title: BALB/c mouse

description: RNA in EVs

hyb_protocol: Hybridized for 16 h at 32 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

source_name: EVs

label_protocol: Extracted total RNA was labeled with Cy5 using the 3D-Gene miRNA labeling kit (Toray, Kamakura, Japan)

extract_protocol: RNA samples were extracted from cells using miRNesy mini kit (Qiagen).

tag: strain

value: BALB/c

value: EVs


title: C57BL/6 mouse

status: Public on Nov 14 2023

type: RNA

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

description: RNA in EVs

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

molecule: total RNA

organism: Mus musculus

tag: cell type


title: DT-resistant, rep5

type: SRA

city: Dresden

first: Dana

last: Westphal

address: Fetscherstrasse 74

department: Department of Dermatology

country: Germany

institute: University Hospital Dresden

library_source: transcriptomic

data_processing:
basecalling software: bcl2fastq2 2.20.0
alignment: Fragments were aligned to the homo sapiens reference genome hg38 with support of the Ensembl 104 splice sites using the aligner STAR (2.7.10b)
gene counts (raw counts): Counts per gene and sample were obtained based on the overlap of the uniquely mapped fragments with the same Ensembl annotation using featureCounts (v2.0.1)
normalised counts: Raw counts were processed within DESeq2 (1.38.3), genes were filtered which had <= 10 fragments over all samples and normalised afterwards
Assembly: hg38
Supplementary files format and content: tab separated file format where columns are gene characteristics and samples and each row lists genes

organism: Homo sapiens

source_name: DT-resistant WM1366

extract_protocol:
Total RNA from 1x106 sensitive or resistant WM1366 cells, which were seeded 72 h beforehand in RPMI containing DMSO (sensitive cells) or BRAFi/MEKi (resistant cells), was isolated according to instructions of the RNeasy Plus Mini Kit (Qiagen). Briefly, cells were immediately lysed by addition of 350 µl buffer RLT Plus including 1% β-mercaptoethanol and resuspended by repeatedly pipetting up and down. Following the procedure of the manufacturer, RNA was isolated and finally eluted with 50 µl RNase-free water
For library preparation, total RNA with an integrity number of ≥ 9 was used. mRNA was isolated from 500 ng total RNA by poly-dT enrichment using the NEBNext Poly(A) mRNA Magnetic Isolation Module according to the manufacturer’s instructions (NEB). Final elution was done in 15ul 2x first strand cDNA synthesis buffer (NEBnext, NEB). After chemical fragmentation by incubating for 15 min at 94°C the sample was directly subjected to the workflow for strand specific RNA-Seq library preparation (Ultra Directional RNA Library Prep, NEB). For ligation custom adaptors were used (Adaptor-Oligo 1: 5'-ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT-3', Adaptor-Oligo 2: 5'-P-GAT CGG AAG AGC ACA CGT CTG AAC TCC AGT CAC-3'). After ligaton adapters were depleted by an XP bead purification (Beckman Coulter) adding bead in a ratio of 1:1. Indexing was done during the following PCR enrichment (12 cycles) using custom amplification primers carrying the index sequence indicated with ‘NNNNNN’. (Primer1: Oligo Seq AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC T, Primer2: GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATC T, Primer3: CAA GCA GAA GAC GGC ATA CGA GAT NNNNNN GTG ACT GGA GTT). After two more XP beads purifications (1:1) libraries were quantified using Qubit dsDNA HS Assay Kit (Invitrogen, Waltham, USA). For Illumina flowcell production, samples were equimolarly pooled sequenced at 40 Mio fragments 100bp paired-end on a NovaSeq 6000 device using a NovaSeq v1.5 S4 flowcell.

tag: cell line

value: DT-resistant WM1366

value: melanoma cell line

tag: treatment

value: dabrafenib/trametinib


title: DT-resistant, rep6


title: Mouse_435850_OLF - AON-TT-DP_10Xv2 [L8TX_190122_01_C06]

city: Seattle

first: Cindy

last: van Velthoven

state: WA

address: 615 Westlake Ave N

country: USA

institute: Allen Institute

description:
WMB_Cell type annotation.xlsx
WMB_sample_metadata.csv
WMB.umap.2d.csv

library_source: transcriptomic single cell

data_processing:
10x libraries were sequenced on the Illumina NovaSeq6000, and sequencing reads were aligned to the mouse reference transcriptome (M21, GRCm38.p6) using the 10x Genomics CellRanger pipeline (version 6.1.1) with default parameters.
To remove low quality cells, cells were first classified into broad cell classes after mapping to an existing, preliminary version of the taxonomy, and cell quality was assessed based on gene detection, qc score, and doublet score. The qc score was calculated by summing the log transformed expression of a set of genes whose expression level is decreased significantly in poor quality cells. These are housekeeping genes that are strongly expressed in nearly all cells with a very tight co-expression pattern that is anti-correlated with the nucleus localized gene Malat1. Out of the 62 QC genes chosen, 30 are annotated as mitochondrial inner membrane category based on GO ontology cellular component, although they are not located on the mitochondrial chromosome. We used this qc score to quantify the integrity of cytoplasmic mRNA content, which tended to show bimodal distribution. Cells at the low end were very similar to single nuclei, which we removed for downstream analysis. Doublets were identified using a modified version of the DoubletFinder algorithm and removed when doublet score > 0.3. Thresholds were tailored to different cell classes. For example, for neurons (excluding granule cells) we used gene counts cutoff of 2,000 and qc score cutoff of 200.
Assembly: M21, GRCm38.p6
Supplementary files format and content: Text file containing information for location viewing and loading associated data
Supplementary files format and content: Excel file containing cell type annotations
Supplementary files format and content: Comma-separated values file containing cell-level metadata
Supplementary files format and content: Comma-separated values file containing UMAP coordinates for all QC-passed cells

source_name: OLF - AON-TT-DP

extract_protocol:
Allen Institute for Brain Science. Mouse Whole Cell Tissue Processing for 10x Genomics Platform V.9. Protocols.io, doi:dx.doi.org/10.17504/protocols.io.q26g7b52klwz/v9 (2022)
Allen Institute for Brain Science. 10Xv2 RNASeq Sample Processing. Protocols.io, doi:dx.doi.org/10.17504/protocols.io.bq68mzhw (2021); Allen Institute for Brain Science. 10Xv3.1 Genomics Sample Processing V.2. Protocols.io, doi:dx.doi.org/10.17504/protocols.io.dm6gpwd8jlzp/v2 (2022).

tag: tissue

value: OLF - AON-TT-DP

tag: genotype

value: Light

tag: age

value: 61 days

tag: donor id


title: DT-resistant, rep2


title: VC-resistant, rep6

source_name: VC-resistant WM1366

value: VC-resistant WM1366

value: vemurafenib/cobimetinib


title: Mouse_435850_OLF - AON-TT-DP_10Xv2 [L8TX_190122_01_B06]


title: VC-resistant, rep5


title: Mouse_352356_MOp_10Xv2 [L8TX_171026_01_H04]

source_name: MOp

value: MOp

value: 57 days


title: Mouse_425671_MOs-FRP_10Xv2 [L8TX_181206_01_H11]

source_name: MOs-FRP

value: MOs-FRP

value: 56 days


title: Mouse_425671_MOs-FRP_10Xv2 [L8TX_181206_01_B12]


title: VC-resistant, rep2


title: EB-resistant, rep5

source_name: EB-resistant WM1366

value: EB-resistant WM1366

value: encorafenib/binimetinib


title: Mouse_352356_MOp_10Xv2 [L8TX_171026_01_F04]


title: Mouse_352356_MOp_10Xv2 [L8TX_171026_01_G04]


title: Mouse_352356_MOp_10Xv2 [L8TX_171026_01_B05]


title: sensitive, rep2

source_name: sensitive WM1366

value: sensitive WM1366

value: DMSO


title: Mouse_352357_MOp_10Xv2 [L8TX_171026_01_F05]

value: 58 days


title: HTR-cells, sgDock180_1

city: Shanghai

first: Yichi

last: Xu

address: 910 Hengshan

country: China

institute: International Peace Maternity And Child Health Hospital, IPMCH

data_processing:
(1) Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
(2) paired-end clean reads were aligned to the reference genome usinghisat2 (v2.0.5)
(3) featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: placenta

growth_protocol: HTR-8 were maintained in DMEM/F12 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
RNA was harvested using Trizol reagent. 0.4 ug of total RNA was used for the construction of sequencing libraries
RNA libraries for RNA-seq were prepared using standard illumina protocols

value: placenta

value: trophoblast cells

value: Dock180 knockout


title: HTR-cells, sgDock180_3


title: sensitive, rep5

value: melanoma cell line


title: Mouse_352357_MOp_10Xv2 [L8TX_171026_01_E05]

value: Light


title: HTR-cells, sgctrl_3

value: ctrl


title: Mouse_434450_CTXsp - CLA-EP-LA-BLA-BMA-PA_10Xv2 [L8TX_190116_01_E04]

source_name: CTXsp - CLA-EP-LA-BLA-BMA-PA

value: CTXsp - CLA-EP-LA-BLA-BMA-PA

value: 61 days


title: Mouse_352357_MOp_10Xv2 [L8TX_171026_01_G05]

value: MOp


title: HTR-cells, sgDock180_2


title: Mouse_455006_OLF - AON-TT-DP_10Xv2 [L8TX_190423_01_G06]

value: OLF - AON-TT-DP

value: 57 days


title: Mouse_414905_AUD_10Xv2 [L8TX_181012_01_H04]

source_name: AUD

value: AUD


title: Mouse_414905_AUD_10Xv2 [L8TX_181012_01_G04]


title: EB-resistant, rep6

value: EB-resistant WM1366


title: HTR-cells, sgctrl_2


title: Mouse_425671_MOs-FRP_10Xv2 [L8TX_181206_01_A12]

value: MOs-FRP

value: 56 days


title: Mouse_414905_AUD_10Xv2 [L8TX_181012_01_E05]


title: HTR-cells, sgctrl_1


title: EB-resistant, rep2

value: encorafenib/binimetinib


title: sensitive, rep6

value: sensitive WM1366

value: DMSO


title: Mouse_414902_AUD_10Xv2 [L8TX_181011_01_H02]


title: TDP-43-HA ON 3

city: Zurich

first: Izaskun

last: Mallona

address: Winterthurerstrasse 190

country: Switzerland

institute: University of Zurich

description: bulk RNA-seq

data_processing:
For the single-cell assay, data was processed with CellRanger for demultiplexing, read alignment to the human reference genome (GRCh38) and filtering to generate a feature-barcode matrix per sample. Cell doublets were removed with scDblFinder and outlier cells were detected and filtered with the “scater” R package.  In short, cells with more than 3 median-absolute-deviations away from the median number of UMIs, the number of features and the percentage of mitochondrial genes were removed. For the 7.5 months old samples, we additionally filtered cells with less than 2000 UMIs and less than 1500 detected features. For the TDP-43 overexpression experiment, we additionally filtered cells with less than 5000 UMIs and less than 2500 detected features. Seurat v3 was used for log-normalization and to identify the top 2000 highly variable genes per sample. Louvain clustering was performed with resolution 0.4 based on a shared nearest neighbor graph constructed from the top 20 principal components (PC).
For bulk RNA-seq data, we ran Salmon (Patro et al. 2017) using ARMOR (Orjuela S et al, 2019) with default parameters and the human reference genome GRCh38.p13 and Gencode v41 annotation.
Assembly: GRCh38
Supplementary files format and content: Count matrices and metadata (sample metadata for bulk RNA-seq; and cell metadata for scRNA-seq cells)

source_name: Neural culture cells

extract_protocol:
Cell cultures were dissociated into single cells suspension using Papain Dissociation System (Worthington #LK003150), passed through 70μm and 40μm cell strainers (Falcon #07-201-431 and #07-201-430), and resuspended in HIB++ media (HibernateTM-E Medium medium (Gibco #A1247601) supplemented with EDTA (1mM final; Invitrogen #AM9260G), HEPES (10mM final; Gibco #15630080), with 1X B27+ supplement (Gibco #17504-044), 1X N2 supplement (Gibco #17502-048); 1X GlutaMAX(Gibco #35050-061), BDNF (PeproTech #450-02), GDNF (Alomone labs #G-240), CNTF (Alomone labs #C-240), NT-3 (PeproTech #450-03) and IGF-1 (Stem Cell #78022) all at 20 ng/ml)) to 1000 cells per μl using CASY Cell Counter (Innovatis AG)
For the single-cell RNA-seq data, 10,000 cells per sample were loaded in to the 10X Chromium controller and library preparation was performed according to the manufacturer’s indications (Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 protocol). For the bulk RNA-seq data, the quality of the isolated RNA was determined with a Fragment Analyzer (Agilent, Santa Clara, California, USA). The TruSeq Stranded mRNA (Illumina, Inc, California, USA) was used in the succeeding steps. Briefly, total RNA samples (100-1000 ng) were poly A enriched and then reverse-transcribed into double-stranded cDNA. The cDNA samples were fragmented, end-repaired and adenylated before ligation of TruSeq adapters containing unique dual indices (UDI) for multiplexing. Fragments containing TruSeq adapters on both ends were selectively enriched with PCR.  The quality and quantity of the enriched libraries were validated using the Fragment Analyzer (Agilent, Santa Clara, California, USA).  The product is a smear with an average fragment size of approximately 260 bp. The libraries were normalized to 10nM in Tris-Cl 10 mM, pH8.5 with 0.1% Tween 20.
For the single-cell RNA-seq data, libraries followed the 10X Genomics recommendations: paired-end reads, R1=28, i7=8, R2=91. For the bulk RNA-seq data, the Novaseq 6000 (Illumina, Inc, California, USA) was used for cluster generation and sequencing according to standard protocol.  Sequencing configuration was paired end 150 bp, 150 million reads depth.

