4

description:
inDrop scRNAseq library containing donor CROPseq KIT cells pooled from 5 recipients - replicate B  (library 4)
ARF2019_Sample5_barcode_list.txt
ARF2019_Sample5_cell_bcs_flat.txt
ARF2019_Sample5_counts_norm.csv.gz
ARF2019_Sample5_genes.txt
ARF2019_Sample5_samp_id_flat.txt
Simultaneous inDrop single cell RNA-seq libraries and sgRNA-targeted RNA-seq libraries


title: CROPseq BM rep A - KIT library 14

description:
inDrop scRNAseq library containing donor CROPseq KIT cells pooled from 5 recipients - replicate A  (library 14)
ARF2019_Sample5_barcode_list.txt
ARF2019_Sample5_cell_bcs_flat.txt
ARF2019_Sample5_counts_norm.csv.gz
ARF2019_Sample5_genes.txt
ARF2019_Sample5_samp_id_flat.txt
Simultaneous inDrop single cell RNA-seq libraries and sgRNA-targeted RNA-seq libraries


title: CROPseq BM rep A - KIT library 13

description:
inDrop scRNAseq library containing donor CROPseq KIT cells pooled from 5 recipients - replicate A  (library 13)
ARF2019_Sample5_barcode_list.txt
ARF2019_Sample5_cell_bcs_flat.txt
ARF2019_Sample5_counts_norm.csv.gz
ARF2019_Sample5_genes.txt
ARF2019_Sample5_samp_id_flat.txt
Simultaneous inDrop single cell RNA-seq libraries and sgRNA-targeted RNA-seq libraries


title: CROPseq BM rep B - HSC library 6

description:
inDrop scRNAseq library containing donor CROPseq HSCs pooled from 5 recipients - replicate B  (library 6)
ARF2019_Sample5_barcode_list.txt
ARF2019_Sample5_cell_bcs_flat.txt
ARF2019_Sample5_counts_norm.csv.gz
ARF2019_Sample5_genes.txt
ARF2019_Sample5_samp_id_flat.txt
Simultaneous inDrop single cell RNA-seq libraries and sgRNA-targeted RNA-seq libraries


title: CROPseq BM rep A - KIT library 11

description:
inDrop scRNAseq library containing donor CROPseq KIT cells pooled from 5 recipients - replicate A  (library 11)
ARF2019_Sample5_barcode_list.txt
ARF2019_Sample5_cell_bcs_flat.txt
ARF2019_Sample5_counts_norm.csv.gz
ARF2019_Sample5_genes.txt
ARF2019_Sample5_samp_id_flat.txt
Simultaneous inDrop single cell RNA-seq libraries and sgRNA-targeted RNA-seq libraries


title: CROPseq BM rep A - KIT library 9

description:
inDrop scRNAseq library containing donor CROPseq KIT cells pooled from 5 recipients - replicate A  (library 9)
ARF2019_Sample5_barcode_list.txt
ARF2019_Sample5_cell_bcs_flat.txt
ARF2019_Sample5_counts_norm.csv.gz
ARF2019_Sample5_genes.txt
ARF2019_Sample5_samp_id_flat.txt
Simultaneous inDrop single cell RNA-seq libraries and sgRNA-targeted RNA-seq libraries


title: CROPseq BM rep A - KIT library 8

description:
inDrop scRNAseq library containing donor CROPseq KIT cells pooled from 5 recipients - replicate A  (library 8)
ARF2019_Sample5_barcode_list.txt
ARF2019_Sample5_cell_bcs_flat.txt
ARF2019_Sample5_counts_norm.csv.gz
ARF2019_Sample5_genes.txt
ARF2019_Sample5_samp_id_flat.txt
Simultaneous inDrop single cell RNA-seq libraries and sgRNA-targeted RNA-seq libraries


title: CROPseq BM rep A - KIT library 10

description:
inDrop scRNAseq library containing donor CROPseq KIT cells pooled from 5 recipients - replicate A  (library 10)
ARF2019_Sample5_barcode_list.txt
ARF2019_Sample5_cell_bcs_flat.txt
ARF2019_Sample5_counts_norm.csv.gz
ARF2019_Sample5_genes.txt
ARF2019_Sample5_samp_id_flat.txt
Simultaneous inDrop single cell RNA-seq libraries and sgRNA-targeted RNA-seq libraries


title: CROPseq BM rep B - HSC library 2

description:
inDrop scRNAseq library containing donor CROPseq HSCs pooled from 5 recipients - replicate B  (library 2)
ARF2019_Sample5_barcode_list.txt
ARF2019_Sample5_cell_bcs_flat.txt
ARF2019_Sample5_counts_norm.csv.gz
ARF2019_Sample5_genes.txt
ARF2019_Sample5_samp_id_flat.txt
Simultaneous inDrop single cell RNA-seq libraries and sgRNA-targeted RNA-seq libraries


title: CROPseq BM rep A - KIT library 12

description:
inDrop scRNAseq library containing donor CROPseq KIT cells pooled from 5 recipients - replicate A  (library 12)
ARF2019_Sample5_barcode_list.txt
ARF2019_Sample5_cell_bcs_flat.txt
ARF2019_Sample5_counts_norm.csv.gz
ARF2019_Sample5_genes.txt
ARF2019_Sample5_samp_id_flat.txt
Simultaneous inDrop single cell RNA-seq libraries and sgRNA-targeted RNA-seq libraries


title: CROPseq BM rep A - KIT library 5

description:
inDrop scRNAseq library containing donor CROPseq KIT cells pooled from 5 recipients - replicate A  (library 5)
ARF2019_Sample5_barcode_list.txt
ARF2019_Sample5_cell_bcs_flat.txt
ARF2019_Sample5_counts_norm.csv.gz
ARF2019_Sample5_genes.txt
ARF2019_Sample5_samp_id_flat.txt
Simultaneous inDrop single cell RNA-seq libraries and sgRNA-targeted RNA-seq libraries


title: CROPseq BM rep A - KIT library 7

description:
inDrop scRNAseq library containing donor CROPseq KIT cells pooled from 5 recipients - replicate A  (library 7)
ARF2019_Sample5_barcode_list.txt
ARF2019_Sample5_cell_bcs_flat.txt
ARF2019_Sample5_counts_norm.csv.gz
ARF2019_Sample5_genes.txt
ARF2019_Sample5_samp_id_flat.txt
Simultaneous inDrop single cell RNA-seq libraries and sgRNA-targeted RNA-seq libraries


title: CROPseq BM rep A - KIT library 2

description:
inDrop scRNAseq library containing donor CROPseq KIT cells pooled from 5 recipients - replicate A  (library 2)
ARF2019_Sample5_barcode_list.txt
ARF2019_Sample5_cell_bcs_flat.txt
ARF2019_Sample5_counts_norm.csv.gz
ARF2019_Sample5_genes.txt
ARF2019_Sample5_samp_id_flat.txt
Simultaneous inDrop single cell RNA-seq libraries and sgRNA-targeted RNA-seq libraries


title: CROPseq BM rep A - KIT library 4

description:
inDrop scRNAseq library containing donor CROPseq KIT cells pooled from 5 recipients - replicate A  (library 4)
ARF2019_Sample5_barcode_list.txt
ARF2019_Sample5_cell_bcs_flat.txt
ARF2019_Sample5_counts_norm.csv.gz
ARF2019_Sample5_genes.txt
ARF2019_Sample5_samp_id_flat.txt
Simultaneous inDrop single cell RNA-seq libraries and sgRNA-targeted RNA-seq libraries


title: CROPseq BM rep A - KIT library 3

description:
inDrop scRNAseq library containing donor CROPseq KIT cells pooled from 5 recipients - replicate A  (library 3)
ARF2019_Sample5_barcode_list.txt
ARF2019_Sample5_cell_bcs_flat.txt
ARF2019_Sample5_counts_norm.csv.gz
ARF2019_Sample5_genes.txt
ARF2019_Sample5_samp_id_flat.txt
Simultaneous inDrop single cell RNA-seq libraries and sgRNA-targeted RNA-seq libraries


title: CROPseq BM rep A - KIT library 6

description:
inDrop scRNAseq library containing donor CROPseq KIT cells pooled from 5 recipients - replicate A  (library 6)
ARF2019_Sample5_barcode_list.txt
ARF2019_Sample5_cell_bcs_flat.txt
ARF2019_Sample5_counts_norm.csv.gz
ARF2019_Sample5_genes.txt
ARF2019_Sample5_samp_id_flat.txt
Simultaneous inDrop single cell RNA-seq libraries and sgRNA-targeted RNA-seq libraries


title: CROPseq BM rep A - KIT library 1

description:
inDrop scRNAseq library containing donor CROPseq KIT cells pooled from 5 replicate - replicate A  (library 1)
ARF2019_Sample5_barcode_list.txt
ARF2019_Sample5_cell_bcs_flat.txt
ARF2019_Sample5_counts_norm.csv.gz
ARF2019_Sample5_genes.txt
ARF2019_Sample5_samp_id_flat.txt
Simultaneous inDrop single cell RNA-seq libraries and sgRNA-targeted RNA-seq libraries