value: Neural culture cells, with TDP-43-HA


title: TDP-43-HA ON 4

description: bulk RNA-seq


title: TDP-43-HA OFF 1

description: bulk RNA-seq

value: Neural culture cells, with TDP-43-HA, OFF control


title: Mouse_414902_AUD_10Xv2 [L8TX_181011_01_G02]


title: TDP-43 KD 1

description: bulk RNA-seq

value: Neural culture cells, with TDP-43 shRNA KD


title: Mouse_414902_AUD_10Xv2 [L8TX_181011_01_C04]

value: Light


title: CTRL KD 2

description: bulk RNA-seq

value: Neural culture cells, with NT shRNA KD


title: Mouse_407906_AUD_10Xv2 [L8TX_180829_01_D10]

value: 55 days


title: TDP-43-HA OFF 2

description: bulk RNA-seq


title: TDP-43 KD 2

description: bulk RNA-seq


title: CTRL KD 1

description: bulk RNA-seq


title: Mouse_410109_AUD_10Xv2 [L8TX_180907_01_F10]


title: Mouse_407906_AUD_10Xv2 [L8TX_180829_01_D09]


title: Mouse_407906_AUD_10Xv2 [L8TX_180829_01_E10]


title: Mouse_396976_AId-AIv-AIp_10Xv2 [L8TX_180712_01_B06]

source_name: AId-AIv-AIp

value: AId-AIv-AIp

value: 59 days


title: Mouse_398348_AId-AIv-AIp_10Xv2 [L8TX_180712_01_C06]

value: 54 days


title: Mouse_396975_AId-AIv_10Xv2 [L8TX_180712_01_G05]

source_name: AId-AIv

value: AId-AIv


title: TDP-43-HA OFF 3

description: bulk RNA-seq


title: TDP-43 KD 3

description: bulk RNA-seq


title: CTRL KD 3

description: bulk RNA-seq


title: TDP-43-HA OFF 4

description: bulk RNA-seq


title: Mouse_392473_AId-AIv_10Xv2 [L8TX_180607_01_C05]


title: TDP-43 KD 4

description: bulk RNA-seq


title: Mouse_374166_AId-AIv-AIp_10Xv2 [L8TX_180221_01_H12]

value: 57 days


title: Mouse_380340_ENT_10Xv2 [L8TX_180406_01_H01]

source_name: ENT

value: ENT


title: CTRL KD 4

description: bulk RNA-seq


title: TDP-43-HA ON 1

description: bulk RNA-seq


title: Mouse_410109_AUD_10Xv2 [L8TX_180907_01_G10]

value: AUD


title: Mouse_373314_AId-AIv_10Xv2 [L8TX_180221_01_E09]

value: 51 days


title: Mouse_372317_AId-AIv-AIp_10Xv2 [L8TX_180221_01_D09]

value: 56 days


title: TDP-43-HA ON 2

description: bulk RNA-seq


title: Mouse_366676_VIS_10Xv2 [L8TX_180115_01_H10]

source_name: VIS

value: VIS


title: Mouse_372317_AId-AIv-AIp_10Xv2 [L8TX_180221_01_C09]


title: Day 96, replicate 5

description: single-cell RNA-seq

value: Neural culture cells


title: Day 52, replicate 3

description: single-cell RNA-seq


title: Mouse_366678_VIS_10Xv2 [L8TX_180115_01_E11]


title: Mouse_446714_RSP_10Xv2 [L8TX_190312_01_H02]

source_name: RSP

value: RSP


title: Mouse_366676_VIS_10Xv2 [L8TX_180115_01_F10]


title: Mouse_446714_RSP_10Xv2 [L8TX_190312_01_F02]


title: NSC, replicate 2

description: single-cell RNA-seq


title: Mouse_446714_RSP_10Xv2 [L8TX_190312_01_E02]


title: NSC, replicate 1

description: single-cell RNA-seq


title: Day 223, replicate 5

description: single-cell RNA-seq


title: Mouse_446714_RSP_10Xv2 [L8TX_190312_01_A03]


title: Mouse_374158_RSP_10Xv2 [L8TX_180221_01_G11]

value: 53 days


title: Day 223, replicate 6

description: single-cell RNA-seq


title: Mouse_374158_RSP_10Xv2 [L8TX_180221_01_F11]


title: TDP43-HA, week 4, DOX on replicate A

description: single-cell RNA-seq

value: Neural culture cells, with TDP-43-HA


title: TDP43-HA, week 4, DOX on replicate B

description: single-cell RNA-seq


title: TDP43-HA, week 4, DOX off

description: single-cell RNA-seq

value: Neural culture cells, with TDP-43-HA, OFF control


title: Mouse_373822_RSP_10Xv2 [L8TX_180221_01_C11]

value: Light

value: 52 days


title: Mouse_373822_RSP_10Xv2 [L8TX_180221_01_D11]


title: TDP43-HA, week 2, DOX on

description: single-cell RNA-seq


title: Day 96, replicate 6

description: single-cell RNA-seq


title: Day 52, replicate 4

description: single-cell RNA-seq


title: Mouse_412204_PTLp_10Xv2 [L8TX_180926_01_E12]

source_name: PTLp

value: PTLp


title: Case_23_Heparin

city: Chicago

first: Xiaolong

last: Cui

state: IL

address: 680 N Lake Shore Drive

department: Department of Preventive Medicine

institute: Northwestern University

library_source: genomic

data_processing:
Sequencing reads were trimmed by Trim_galore to remove low-quality nucleotides.
Clean reads were aligned to hg19 reference genome by Bowtie2.
PCR duplicates were removed by Samtools.
Uniquely mapped reads were counted on gene-bodies by FeatureCounts.
Assembly: hg19
Supplementary files format and content: Bigwig files normalized to show RPKM.

molecule: genomic DNA

source_name: Plasma

extract_protocol:
Plasma were separated from blood,then cfDNA were extracted from plasma using zymo research Quick-cfRNA Serum & Plasma, 10ng cfDNA was used for library construction.
DNA libraries were prepared for sequencing using standard Illumina protocols

value: Plasma

tag: race

value: White, Non-Hispanic

tag: gender

value: M

tag: anticoagulants

value: Heparin

tag: condition

value: CRC


title: Mouse_374158_RSP_10Xv2 [L8TX_180221_01_E11]


title: Control_25_EDTA

value: EDTA

value: Control


title: Mouse_373822_RSP_10Xv2 [L8TX_180221_01_B11]


title: Mouse_372312_PL-ILA-ORB_10Xv2 [L8TX_180221_01_D10]

source_name: PL-ILA-ORB

value: PL-ILA-ORB


title: Case_17_EDTA

value: F


title: Case_6_EDTA


title: Mouse_426004_MOs-FRP_10Xv2 [L8TX_181206_01_F12]

value: MOs-FRP

value: 61 days


title: Control_12_EDTA


title: Mouse_426004_MOs-FRP_10Xv2 [L8TX_181206_01_D12]


title: Mouse_426004_MOs-FRP_10Xv2 [L8TX_181206_01_E12]


title: Case_23_EDTA


title: Case_29_EDTA


title: Mouse_426004_MOs-FRP_10Xv2 [L8TX_181206_01_C12]


title: Control_28_EDTA


title: Mouse_352353_MOp_10Xv2 [L8TX_171026_01_G03]

value: MOp

value: 57 days


title: Case_13_EDTA


title: Case_12_Heparin


title: Mouse_352353_MOp_10Xv2 [L8TX_171026_01_F03]


title: Control_17_EDTA


title: Mouse_352353_MOp_10Xv2 [L8TX_171026_01_B04]


title: Case_17_Heparin


title: Control_7_EDTA


title: Mouse_352357_MOp_10Xv2 [L8TX_171026_01_H05]

value: 58 days


title: Case_13_Heparin


title: Mouse_352356_MOp_10Xv2 [L8TX_171026_01_A05]

value: Light


title: Case_24_Heparin


title: Mouse_352357_MOp_10Xv2 [L8TX_171026_01_D05]


title: Mouse_352357_MOp_10Xv2 [L8TX_171026_01_C05]


title: Case_22_EDTA


title: Mouse_352353_MOp_10Xv2 [L8TX_171026_01_A04]


title: Case_11_Heparin


title: Control_18_Heparin


title: Mouse_380340_ENT_10Xv2 [L8TX_180406_01_G02]

value: ENT

value: 56 days


title: Control_7_Heparin

value: Plasma


title: Case_2_Heparin

value: White, Non-Hispanic


title: Mouse_380345_ENT_10Xv2 [L8TX_180406_01_E06]


title: Case_20_EDTA


title: Control_30_Heparin

value: M


title: Mouse_380340_ENT_10Xv2 [L8TX_180406_01_E02]


title: Mouse_352353_MOp_10Xv2 [L8TX_171026_01_H03]


title: Mouse_380345_ENT_10Xv2 [L8TX_180406_01_E07]


title: Mouse_380345_ENT_10Xv2 [L8TX_180406_01_C08]


title: Case_25_EDTA


title: Case_24_EDTA


title: Mouse_371230_ACA_10Xv2 [L8TX_180221_01_G09]

source_name: ACA

value: ACA

value: 55 days


title: Mouse_371230_ACA_10Xv2 [L8TX_180221_01_H09]


title: Control_14_EDTA

value: EDTA


title: Case_12_EDTA

value: CRC


title: Mouse_371232_ACA_10Xv2 [L8TX_180221_01_B10]


title: Control_8_EDTA

value: Control


title: Control_18_EDTA

value: F


title: Mouse_371232_ACA_10Xv2 [L8TX_180221_01_C10]


title: Mouse_371232_ACA_10Xv2 [L8TX_180221_01_A10]


title: Mouse_380340_ENT_10Xv2 [L8TX_180406_01_H02]


title: Control_20_Heparin

value: Heparin


title: Mouse_381296_ACA_10Xv2 [L8TX_180406_01_F02]


title: Mouse_381296_ACA_10Xv2 [L8TX_180406_01_C06]


title: Mouse_366678_VIS_10Xv2 [L8TX_180115_01_H11]

value: VIS

value: 59 days


title: Control_8_Heparin


title: Case_10_EDTA


title: Mouse_366292_VIS_10Xv2 [L8TX_180115_01_H09]

value: 57 days


title: Control_9_Heparin


title: Case_3_EDTA


title: Case_18_Heparin


title: Control_1_Heparin


title: Mouse_366678_VIS_10Xv2 [L8TX_180115_01_F11]


title: Case_25_Heparin


title: Control_5_Heparin


title: Mouse_365619_VIS_10Xv2 [L8TX_180115_01_F09]


title: Mouse_365617_VISl_10Xv2 [L8TX_180115_01_G08]

source_name: VISl

value: VISl

value: 58 days


title: Mouse_371230_ACA_10Xv2 [L8TX_180221_01_F09]

value: Light


title: Control_2_Heparin


title: Control_24_Heparin


title: Mouse_366676_VIS_10Xv2 [L8TX_180115_01_E10]


title: Control_6_EDTA


title: Mouse_365617_VISp_10Xv2 [L8TX_180115_01_F08]

source_name: VISp

value: VISp


title: Mouse_366678_VIS_10Xv2 [L8TX_180115_01_D11]


title: Case_2_EDTA

value: Plasma


title: Mouse_365619_VIS_10Xv2 [L8TX_180115_01_C09]


title: Case_8_Heparin

value: White, Non-Hispanic


title: Mouse_366676_VIS_10Xv2 [L8TX_180115_01_B11]


title: Mouse_365619_VIS_10Xv2 [L8TX_180115_01_D09]


title: Control_3_Heparin

value: M


title: Mouse_365619_VIS_10Xv2 [L8TX_180115_01_B09]


title: Control_4_EDTA


title: Mouse_366292_VIS_10Xv2 [L8TX_180115_01_B10]


title: Case_4_Heparin


title: Mouse_366678_VIS_10Xv2 [L8TX_180115_01_G11]


title: Mouse_366676_VIS_10Xv2 [L8TX_180115_01_A11]


title: Control_26_EDTA


title: Mouse_365619_VIS_10Xv2 [L8TX_180115_01_A09]


title: Mouse_355878_VISl_10Xv2 [L8TX_171120_01_H07]


title: Case_19_EDTA


title: Mouse_355877_VISa_10Xv2 [L8TX_171120_01_H06]

source_name: VISa

value: VISa


title: Control_30_EDTA


title: Control_12_Heparin


title: Mouse_355878_VISp_10Xv2 [L8TX_171120_01_F07]


title: Case_27_EDTA


title: Control_22_EDTA


title: Mouse_355878_VISm_10Xv2 [L8TX_171120_01_C07]

source_name: VISm

value: VISm


title: Mouse_525798_TEa-PERI-ECT_10Xv2 [L8TX_200611_02_A05]

source_name: TEa-PERI-ECT

value: TEa-PERI-ECT

value: 69 days


title: Mouse_414906_SSs-GU-VISC-AIp_10Xv2 [L8TX_181011_01_H03]

source_name: SSs-GU-VISC-AIp

value: SSs-GU-VISC-AIp


title: Mouse_414906_SSs-GU-VISC-AIp_10Xv2 [L8TX_181011_01_C03]


title: Control_1_EDTA

value: EDTA

value: Control


title: Case_8_EDTA

value: F

value: CRC


title: Control_11_Heparin

value: Heparin


title: Mouse_414906_SSs-GU-VISC-AIp_10Xv2 [L8TX_181011_01_B03]

value: 59 days


title: Control_2_EDTA


title: Mouse_414906_SSs-GU-VISC-AIp_10Xv2 [L8TX_181011_01_A03]


title: Case_1_Heparin


title: Mouse_412866_SSs-GU-VISC-AIp_10Xv2 [L8TX_180926_01_H12]

value: 56 days


title: Control_19_Heparin


title: Case_14_Heparin


title: Mouse_412866_SSs-GU-VISC-AIp_10Xv2 [L8TX_180926_01_G12]

value: Light


title: Case_11_EDTA


title: Control_15_Heparin


title: Mouse_412866_SSs-GU-VISC-AIp_10Xv2 [L8TX_180926_01_F12]


title: Mouse_355878_VISl_10Xv2 [L8TX_171120_01_G07]

value: VISl


title: Mouse_395342_TEa-PERI-ECT_10Xv2 [L8TX_180712_01_F05]


title: Control_21_Heparin

value: Plasma


title: Mouse_443644_OLF - PIR_10Xv2 [L8TX_190228_01_F11]

source_name: OLF - PIR

value: OLF - PIR

value: 58 days


title: Case_22_Heparin

value: White, Non-Hispanic


title: Mouse_395345_TEa-PERI-ECT_10Xv2 [L8TX_180712_01_H05]


title: Control_21_EDTA


title: Mouse_441865_OLF - PIR_10Xv2 [L8TX_190214_01_E10]

value: 53 days


title: Case_30_EDTA

value: M


title: Mouse_374165_HIP_10Xv2 [L8TX_180221_01_G12]

source_name: HIP

value: HIP


title: Case_30_Heparin


title: Control_19_EDTA


title: Control_26_Heparin


title: Mouse_404122_TH - Anterior_10Xv2 [L8TX_180815_01_C07]

source_name: TH - Anterior

value: TH - Anterior


title: Control_29_Heparin


title: Control_20_EDTA

value: EDTA


title: Case_3_Heparin


title: Mouse_404124_TH - Posterior_10Xv2 [L8TX_180815_01_H08]

source_name: TH - Posterior

value: TH - Posterior


title: Case_10_Heparin

value: F


title: Case_4_EDTA

value: CRC


title: Mouse_381295_PAR-POST-PRE-SUB-ProS_10Xv2 [L8TX_180406_01_G01]

source_name: PAR-POST-PRE-SUB-ProS

value: PAR-POST-PRE-SUB-ProS

value: 54 days


title: Mouse_374165_HIP_10Xv2 [L8TX_180221_01_F12]

value: 56 days


title: Mouse_434450_CTXsp - CLA-EP-LA-BLA-BMA-PA_10Xv2 [L8TX_190116_01_C04]

source_name: CTXsp - CLA-EP-LA-BLA-BMA-PA

value: CTXsp - CLA-EP-LA-BLA-BMA-PA

value: Light

value: 61 days


title: Case_1_EDTA

value: Plasma


title: Mouse_443644_OLF - PIR_10Xv2 [L8TX_190228_01_A01]

value: OLF - PIR

value: 58 days


title: Control_10_Heparin

value: White, Non-Hispanic

value: Heparin

value: Control


title: Mouse_381293_PAR-POST-PRE-SUB-ProS_10Xv2 [L8TX_180406_01_F01]

value: 53 days


title: Control_15_EDTA

value: M

value: EDTA


title: Mouse_381295_PAR-POST-PRE-SUB-ProS_10Xv2 [L8TX_180406_01_D01]


title: Mouse_381295_PAR-POST-PRE-SUB-ProS_10Xv2 [L8TX_180406_01_D02]


title: Mouse_381917_HIP_10Xv2 [L8TX_180406_01_B07]

value: HIP


title: Control_16_Heparin

value: F


title: Mouse_381295_PAR-POST-PRE-SUB-ProS_10Xv2 [L8TX_180406_01_E01]

value: PAR-POST-PRE-SUB-ProS


title: Control_24_EDTA


title: Case_26_Heparin

value: CRC


title: Case_7_EDTA


title: Mouse_381295_PAR-POST-PRE-SUB-ProS_10Xv2 [L8TX_180406_01_C02]

value: 54 days


title: Mouse_374165_HIP_10Xv2 [L8TX_180221_01_E12]

value: 56 days


title: Case_5_EDTA


title: Mouse_381293_PAR-POST-PRE-SUB-ProS_10Xv2 [L8TX_180406_01_C01]

value: Light


title: Mouse_381293_PAR-POST-PRE-SUB-ProS_10Xv2 [L8TX_180406_01_B02]


title: Case_15_EDTA


title: Mouse_404122_TH - Anterior_10Xv2 [L8TX_180815_01_D07]

value: TH - Anterior


title: Mouse_381293_PAR-POST-PRE-SUB-ProS_10Xv2 [L8TX_180406_01_B01]


title: Case_21_EDTA

value: Plasma


title: Mouse_529272_HIP_10Xv2 [L8TX_200625_02_G11]

value: 62 days


title: Case_19_Heparin


title: Case_20_Heparin


title: Mouse_529270_HIP_10Xv2 [L8TX_200625_02_E11]

value: 61 days


title: Mouse_529272_HIP_10Xv2 [L8TX_200625_02_F11]


title: Control_17_Heparin

value: White, Non-Hispanic


title: Case_16_EDTA


title: Mouse_381917_HIP_10Xv2 [L8TX_180406_01_G07]


title: Mouse_381917_HIP_10Xv2 [L8TX_180406_01_F07]


title: Mouse_381917_HIP_10Xv2 [L8TX_180406_01_F06]


title: Mouse_381917_HIP_10Xv2 [L8TX_180406_01_D07]


title: Control_6_Heparin

value: Heparin


title: Control_23_EDTA

value: Control


title: Control_13_EDTA


title: Mouse_381917_HIP_10Xv2 [L8TX_180406_01_D06]


title: TC2Ras tumor + unprimed_ASC  replicate3

city: West Lafayette

first: Sagar

middle: M

last: Utturkar

state: IN

address: 201 S University St

department: Institute for Cancer Research

institute: Purdue University

data_processing:
Cutadaptand perl scripts in house were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases, followed by sequence quality verification using FASTQC.
HISAT2 was used to map reads to the human genome.
The mapped reads of each sample were assembled using StringTie. All transcriptomes were merged to reconstruct a comprehensive transcriptome using perl scripts and gffcompare. After the ﬁnal transcriptome was generated, StringTie and ballgown was used to estimate the expression levels of all transcripts.
StringTie was used to perform expression level for mRNAs by calculating FPKM. mRNAs differential expression analysis were performed by R package DESeq2.
Assembly: GRCm38
Supplementary files format and content: Excel file containing raw counts for each sample

source_name: prostate tumor SC

growth_protocol: Human ASC from a male Caucasian donor (65 years old and BMI 33.19) were obtained from LaCell/Obatala. ASC were cultured on fibronectin-coated plasticware in modified media (ASC media) (Shearer et al., 2016). At passage 4, cells were transduced with a lentivirus to express renilla luciferase (LV-Rluc-Puro; G&P Bioscience, Santa Clara, CA) at MOI 2, using a ViraDuctin Lentivirus Transduction Kit (Cell BioLabs, San Diego, CA). Selection for transduced cells was performed for 2 weeks by supplementing growth media with 1 ug/mL of puromycin (Sigma-Aldrich). Mouse TRAMP-C2 (TC2) cells are advanced prostate adenocarcinoma cells (ATCC, CRL-2731), derived from a primary tumor in the prostate of Probasin-SV40-T antigen (TRAMP) adult C57/BL6 male mouse (Foster et al., 1997). Our group has further transduced TC2 with a lentivirus to express activated H-ras G12V and mouse androgen receptor (TC2R) (Zolochevska et al., 2013), observing significantly more rapid growth of these cells relative to the parental TC2 (Umbaugh, 2018). The TC2R cells are serve as a model of aggressive PrCa to be examined in C57/BL6 immune competent mice. These cells were maintained in DMEM-F12 supplemented with 10% FBS and 1% anti-anti.

extract_protocol:
QIAGEN Rneasy kit
Poly(A) RNA sequencing library was prepared following Illumina’s TruSeq-stranded-mRNA sample preparation protocol. RNA integrity was checked with Agilent Technologies 2100 Bioanalyzer. Poly(A) tail-containing mRNAs were purified using oligo-(dT) magnetic beads with two rounds of purification. After purification, poly(A) RNA was fragmented using divalent cation buffer in elevated temperature. The DNA library construction is shown in the following workflow. Quality control analysis and quantification of the sequencing library were performed using Agilent Technologies 2100 Bioanalyzer High Sensitivity DNA Chip.

treatment_protocol: ASC were thawed and expanded as described above. After expansion, cells were seeded in non-coated 6-well plates at a density of 3 x 105 cells/well and allowed to attach overnight in complete media. ASC were primed for 1 hour in priming media containing DMEM-F12 (Corning) supplemented with 16.5% FBS (ATCC), 1X Anti-Anti. Unprimed MSC, incubated in priming media, were used as control. TLR agonists were added to the priming media as follows: Poly I:C 1 µg/mL (1:1 mix of HMW and LMW poly I:C, Invivogen), or LPS 10 ng/mL (Millipore) (Waterman et al., 2010). After the completion of the hour, cell cultures were washed twice with PBS and comixed with PrCa cells as described below.

value: prostate tumor SC

value: prostate adenocarcinoma


title: Control_4_Heparin

value: M


title: Control_27_EDTA

value: EDTA


title: TC2Ras tumor + unprimed_ASC  replicate2


title: Case_7_Heparin

value: F


title: Control_13_Heparin


title: TC2Ras tumor + ASC_polyI:C  replicate3


title: Case_9_EDTA


title: TC2Ras tumor + ASC_polyI:C  replicate1


title: TC2Ras tumor + ASC_polyI:C replicate2


title: Case_29_Heparin


title: Case_16_Heparin


title: Case_28_Heparin


title: Case_5_Heparin


title: Control_29_EDTA


title: Control_11_EDTA


title: TC2Ras tumor + ASC_LPS  replicate3


title: TC2Ras tumor + noASC  replicate1

value: noASC


title: TC2Ras tumor + noASC  replicate3


title: Case_18_EDTA

value: CRC


title: TC2Ras tumor + noASC  replicate2


title: Mouse_381917_HIP_10Xv2 [L8TX_180406_01_B08]

value: HIP


title: Control_9_EDTA


title: Control_27_Heparin


title: TC2Ras tumor + ASC_LPS replicate1


title: TC2Ras tumor + ASC_LPS replicate2


title: Control_14_Heparin


title: Ligation

first: Guangzheng

last: Shi

address: No. 197, Ruijin Second Road

department: Ruijin Hospital

institute: Shanghai Jiao Tong University School of Medicine

description:
tissue: mice cartoid artery treatment: ligation age: 8 weeks strain：C57/BL6
10x Genomics

data_processing:
1. Genome Alignment Cell Ranger (http://support.10xgenomics.com/single-cell/software/overview/welcome) uses an aligner called STAR (https://github.com/alexdobin/STAR), which peforms splicing-aware alignment of reads to the genome. Cell Ranger then uses the transcript annotation GTF to bucket the reads into exonic, intronic, and intergenic, and by whether the reads align (confidently) to the genome. A read is exonic if at least 50% of it intersects an exon, intronic if it is non-exonic and intersects an intron, and intergenic otherwise. Cell Ranger further aligns exonic reads to annotated transcripts, looking for compatibility. A read  that is compatible with the exons of an annotated transcript, and aligned to the same strand, is  considered mapped to the transcriptome. If the read is compatible with a single gene annotation, it  is considered uniquely (confidently) mapped to the transcriptome. Only reads that are confidently  mapped to the transcriptome are used for UMI countin
2.Calling Cell Barcodes Cell Ranger takes as input the expected number of recovered cells, N. Let m be a robust estimate of the maximum total UMI counts, taken as the 99th percentile of the top N barcodes by total UMI counts. All barcodes whose total UMI counts exceed m/10 are called as cells.
3.Depth normalization When combining data from multiple libraries, we recommend equalizing the read depth between libraries before merging, to reduce the batch effect introduced by sequencing. Subsample reads from higher-depth libraries until they all have an equal number of total reads per cell.
Assembly: m/10
Supplementary files format and content: Seurat was use to perform QC, analysis, and exploration of scRNA-seq data.

source_name: carotid artery

extract_protocol:
Euthanized mice were perfused with PBS. Carotid arteries were extracted and placed on ice in DMEM containing 10% fetal bovine serum. To get single-cell suspensions, arteries were washed three times with PBS, cut into fine pieces, and digested for 30 minutes at 37 °C with reciprocal shaking in a mixed digesting solution containing collagenase I (1mg/ml). Single cells were resuspended in DMEM with 10% FBS. At the completion of the digestion process, all digested cells from a single sample were pooled together. Cells were collected after being filtered through a 40um cell strainer and centrifuged for 8 minutes at 500g speed at 4 °C. Subsequently, cell pellet was suspended in HBSS for further experiments.
R1 (read 1 primer sequence) are added to the molecules during GEM incubation. P5, P7, a sample index, and R2 (read 2 primer sequence) are added during library construction via End Repair, A_x0002_tailing, Adaptor Ligation, and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification.