title: CROPseq BM rep A - HSC library 4

description:
inDrop scRNAseq library containing donor CROPseq HSCs pooled from 5 recipients - replicate A  (library 4)
ARF2019_Sample5_barcode_list.txt
ARF2019_Sample5_cell_bcs_flat.txt
ARF2019_Sample5_counts_norm.csv.gz
ARF2019_Sample5_genes.txt
ARF2019_Sample5_samp_id_flat.txt
Simultaneous inDrop single cell RNA-seq libraries and sgRNA-targeted RNA-seq libraries


title: CROPseq BM rep A - HSC library 3

description:
inDrop scRNAseq library containing donor CROPseq HSCs pooled from 5 recipients - replicate A  (library 3)
ARF2019_Sample5_barcode_list.txt
ARF2019_Sample5_cell_bcs_flat.txt
ARF2019_Sample5_counts_norm.csv.gz
ARF2019_Sample5_genes.txt
ARF2019_Sample5_samp_id_flat.txt
Simultaneous inDrop single cell RNA-seq libraries and sgRNA-targeted RNA-seq libraries


title: CROPseq BM rep A - HSC library 7

description:
inDrop scRNAseq library containing donor CROPseq HSCs pooled from 5 recipients - replicate A  (library 7)
ARF2019_Sample5_barcode_list.txt
ARF2019_Sample5_cell_bcs_flat.txt
ARF2019_Sample5_counts_norm.csv.gz
ARF2019_Sample5_genes.txt
ARF2019_Sample5_samp_id_flat.txt
Simultaneous inDrop single cell RNA-seq libraries and sgRNA-targeted RNA-seq libraries


title: CROPseq BM rep A - HSC library 2

description:
inDrop scRNAseq library containing donor CROPseq HSCs pooled from 5 recipients - replicate A  (library 2)
ARF2019_Sample5_barcode_list.txt
ARF2019_Sample5_cell_bcs_flat.txt
ARF2019_Sample5_counts_norm.csv.gz
ARF2019_Sample5_genes.txt
ARF2019_Sample5_samp_id_flat.txt
Simultaneous inDrop single cell RNA-seq libraries and sgRNA-targeted RNA-seq libraries


title: CROPseq BM rep A - HSC library 8

description:
inDrop scRNAseq library containing donor CROPseq HSCs pooled from 5 recipients - replicate A  (library 8)
ARF2019_Sample5_barcode_list.txt
ARF2019_Sample5_cell_bcs_flat.txt
ARF2019_Sample5_counts_norm.csv.gz
ARF2019_Sample5_genes.txt
ARF2019_Sample5_samp_id_flat.txt
Simultaneous inDrop single cell RNA-seq libraries and sgRNA-targeted RNA-seq libraries


title: CROPseq BM rep A - HSC library 6

description:
inDrop scRNAseq library containing donor CROPseq HSCs pooled from 5 recipients - replicate A  (library 6)
ARF2019_Sample5_barcode_list.txt
ARF2019_Sample5_cell_bcs_flat.txt
ARF2019_Sample5_counts_norm.csv.gz
ARF2019_Sample5_genes.txt
ARF2019_Sample5_samp_id_flat.txt
Simultaneous inDrop single cell RNA-seq libraries and sgRNA-targeted RNA-seq libraries


title: CROPseq BM rep A - HSC library 5

description:
inDrop scRNAseq library containing donor CROPseq HSCs pooled from 5 recipients - replicate A  (library 5)
ARF2019_Sample5_barcode_list.txt
ARF2019_Sample5_cell_bcs_flat.txt
ARF2019_Sample5_counts_norm.csv.gz
ARF2019_Sample5_genes.txt
ARF2019_Sample5_samp_id_flat.txt
Simultaneous inDrop single cell RNA-seq libraries and sgRNA-targeted RNA-seq libraries


title: Recipient 7 - KIT library 3

description:
inDrop scRNAseq library containing a sample of remaining donor KIT cells from mouse recipient 7 (library 3)
ARF2019_Sample4_barcode_list.txt
ARF2019_Sample4_cell_bcs_flat.txt
ARF2019_Sample4_counts_norm.csv.gz
ARF2019_Sample4_genes.txt
ARF2019_Sample4_samp_id_flat.txt
Simultaneous inDrop single cell RNA-seq libraries and barcode-targeted RNA-seq libraries

extract_protocol:
EGFP-labeled SLAM HSCs and a sample of the remaining of Kit+ cells were extracted from bone marrow, 16 weeks after transplantation, and encapsulated using inDrop (Zillionis et al. 2017).
After RNA amplification, half of the RNA was used to construct whole transcriptome libraries as in (Zilionis et al. 2017) and the other half of the RNA was used to construct barcode targeted libraries as in (Wagner et al. 2018).
Whole bone marrow from large bones (except the cranium) was prepared by crushing in 2% FBS-supplemented PBS. Red blood cells were removed by specific cell lysis (RBC lysis). HSC and Kit cells were enriched by magnetic separation using CD117 (cKit) beads from Miltenyi corporation, and further purified by FACS to isolate the SLAM+ LT-HSCs (HSC libraries) and the rest of cKit cells (KIT libraries). After encapsulation with inDrop, libraries were distributed into equal parts of approximately 2000-3000 cells  each.
Library construction protocol was as in Zilionis et al. Nature Protocols 2017.

treatment_protocol:
Donor LT-HSCs were labeled with the LARRY single-cell expressible barcoding lentiviral library
Donor mice were euthanized and the entire LT-HSC compartment was isolated and labeled with a lentivirus for over-night. Recipient mice were lethally irradiated (split dose of 550 cGy) and transplanted with the barcoded LT-HSCs. Recipients were allowed to reconstitute the bone marrow for 4 months, before proceeding to euthanasia.


title: CROPseq BM rep A - HSC library 9

description:
inDrop scRNAseq library containing donor CROPseq HSCs pooled from 5 recipients - replicate A  (library 9)
ARF2019_Sample5_barcode_list.txt
ARF2019_Sample5_cell_bcs_flat.txt
ARF2019_Sample5_counts_norm.csv.gz
ARF2019_Sample5_genes.txt
ARF2019_Sample5_samp_id_flat.txt
Simultaneous inDrop single cell RNA-seq libraries and sgRNA-targeted RNA-seq libraries


title: Recipient 7 - KIT library 2

description:
inDrop scRNAseq library containing a sample of remaining donor KIT cells from mouse recipient 7 (library 2)
ARF2019_Sample4_barcode_list.txt
ARF2019_Sample4_cell_bcs_flat.txt
ARF2019_Sample4_counts_norm.csv.gz
ARF2019_Sample4_genes.txt
ARF2019_Sample4_samp_id_flat.txt
Simultaneous inDrop single cell RNA-seq libraries and barcode-targeted RNA-seq libraries


title: CROPseq BM rep A - HSC library 1

description:
inDrop scRNAseq library containing donor CROPseq HSCs pooled from 5 recipients - replicate A  (library 1)
ARF2019_Sample5_barcode_list.txt
ARF2019_Sample5_cell_bcs_flat.txt
ARF2019_Sample5_counts_norm.csv.gz
ARF2019_Sample5_genes.txt
ARF2019_Sample5_samp_id_flat.txt
Simultaneous inDrop single cell RNA-seq libraries and sgRNA-targeted RNA-seq libraries


title: Recipient 7 - KIT library 1

description:
inDrop scRNAseq library containing a sample of remaining donor KIT cells from mouse recipient 7 (library 1)
ARF2019_Sample4_barcode_list.txt
ARF2019_Sample4_cell_bcs_flat.txt
ARF2019_Sample4_counts_norm.csv.gz
ARF2019_Sample4_genes.txt
ARF2019_Sample4_samp_id_flat.txt
Simultaneous inDrop single cell RNA-seq libraries and barcode-targeted RNA-seq libraries


title: Recipient 7 - HSC library 2

description:
inDrop scRNAseq library containing donor HSCs from mouse recipient 7 (library 2)
ARF2019_Sample4_barcode_list.txt
ARF2019_Sample4_cell_bcs_flat.txt
ARF2019_Sample4_counts_norm.csv.gz
ARF2019_Sample4_genes.txt
ARF2019_Sample4_samp_id_flat.txt
Simultaneous inDrop single cell RNA-seq libraries and barcode-targeted RNA-seq libraries


title: Recipient 7 - HSC library 1

description:
inDrop scRNAseq library containing donor HSCs from mouse recipient 7 (library 1)
ARF2019_Sample4_barcode_list.txt
ARF2019_Sample4_cell_bcs_flat.txt
ARF2019_Sample4_counts_norm.csv.gz
ARF2019_Sample4_genes.txt
ARF2019_Sample4_samp_id_flat.txt
Simultaneous inDrop single cell RNA-seq libraries and barcode-targeted RNA-seq libraries


title: Recipient 6 - KIT library 1

description:
inDrop scRNAseq library containing a sample of remaining donor KIT cells from mouse recipient 6 (library 1)
ARF2019_Sample4_barcode_list.txt
ARF2019_Sample4_cell_bcs_flat.txt
ARF2019_Sample4_counts_norm.csv.gz
ARF2019_Sample4_genes.txt
ARF2019_Sample4_samp_id_flat.txt
Simultaneous inDrop single cell RNA-seq libraries and barcode-targeted RNA-seq libraries