value: carotid artery

value: 8 weeks

value: ligation


title: lung_sc_rtx_rep3

city: New York

first: BiNGS

last: Core

address: 1470 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

description:
subcutaneous resiniferatoxin injection
raw_gene_counts_salmon_figure_3S.csv

data_processing:
FastQC (v0.11.8) was used to assess raw data quality
Trim Galore! (v0.6.6) was used to trim adapters with a quality threshold of 20
Salmon (v1.2.1) was used to obtain gene level read counts from trimmed fastqs
STAR aligner (v2.7.5b) was used to align reads to reference genome. All samples have passed the alignment quality control requirements with > 90% of reads uniquely mapping (>10M uniquely mapped reads for each library)
Assembly: grcm38
Supplementary files format and content: Processed data contains ENSEMBL gene id, gene name, and raw read counts for each sample

source_name: Lung

extract_protocol:
RNA was harvested using Rneasy plus universal mini kit (Qiagen).
The RNA sequencing library was prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer’s instructions (New England Biolabs, Ipswich, MA, USA). Briefly, mRNAs were initially enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing library was validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).

treatment_protocol:
Recipient mice (WT or human JAK1 GOF) received the same number of cells, at 1 x 107 live BM cells per mouse, through intravenous (i.v.) injection within 24 hours after irradiation.
WT C57BL/6 mice were injected daily intrathecally (i.t.) in the L5-L6 region with RTX (25 ng/mouse for two consecutive days) or given vehicle (10 μl saline)
WT C57BL/6 mice were injected daily subcutaneously (s.c.) in the flank in increasing doses of RTX (30, 70, 100 μg/kg for three consecutive days) or given vehicle (100 μl saline).
Mice were administered Alternaria alternata extract ( 2 mg/dose in 40 μl of sterile phosphate-buffered saline [PBS]) intranasally for four consecutive days (Day 0, 1, 2, and 3) for the induction of allergic lung inflammation.

value: Lung

value: WT

value: intranasal Alternaria alternata


title: lung_sc_rtx_rep2


title: Control_23_Heparin

source_name: Plasma

value: Plasma

value: White, Non-Hispanic


title: TC2Ras tumor + unprimed_ASC  replicate1


title: Sham

description:
tissue: mice cartoid artery treatment: none age: 8 weeks strain：C57/BL6
10x Genomics


title: Control_10_EDTA

value: Control


title: Control_5_EDTA


title: Case_6_Heparin

value: Heparin


title: lung_sc_rtx_rep1


title: Case_14_EDTA


title: lung_sc_vehicle_rep2

description:
subcutaneous vehicle injection
raw_gene_counts_salmon_figure_3S.csv


title: lung_sc_vehicle_rep1


title: Case_27_Heparin


title: Case_9_Heparin


title: Control_25_Heparin


title: lung_it_rtx_rep3

description:
intrathecal resiniferatoxin injection
raw_gene_counts_salmon_figure_3L.csv


title: Control_28_Heparin


title: lung_it_vehicle_rep2

description:
intrathecal vehicle injection
raw_gene_counts_salmon_figure_3L.csv


title: Control_22_Heparin


title: lung_it_rtx_rep2


title: lung_it_vehicle_rep1


title: Case_26_EDTA


title: Control_3_EDTA


title: Case_21_Heparin


title: lung_wt_to_humanJAK1GOF_rep1

description:
BM chimera: WT_to_human JAK1 GOF
raw_gene_counts_salmon_figure_2M.csv

value: human JAK1 GOF


title: lung_it_rtx_rep1


title: Case_28_EDTA


title: lung_wt_to_humanJAK1GOF_rep2


title: Case_15_Heparin

value: M


title: lung_wt_to_wt_rep2

description:
BM chimera: WT_to_WT
raw_gene_counts_salmon_figure_2M.csv


title: Control_16_EDTA

value: EDTA


title: lung_wt_to_wt_rep1


title: Human 160h embryo spent media, participant 013, rep1 [P-013-160-1]

city: La Jolla

first: Sheng

last: Zhong

address: 9500 Gilman Dr

institute: UCSD

data_processing:
Adapters and low-quality bases were trimmed by Trimmomatic (version 0.36).
The trimmed sequences were aligned to the human reference genome (GRCh38/hg38) by STAR (version 2.5.4b) and de-duplicated by UMI.
Read counts per gene were calculated by featureCounts (version 1.6.1) with the RefSeq gene annotation GTF file (GRCh38/p14).
Read counts were converted to normalized counts (NC) by DESeq2 in R (R package DESeq2).
Assembly: hg38
Supplementary files format and content: IVF_NC.tsv: normalized counts level for each gene and sample with genes in rows and samples in columns
Library strategy: SILVER-seq

extract_protocol:
The spent media in their original culture dishes were obtained immediately after embryo transfer to fresh media. The fertility center follows a 7-day standard procedure. In this procedure, the collected oocytes are screened for maturity (the time of screening is designated as the 0th hour). The mature oocytes (MII oocytes) undergo intracytoplasmic sperm injection and are subsequently cultured in G-1™ PLUS media (G1). At the 18th hour, the embryos are washed and transferred to new G1 media. The spent G1 media are collected (18h spent media, 62 droplets). At the 68th hour, the embryos are transferred to new G-2™ PLUS media (G2), and the spent G1 media are collected (68h spent media, 70 droplets). At the 120th hour, the embryos are evaluated, and the spent media are (120h spent media, 69 droplets). Depending on the evaluation, the embryos are either frozen for transferring to the uterus or transferred to fresh G2 media for additional culturing. Those embryos subjected to additional culturing are collected at the 160th hour (160h spent media, 60 droplets).
The spent media were carefully aspirated out from the original culture dishes and centrifuged at 500 ×g for 3 min under 4°C. The supernatant was aspirated and centrifuged again. A 7 μL aliquot of the supernatant of the 2nd round of centrifugation was used as the input to SILVER-seq.

value: Human embryo spent media

tag: participant id

tag: collection time

tag: arrest status

tag: uniquely mapped_ratio_>_25%

value: N

tag: cultured w/_cumulus_cells


title: Human 160h embryo spent media, participant 028, rep1 [P-028-160-2]

value: Arrest


title: Human 160h embryo spent media, participant 028, rep1 [P-028-160-1]


title: Sample_VEH2-9_IGO_12061_107

first: Stanislav

last: Dikiy

state: CA

address: 10550 North Torrey Pines Road

department: Immunology

institute: Scripps Research

description: single cell

data_processing:
Adapter trimming: Trimmomatic (version 0.39): TrimmomaticPE Sample_R1.fastq.gz Sample_R2.fastq.gz -baseout Sample.fastq.gz ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Alignment: STAR (version 2.7.3a): STAR --runThreadN 6 --runMode alignReads --genomeLoad NoSharedMemory --readFilesCommand zcat --genomeDir mm39_100_RNA --readFilesIn Sample_1P.fastq.gz Sample_2P.fastq.gz --outFileNamePrefix Sample --outSAMtype BAM Unsorted --outBAMcompression 6 --outFilterMultimapNmax 1 --outFilterMismatchNoverLmax 0.06 --outFilterMatchNminOverLread 0.35 --outFilterMatchNmin 30 --alignEndsType EndToEnd
Sort: samtools (version 1.12): samtools sort -@ 4 -n -o Sample.bam SampleAligned.out.bam
Mate coordinates: samtools (version 1.12): samtools fixmate -@ 4 -rm Sample.bam Sample.fixmate.bam
Sort: samtools (version 1.12): samtools sort -@ 4 -o Sample.resort.bam Sample.fixmate.bam
Remove duplicates: samtools (version 1.12): samtools markdup -@ 4 -l 1500 -r -d 100 -s Sample.resort.bam Sample.duprm.bam
Index: samtools (version 1.12): samtools index -@ 4 -b Sample.duprm.bam
Count reads: GenomicAlignments (R, version 1.26.0): summarizeOverlaps (default parameters)
Assembly: mm39 (modified)
Supplementary files format and content: mtx file with counts (aligned to gene) against all samples
Supplementary files format and content: genes.tsv: gene names corresponding to row names of mtx file
Supplementary files format and content: cells.tsv: cell (sample) corresponding to column names of mtx file

source_name: Skin

extract_protocol:
Cells were sorted into Buffer RLT (Qiagen catalog # 79216) and RNA was purified using the Agencourt RNAClean XP beads (Beckman Coulter catalog # A63987) at a 2.2X ratio.
First-strand cDNA synthesis was achieved using Maxima H Minus Reverse Transcriptase (ThermoFisher catalog # EP0751) according to the manufacturer’s protocol using oligo dT primers, plus the addition of a custom template-switch oligo in a 1mM final concentration. cDNA was amplified for 24 cycles using KAPA HiFi HotStart ReadyMix (Kapa Biosystems KK2601). After PicoGreen quantification, 0.1-20 ng of cDNA was used to prepare libraries with the Nextera XT DNA Library Preparation Kit (Illumina catalog # FC-131-1024) in a total volume of 6.25 µL with 12 cycles of PCR. Indexed libraries were pooled by volume and cleaned by aMPure XP beads (Beckman Coulter catalog # A63882) at a 2X ratio.

treatment_protocol: Mice were treated topically on the ears with either imiquimod or vehicle control for 3 days. Cells were isolated from skin and Treg cells were sorted into single wells.

value: Skin

value: regulatory T cell

value: vehicle


title: Sample_VEH2-87_IGO_12061_191

description: single cell


title: Human 160h embryo spent media, participant 014, rep1 [P-014-160-3]


title: Sample_VEH2-84_IGO_12061_188

description: single cell


title: Human 160h embryo spent media, participant 014, rep1 [P-014-160-2]


title: Sample_VEH2-83_IGO_12061_187

description: single cell


title: Human 160h embryo spent media, participant 014, rep1 [P-014-160-1]

value: Developing


title: Human 160h embryo spent media, participant 023, rep1 [P-023-160-2]


title: Sample_VEH2-82_IGO_12061_186

description: single cell


title: Human 160h embryo spent media, participant 027, rep1 [P-027-160-4]


title: Human 160h embryo spent media, participant 027, rep1 [P-027-160-3]


title: Human 160h embryo spent media, participant 027, rep1 [P-027-160-2]


title: Sample_VEH2-81_IGO_12061_185

description: single cell


title: Sample_VEH2-80_IGO_12061_183

description: single cell


title: Sample_VEH2-8_IGO_12061_106

description: single cell


title: Human 160h embryo spent media, participant 023, rep1 [P-023-160-1]


title: Sample_VEH2-76_IGO_12061_179

description: single cell


title: Sample_VEH2-75_IGO_12061_178

description: single cell


title: Sample_VEH2-86_IGO_12061_190

description: single cell


title: Sample_VEH2-74_IGO_12061_177

description: single cell


title: Sample_VEH2-77_IGO_12061_180

description: single cell


title: Human 160h embryo spent media, participant 018, rep1 [P-018-160-4]


title: Human 160h embryo spent media, participant 001, rep1 [P-001-160-6]


title: Sample_VEH2-73_IGO_12061_175

description: single cell


title: Sample_VEH2-78_IGO_12061_181

description: single cell


title: Sample_VEH2-85_IGO_12061_189

description: single cell


title: Human 160h embryo spent media, participant 006, rep1 [P-006-160-4]


title: Human 160h embryo spent media, participant 003, rep1 [P-003-160-1]


title: Human 160h embryo spent media, participant 018, rep1 [P-018-160-3]


title: Human 120h embryo spent media, participant 014, rep1 [P-014-120-3]


title: Human 120h embryo spent media, participant 014, rep1 [P-014-120-2]


title: Human 120h embryo spent media, participant 023, rep1 [P-023-120-3]


title: Sample_VEH2-79_IGO_12061_182

description: single cell


title: Sample_VEH2-70_IGO_12061_172

description: single cell


title: Sample_VEH2-7_IGO_12061_104

description: single cell


title: Sample_VEH2-69_IGO_12061_171

description: single cell


title: Human 120h embryo spent media, participant 015, rep1 [P-015-120-2]


title: Human 120h embryo spent media, participant 015, rep1 [P-015-120-1]


title: Human 160h embryo spent media, participant 027, rep1 [P-027-160-1]


title: Sample_VEH2-68_IGO_12061_170

description: single cell


title: Human 120h embryo spent media, participant 027, rep1 [P-027-120-4]


title: Sample_VEH2-67_IGO_12061_169

description: single cell


title: Human 120h embryo spent media, participant 027, rep1 [P-027-120-3]


title: Sample_VEH2-66_IGO_12061_167

description: single cell


title: Sample_VEH2-65_IGO_12061_166

description: single cell


title: Human 120h embryo spent media, participant 027, rep1 [P-027-120-2]


title: Sample_VEH2-72_IGO_12061_174

description: single cell


title: Human 120h embryo spent media, participant 027, rep1 [P-027-120-1]


title: Human 120h embryo spent media, participant 018, rep1 [P-018-120-4]


title: Human 120h embryo spent media, participant 018, rep1 [P-018-120-3]


title: Sample_VEH2-64_IGO_12061_165

description: single cell


title: Human 120h embryo spent media, participant 018, rep1 [P-018-120-2]


title: Human 120h embryo spent media, participant 018, rep1 [P-018-120-1]


title: Sample_VEH2-62_IGO_12061_163

description: single cell


title: Sample_VEH2-61_IGO_12061_162

description: single cell


title: Human 120h embryo spent media, participant 001, rep1 [P-001-120-6]


title: Sample_VEH2-60_IGO_12061_161

description: single cell


title: Sample_VEH2-71_IGO_12061_173

description: single cell


title: Sample_VEH2-63_IGO_12061_164

description: single cell


title: Human 120h embryo spent media, participant 003, rep1 [P-003-120-1]


title: Sample_VEH2-6_IGO_12061_103

description: single cell


title: Sample_VEH2-59_IGO_12061_159

description: single cell


title: Human 120h embryo spent media, participant 024, rep1 [P-024-120-3]


title: Human 120h embryo spent media, participant 005, rep1 [P-005-120-5]


title: Human 120h embryo spent media, participant 024, rep1 [P-024-120-2]


title: Sample_VEH2-58_IGO_12061_158

description: single cell


title: Human 160h embryo spent media, participant 029, rep1 [P-029-160-1]

value: Y


title: Sample_VEH2-57_IGO_12061_157

description: single cell


title: Sample_VEH2-56_IGO_12061_156

description: single cell


title: Sample_VEH2-54_IGO_12061_154

description: single cell


title: Human 160h embryo spent media, participant 026, rep1 [P-026-160-2]


title: Human 160h embryo spent media, participant 026, rep1 [P-026-160-1]


title: Sample_VEH2-52_IGO_12061_152

description: single cell


title: Sample_VEH2-53_IGO_12061_153

description: single cell


title: Human 160h embryo spent media, participant 007, rep1 [P-007-160-2]


title: Human 160h embryo spent media, participant 020, rep1 [P-020-160-2]


title: Human 160h embryo spent media, participant 004, rep1 [P-004-160-2]


title: Human 160h embryo spent media, participant 020, rep1 [P-020-160-1]


title: Sample_VEH2-51_IGO_12061_151

description: single cell


title: Human 160h embryo spent media, participant 007, rep1 [P-007-160-1]


title: Sample_VEH2-5_IGO_12061_102

description: single cell


title: Sample_VEH2-49_IGO_12061_149

description: single cell


title: Human 160h embryo spent media, participant 004, rep1 [P-004-160-1]


title: Sample_VEH2-47_IGO_12061_147

description: single cell


title: Sample_VEH2-48_IGO_12061_148

description: single cell


title: Human 160h embryo spent media, participant 015, rep1 [P-015-160-1]


title: Human 160h embryo spent media, participant 018, rep1 [P-018-160-2]


title: Sample_VEH2-46_IGO_12061_146

description: single cell


title: Human 160h embryo spent media, participant 026, rep1 [P-026-160-3]


title: Human 160h embryo spent media, participant 018, rep1 [P-018-160-1]


title: Sample_VEH2-55_IGO_12061_155

description: single cell


title: Sample_VEH2-44_IGO_12061_144

description: single cell


title: Sample_VEH2-45_IGO_12061_145

description: single cell


title: Human 160h embryo spent media, participant 002, rep1 [P-002-160-1]


title: Sample_VEH2-42_IGO_12061_142

description: single cell


title: Sample_VEH2-41_IGO_12061_141

description: single cell


title: Sample_VEH2-43_IGO_12061_143

description: single cell


title: Human 160h embryo spent media, participant 002, rep1 [P-002-160-2]


title: Human 160h embryo spent media, participant 001, rep1 [P-001-160-5]


title: Human 160h embryo spent media, participant 001, rep1 [P-001-160-4]


title: Sample_VEH2-50_IGO_12061_150

description: single cell


title: Human 160h embryo spent media, participant 001, rep1 [P-001-160-3]


title: Sample_VEH2-40_IGO_12061_140

description: single cell


title: Sample_VEH2-4_IGO_12061_101

description: single cell


title: Human 160h embryo spent media, participant 001, rep1 [P-001-160-2]


title: Human 160h embryo spent media, participant 001, rep1 [P-001-160-1]


title: Sample_VEH2-39_IGO_12061_139

description: single cell


title: Sample_VEH2-38_IGO_12061_138

description: single cell


title: Human 160h embryo spent media, participant 021, rep1 [P-021-160-1]


title: Sample_VEH2-37_IGO_12061_137

description: single cell


title: Human 160h embryo spent media, participant 024, rep1 [P-024-160-2]


title: Human 160h embryo spent media, participant 024, rep1 [P-024-160-1]


title: Sample_VEH2-36_IGO_12061_136

description: single cell


title: Human 160h embryo spent media, participant 006, rep1 [P-006-160-3]


title: Sample_VEH2-35_IGO_12061_135

description: single cell


title: Sample_VEH2-34_IGO_12061_134

description: single cell


title: Sample_VEH2-33_IGO_12061_133

description: single cell


title: Sample_VEH2-32_IGO_12061_132

description: single cell


title: Human 160h embryo spent media, participant 006, rep1 [P-006-160-1]


title: Human 160h embryo spent media, participant 019, rep1 [P-019-160-1]


title: Human 160h embryo spent media, participant 006, rep1 [P-006-160-2]


title: Sample_VEH2-30_IGO_12061_130

description: single cell


title: Sample_VEH2-31_IGO_12061_131

description: single cell


title: Human 160h embryo spent media, participant 012, rep1 [P-012-160-2]


title: Human 160h embryo spent media, participant 012, rep1 [P-012-160-1]


title: Human 160h embryo spent media, participant 011, rep1 [P-011-160-1]


title: Sample_VEH2-3_IGO_12061_100

description: single cell


title: Sample_VEH2-28_IGO_12061_128

description: single cell


title: Sample_VEH2-29_IGO_12061_129

description: single cell


title: Human 160h embryo spent media, participant 024, rep1 [P-024-160-3]


title: Human 160h embryo spent media, participant 022, rep1 [P-022-160-2]


title: Human 160h embryo spent media, participant 011, rep1 [P-011-160-2]


title: Sample_VEH2-27_IGO_12061_127

description: single cell


title: Human 160h embryo spent media, participant 022, rep1 [P-022-160-1]


title: Sample_VEH2-26_IGO_12061_126

description: single cell


title: Human 160h embryo spent media, participant 009, rep1 [P-009-160-3]


title: Sample_VEH2-25_IGO_12061_125

description: single cell


title: Human 160h embryo spent media, participant 009, rep1 [P-009-160-1]


title: Sample_VEH2-23_IGO_12061_123

description: single cell


title: Human 160h embryo spent media, participant 005, rep1 [P-005-160-5]


title: Sample_VEH2-20_IGO_12061_119

description: single cell


title: Human 160h embryo spent media, participant 005, rep1 [P-005-160-4]


title: Human 160h embryo spent media, participant 025, rep1 [P-025-160-1]


title: Human 160h embryo spent media, participant 005, rep1 [P-005-160-2]


title: Human 160h embryo spent media, participant 005, rep1 [P-005-160-3]


title: Human 160h embryo spent media, participant 005, rep1 [P-005-160-1]


title: Sample_VEH2-18_IGO_12061_117

description: single cell


title: Sample_VEH2-2_IGO_12061_99

description: single cell


title: Sample_VEH2-19_IGO_12061_118

description: single cell


title: Sample_VEH2-17_IGO_12061_116

description: single cell


title: Human 120h embryo spent media, participant 013, rep1 [P-013-120-1]


title: Human 120h embryo spent media, participant 013, rep1 [P-013-120-2]


title: Sample_VEH2-16_IGO_12061_115

description: single cell


title: Human 160h embryo spent media, participant 009, rep1 [P-009-160-2]


title: Sample_VEH2-14_IGO_12061_112

description: single cell


title: Sample_VEH2-22_IGO_12061_122

description: single cell


title: Human 120h embryo spent media, participant 029, rep1 [P-029-120-1]


title: Human 120h embryo spent media, participant 026, rep1 [P-026-120-2]


title: Human 120h embryo spent media, participant 028, rep1 [P-028-120-3]


title: Human 120h embryo spent media, participant 026, rep1 [P-026-120-3]


title: Sample_VEH2-15_IGO_12061_114

description: single cell


title: Sample_VEH2-12_IGO_12061_110

description: single cell


title: Sample_VEH2-13_IGO_12061_111

description: single cell


title: Sample_VEH2-11_IGO_12061_109

description: single cell


title: Human 120h embryo spent media, participant 028, rep1 [P-028-120-2]


title: Human 120h embryo spent media, participant 028, rep1 [P-028-120-1]


title: Sample_VEH2-24_IGO_12061_124

description: single cell


title: Sample_VEH2-1_IGO_12061_98

description: single cell


title: Sample_VEH2-10_IGO_12061_108

description: single cell


title: Sample_VEH-9_IGO_12061_11

description: single cell


title: Human 120h embryo spent media, participant 017, rep1 [P-017-120-3]


title: Sample_VEH2-21_IGO_12061_120

description: single cell


title: Human 120h embryo spent media, participant 017, rep1 [P-017-120-2]


title: Sample_VEH-87_IGO_12061_95

description: single cell


title: Human 120h embryo spent media, participant 017, rep1 [P-017-120-1]


title: Sample_VEH-86_IGO_12061_94

description: single cell


title: Sample_VEH-85_IGO_12061_93

description: single cell


title: Sample_VEH-84_IGO_12061_92

description: single cell


title: Human 120h embryo spent media, participant 026, rep1 [P-026-120-1]


title: Human 120h embryo spent media, participant 007, rep1 [P-007-120-1]


title: Human 120h embryo spent media, participant 007, rep1 [P-007-120-2]


title: Human 120h embryo spent media, participant 004, rep1 [P-004-120-1]


title: Sample_VEH-81_IGO_12061_89

description: single cell


title: Sample_VEH-83_IGO_12061_91

description: single cell


title: Sample_VEH-82_IGO_12061_90

description: single cell


title: Human 120h embryo spent media, participant 020, rep1 [P-020-120-1]


title: Human 120h embryo spent media, participant 023, rep1 [P-023-120-2]


title: Human 120h embryo spent media, participant 004, rep1 [P-004-120-2]


title: Human 120h embryo spent media, participant 020, rep1 [P-020-120-2]


title: Sample_VEH-80_IGO_12061_87

description: single cell


title: Sample_VEH-79_IGO_12061_86

description: single cell


title: Sample_VEH-78_IGO_12061_85

description: single cell


title: Sample_VEH-77_IGO_12061_84

description: single cell


title: Human 120h embryo spent media, participant 002, rep1 [P-002-120-2]


title: Sample_VEH-76_IGO_12061_83

description: single cell


title: Sample_VEH-8_IGO_12061_10

description: single cell


title: Sample_VEH-74_IGO_12061_81

description: single cell


title: Human 120h embryo spent media, participant 002, rep1 [P-002-120-1]


title: Human 120h embryo spent media, participant 001, rep1 [P-001-120-5]


title: Human 120h embryo spent media, participant 001, rep1 [P-001-120-4]


title: Sample_VEH-73_IGO_12061_79

description: single cell


title: Human 120h embryo spent media, participant 001, rep1 [P-001-120-3]


title: Human 120h embryo spent media, participant 001, rep1 [P-001-120-2]


title: Sample_VEH-71_IGO_12061_77

description: single cell


title: Human 120h embryo spent media, participant 014, rep1 [P-014-120-1]


title: Human 120h embryo spent media, participant 001, rep1 [P-001-120-1]


title: Sample_VEH-70_IGO_12061_76

description: single cell


title: Human 120h embryo spent media, participant 021, rep1 [P-021-120-2]


title: Sample_VEH-69_IGO_12061_75

description: single cell


title: Human 120h embryo spent media, participant 006, rep1 [P-006-120-4]


title: Human 120h embryo spent media, participant 024, rep1 [P-024-120-1]


title: Human 120h embryo spent media, participant 021, rep1 [P-021-120-1]


title: Human 120h embryo spent media, participant 023, rep1 [P-023-120-1]


title: Sample_VEH-68_IGO_12061_74

description: single cell


title: Sample_VEH-7_IGO_12061_8

description: single cell


title: Sample_VEH-64_IGO_12061_69

description: single cell


title: Sample_VEH-65_IGO_12061_70

description: single cell


title: Sample_VEH-75_IGO_12061_82

description: single cell


title: Human 120h embryo spent media, participant 025, rep1 [P-025-120-1]


title: Human 120h embryo spent media, participant 006, rep1 [P-006-120-2]


title: Sample_VEH-63_IGO_12061_68

description: single cell


title: Human 120h embryo spent media, participant 019, rep1 [P-019-120-1]


title: Sample_VEH-62_IGO_12061_67

description: single cell


title: Human 120h embryo spent media, participant 010, rep1 [P-010-120-1]


title: Sample_VEH-61_IGO_12061_66

description: single cell


title: Human 120h embryo spent media, participant 012, rep1 [P-012-120-2]


title: Sample_VEH-72_IGO_12061_78

description: single cell


title: Human 120h embryo spent media, participant 012, rep1 [P-012-120-1]


title: Sample_VEH-60_IGO_12061_65

description: single cell


title: Human 120h embryo spent media, participant 011, rep1 [P-011-120-2]


title: Human 120h embryo spent media, participant 006, rep1 [P-006-120-3]


title: Human 120h embryo spent media, participant 011, rep1 [P-011-120-1]


title: Human 120h embryo spent media, participant 006, rep1 [P-006-120-1]


title: Human 120h embryo spent media, participant 022, rep1 [P-022-120-2]


title: Human 120h embryo spent media, participant 022, rep1 [P-022-120-1]