title: Recipient 6 - KIT library 2

description:
inDrop scRNAseq library containing a sample of remaining donor KIT cells from mouse recipient 6 (library 2)
ARF2019_Sample4_barcode_list.txt
ARF2019_Sample4_cell_bcs_flat.txt
ARF2019_Sample4_counts_norm.csv.gz
ARF2019_Sample4_genes.txt
ARF2019_Sample4_samp_id_flat.txt
Simultaneous inDrop single cell RNA-seq libraries and barcode-targeted RNA-seq libraries


title: Recipient 5 - KIT library 5

description:
inDrop scRNAseq library containing a sample of remaining donor KIT cells from mouse recipient 5 (library 5)
ARF2019_Sample3_barcode_list.txt
ARF2019_Sample3_cell_bcs_flat.txt
ARF2019_Sample3_counts_norm.csv.gz
ARF2019_Sample3_genes.txt
ARF2019_Sample3_projected_to_referenceclusters.csv
ARF2019_Sample3_samp_id_flat.txt
ARF2019_Sample3_samp_id_flat2.txt
Simultaneous inDrop single cell RNA-seq libraries and barcode-targeted RNA-seq libraries


title: Recipient 6 - HSC library 2

description:
inDrop scRNAseq library containing donor HSCs from mouse recipient 6 (library 2)
ARF2019_Sample4_barcode_list.txt
ARF2019_Sample4_cell_bcs_flat.txt
ARF2019_Sample4_counts_norm.csv.gz
ARF2019_Sample4_genes.txt
ARF2019_Sample4_samp_id_flat.txt
Simultaneous inDrop single cell RNA-seq libraries and barcode-targeted RNA-seq libraries


title: Recipient 5 - HSC library 3

description:
inDrop scRNAseq library containing donor HSCs from mouse recipient 5 (library 3)
ARF2019_Sample3_barcode_list.txt
ARF2019_Sample3_cell_bcs_flat.txt
ARF2019_Sample3_counts_norm.csv.gz
ARF2019_Sample3_genes.txt
ARF2019_Sample3_projected_to_referenceclusters.csv
ARF2019_Sample3_samp_id_flat.txt
ARF2019_Sample3_samp_id_flat2.txt
Simultaneous inDrop single cell RNA-seq libraries and barcode-targeted RNA-seq libraries


title: Recipient 5 - HSC library 2

description:
inDrop scRNAseq library containing donor HSCs from mouse recipient 5 (library 2)
ARF2019_Sample3_barcode_list.txt
ARF2019_Sample3_cell_bcs_flat.txt
ARF2019_Sample3_counts_norm.csv.gz
ARF2019_Sample3_genes.txt
ARF2019_Sample3_projected_to_referenceclusters.csv
ARF2019_Sample3_samp_id_flat.txt
ARF2019_Sample3_samp_id_flat2.txt
Simultaneous inDrop single cell RNA-seq libraries and barcode-targeted RNA-seq libraries


title: Recipient 4 - KIT library 4

description:
inDrop scRNAseq library containing a sample of remaining donor KIT cells from mouse recipient 4 (library 4)
ARF2019_Sample2_barcode_list.txt
ARF2019_Sample2_cell_bcs_flat.txt
ARF2019_Sample2_counts_norm.csv.gz
ARF2019_Sample2_genes.txt
ARF2019_Sample2_projected_clusters.csv
ARF2019_Sample2_samp_id_flat_for_clonal_annotation.txt
ARF2019_Sample2_samp_id_flat.txt
Simultaneous inDrop single cell RNA-seq libraries and barcode-targeted RNA-seq libraries


title: Recipient 5 - KIT library 3

description:
inDrop scRNAseq library containing a sample of remaining donor KIT cells from mouse recipient 5 (library 3)
ARF2019_Sample3_barcode_list.txt
ARF2019_Sample3_cell_bcs_flat.txt
ARF2019_Sample3_counts_norm.csv.gz
ARF2019_Sample3_genes.txt
ARF2019_Sample3_projected_to_referenceclusters.csv
ARF2019_Sample3_samp_id_flat.txt
ARF2019_Sample3_samp_id_flat2.txt
Simultaneous inDrop single cell RNA-seq libraries and barcode-targeted RNA-seq libraries


title: Recipient 5 - KIT library 2

description:
inDrop scRNAseq library containing a sample of remaining donor KIT cells from mouse recipient 5 (library 2)
ARF2019_Sample3_barcode_list.txt
ARF2019_Sample3_cell_bcs_flat.txt
ARF2019_Sample3_counts_norm.csv.gz
ARF2019_Sample3_genes.txt
ARF2019_Sample3_projected_to_referenceclusters.csv
ARF2019_Sample3_samp_id_flat.txt
ARF2019_Sample3_samp_id_flat2.txt
Simultaneous inDrop single cell RNA-seq libraries and barcode-targeted RNA-seq libraries


title: Recipient 5 - HSC library 1

description:
inDrop scRNAseq library containing donor HSCs from mouse recipient 5 (library 1)
ARF2019_Sample3_barcode_list.txt
ARF2019_Sample3_cell_bcs_flat.txt
ARF2019_Sample3_counts_norm.csv.gz
ARF2019_Sample3_genes.txt
ARF2019_Sample3_projected_to_referenceclusters.csv
ARF2019_Sample3_samp_id_flat.txt
ARF2019_Sample3_samp_id_flat2.txt
Simultaneous inDrop single cell RNA-seq libraries and barcode-targeted RNA-seq libraries


title: Recipient 5 - KIT library 1

description:
inDrop scRNAseq library containing a sample of remaining donor KIT cells from mouse recipient 5 (library 1)
ARF2019_Sample3_barcode_list.txt
ARF2019_Sample3_cell_bcs_flat.txt
ARF2019_Sample3_counts_norm.csv.gz
ARF2019_Sample3_genes.txt
ARF2019_Sample3_projected_to_referenceclusters.csv
ARF2019_Sample3_samp_id_flat.txt
ARF2019_Sample3_samp_id_flat2.txt
Simultaneous inDrop single cell RNA-seq libraries and barcode-targeted RNA-seq libraries


title: Recipient 4 - KIT library 2

description:
inDrop scRNAseq library containing a sample of remaining donor KIT cells from mouse recipient 4 (library 2)
ARF2019_Sample2_barcode_list.txt
ARF2019_Sample2_cell_bcs_flat.txt
ARF2019_Sample2_counts_norm.csv.gz
ARF2019_Sample2_genes.txt
ARF2019_Sample2_projected_clusters.csv
ARF2019_Sample2_samp_id_flat_for_clonal_annotation.txt
ARF2019_Sample2_samp_id_flat.txt
Simultaneous inDrop single cell RNA-seq libraries and barcode-targeted RNA-seq libraries


title: CROPseq BM rep A - KIT library 15

description:
inDrop scRNAseq library containing donor CROPseq KIT cells pooled from 5 recipients - replicate A  (library 15)
ARF2019_Sample5_barcode_list.txt
ARF2019_Sample5_cell_bcs_flat.txt
ARF2019_Sample5_counts_norm.csv.gz
ARF2019_Sample5_genes.txt
ARF2019_Sample5_samp_id_flat.txt
Simultaneous inDrop single cell RNA-seq libraries and sgRNA-targeted RNA-seq libraries


title: Recipient 4 - HSC library 4

description:
inDrop scRNAseq library containing donor HSCs from mouse recipient 4 (library 4)
ARF2019_Sample2_barcode_list.txt
ARF2019_Sample2_cell_bcs_flat.txt
ARF2019_Sample2_counts_norm.csv.gz
ARF2019_Sample2_genes.txt
ARF2019_Sample2_projected_clusters.csv
ARF2019_Sample2_samp_id_flat_for_clonal_annotation.txt
ARF2019_Sample2_samp_id_flat.txt
Simultaneous inDrop single cell RNA-seq libraries and barcode-targeted RNA-seq libraries


title: Recipient 5 - KIT library 4

description:
inDrop scRNAseq library containing a sample of remaining donor KIT cells from mouse recipient 5 (library 4)
ARF2019_Sample3_barcode_list.txt
ARF2019_Sample3_cell_bcs_flat.txt
ARF2019_Sample3_counts_norm.csv.gz
ARF2019_Sample3_genes.txt
ARF2019_Sample3_projected_to_referenceclusters.csv
ARF2019_Sample3_samp_id_flat.txt
ARF2019_Sample3_samp_id_flat2.txt
Simultaneous inDrop single cell RNA-seq libraries and barcode-targeted RNA-seq libraries


title: Recipient 4 - KIT library 1

description:
inDrop scRNAseq library containing a sample of remaining donor KIT cells from mouse recipient 4 (library 1)
ARF2019_Sample2_barcode_list.txt
ARF2019_Sample2_cell_bcs_flat.txt
ARF2019_Sample2_counts_norm.csv.gz
ARF2019_Sample2_genes.txt
ARF2019_Sample2_projected_clusters.csv
ARF2019_Sample2_samp_id_flat_for_clonal_annotation.txt
ARF2019_Sample2_samp_id_flat.txt
Simultaneous inDrop single cell RNA-seq libraries and barcode-targeted RNA-seq libraries