title: Sample_VEH-58_IGO_12061_62

description: single cell


title: Sample_VEH-57_IGO_12061_61

description: single cell


title: Sample_VEH-66_IGO_12061_71

description: single cell


title: Sample_VEH-56_IGO_12061_60

description: single cell


title: Human 120h embryo spent media, participant 009, rep1 [P-009-120-3]


title: Sample_VEH-67_IGO_12061_73

description: single cell


title: Human 120h embryo spent media, participant 009, rep1 [P-009-120-1]


title: Sample_VEH-59_IGO_12061_63

description: single cell


title: Sample_VEH-53_IGO_12061_57

description: single cell


title: Human 120h embryo spent media, participant 009, rep1 [P-009-120-2]


title: Sample_VEH-52_IGO_12061_56

description: single cell


title: Sample_VEH-55_IGO_12061_59

description: single cell


title: Human 120h embryo spent media, participant 005, rep1 [P-005-120-3]


title: Human 120h embryo spent media, participant 005, rep1 [P-005-120-2]


title: Human 120h embryo spent media, participant 005, rep1 [P-005-120-4]


title: Sample_VEH-51_IGO_12061_55

description: single cell


title: Human 120h embryo spent media, participant 005, rep1 [P-005-120-1]


title: Sample_VEH-50_IGO_12061_54

description: single cell


title: Sample_VEH-5_IGO_12061_6

description: single cell


title: Human 68h embryo spent media, participant 013, rep1 [P-013-68-2]


title: Sample_VEH-49_IGO_12061_53

description: single cell


title: Sample_VEH-6_IGO_12061_7

description: single cell


title: Human 68h embryo spent media, participant 013, rep1 [P-013-68-1]


title: Human 68h embryo spent media, participant 026, rep1 [P-026-68-2]


title: Sample_VEH-48_IGO_12061_52

description: single cell


title: Human 68h embryo spent media, participant 026, rep1 [P-026-68-1]


title: Human 68h embryo spent media, participant 028, rep1 [P-028-68-2]


title: Human 68h embryo spent media, participant 028, rep1 [P-028-68-1]


title: Human 68h embryo spent media, participant 017, rep1 [P-017-68-3]


title: Sample_VEH-44_IGO_12061_48

description: single cell


title: Sample_VEH-54_IGO_12061_58

description: single cell


title: Sample_VEH-43_IGO_12061_47

description: single cell


title: Sample_VEH-42_IGO_12061_46

description: single cell


title: Human 68h embryo spent media, participant 017, rep1 [P-017-68-2]


title: Human 68h embryo spent media, participant 007, rep1 [P-007-68-2]


title: Sample_VEH-41_IGO_12061_45

description: single cell


title: Human 68h embryo spent media, participant 017, rep1 [P-017-68-1]


title: Human 68h embryo spent media, participant 007, rep1 [P-007-68-1]


title: Sample_VEH-39_IGO_12061_43

description: single cell


title: Sample_VEH-4_IGO_12061_5

description: single cell


title: Human 68h embryo spent media, participant 004, rep1 [P-004-68-2]


title: Sample_VEH-38_IGO_12061_42

description: single cell


title: Human 68h embryo spent media, participant 004, rep1 [P-004-68-1]


title: Sample_VEH-37_IGO_12061_41

description: single cell


title: Sample_VEH-36_IGO_12061_40

description: single cell


title: Human 68h embryo spent media, participant 014, rep1 [P-014-68-3]


title: Sample_VEH-35_IGO_12061_39

description: single cell


title: Human 68h embryo spent media, participant 014, rep1 [P-014-68-2]


title: Sample_VEH-46_IGO_12061_50

description: single cell


title: Sample_VEH-47_IGO_12061_51

description: single cell


title: Sample_VEH-34_IGO_12061_38

description: single cell


title: Human 68h embryo spent media, participant 014, rep1 [P-014-68-1]


title: Sample_VEH-45_IGO_12061_49

description: single cell


title: Sample_VEH-33_IGO_12061_37

description: single cell


title: Human 68h embryo spent media, participant 023, rep1 [P-023-68-3]


title: Human 68h embryo spent media, participant 023, rep1 [P-023-68-2]


title: Sample_VEH-31_IGO_12061_35

description: single cell


title: Sample_VEH-32_IGO_12061_36

description: single cell


title: Human 68h embryo spent media, participant 023, rep1 [P-023-68-1]


title: Human 68h embryo spent media, participant 015, rep1 [P-015-68-3]


title: Sample_VEH-3_IGO_12061_4

description: single cell


title: Human 68h embryo spent media, participant 020, rep1 [P-020-68-2]


title: Human 68h embryo spent media, participant 015, rep1 [P-015-68-2]


title: Sample_VEH-40_IGO_12061_44

description: single cell


title: Human 68h embryo spent media, participant 016, rep1 [P-016-68-4]


title: Human 68h embryo spent media, participant 015, rep1 [P-015-68-1]


title: Sample_VEH-30_IGO_12061_34

description: single cell


title: Sample_VEH-29_IGO_12061_33

description: single cell


title: Human 68h embryo spent media, participant 020, rep1 [P-020-68-1]


title: Human 68h embryo spent media, participant 016, rep1 [P-016-68-3]


title: Sample_VEH-27_IGO_12061_31

description: single cell


title: Sample_VEH-26_IGO_12061_30

description: single cell


title: Sample_VEH-28_IGO_12061_32

description: single cell


title: Human 68h embryo spent media, participant 016, rep1 [P-016-68-2]


title: Sample_VEH-25_IGO_12061_29

description: single cell


title: Human 68h embryo spent media, participant 016, rep1 [P-016-68-1]


title: Human 68h embryo spent media, participant 027, rep1 [P-027-68-2]


title: Human 68h embryo spent media, participant 027, rep1 [P-027-68-1]


title: Human 68h embryo spent media, participant 018, rep1 [P-018-68-4]


title: Sample_VEH-23_IGO_12061_27

description: single cell


title: Sample_VEH-24_IGO_12061_28

description: single cell


title: Sample_VEH-20_IGO_12061_23

description: single cell


title: Sample_VEH-21_IGO_12061_24

description: single cell


title: Sample_VEH-22_IGO_12061_26

description: single cell


title: Human 68h embryo spent media, participant 018, rep1 [P-018-68-3]


title: Human 68h embryo spent media, participant 018, rep1 [P-018-68-2]


title: Human 68h embryo spent media, participant 018, rep1 [P-018-68-1]


title: Sample_VEH-2_IGO_12061_3

description: single cell


title: Sample_VEH-19_IGO_12061_22

description: single cell


title: Human 68h embryo spent media, participant 002, rep1 [P-002-68-2]


title: Human 68h embryo spent media, participant 002, rep1 [P-002-68-1]


title: Human 68h embryo spent media, participant 001, rep1 [P-001-68-5]


title: Sample_VEH-17_IGO_12061_20

description: single cell


title: Human 68h embryo spent media, participant 001, rep1 [P-001-68-3]


title: Human 68h embryo spent media, participant 001, rep1 [P-001-68-4]


title: Sample_VEH-16_IGO_12061_19

description: single cell


title: Sample_VEH-14_IGO_12061_16

description: single cell


title: Human 68h embryo spent media, participant 001, rep1 [P-001-68-1]


title: Human 68h embryo spent media, participant 001, rep1 [P-001-68-2]


title: Sample_VEH-13_IGO_12061_15

description: single cell


title: Sample_VEH-12_IGO_12061_14

description: single cell


title: Human 68h embryo spent media, participant 003, rep1 [P-003-68-1]


title: Human 68h embryo spent media, participant 021, rep1 [P-021-68-2]


title: Human 68h embryo spent media, participant 003, rep1 [P-003-68-2]


title: Sample_VEH-10_IGO_12061_12

description: single cell


title: Sample_VEH-1_IGO_12061_2

description: single cell


title: Human 68h embryo spent media, participant 021, rep1 [P-021-68-1]


title: Human 68h embryo spent media, participant 024, rep1 [P-024-68-3]


title: Sample_POS4-3_IGO_12061_368

description: positive control (ten cells)


title: Sample_POS4-2_IGO_12061_360

description: positive control (ten cells)


title: Sample_POS4-1_IGO_12061_352

description: positive control (ten cells)


title: Human 68h embryo spent media, participant 006, rep1 [P-006-68-2]


title: Human 68h embryo spent media, participant 024, rep1 [P-024-68-1]


title: Human 68h embryo spent media, participant 024, rep1 [P-024-68-2]


title: Human 68h embryo spent media, participant 006, rep1 [P-006-68-1]


title: Sample_POS3-4_IGO_12061_280

description: positive control (ten cells)


title: Human 68h embryo spent media, participant 025, rep1 [P-025-68-1]


title: Sample_VEH-18_IGO_12061_21

description: single cell


title: Sample_VEH-15_IGO_12061_18

description: single cell


title: Sample_POS3-3_IGO_12061_272

description: positive control (ten cells)


title: Sample_POS3-2_IGO_12061_264

description: positive control (ten cells)


title: Sample_POS3-1_IGO_12061_256

description: positive control (ten cells)


title: Sample_VEH-11_IGO_12061_13

description: single cell


title: Sample_POS2-4_IGO_12061_184

description: positive control (ten cells)


title: Human 68h embryo spent media, participant 012, rep1 [P-012-68-2]


title: Human 68h embryo spent media, participant 012, rep1 [P-012-68-1]


title: Sample_POS4-4_IGO_12061_376

description: positive control (ten cells)


title: Sample_POS2-3_IGO_12061_176

description: positive control (ten cells)


title: Human 68h embryo spent media, participant 011, rep1 [P-011-68-1]


title: Sample_POS-4_IGO_12061_88

description: positive control (ten cells)


title: Human 68h embryo spent media, participant 019, rep1 [P-019-68-1]


title: Human 68h embryo spent media, participant 011, rep1 [P-011-68-2]


title: Human 68h embryo spent media, participant 022, rep1 [P-022-68-1]


title: Sample_POS-3_IGO_12061_80

description: positive control (ten cells)


title: Human 68h embryo spent media, participant 022, rep1 [P-022-68-2]


title: Human 68h embryo spent media, participant 009, rep1 [P-009-68-3]


title: Sample_POS2-1_IGO_12061_160

description: positive control (ten cells)


title: Sample_POS-2_IGO_12061_72

description: positive control (ten cells)


title: Human 68h embryo spent media, participant 009, rep1 [P-009-68-1]


title: Human 68h embryo spent media, participant 009, rep1 [P-009-68-2]


title: Sample_POS-1_IGO_12061_64

description: positive control (ten cells)


title: Sample_NegCTRL4-1_IGO_12061_384

description: control (no cell)

source_name: Empty well

value: Empty well


title: Human 68h embryo spent media, participant 005, rep1 [P-005-68-4]


title: Sample_NegCTRL3-1_IGO_12061_288

description: control (no cell)


title: Sample_NegCTRL-1_IGO_12061_96

description: control (no cell)


title: Human 68h embryo spent media, participant 005, rep1 [P-005-68-2]


title: Human 68h embryo spent media, participant 005, rep1 [P-005-68-3]


title: Human 68h embryo spent media, participant 010, rep1 [P-010-68-1]


title: Sample_NegCTRL2-1_IGO_12061_192

description: control (no cell)


title: Sample_POS2-2_IGO_12061_168

description: positive control (ten cells)


title: Human 68h embryo spent media, participant 005, rep1 [P-005-68-1]


title: Human 18h embryo spent media, participant 026, rep1 [P-026-18-2]


title: Sample_IMQ1-9_IGO_12061_299

description: single cell

value: Imiquimod


title: Sample_IMQ1-87_IGO_12061_383

description: single cell


title: Human 18h embryo spent media, participant 026, rep1 [P-026-18-1]


title: Sample_IMQ1-86_IGO_12061_382

description: single cell


title: Sample_IMQ1-85_IGO_12061_381

description: single cell


title: Human 18h embryo spent media, participant 017, rep1 [P-017-18-2]


title: Sample_IMQ1-83_IGO_12061_379

description: single cell


title: Human 18h embryo spent media, participant 017, rep1 [P-017-18-1]


title: Human 18h embryo spent media, participant 007, rep1 [P-007-18-1]


title: Human 18h embryo spent media, participant 007, rep1 [P-007-18-2]


title: Human 18h embryo spent media, participant 020, rep1 [P-020-18-2]


title: Sample_IMQ1-81_IGO_12061_377

description: single cell


title: Human 18h embryo spent media, participant 020, rep1 [P-020-18-1]


title: Sample_IMQ1-8_IGO_12061_298

description: single cell


title: Sample_IMQ1-80_IGO_12061_375

description: single cell


title: Human 18h embryo spent media, participant 014, rep1 [P-014-18-2]


title: Sample_IMQ1-79_IGO_12061_374

description: single cell


title: Human 18h embryo spent media, participant 004, rep1 [P-004-18-1]


title: Human 18h embryo spent media, participant 014, rep1 [P-014-18-1]


title: Sample_IMQ1-78_IGO_12061_373

description: single cell


title: Sample_IMQ1-76_IGO_12061_371

description: single cell


title: Sample_IMQ1-77_IGO_12061_372

description: single cell


title: Human 18h embryo spent media, participant 023, rep1 [P-023-18-2]


title: Human 18h embryo spent media, participant 023, rep1 [P-023-18-1]


title: Sample_IMQ1-75_IGO_12061_370

description: single cell


title: Human 18h embryo spent media, participant 023, rep1 [P-023-18-3]


title: Sample_IMQ1-74_IGO_12061_369

description: single cell


title: Sample_IMQ1-72_IGO_12061_366

description: single cell


title: Sample_IMQ1-73_IGO_12061_367

description: single cell


title: Human 18h embryo spent media, participant 017, rep1 [P-017-18-3]


title: Sample_IMQ1-84_IGO_12061_380

description: single cell


title: Human 18h embryo spent media, participant 015, rep1 [P-015-18-2]


title: Human 18h embryo spent media, participant 015, rep1 [P-015-18-1]


title: Sample_IMQ1-71_IGO_12061_365

description: single cell


title: Sample_IMQ1-82_IGO_12061_378

description: single cell


title: Human 18h embryo spent media, participant 016, rep1 [P-016-18-3]


title: Sample_IMQ1-70_IGO_12061_364

description: single cell


title: Human 18h embryo spent media, participant 016, rep1 [P-016-18-2]


title: Human 18h embryo spent media, participant 016, rep1 [P-016-18-1]


title: Human 18h embryo spent media, participant 027, rep1 [P-027-18-1]


title: Sample_IMQ1-7_IGO_12061_296

description: single cell


title: Sample_IMQ1-68_IGO_12061_362

description: single cell


title: Human 18h embryo spent media, participant 027, rep1 [P-027-18-2]


title: Sample_IMQ1-69_IGO_12061_363

description: single cell


title: Human 18h embryo spent media, participant 018, rep1 [P-018-18-3]


title: Sample_IMQ1-66_IGO_12061_359

description: single cell


title: Human 18h embryo spent media, participant 018, rep1 [P-018-18-2]


title: Sample_IMQ1-67_IGO_12061_361

description: single cell


title: Human 18h embryo spent media, participant 018, rep1 [P-018-18-1]


title: Sample_IMQ1-65_IGO_12061_358

description: single cell


title: Human 18h embryo spent media, participant 002, rep1 [P-002-18-2]


title: Human 18h embryo spent media, participant 002, rep1 [P-002-18-1]


title: Human 18h embryo spent media, participant 001, rep1 [P-001-18-3]


title: Sample_IMQ1-64_IGO_12061_357

description: single cell


title: Sample_IMQ1-60_IGO_12061_353

description: single cell


title: Sample_IMQ1-6_IGO_12061_295

description: single cell


title: Human 18h embryo spent media, participant 021, rep1 [P-021-18-2]


title: Human 18h embryo spent media, participant 003, rep1 [P-003-18-1]


title: Sample_IMQ1-62_IGO_12061_355

description: single cell


title: Human 18h embryo spent media, participant 001, rep1 [P-001-18-1]


title: Sample_IMQ1-63_IGO_12061_356

description: single cell


title: Human 18h embryo spent media, participant 024, rep1 [P-024-18-2]


title: Sample_IMQ1-57_IGO_12061_349

description: single cell


title: Sample_IMQ1-58_IGO_12061_350

description: single cell


title: Sample_IMQ1-59_IGO_12061_351

description: single cell


title: Human 18h embryo spent media, participant 021, rep1 [P-021-18-1]


title: Sample_IMQ1-56_IGO_12061_348

description: single cell


title: Human 18h embryo spent media, participant 006, rep1 [P-006-18-4]


title: Human 18h embryo spent media, participant 024, rep1 [P-024-18-1]


title: Human 18h embryo spent media, participant 006, rep1 [P-006-18-1]


title: Sample_IMQ1-53_IGO_12061_345

description: single cell


title: Human 18h embryo spent media, participant 006, rep1 [P-006-18-3]


title: Sample_IMQ1-61_IGO_12061_354

description: single cell


title: Sample_IMQ1-52_IGO_12061_344

description: single cell


title: Sample_IMQ1-54_IGO_12061_346

description: single cell


title: Sample_IMQ1-51_IGO_12061_343

description: single cell


title: Human 18h embryo spent media, participant 010, rep1 [P-010-18-1]


title: Human 18h embryo spent media, participant 025, rep1 [P-025-18-1]


title: Human 18h embryo spent media, participant 001, rep1 [P-001-18-2]


title: Sample_IMQ1-50_IGO_12061_342

description: single cell


title: Human 18h embryo spent media, participant 019, rep1 [P-019-18-1]


title: Human 18h embryo spent media, participant 012, rep1 [P-012-18-1]


title: Sample_IMQ1-49_IGO_12061_341

description: single cell


title: Sample_IMQ1-48_IGO_12061_340

description: single cell


title: Sample_IMQ1-5_IGO_12061_294

description: single cell


title: Sample_IMQ1-46_IGO_12061_338

description: single cell


title: Sample_IMQ1-47_IGO_12061_339

description: single cell


title: Human 18h embryo spent media, participant 011, rep1 [P-011-18-2]


title: Human 18h embryo spent media, participant 012, rep1 [P-012-18-2]


title: Human 18h embryo spent media, participant 011, rep1 [P-011-18-1]


title: H4_B3_neg_GACGAC

city: Stanford

first: Jesse

last: Engreitz

address: 240 Pasteur Drive

institute: Stanford University

data_processing:
Fastq files were de-multiplexed by index primer
Demultiplexed fastq files for the same sample were concatenated
Reads were mapped to the human transcriptome using Kallisto
Read counts in transcripts were measured using Kallisto
Assembly: hg38
Supplementary files format and content: All_bulk_RNAseq_TPM_by_Symbol.txt. Contains TPM calls for all samples from Kallisto. Column names are the same as library ID & title.

molecule: polyA RNA

source_name: Vascular

growth_protocol: Telomerase-immortalized human aortic endothelial cells (TeloHAEC) were purchased from ATCC, and grown in Lifeline VEGF endothelial cell media with 1x Penn/Strep. TeloHAEC were plated at a density of 0.5-1.0 x 106 cells per 10cm plate and split before reaching 4 x 10^6/plate (3 to 4 days).

extract_protocol:
Total RNA was harvested from TeloHAEC (parental or CRISPRi lines) by Qiagen RNeasy kit, washed with 350 ul of buffer RW1 and treated for 20 mins at room temperature with 10 ul Purelink DNAse (InVitrogen 12185010)  in 80 ul of 1x buffer, with subsequent steps according to the supplier's method. For shear stress (flow) versus static cells, RNA was instead harvested with 300 ul of Trizol and extracted with 60ul of chloroform. After addition of 1 volume 70% ethanol, RNA was loaded onto a Qiagen RNeasy spin column, with subsequent steps as per the Qiagen RNeasy protocol, above. mRNA was purified from 400ng to 1 ug of total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation module (NEB).
NEBNext Ultra II RNA Library Kit for Illumina (NEB), according to manufacturer's protocol, and index primers specific for each library

treatment_protocol: 1) To create the TeloHAEC CRISPRi line, cells were transduced with lentiviral vectors containing a) dox-inducible (tetracycline operator controlled) dCas9-KRAB-BFP (CRISPRi machinery, which targets epigenetic repressors to efficiently silence enhancers or promoters58–60) and b) rtTA (tetracycline activator) with a hygromycin marker. After hygromycin selection (250ug/ml for 4 days), cells were treated with 1 ug/ml doxycycline (dox, a stable tetracycline analogue) for 3 days before FACS sorting for the top 15% of BFP positive cells, and after a period in culture without dox, treated again with dox and re-sorted. 2) To study the effects of gene perturbations, CRISPRi TeloHAEC were transduced with Lentivirus carrying single guide RNAs against the promoters of the indicated genes,  in a CROP-opti-blast backbone, selected for blasticidin resistance (15ug/ml) for 3 to 4 days, and then treated for 5 days with 2ug/ml doxycycline to induce the CRISPRi machinery. 3) To study responses to laminar flow, 200,000 CRISPRi TeloHAEC with the indicated single guides were seeded on flow chamber slides (80176, Ibidi) that had been pre-coated with 0.2% gelatin. After 24 hours, cells were cultured under laminar flow (12 dynes/cm2) for 48 hours (10902, Ibidi pump system). Static culture controls were seeded at the same density. Cells were treated with 2 ug/ml doxycycline for 2 days prior to seeding, and throughout, for a total of 5 days. 4) To study the combined knockdown effects of CCM2 or TLNRD1 with MAP3K3, 150,000 TeloHAEC were nucleofected with Synthego’s Gene Knockout Kit v2 for non-targeting negative control or MAP3K3  using the Lonza 4D-Nucleofector system (20 pmol of Cas9 and 50 pmol of sgRNA), program CA-210, using SG cell line nucleofection solution (Lonza; V4XC-3024). The nucleofected cells were harvested 48 hrs later. To induce CRISPRIi, cells were treated with 2 ug/ml doxycycline for 72 hours before nucleofection, and for the 48 hours afterwards.

value: Vascular

value: Endothelial

value: Transduced with sgRNA to MESDC1:GTGGCTGCGCCGCCGCCCGCA

value: NegCtrlGuide


title: Sample_IMQ1-45_IGO_12061_337

description: single cell


title: H2_D12_SS2_GTAGAG

value: Transduced with sgRNA to MESDC1:GCCTCCGGCAGCCCCTGCGGG

value: ShearStress


title: Sample_IMQ1-55_IGO_12061_347

description: single cell


title: H1_D2_SS2_ATCACG

value: Transduced with non-targeting control sgRNA:GTGGTTCACAACCGGACCCA


title: Human 18h embryo spent media, participant 006, rep1 [P-006-18-2]

value: Human embryo spent media


title: G4_D12_neg_TAATCG


title: Human 18h embryo spent media, participant 022, rep1 [P-022-18-2]

value: N


title: Sample_IMQ1-44_IGO_12061_336

description: single cell


title: G1_C2_SS2_CGATGT

value: Transduced with sgRNA to CCM2:GGCAAGAAGGTGAGCGTGCG


title: Human 18h embryo spent media, participant 022, rep1 [P-022-18-1]


title: Human 18h embryo spent media, participant 022, rep1 [P-022-18-3]


title: Sample_IMQ1-43_IGO_12061_335

description: single cell

value: Skin


title: F4_D2_M3K_TACAGC


title: Human 18h embryo spent media, participant 009, rep1 [P-009-18-3]


title: F1_B3_SS2_TTAGGC


title: G2_B6_sta2_GGTAGC

value: Transduced with non-targeting negative sgRNA:GCAACGGTGTACCGCGGATC

value: Static


title: Sample_IMQ1-41_IGO_12061_333

description: single cell

value: regulatory T cell


title: E2_D12_sta2_CAAAAG


title: Sample_IMQ1-42_IGO_12061_334

description: single cell


title: Sample_IMQ1-40_IGO_12061_332

description: single cell


title: D4_C2_M3K_TCATTC


title: E4_B6_M3K_TATAAT


title: Human 18h embryo spent media, participant 009, rep1 [P-009-18-2]

value: Y


title: Human 18h embryo spent media, participant 009, rep1 [P-009-18-1]


title: Sample_IMQ1-4_IGO_12061_293

description: single cell


title: Human 18h embryo spent media, participant 005, rep1 [P-005-18-5]


title: D3_D2_neg_CGGAAT


title: E1_D2_sta2_TGACCA


title: C4_F6_M3K_TCCCGA

value: Transduced with sgRNA to CCM2:GAGCCGCTACATGCTCGACCC


title: F2_F6_sta2_ATGAGC


title: Human 18h embryo spent media, participant 005, rep1 [P-005-18-4]


title: C3_B6_neg_CTAGCT


title: C1_B3_sta3_GCCAAT


title: Sample_IMQ1-38_IGO_12061_330

description: single cell

value: Imiquimod


title: Sample_IMQ1-39_IGO_12061_331

description: single cell


title: B4_B3_M3K_TCGAAG

value: Vascular


title: B3_C2_neg_CTATAC

value: Endothelial


title: Sample_IMQ1-37_IGO_12061_329

description: single cell


title: Human 18h embryo spent media, participant 005, rep1 [P-005-18-2]


title: B1_B6_SS2_CAGATC


title: A4_D12_M3K_TCGGCA


title: A3_F6_neg_GTGATC


title: Human 18h embryo spent media, participant 005, rep1 [P-005-18-1]


title: A1_F6_SS2_ACTTGA


title: NEA_33 scRNAseq

city: Tucson

first: Darren

middle: A.