title: Recipient 4 - HSC library 3

description:
inDrop scRNAseq library containing donor HSCs from mouse recipient 4 (library 3)
ARF2019_Sample2_barcode_list.txt
ARF2019_Sample2_cell_bcs_flat.txt
ARF2019_Sample2_counts_norm.csv.gz
ARF2019_Sample2_genes.txt
ARF2019_Sample2_projected_clusters.csv
ARF2019_Sample2_samp_id_flat_for_clonal_annotation.txt
ARF2019_Sample2_samp_id_flat.txt
Simultaneous inDrop single cell RNA-seq libraries and barcode-targeted RNA-seq libraries


title: Recipient 3 - KIT library 4

description:
inDrop scRNAseq library containing a sample of remaining donor KIT cells from mouse recipient 3 (library 4)
ARF2019_Sample2_barcode_list.txt
ARF2019_Sample2_cell_bcs_flat.txt
ARF2019_Sample2_counts_norm.csv.gz
ARF2019_Sample2_genes.txt
ARF2019_Sample2_projected_clusters.csv
ARF2019_Sample2_samp_id_flat_for_clonal_annotation.txt
ARF2019_Sample2_samp_id_flat.txt
Simultaneous inDrop single cell RNA-seq libraries and barcode-targeted RNA-seq libraries


title: Recipient 4 - HSC library 2

description:
inDrop scRNAseq library containing donor HSCs from mouse recipient 4 (library 2)
ARF2019_Sample2_barcode_list.txt
ARF2019_Sample2_cell_bcs_flat.txt
ARF2019_Sample2_counts_norm.csv.gz
ARF2019_Sample2_genes.txt
ARF2019_Sample2_projected_clusters.csv
ARF2019_Sample2_samp_id_flat_for_clonal_annotation.txt
ARF2019_Sample2_samp_id_flat.txt
Simultaneous inDrop single cell RNA-seq libraries and barcode-targeted RNA-seq libraries


title: Recipient 6 - KIT library 3

description:
inDrop scRNAseq library containing a sample of remaining donor KIT cells from mouse recipient 6 (library 3)
ARF2019_Sample4_barcode_list.txt
ARF2019_Sample4_cell_bcs_flat.txt
ARF2019_Sample4_counts_norm.csv.gz
ARF2019_Sample4_genes.txt
ARF2019_Sample4_samp_id_flat.txt
Simultaneous inDrop single cell RNA-seq libraries and barcode-targeted RNA-seq libraries


title: Recipient 3 - KIT library 1

description:
inDrop scRNAseq library containing a sample of remaining donor KIT cells from mouse recipient 3 (library 1)
ARF2019_Sample2_barcode_list.txt
ARF2019_Sample2_cell_bcs_flat.txt
ARF2019_Sample2_counts_norm.csv.gz
ARF2019_Sample2_genes.txt
ARF2019_Sample2_projected_clusters.csv
ARF2019_Sample2_samp_id_flat_for_clonal_annotation.txt
ARF2019_Sample2_samp_id_flat.txt
Simultaneous inDrop single cell RNA-seq libraries and barcode-targeted RNA-seq libraries


title: Recipient 3 - KIT library 3

description:
inDrop scRNAseq library containing a sample of remaining donor KIT cells from mouse recipient 3 (library 3)
ARF2019_Sample2_barcode_list.txt
ARF2019_Sample2_cell_bcs_flat.txt
ARF2019_Sample2_counts_norm.csv.gz
ARF2019_Sample2_genes.txt
ARF2019_Sample2_projected_clusters.csv
ARF2019_Sample2_samp_id_flat_for_clonal_annotation.txt
ARF2019_Sample2_samp_id_flat.txt
Simultaneous inDrop single cell RNA-seq libraries and barcode-targeted RNA-seq libraries


title: Recipient 3 - KIT library 2

description:
inDrop scRNAseq library containing a sample of remaining donor KIT cells from mouse recipient 3 (library 2)
ARF2019_Sample2_barcode_list.txt
ARF2019_Sample2_cell_bcs_flat.txt
ARF2019_Sample2_counts_norm.csv.gz
ARF2019_Sample2_genes.txt
ARF2019_Sample2_projected_clusters.csv
ARF2019_Sample2_samp_id_flat_for_clonal_annotation.txt
ARF2019_Sample2_samp_id_flat.txt
Simultaneous inDrop single cell RNA-seq libraries and barcode-targeted RNA-seq libraries


title: Recipient 3 - HSC library 3

description:
inDrop scRNAseq library containing donor HSCs from mouse recipient 3 (library 3)
ARF2019_Sample2_barcode_list.txt
ARF2019_Sample2_cell_bcs_flat.txt
ARF2019_Sample2_counts_norm.csv.gz
ARF2019_Sample2_genes.txt
ARF2019_Sample2_projected_clusters.csv
ARF2019_Sample2_samp_id_flat_for_clonal_annotation.txt
ARF2019_Sample2_samp_id_flat.txt
Simultaneous inDrop single cell RNA-seq libraries and barcode-targeted RNA-seq libraries


title: Recipient 4 - HSC library 1

description:
inDrop scRNAseq library containing donor HSCs from mouse recipient 4 (library 1)
ARF2019_Sample2_barcode_list.txt
ARF2019_Sample2_cell_bcs_flat.txt
ARF2019_Sample2_counts_norm.csv.gz
ARF2019_Sample2_genes.txt
ARF2019_Sample2_projected_clusters.csv
ARF2019_Sample2_samp_id_flat_for_clonal_annotation.txt
ARF2019_Sample2_samp_id_flat.txt
Simultaneous inDrop single cell RNA-seq libraries and barcode-targeted RNA-seq libraries


title: Recipient 3 - HSC library 4

description:
inDrop scRNAseq library containing donor HSCs from mouse recipient 3 (library 4)
ARF2019_Sample2_barcode_list.txt
ARF2019_Sample2_cell_bcs_flat.txt
ARF2019_Sample2_counts_norm.csv.gz
ARF2019_Sample2_genes.txt
ARF2019_Sample2_projected_clusters.csv
ARF2019_Sample2_samp_id_flat_for_clonal_annotation.txt
ARF2019_Sample2_samp_id_flat.txt
Simultaneous inDrop single cell RNA-seq libraries and barcode-targeted RNA-seq libraries


title: Recipient 3 - HSC library 1

description:
inDrop scRNAseq library containing donor HSCs from mouse recipient 3 (library 1)
ARF2019_Sample2_barcode_list.txt
ARF2019_Sample2_cell_bcs_flat.txt
ARF2019_Sample2_counts_norm.csv.gz
ARF2019_Sample2_genes.txt
ARF2019_Sample2_projected_clusters.csv
ARF2019_Sample2_samp_id_flat_for_clonal_annotation.txt
ARF2019_Sample2_samp_id_flat.txt
Simultaneous inDrop single cell RNA-seq libraries and barcode-targeted RNA-seq libraries


title: Recipient 4 - KIT library 3

description:
inDrop scRNAseq library containing a sample of remaining donor KIT cells from mouse recipient 4 (library 3)
ARF2019_Sample2_barcode_list.txt
ARF2019_Sample2_cell_bcs_flat.txt
ARF2019_Sample2_counts_norm.csv.gz
ARF2019_Sample2_genes.txt
ARF2019_Sample2_projected_clusters.csv
ARF2019_Sample2_samp_id_flat_for_clonal_annotation.txt
ARF2019_Sample2_samp_id_flat.txt
Simultaneous inDrop single cell RNA-seq libraries and barcode-targeted RNA-seq libraries


title: Recipient 3 - HSC library 2

description:
inDrop scRNAseq library containing donor HSCs from mouse recipient 3 (library 2)
ARF2019_Sample2_barcode_list.txt
ARF2019_Sample2_cell_bcs_flat.txt
ARF2019_Sample2_counts_norm.csv.gz
ARF2019_Sample2_genes.txt
ARF2019_Sample2_projected_clusters.csv
ARF2019_Sample2_samp_id_flat_for_clonal_annotation.txt
ARF2019_Sample2_samp_id_flat.txt
Simultaneous inDrop single cell RNA-seq libraries and barcode-targeted RNA-seq libraries


title: Recipient 2 - KIT library 2

description:
inDrop scRNAseq library containing a sample of remaining donor KIT cells from mouse recipient 2 (library 2)
ARF2019_Sample1_all_cellids.txt
ARF2019_Sample1_barcode_list.txt
ARF2019_Sample1_counts_norm.csv.gz
ARF2019_Sample1_genes.txt
ARF2019_Sample1_samp_id.txt
Simultaneous inDrop single cell RNA-seq libraries and barcode-targeted RNA-seq libraries

extract_protocol:
EGFP-labeled SLAM HSCs and a sample of the remaining Kit+ cells were extracted from bone marrow, 16 weeks after transplantation, and encapsulated using inDrop (Zillionis et al. 2017).
After RNA amplification, half of the RNA was used to construct whole transcriptome libraries as in (Zilionis et al. 2017) and the other half of the RNA was used to construct barcode targeted libraries as in (Wagner et al. 2018).
Whole bone marrow from large bones (except the cranium) was prepared by crushing in 2% FBS-supplemented PBS. Red blood cells were removed by specific cell lysis (RBC lysis). HSC and Kit cells were enriched by magnetic separation using CD117 (cKit) beads from Miltenyi corporation, and further purified by FACS to isolate the SLAM+ LT-HSCs (HSC libraries) and the rest of cKit cells (KIT libraries). After encapsulation with inDrop, libraries were distributed into equal parts of approximately 2000-3000 cells  each.
Library construction protocol was as in Zilionis et al. Nature Protocols 2017.


title: Recipient 2 - HSC library 1

description:
inDrop scRNAseq library containing donor HSCs from mouse recipient 2 (library 1)
ARF2019_Sample1_all_cellids.txt
ARF2019_Sample1_barcode_list.txt
ARF2019_Sample1_counts_norm.csv.gz
ARF2019_Sample1_genes.txt
ARF2019_Sample1_samp_id.txt
Simultaneous inDrop single cell RNA-seq libraries and barcode-targeted RNA-seq libraries


title: Recipient 2 - HSC library 2

description:
inDrop scRNAseq library containing donor HSCs from mouse recipient 2 (library 2)
ARF2019_Sample1_all_cellids.txt
ARF2019_Sample1_barcode_list.txt
ARF2019_Sample1_counts_norm.csv.gz
ARF2019_Sample1_genes.txt
ARF2019_Sample1_samp_id.txt
Simultaneous inDrop single cell RNA-seq libraries and barcode-targeted RNA-seq libraries


title: Recipient 1 - HSC library 1

description:
inDrop scRNAseq library containing donor HSCs from mouse recipient 1 (library 1)
ARF2019_Sample1_all_cellids.txt
ARF2019_Sample1_barcode_list.txt
ARF2019_Sample1_counts_norm.csv.gz
ARF2019_Sample1_genes.txt
ARF2019_Sample1_samp_id.txt
Simultaneous inDrop single cell RNA-seq libraries and barcode-targeted RNA-seq libraries


title: Recipient 1 - KIT library 1

description:
inDrop scRNAseq library containing a sample of remaining donor KIT cells from mouse recipient 1 (library 1)
ARF2019_Sample1_all_cellids.txt
ARF2019_Sample1_barcode_list.txt
ARF2019_Sample1_counts_norm.csv.gz
ARF2019_Sample1_genes.txt
ARF2019_Sample1_samp_id.txt
Simultaneous inDrop single cell RNA-seq libraries and barcode-targeted RNA-seq libraries


title: Recipient 1 - KIT library 2

description:
inDrop scRNAseq library containing a sample of remaining donor KIT cells from mouse recipient 1 (library 2)
ARF2019_Sample1_all_cellids.txt
ARF2019_Sample1_barcode_list.txt
ARF2019_Sample1_counts_norm.csv.gz
ARF2019_Sample1_genes.txt
ARF2019_Sample1_samp_id.txt
Simultaneous inDrop single cell RNA-seq libraries and barcode-targeted RNA-seq libraries


title: Recipient 1 - HSC library 2

description:
inDrop scRNAseq library containing donor HSCs from mouse recipient 1 (library 2)
ARF2019_Sample1_all_cellids.txt
ARF2019_Sample1_barcode_list.txt
ARF2019_Sample1_counts_norm.csv.gz
ARF2019_Sample1_genes.txt
ARF2019_Sample1_samp_id.txt
Simultaneous inDrop single cell RNA-seq libraries and barcode-targeted RNA-seq libraries


title: Recipient 6 - HSC library 1

description:
inDrop scRNAseq library containing donor HSCs from mouse recipient 6 (library 1)
ARF2019_Sample4_barcode_list.txt
ARF2019_Sample4_cell_bcs_flat.txt
ARF2019_Sample4_counts_norm.csv.gz
ARF2019_Sample4_genes.txt
ARF2019_Sample4_samp_id_flat.txt
Simultaneous inDrop single cell RNA-seq libraries and barcode-targeted RNA-seq libraries


title: TAP_REDESIGN, original panel 2

description: Panel 2 was redesigned twice and aplied to K562 cells carying a set of control perturbations (gRNAs targeting the promoters of DSSC1, LRRC1, OXR1, RIPK2, STK3 and UBR5 as well as gRNAs targeting the enhancers of GATA1, ZFPM2 and MYC and the HS2 enhancer)

data_processing:
Genome_build: Homo Sapiens hg38
Conversion of paired end fastq files to unaligned bam; Picard Tools FastqToSam (v. 2.18.14)
Extraction of UMI observations using the Drop-seq tools workflow (v. 1.13; http://mccarrolllab.org/dropseq/) with STAR (v. 2.5.3a) for read alignment.
Filtering for chimeric reads and UMI count extraction using an approach adapted from Dixit et al. (python v. 3.6.6 ; https://www.biorxiv.org/content/10.1101/093237v1.full)
Extraction of perturbation status for each cell based on a cutoff on detected vector molecule counts (R v. 3.5.1).
Supplementary_files_format_and_content: Count tables (.counts.csv) and binary tables specifyng perturbation status (.pertStatus.csv)

growth_protocol: K562 cells (ATCC CCL-243) stably infected with dCas9-BFP-KRAB were routinely cultivated in RPMI + 10 % FCS + Pen/Strep and replated twice a week. Cells infected with lentivirus were selected using Puromycn and kept under Puromycin selection upon stable growth.

extract_protocol:
Cells were collected using centrifugation, FACS-sorted (high dCas9-BFP-KRAB expression,  viability with Draq7) and  subjectd to single-cell RNAseq using 10X Genomics or DropSeq technologies.
TAP-seq, 10x genomics based
Libraries were prepared according to DropSeq protocol (Macosko Cell 2015) or 10X Genomics single-cell RNAseq v2 (Chromium 3' Reagent Kits v2 User Guide Rev C "CG00052") for whole transcriptome or TAP-seq protocol for targeted transcriptome readouts.

value: Chromosome 8 panel

value: Control perturbations (reduced set)


title: TAP_REDESIGN,  panel 2, 2nd redesign

value: Chromosome 8 panel (Redesign 2)


title: WTX_REF, 10x genomics (deeper sequencing, less cells)

description: 10x genomics of K562 cells

extract_protocol:
Cells were collected using centrifugation, FACS-sorted (high dCas9-BFP-KRAB expression,  viability with Draq7) and  subjectd to single-cell RNAseq using 10X Genomics or DropSeq technologies.
Default library production protocol, 10x genomics, Pleasanton, CA
Libraries were prepared according to DropSeq protocol (Macosko Cell 2015) or 10X Genomics single-cell RNAseq v2 (Chromium 3' Reagent Kits v2 User Guide Rev C "CG00052") for whole transcriptome or TAP-seq protocol for targeted transcriptome readouts.


title: TAP_REDESIGN,  panel 2, 1st redesign

value: Chromosome 8 panel (Redesign 1)


title: TSC_TAR, L1000 panel

description: The basic TAP-Seq protocol was performed with indicated target gene panel.

value: L1000 panel


title: TAP_DEEP, panel 2


title: 2_CONTROL

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

description:
481_Yin_8RNASeq_RawCounts.txt
481_Yin_8RNASeq_DESeq2_NormCounts.txt

data_processing:
Illumina bcl2fastq v2.17.1.14 was used for demultiplexing.
Reads were mapped to the Ensebl mouse (GRCm38.p3) genomic reference with STAR (v2.5.2b) with default alignment parameters.
Abundance estimation of raw read counts per transcript was done internally with STAR using the algorithm of htseq-count.
Normalized expression (normalized read counts) was performed with DESeq2 (v1.10.1)
Genome_build: GRCm38.p3
Supplementary_files_format_and_content: tab delimited text file containing normalized read counts for each sample (in columns) and each annotated transcript (in rows).

source_name: Corpus callosum

growth_protocol: Age-matched PLP-150Q mice were bred and maintained in the animal facility under specific pathogen-free conditions

extract_protocol:
Corpus callosum were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 3-month-old PLP-150Q mice were treated with 5 mg/kg LAQ or purified water for two months.

value: brain (Corpus callosum)

tag: age

value: five-months-old

value: Vehicle


title: TAP_SCREEN, chromosome 11 screen, sample 11

description: K562 cells expressing dCas9-KRAB were infected with a lentiviral gRNA library targeting all enhancers on a defined region of chromosome 11. Binary Perturbation status per cell is contained in the pertStatus.csv.gz file.