last: Cusanovich

state: AZ

address: 1230 N Cherry Avenue, BSRL 421

department: Cellular and Molecular Medicine

institute: University of Arizona

description:
NEA_33
10x Genomics 5' v1.1

data_processing:
Raw sequencing data were processed using the 10X Genomics Cell Ranger pipeline. FASTQ files for Batch 1 were generated with default arguments. FASTQ files of Batch 2 samples were generated with Cell Ranger ‘mkfastq’ and the base mask argument ‘--use-bases-mask’ to create FASTQ files of Read 1=26 and Index 1=8.
Doublets were identified using the Python package Scrublet v0.2.1. Potential doublets were removed from subsequent analysis.
To adjust for cell-free RNA contamination, the Cell Ranger outputs were loaded into the R package SoupX using the ‘load10x’ function. Ambient RNA contamination was estimated with ‘autoEstCont’ function and argument tfidfMin = 0.7 for all samples and decontaminated with the function ‘adjustCounts.’
Cells with less than 200 genes per cell and/or greater than 20% mitochondrial reads were filtered from downstream analysis.
Assembly: hg38
Supplementary files format and content: processed_matrix.txt: tab-separated matrix (genes x cells) containing SoupX-corrected UMI counts. Each column is a cell (with the column header indicating the cell barcode). Each row is a gene (gene names are provided in processed_genes.txt).
Supplementary files format and content: processed_metadata.txt: tab-separated matrix of metadata associated with each cell. Contains the following columns: "CellID" - cell barcode; "SubjectID" - subject cell was obtained from; "TotalUMIsperCell" - total UMI count for that cell; "TotalGenesperCell" - total genes detected for that cell; "PercentMTReads" - percent of reads arising from mitochondrial genes; "Sex" - inferred sex of subject (using sex chromosome reads); "Batch" - batch sample was processed in (either "B1" or "B2"); "Cluster" - cluster cell was assigned to after UMAP dimensionality reduction; "CellType" - final cell type annotation; "Travaglini_MaxPredictionScore" - score for best matching annotation for label transfer from Travaglini et al; "Travaglini_ID" - best matching annotation from Travaglini et al; "Adams_MaxPredictionScore" - score for best matching annotation for label transfer from Adams et al; "Adams_ID" - best matching annotation from Adams et al; "SingleR_ID" - annotation obtained from SingleR.
Supplementary files format and content: processed_genes.txt: gene names for genes included in final data set.
Supplementary files format and content: NEA_*_matrix.mtx: matrix market formatted gene x cell matrix of UMI counts for each individual (generated from CellRanger).
Supplementary files format and content: NEA_*_features.tsv: gene names for genes included in the .mtx file for each individual (generated from CellRanger).
Supplementary files format and content: NEA_*_barcodes.tsv: cell barcodes for each cell for each individual (generated from CellRanger).

source_name: endotracheal aspirate

extract_protocol:
Endotracheal aspirates were collected from premature neonates (23-28 weeks gestational age, gestational birth weight < 1250 gram) in whom endotracheal tubes had been placed for clinical reasons. Within 60 minutes of birth, while still in the delivery suite, aspirate samples were collected immediately following placement of the tracheal tube before administering any surfactants or other medications. The aspirate samples were collected by instilling a 1 mL saline solution into the tracheal tube followed by immediate suction. After 1-2 mL of DMEM (Corning 10-013-CV) was added to the sample, it was stored at 4°C until it could be transferred on ice to the laboratory for cryopreservation. After receipt from the clinic, each sample was transferred to a 50mL conical tube and a viability count was estimated with Trypan Blue staining using the Countess II FL. Samples were washed with 10 volumes of ice-cold DPBS and were centrifuged at 500 x g for 5 minutes at 4°C, aspirated, and the cell pellet was resuspended in 1 mL freezing media (RPMI 40% FBS 10% DMSO). Mucus in the samples was relatively minor. Samples were transferred to a cryotube and frozen overnight in CoolCells (Corning) in the -80°C freezer, and then transferred to liquid nitrogen the following day for storage. On the day of library generation, samples were thawed quickly in a 37°C water bath, transferred to 10mL media (RPMI 15% FBS), and centrifuged at 500 x g for 5 minutes at 4°C. After, the cells were resuspended in 0.04% BSA in PBS, counted on a Countess (Bio-Rad) after staining with Trypan Blue, and adjusted to a concentration of 1x10^6 cells/mL.
All libraries were generated using the 10X Chromium Single Cell 5ʹ GEM, Library & Gel Bead Kit v1.1 across two batches with five samples in each batch. Based on the cell counts described above, the maximum number of cells (16,000) were loaded for each sample, unless the concentration was too low, in which case 37.8 ul of the sample (the maximum volume possible in this reaction) was loaded regardless of concentration. Consequently, in the first batch, we loaded an estimated 16,000 cells for NEA_13, 16,000 cells for NEA_15, 4,914 cells for NEA_20, 4,158 cells for NEA_22, and 7,938 cells for NEA_23 on the Chromium Controller. In the second batch (processed at a later date), we loaded an estimated 12,474 cells for NEA_26, 10,584 cells for NEA_28, 11,340 cells for NEA_29, 16,000 cells for NEA_31, and 7,560 cells for NEA_33. All samples were processed according to the 10X protocol.

value: endotracheal aspirate

tag: Sex

value: Male

value: Premature neonate


title: D1_C2_sta2_ACAGTG

tag: cell type


title: NEA_31 scRNAseq

description:
NEA_31
10x Genomics 5' v1.1


title: Sample_IMQ1-35_IGO_12061_327

description: single cell


title: Sample_IMQ1-34_IGO_12061_326

description: single cell


title: Human oocyte spent media, participant 013, rep 1 [P-013-0-4]

value: Human oocyte spent media


title: Sample_IMQ1-33_IGO_12061_325

description: single cell


title: Human oocyte spent media, participant 013, rep 1 [P-013-0-5]


title: Human oocyte spent media, participant 013, rep 1 [P-013-0-3]


title: NEA_28 scRNAseq

description:
NEA_28
10x Genomics 5' v1.1


title: Human oocyte spent media, participant 013, rep 1 [P-013-0-2]


title: NEA_26 scRNAseq

description:
NEA_26
10x Genomics 5' v1.1

value: Female


title: Human 18h embryo spent media, participant 005, rep1 [P-005-18-3]

value: Human embryo spent media


title: NEA_20 scRNAseq

description:
NEA_20
10x Genomics 5' v1.1


title: Sample_IMQ1-31_IGO_12061_323

description: single cell


title: NEA_15 scRNAseq

description:
NEA_15
10x Genomics 5' v1.1


title: NEA_13 scRNAseq

description:
NEA_13
10x Genomics 5' v1.1


title: Human oocyte spent media, participant 008, rep 1 [P-008-0-1]

value: N


title: Sample_IMQ1-3_IGO_12061_292

description: single cell


title: Human oocyte spent media, participant 028, rep 1 [P-028-0-2]


title: NEA_29 scRNAseq

description:
NEA_29
10x Genomics 5' v1.1


title: Sample_IMQ1-36_IGO_12061_328

description: single cell


title: NEA_23 scRNAseq

description:
NEA_23
10x Genomics 5' v1.1


title: Sample_IMQ1-32_IGO_12061_324

description: single cell


title: LELab_IHF_manuscript_sample_38

city: Norwich

first: Tung

middle: Ba  Khanh

last: Le

state: Norfolk

address: Colney Lane

department: Department of Molecular Microbiology

country: United Kingdom

institute: John Innes Centre

description: submitter provided name: Caulobacter crecentus CB15N

data_processing:
For analysis of ChIP-seq data, Hiseq 2500 Illumina short reads (50 bp) or NextSeq550 short reads (75bp) were mapped back to the Caulobacter NA1000 reference genome (NCBI Reference Sequence: NC_011916.1) using Bowtie 1 (Langmead et al., 2009) and the following command:bowtie -m 1 -n 1 --best --strata -p 4 --chunkmbs 512 NA1000-bowtie --sam *.fastq > output.sam. Subsequently, the sequencing coverage at each nucleotide position was computed using BEDTools (Quinlan and Hall, 2010) using the following command: bedtools genomecov -d -ibam output.sorted.bam -g NA1000.fna > coverage_output.txt. Finally, ChIP-seq profiles were plotted with the x-axis representing genomic positions and the y-axis is the number of reads per base pair per million mapped reads (RPBPM) using custom R scripts.
Assembly: NC_011916.1
Supplementary files format and content: Files starting with LeLab_coverage_output_: tab-delimited text file of nucleotide-resolution coverage from ChIP-seq data (column 1: genome ID, column 2: nucleotide position, column 3: coverage)

organism: Caulobacter vibrioides

source_name: mixed population, stationary phase

growth_protocol: C. crescentus cell cultures (50 mL) were grown in PYE to a stationary phase and fixed with formaldehyde to a final concentration of 1%. When appropriate, media were supplemented with antibiotics at the following concentrations (liquid/solid media for C. crescentus): kanamycin (5/25); spectinomycin (25/100); oxytetracycline (1/2). Fixed cells were incubated at room temperature for 30 min, then quenched with 0.125 M glycine for 15 min. Cells were washed three times with 1x PBS (pH 7.4) and resuspended in 1 mL of buffer 1 (20 mM K-HEPES pH 7.9, 50 mM KCl, 10% glycerol, and Roche EDTA-free protease inhibitors). Subsequently

extract_protocol:
DNA was isolated using the Qiagen Cell Lysis and Protein Precipitation solutions. Detailed protocols are listed in the Supplementary Materials
Standard library construction for Illumina Hiseq2500 or NextSeq550 sequencing platform

value: mixed population, stationary phase

value: delta_rogA gafZ::gafZ-FLAG

value: anti-VSVG


title: LELab_IHF_manuscript_sample_49

value: delta_rogA rpoD::flag-rpoD

value: anti-FLAG


title: Human oocyte spent media, participant 017, rep 1 [P-017-0-1]

value: Y


title: Sample_IMQ1-28_IGO_12061_320

description: single cell

value: Skin

value: regulatory T cell


title: LELab_IHF_manuscript_sample_43

value: delta_rogA gafZ::gafZ-FLAG ZBE5


title: LELab_IHF_manuscript_sample_36


title: LELab_IHF_manuscript_sample_34

value: delta_rogA rpoC::rpoC-3xflag


title: NEA_22 scRNAseq

description:
NEA_22
10x Genomics 5' v1.1

value: endotracheal aspirate


title: Sample_IMQ1-27_IGO_12061_319

description: single cell

value: Imiquimod


title: Human oocyte spent media, participant 007, rep 1 [P-007-0-2]


title: Sample_IMQ1-29_IGO_12061_321

description: single cell


title: Sample_IMQ1-26_IGO_12061_318

description: single cell


title: Human oocyte spent media, participant 028, rep 1 [P-028-0-1]


title: LELab_IHF_manuscript_sample_37


title: LELab_IHF_manuscript_sample_33


title: Human oocyte spent media, participant 013, rep 1 [P-013-0-1]


title: LELab_IHF_manuscript_sample_47

value: delta_rogA YBE6

value: anti-GafY


title: Human oocyte spent media, participant 007, rep 1 [P-007-0-1]

value: Human oocyte spent media


title: Sample_IMQ1-30_IGO_12061_322

description: single cell


title: Sample_IMQ1-25_IGO_12061_317

description: single cell


title: Human oocyte spent media, participant 014, rep 1 [P-014-0-1]


title: LELab_IHF_manuscript_sample_35


title: LELab_IHF_manuscript_sample_22

value: delta_rogA gtaT IBE2-3-4-5 (TT to GG)


title: Human oocyte spent media, participant 015, rep 1 [P-015-0-1]


title: Sample_IMQ1-24_IGO_12061_316

description: single cell


title: Human oocyte spent media, participant 016, rep 1 [P-016-0-1]


title: LELab_IHF_manuscript_sample_21


title: Sample_IMQ1-23_IGO_12061_315

description: single cell


title: LELab_IHF_manuscript_sample_20

value: delta_rogA gafY IBE (TT to GG) ihfB::ihfB-flag


title: LELab_IHF_manuscript_sample_16

value: mixed population, stationary phase

value: delta_rogA gafY IBE (TT to GG)


title: Sample_IMQ1-22_IGO_12061_314

description: single cell


title: LELab_IHF_manuscript_sample_23

value: delta_rogA gtaT IBE2-3-4-5 (TT to GG) ihfB::ihfB-flag


title: LELab_IHF_manuscript_sample_18

value: delta_rogA gtaT IBE (TT to GG)  ihfB::ihfB-flag


title: LELab_IHF_manuscript_sample_15

value: anti-FLAG


title: Human oocyte spent media, participant 002, rep 1 [P-002-0-1]

value: Y

value: N


title: LELab_IHF_manuscript_sample_19


title: LELab_IHF_manuscript_sample_17


title: Sample_IMQ1-21_IGO_12061_312

description: single cell

value: Skin

value: regulatory T cell


title: LELab_IHF_manuscript_sample_13

value: delta_rogA gtaT IBE (TT to GG)


title: LELab_IHF_manuscript_sample_12

value: delta_rogA ihfA::ihfA-flag


title: LELab_IHF_manuscript_sample_14


title: Human oocyte spent media, participant 003, rep 1 [P-001-0-1]


title: Human oocyte spent media, participant 003, rep 1 [P-003-0-1]


title: LELab_IHF_manuscript_sample_11


title: Sample_IMQ1-20_IGO_12061_311

description: single cell

value: Imiquimod


title: Sample_IMQ1-2_IGO_12061_291

description: single cell


title: LELab_IHF_manuscript_sample_9

value: CB15N ihfA::ihfA-flag


title: LELab_IHF_manuscript_sample_10


title: Sample_IMQ1-19_IGO_12061_310

description: single cell


title: Human oocyte spent media, participant 021, rep 1 [P-021-0-1]


title: Human oocyte spent media, participant 006, rep 1 [P-006-0-2]


title: LELab_IHF_manuscript_sample_6


title: LELab_IHF_manuscript_sample_4

value: CB15N ihfB::ihfB-flag


title: Human oocyte spent media, participant 006, rep 1 [P-006-0-1]

value: Human oocyte spent media


title: LELab_IHF_manuscript_sample_3


title: LELab_IHF_manuscript_sample_2

value: CB15N WT


title: Human oocyte spent media, participant 012, rep 1 [P-012-0-2]


title: Sample_IMQ1-16_IGO_12061_307

description: single cell


title: Human oocyte spent media, participant 012, rep 1 [P-012-0-1]


title: Human oocyte spent media, participant 012, rep 1 [P-012-0-3]


title: Sample_IMQ1-14_IGO_12061_304

description: single cell


title: Sample_IMQ1-15_IGO_12061_306

description: single cell