data_processing:
Homo Sapiens hg38
Conversion of paired end fastq files to unaligned bam; Picard Tools FastqToSam (v. 2.18.14)
Extraction of UMI observations using the Drop-seq tools workflow (v. 1.13; http://mccarrolllab.org/dropseq/) with STAR (v. 2.5.3a) for read alignment.
Filtering for chimeric reads and UMI count extraction using an approach adapted from Dixit et al. (python v. 3.6.6 ; https://www.biorxiv.org/content/10.1101/093237v1.full)
Extraction of perturbation status for each cell based on a cutoff on detected vector molecule counts (R v. 3.5.1).
Supplementary_files_format_and_content: Count tables (.counts.csv) and binary tables specifyng perturbation status (.pertStatus.csv)

source_name: K562 dCas9-KRAB

value: K562 Cell line

value: Chromosome 11 panel

value: Chromosome 11 enhancer perturbations


title: 3_CONTROL

tag: tissue


title: 1_CONTROL


title: 5_LAQ5MG

value: LAQ 5mg


title: E12.5_Input

data_processing:
Paired end 2x 150bp reads were  gained using Illumina HiSeq 2500, and aligned to the mouse genome mm10 with Bowtie2
After filtration, the bigwig file of ChIP was performed using bamCompare through normalization to input.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig file including peaks

extract_protocol:
The anterior palate mesenchyme from E12.5 Meis2HA mouse embryos was fixed in 1% formaldehyde for 10 min and quenched by glycine for 5 min at room temperature. After washing with ice-cold PBS containing cocktail protease inhibitor, tissues were dispersed into single cell suspension on ice.
ChIP-seq DNA Library Prep Kit for Illumina

tag: strain background

value: anterior palate mesenchyme


title: 4_CONTROL


title: 7_LAQ5MG


title: Recipient 2 - KIT library 1

description:
inDrop scRNAseq library containing a sample of remaining donor KIT cells from mouse recipient 2 (library 1)
ARF2019_Sample1_all_cellids.txt
ARF2019_Sample1_barcode_list.txt
ARF2019_Sample1_counts_norm.csv.gz
ARF2019_Sample1_genes.txt
ARF2019_Sample1_samp_id.txt
Simultaneous inDrop single cell RNA-seq libraries and barcode-targeted RNA-seq libraries


title: TAP_DEEP, panel 1


title: TAP_SCREEN, chromosome 11 screen, sample 10


title: 6_LAQ5MG


title: AcKO.3

city: Chongqing

first: Zhe

last: Chen

address: 1 Yixueyuan Road, Yuzhong District

institute: Chongqing 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 mm10 whole genome using bowtie v0.12.9.
FPKM was performed with Cufflinks v2.1.1, aligned reads were counted with HTSeq.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM

source_name: Skeletal Muscle

extract_protocol:
About 800 SCs were isolated by FACS and the mRNA library constructed using QIAseq FX Single Cell RNA Library Kit (QIAGEN) according to the manufacturer’s instruction
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The  FoxM1fl/fl (floxp) and FoxM1fl/fl,Pax7Cre/+ (cKO) mice were treated with or without Bacl2. To induce injury, 50ul 1.2% BaCl2 in PBS or PBS alone was injected into and along the length of tibialis anterior  and gastrocnemius muscles.

value: Muscle satellite cells (SCs)

tag: cell states

value: Activated


title: 8_LAQ5MG


title: AcKO.2

tag: genotype/variation


title: TAP_SCREEN, chromosome 11 screen, sample 9


title: TAP_SCREEN, chromosome 11 screen, sample 8


title: TAP_SCREEN, chromosome 11 screen, sample 14


title: AcKO.1


title: Aflxop.2

value: Control


title: TAP_SCREEN, chromosome 11 screen, sample 5


title: Aflxop.1


title: TAP_SCREEN, chromosome 11 screen, sample 6


title: QcKO.3

value: Quiescent


title: QcKO.2


title: Qflxop.2


title: Qflxop.3


title: TAP_SCREEN, chromosome 11 screen, sample 1


title: QcKO.1


title: TAP_SCREEN, chromosome 8 screen, sample 14

description: K562 cells expressing dCas9-KRAB were infected with a lentiviral gRNA library targeting all enhancers on a defined region of chromosome 8. Binary Perturbation status per cell is contained in the pertStatus.csv.gz file.

value: Chromosome 8 panel

value: Chromosome 8 enhancer perturbations


title: Aflxop.3


title: Qflxop.1


title: TAP_SCREEN, chromosome 11 screen, sample 2


title: TAP_SCREEN, chromosome 8 screen, sample 12


title: TAP_SCREEN, chromosome 8 screen, sample 11


title: WT_19pos_H3K36me3_rep2

first: Richard

last: Koche

state: New York

institute: Memorial Sloan Kettering Cancer Center

data_processing:
ChIP-seq reads were filtered for quality and 3' trimmed for adapter sequences.
Reads were aligned to mouse assembly mm9 using bowtie2 (v2.2.2) with default parameters.
To create density files, read overlap density was calculated with an extension of the average fragment size, the signal was then normalized to ten million mapped reads and converted to BigWig using BEDTools.
Genome_build: mm9
Supplementary_files_format_and_content: BigWig files containing read densities normalized to 10 million reads

source_name: sorted Cd19+ proB cells

growth_protocol: Setd2f/f mice were bred to Mx1, Vav1, Cd19, Mb1, Cd2-cre mice to homozygosity. At 6-8 weeks of age, mice were sacrificed and bone marrow from femurs, tibias, hips, and spines were isolated. BM was then RBC lysed and stained with B220-biotin (BD pharmingen) and subsequently stained with Anti-biotin microbeads (Miltenyi) and applied on a LS column. Subsequent staining for cellular antigens was conducted. For VDJ recombination product assessment, RNA-Seq, ChIP-Seq, ChIP-PCR, qPCR proB and preB cells were isolated as follows: cells were then stained and sorted by FACS (BD-Aria) for B220+Cd43+IgM-Cd25- Cd19- proB cells

extract_protocol: Libraries were prepared using a ThruPLEX DNA-seq Kit (Rubicon Genomics) and validated using a TapeStation (Agilent Technologies) and Qubit 2.0 Flurometer (Thermo Fisher Scientific).

value: sorted Cd19+ proB cells

value: Setd2 WT

tag: chip antibody

value: H3K36me3 Ab from Active Motif (catalogue #61101)


title: WT_19pos_H3K36me3_rep3

tag: genotype


title: TAP_SCREEN, chromosome 8 screen, sample 10

tag: cell line


title: TAP_SCREEN, chromosome 8 screen, sample 9


title: TAP_SCREEN, chromosome 8 screen, sample 8


title: WT_19neg_H3K36me3_rep3

source_name: sorted Cd19- proB cells

value: sorted Cd19- proB cells


title: TAP_SCREEN, chromosome 11 screen, sample 4


title: TAP_SCREEN, chromosome 8 screen, sample 7


title: WT_19neg_H3K36me3_rep2


title: WT_19pos_H3K36me3_rep1


title: WT_19neg_H3K36me3_rep1


title: TAP_SCREEN, chromosome 8 screen, sample 5


title: TAP_SCREEN, chromosome 8 screen, sample 6


title: SETD2KO_19pos_H3K36me3_rep2

value: Setd2 KO


title: TAP_SCREEN, chromosome 8 screen, sample 13


title: TAP_SCREEN, chromosome 8 screen, sample 2


title: SETD2KO_19pos_H3K36me3_rep3


title: SETD2KO_19neg_H3K36me3_rep1

value: Cd19- proB cells


title: TAP_SCREEN, chromosome 8 screen, sample 1

value: K562 Cell line


title: SETD2KO_19neg_H3K36me3_rep3


title: SETD2KO_19pos_H3K36me3_rep1


title: SETD2KO_19neg_H3K36me3_rep2


title: TAP_SCREEN, chromosome 11 screen, sample 3

value: Chromosome 11 panel


title: TAP_SCREEN, chromosome 8 screen, sample 4


title: RNA_WTLSK6

data_processing:
RNA-seq reads were filtered for quality and 3' trimmed for adapter sequences.
Reads were aligned to mouse assembly mm9 using STAR (v2.4) with default parameters.
Read count tables were created using HTSeq v0.6.1.
Normalization and differential expression analysis was performed with DESeq2.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text file with un-normalized read counts over all genes.

source_name: WBM LSK

growth_protocol: LSKs were obtained by lineage depletion of WBM and conducted as per manufacturer’s protocols with biotin-labeled antibodies for CD3, Gr1, Ter119, and B220 (BD pharmingen) and subsequently subjected to magnetic depletion with anti-biotin microbeads and depletion on a LD column (Miltenyi).  Lineage depleted cells were then stained with cKit and Sca1 and sorted on a FACS cell sorter (BDAria).

extract_protocol:
Qiagen RNA kits were used as per manufacturer’s protocol for RNA isolation and purity was confirmed by RNA Tapestation (Illumina).
RNA-seq librariers were amplified with SMARTer Ultra Low Input RNA Kit for Illumina Sequencing.

value: LSK


title: WTX_DIFFEX, sample 4

description: K562 cells expressing dCas9-KRAB were infected with a lentiviral gRNA library targeting 16 control promoters and enhancers. Binary Perturbation status per cell is contained in the pertStatus.csv.gz file.

extract_protocol:
Cells were collected using centrifugation, FACS-sorted (high dCas9-BFP-KRAB expression,  viability with Draq7) and  subjectd to single-cell RNAseq using 10X Genomics or DropSeq technologies.
Default library production protocol, 10x genomics, Pleasanton, CA; additionally, CROP-Seq vector transcripts were amplified and sequenced separately.
Libraries were prepared according to DropSeq protocol (Macosko Cell 2015) or 10X Genomics single-cell RNAseq v2 (Chromium 3' Reagent Kits v2 User Guide Rev C "CG00052") for whole transcriptome or TAP-seq protocol for targeted transcriptome readouts.

value: Control perturbations


title: WTX_DIFFEX, sample 2


title: WTX_DIFFEX, sample 3


title: RNA_WTLSK5


title: RNA_WTLSK4


title: WTX_DIFFEX, sample 1


title: RNA_WTLSK3


title: TAP_DIFFEX, sample 1


title: TAP_SCREEN, chromosome 8 screen, sample 3


title: RNA_WTLSK2


title: RNA_WTLSK1


title: WTX_REF, DropSeq

description: DropSeq of K562 cells

extract_protocol:
Cells were collected using centrifugation, FACS-sorted (high dCas9-BFP-KRAB expression,  viability with Draq7) and  subjectd to single-cell RNAseq using 10X Genomics or DropSeq technologies.
Default DropSeq protocol (MacKosco et al.)
Libraries were prepared according to DropSeq protocol (Macosko Cell 2015) or 10X Genomics single-cell RNAseq v2 (Chromium 3' Reagent Kits v2 User Guide Rev C "CG00052") for whole transcriptome or TAP-seq protocol for targeted transcriptome readouts.


title: TAP_DIFFEX, sample 2


title: WTX_REF, 10x genomics

description: 10x genomics of K562 cells


title: RNA_SETD2KOLSK4


title: TAP_TAR, panel 1, DropSeq

extract_protocol:
Cells were collected using centrifugation, FACS-sorted (high dCas9-BFP-KRAB expression,  viability with Draq7) and  subjectd to single-cell RNAseq using 10X Genomics or DropSeq technologies.
TAP-seq, Drop-Seq based
Libraries were prepared according to DropSeq protocol (Macosko Cell 2015) or 10X Genomics single-cell RNAseq v2 (Chromium 3' Reagent Kits v2 User Guide Rev C "CG00052") for whole transcriptome or TAP-seq protocol for targeted transcriptome readouts.


title: RNA_SETD2KOLSK5


title: RNA_SETD2KOLSK3


title: TAP_TAR, panel 1 + 2

value: Chromosome 8 panel + chromosome 11 panel


title: RNA_SETD2KOLSK6


title: RNA_SETD2KOLSK2


title: RNA_SETD2KOLSK1


title: TAP_SCREEN, chromosome 11 screen, sample 7

value: Chromosome 11 enhancer perturbations


title: PCR-variable experiment replicate 3 0.2X Tn5

city: Ann Arbor

first: Stephen

last: Parker

state: MI

address: 100 Washtenaw Avenue

institute: University of Michigan

data_processing:
Basecalls performed using Illumina CASAVA bcl2fastq v2.17.1.14
Adapters were trimmed using cta (v. 0.1.2) with default settings
Reads were aligned to hg19 using bwa mem (v. 0.7.15-r1140; using the -M flag)
Read groups (corresponding to fastq files with '_1964'/'_1979') for PCR-constant samples were merged within each sample using samtools merge (v. 1.7)
Duplicates were marked using picard MarkDuplicates (v. 2.18.27) with VALIDATION_STRINGENCY=LENIENT
Reads were filtered to autosomal reads using samtools view with options -f 3 -F 4 -F 8 -F 256 -F 1024 -F 2048 -q 30
Peak calling was performed using MACS2 (v. 2.1.1.20160309; options: --nomodel --broad --shift -100 --extsize 200 --keep-dup all)
Peaks were filtered against the ENCODE hg19 blacklists (downloaded from  http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeMapability/wgEncodeDacMapabilityConsensusExcludable.bed.gz and http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeMapability/wgEncodeDukeMapabilityRegionsExcludable.bed.gz)
To generate the list of "master peaks" (peaks that would be used for downstream analysis) for the PCR-variable and the PCR-constant experiments, we took all blacklist-filtered, FDR 1% peak calls from the 1X Tn5 libraries in that experiment, merged these peaks (bedtools merge; v. 2.27.1), and kept (as master peaks) those merged intervals that overlapped with the blacklist filtered, FDR 1% peak calls from at least two of the 1X Tn5 libraries in that experiment
Genome_build: hg19
Supplementary_files_format_and_content: broadPeak files contain the peak calls as output by MACS2. Each of the PCR-constant samples has only one set of peak calls, but the PCR-variable samples each have two sets of peak calls ('_low' and '_high'), since each of these samples was sequenced on a sequencing run with high cluster density as well as a sequencing run with low cluster density. The bedgraph files represent the 'treat_pileup' bedgraph files output by macs2 during peak calling. The 'counts' BED files represent read counts in master peaks, generated using bedtool's coverageBed (v. 2.27.1; with -counts flag) on each sample's filtered bam file.

growth_protocol: We cultured GM12878 cells following the ENCODE GM12878 cell culture protocol (available at https://www.encodeproject.org/documents/1bb75b62-ac29-4368-9855-68d410e1963a/), except that we added plasmocin (Invivogen; 50 ug/mL) to the growth media to prevent mycoplasma contamination.

extract_protocol:
We isolated nuclei from three independent cultures for the PCR-variable experiment and six additional cultures for the PCR-constant experiment.
We conducted ATAC-seq as described in (Buenrostro et al. 2015) using a home-made Tn5 that we synthesized as described in (Picelli et al. 2014). For each replicate we incubated 50,000 nuclei with various concentrations of enzyme (1/5X, 1/2X, 2/3X, 1X, 1.5X, 2X, 5X; 1X corresponds to 2.5 uL of 1:1 Tn5-A/B mix) at 37 degrees C for 30 minutes in a 50 uL reaction. We column-purified the tagmented DNA using the Zymo DNA Clean & Concentrator-5 kit (Zymo Research, Irvine, CA). In the PCR-variable experiment, we PCR-amplified the entire eluate until amplification curve reached its mid-log phase (1/3 to 1/2 of max signal); whereas in the PCR-constant experiment, we amplified the entire eluate with a fixed number of PCR cycles (16) for all samples. We purified the products using SPRI beads prepared as in (Rohland and Reich, 2012) and eluted in 20 uL of TE buffer with Tween-20 (10 mM Tris-HCl, 0.1 mM EDTA, 0.05% Tween-20, pH 8)

tag: pcr cycles


title: TAP_TAR, panel 1 rep. 2

tag: targeting panel


title: TAP_TAR, panel 1 rep. 1

tag: perturbations


title: TAP_TAR, panel 2 rep. 1


title: TAP_TAR, panel 2 rep. 2


title: PCR-variable experiment replicate 3 1X Tn5


title: TAP_TAR, panel 1+2+3

value: Chromosome 8 panel + chromosome 11 panel + supplementary panel


title: PCR-variable experiment replicate 3 0.66X Tn5


title: PCR-variable experiment replicate 3 2X Tn5


title: PCR-variable experiment replicate 3 1.5X Tn5


title: PCR-variable experiment replicate 3 5X Tn5


title: PCR-variable experiment replicate 2 0.5X Tn5


title: PCR-variable experiment replicate 2 0.2X Tn5


title: PCR-variable experiment replicate 2 0.66X Tn5


title: PCR-variable experiment replicate 2 1X Tn5


title: PCR-variable experiment replicate 2 5X Tn5


title: PCR-variable experiment replicate 1 0.2X Tn5


title: PCR-variable experiment replicate 1 0.5X Tn5


title: PCR-variable experiment replicate 2 2X Tn5


title: PCR-variable experiment replicate 2 1.5X Tn5


title: PCR-variable experiment replicate 1 0.66X Tn5


title: 12 ARG (12A-2)

type: RNA

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

hyb_protocol: Hybridization was performed according to the manufacturer’s instructions.

scan_protocol: Data are run on the iScan system (Illumina).

data_processing: Data processed using limma package in R version 3.2.0

label: biotin

source_name: iMSC

label_protocol: The samples were prepared using SuperScript III Reverse Transcriptase (ThermoFisher) and TargetAmp Nano Labeling kit (Lucigen).

growth_protocol: All lines were propagated in α Minimum Essential Medium (αMEM, Thermo Fisher) supplemented with 10% human platelet lysate (hPL) (Cook Regentec).

extract_protocol: Total RNA was isolated from cells using the QIAgen RNeasy Mini kit (Qiagen). The RNA quality was assessed using Agilent RNA 6000 Nano Kit and the 2100 Bioanalyser (Agilent).

treatment_protocol: For the HumanHT-12 v4 Expression BeadChip (Illumina) assay RNA was isolated from cells with and without 18 h IFNG treatment.

tag: donor

tag: protocol

value: ARG

value: iMSC

value: control (non-treated)


title: 13 ARG (13A-2)


title: 13 ARG (13A-1)


title: 12 ARG (12A-T1)

value: IFNG-treated


title: 12 ARG (12A-T3)


title: 13 ARG (13A-T3)


title: 12 ARG (12A-1)


title: 13 ARG (13A-T2)


title: 12 ARG (12A-T2)


title: 13 ARG (13A-T1)


title: PCR-variable experiment replicate 1 1X Tn5


title: 12 TEX (12TX-T3)

value: TEX


title: 12 TEX (12TX-T2)


title: 12 TEX (12TX-T1)


title: 12 ARG (12A-3)


title: PCR-variable experiment replicate 1 2X Tn5


title: PCR-constant experiment replicate 6 0.2X Tn5


title: 12 TEX (12TX-2)


title: 13 native (13N-T2)

source_name: nMSC

value: native

value: nMSC


title: 12 TEX (12TX-1)


title: PCR-constant experiment replicate 6 0.5X Tn5


title: PCR-constant experiment replicate 6 1X Tn5


title: 13 native (13N-T3)


title: PCR-constant experiment replicate 6 2X Tn5


title: PCR-constant experiment replicate 6 5X Tn5


title: 12 TEX (12TX-3)


title: 34 ARG (34A-T3)

source_name: eMSC

value: embryonic stem cell line KCL034

value: eMSC


title: PCR-constant experiment replicate 5 0.2X Tn5


title: 13 native (13N-1)


title: 34 ARG (34A-T2)


title: PCR-constant experiment replicate 5 0.66X Tn5


title: 13 native (13N-3)


title: 34 ARG (34A-T1)


title: PCR-constant experiment replicate 6 1.5X Tn5


title: 34 ARG (34A-3)


title: 34 ARG (34A-2)


title: 13 ARG (13A-3)


title: 13 native (13N-2)


title: PCR-constant experiment replicate 5 1.5X Tn5


title: PCR-constant experiment replicate 5 2X Tn5


title: 13 native (13N-T1)


title: PCR-constant experiment replicate 5 1X Tn5


title: PCR-constant experiment replicate 6 0.66X Tn5


title: PCR-constant experiment replicate 5 0.5X Tn5


title: 13 TEX (13TX-3)


title: 13 TEX (13TX-T1)


title: 13 TEX (13TX-T3)


title: 13 TEX (13TX-1)


title: PCR-constant experiment replicate 4 0.2X Tn5


title: PCR-constant experiment replicate 4 0.5X Tn5


title: 13 TEX (13TX-T2)


title: PCR-constant experiment replicate 4 1.5X Tn5


title: PCR-constant experiment replicate 4 0.66X Tn5


title: PCR-constant experiment replicate 4 1X Tn5


title: 46: Psoriasis

first: Michael

middle: Seth

last: Garshick

address: 435 East 30th Street

institute: NYU Langone Health

description: Paxgene tubes

data_processing:
Mapped to reference human genome GRCH37/hg19
Read counts with HTSeq V 0.60
Normalization with DSEeq v3.7
Supplementary_files_format_and_content: Tab-deliminated tet files lincluding FPKM values

source_name: Whole blood RNA

extract_protocol:
Automatic QIAsymphony PAXgene Blood RNA Kit
Illumina TruSeq
200ng, 12 cyles of amplication 2 lanes of single read 50 on an Illumina HiSeq 4000 Sequencer

tag: disease state

value: Psoriasis

value: Whole blood


title: PCR-constant experiment replicate 4 2X Tn5


title: 34 TEX (34TX-T3)

tag: treatment


title: PCR-constant experiment replicate 3 0.2X Tn5


title: PCR-constant experiment replicate 3 0.5X Tn5


title: 34 TEX (34TX-T1)

tag: cell type


title: PCR-constant experiment replicate 4 5X Tn5


title: 34 TEX (34TX-2)


title: 34 TEX (34TX-3)


title: 34 TEX (34TX-T2)


title: 37: Control

description: Paxgene tubes

value: Control


title: 34 TEX (34TX-1)


title: 12 native (12N-T3)


title: 12 native (12N-T2)


title: 13 TEX (13TX-2)


title: 36: Control

description: Paxgene tubes


title: 12 native (12N-2)


title: 12 native (12N-T1)


title: PCR-constant experiment replicate 3 1X Tn5


title: 35: Control

description: Paxgene tubes


title: PCR-constant experiment replicate 3 1.5X Tn5


title: 34: Control

description: Paxgene tubes


title: 32: Control

description: Paxgene tubes


title: PCR-constant experiment replicate 3 0.66X Tn5


title: 12 native (12N-1)


title: 12 native (12N-3)


title: Mononuclear_cells_patient_11_rifampicin

city: Kuopio

first: Jaana

last: Rysae

address: Yliopistonranta 1C

department: School of Pharmacy

country: Finland

institute: University of Eastern Finland

description:
Gene expression data from patient no:11 after administration of rifampicin for one week.
084-11K2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data was log2-transformed, normalized with shift to 75 percentile and baseline transformed to median of all samples in GeneSpring 12.6 Software

label: Biotin

label_protocol: Biotinylated cRNA were prepared with the Illumina® Total PrepT RNA Ampification kit (Life Technologies) for Illumina arrays

extract_protocol: Blood samples were collected, and peripheral blood mononuclear cells were separated. part of the cell suspension was isolated and centrifuged at 800 x g for 8 min at 22°C to collect the mononuclear cell pellet. The harvested cells were then lysed by suspending in RLT-buffer (RNeasy® Mini Kit; Qiagen, Hilden, Germany) containing 1%-β-mercaptoethanol. For the homogenization of samples and elimination of unsolubilized cellular particles both the macrophage and mononuclear cell lysates were centrifuged at 16 000 x g for 2 min through QIAshredder (Qiagen) spin columns, and RNA was extracted with RNeasy® Mini Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Healthy volunteers, aged 19-38 years, were administered 600 mg rifampicin (Rimapen; Orion Corporation, Espoo, Finland) or placebo daily for a week with at least a 4-week washout period before the next treatment arm. At the end of each arm, blood samples were collected on the morning of the eighth day.

value: blood

tag: individual

value: patient 11

tag: gender

value: male

value: rifampicin

value: Peripheral blood mononuclear cells


title: Mononuclear_cells_patient_12_rifampicin

description:
Gene expression data from patient no:12 after administration of rifampicin for one week.
084-12K1

tag: tissue

value: patient 12


title: 29: Psoriasis

description: Paxgene tubes


title: PCR-constant experiment replicate 3 2X Tn5


title: Mononuclear_cells_patient_11_placebo

description:
Gene expression data from patient no:11 after administration of placebo for one week.
084-11K1

value: Placebo


title: PCR-constant experiment replicate 3 5X Tn5


title: Mononuclear_cells_patient_12_placebo

description:
Gene expression data from patient no:12 after administration of placebo for one week.
084-12K2


title: PCR-constant experiment replicate 2 0.2X Tn5


title: 28: Control

description: Paxgene tubes


title: PCR-constant experiment replicate 2 0.66X Tn5


title: 26: Psoriasis

description: Paxgene tubes


title: 25: Psoriasis

description: Paxgene tubes


title: Mononuclear_cells_patient_8_placebo

description:
Gene expression data from patient no:8 after administration of placebo for one week.
084-8K1

value: patient 8


title: Mononuclear_cells_patient_7_placebo

description:
Gene expression data from patient no:7 after administration of placebo for one week.
084-7K2

value: patient 7


title: 22: Psoriasis

description: Paxgene tubes


title: Mononuclear_cells_patient_9_rifampicin

description:
Gene expression data from patient no:9 after administration of rifampicin for one week.
084-9K1

value: patient 9


title: Mononuclear_cells_patient_9_placebo

description:
Gene expression data from patient no:9 after administration of placebo for one week.
084-9K2


title: Mononuclear_cells_patient_7_rifampicin

description:
Gene expression data from patient no:7 after administration of rifampicin for one week.
084-7K1


title: Mononuclear_cells_patient_8_rifampicin

description:
Gene expression data from patient no:8 after administration of rifampicin for one week.
084-8K2


title: PCR-constant experiment replicate 2 0.5X Tn5


title: Mononuclear_cells_patient_6_placebo

description:
Gene expression data from patient no:6 after administration of placebo for one week.
084-6K2

value: patient 6


title: Mononuclear_cells_patient_10_rifampicin

description:
Gene expression data from patient no:10 after administration of rifampicin for one week.
084-10K2

value: patient 10

value: female


title: Mononuclear_cells_patient_10_placebo

description:
Gene expression data from patient no:10 after administration of placebo for one week.
084-10K1


title: PCR-constant experiment replicate 2 1X Tn5


title: 27: Psoriasis

description: Paxgene tubes


title: PCR-constant experiment replicate 2 2X Tn5


title: PCR-constant experiment replicate 2 1.5X Tn5


title: Mononuclear_cells_patient_5_rifampicin

description:
Gene expression data from patient no:5 after administration of rifampicin for one week.
084-5K2

value: patient 5


title: Mononuclear_cells_patient_5_placebo

description:
Gene expression data from patient no:5 after administration of placebo for one week.
084-5K1


title: 34 ARG (34A-1)

value: embryonic stem cell line KCL034

value: ARG

value: eMSC

value: control (non-treated)


title: PCR-variable experiment replicate 1 1.5X Tn5


title: Mononuclear_cells_patient_4_rifampicin

description:
Gene expression data from patient no:4 after administration of rifampicin for one week.
084-4K2

value: blood

value: patient 4


title: PCR-variable experiment replicate 1 5X Tn5


title: Mononuclear_cells_patient_4_placebo

description:
Gene expression data from patient no:4 after administration of placebo for one week.
084-4K1

value: male


title: Mononuclear_cells_patient_3_placebo

description:
Gene expression data from patient no:3 after administration of placebo for one week.
084-3K2

value: patient 3

value: Peripheral blood mononuclear cells


title: 20: Psoriasis

description: Paxgene tubes

value: Psoriasis

value: Whole blood


title: PCR-constant experiment replicate 5 5X Tn5


title: 10: Psoriasis

description: Paxgene tubes


title: PCR-constant experiment replicate 1 0.2X Tn5


title: PCR-constant experiment replicate 1 0.5X Tn5


title: PCR-constant experiment replicate 2 5X Tn5


title: 16: Control

description: Paxgene tubes

value: Control


title: 19: Psoriasis

description: Paxgene tubes