title: BEV MSN05-01R-CM Rep 2 (Conv)


title: AZA MSN02-04R-CM Rep 3 (Conv)

status: Public on Nov 14 2022

type: SRA

city: New York

first: Ravi

last: Iyengar

state: NY

address: 1425 Madison Avenue, Room 12-70C

department: Pharmacological Sciences

country: USA

institute: Icahn School of Medicine at Mount Sinai

library_source: transcriptomic

data_processing:
Preparing required software packages (README.pdf for details)
Preparing required input data files (README.pdf for details)
Aligning random-primed mRNA sequence reads (README.pdf for details)
Mapping aligned sequence reads to reference genes (README.pdf for details)
Identifying differentially expressed genes under drug treatments (README.pdf for details)
Assembly: Reference-Library.tar.gz: a compressed file containing the UCSC human genome referece library (version hg38)
Supplementary files format and content: Conv-RNAseq-Experiment-Design.tsv.gz: a compressed file containing the experiment design table of all the samples from the conventional dataset to be used by the DEG-comparison pipeline
Supplementary files format and content: Conv-RNAseq-Read-Counts.tsv.gz: a compressed file containing the read counts table of the uniquely aligned sequence fragments for the conventional dataset
Supplementary files format and content: Conv-RNAseq-Configs.tar.gz: a compressed file containing the configuration of the DEG-comparison pipeline file for the conventional dataset
Supplementary files format and content: Conv-RNAseq-Params.tar.gz: a compressed file containing the input parameter files of the DEG-comparison pipeline file for the conventional dataset
Supplementary files format and content: Conv-DEG-Calc-FDR-0.1.tar.gz: a compressed file containing a set of statistical comparison results of differentially expressed genes at each drug-treated condition with the file names in a form of Human-[Cell Line]-Hour-48-Plate-[Plate Number]-Calc.CTRL-[Drug Name].tsv for the conventional dataset
Supplementary files format and content: Program-Source-Codes.tar.gz: a compressed file containing the source codes for sequence alignment, feature counts, and differential comparison.
Supplementary files format and content: README.pdf.gz: a compressed PDF file containing detailed instructions for running the pipeline

molecule: total RNA

organism: Homo sapiens

source_name: induced pluripotent stem cell

growth_protocol: Cultured under growth conditions with E8 media and differentiated for 20 days with differentiation media,start Lactate Metabolic Selection for one week,Plate 240k cells into one well of 24-well plate and growth for one week for drug treatment. (see DToxS SOP CE)

extract_protocol:
Total RNA was isolated using Trizol (see DToxS SOP A – 1.0: Total RNA Isolation)
Library was prepared using 300 ng of total RNA enriched for mRNA using polyA beads and the TruSeq RNA Library Prep Kit (Illumina, Cat: RS-122-2001) per manufacturer’s instructions (See DToxS SOP A - 6.0: High-throughput mRNA Seq Library Construction for 3' Digital Gene Expression (DGE)

treatment_protocol: Fully confluent and differentiated cells were treated with drugs or vehicle (DMSO) for 48 hours (see DToxS SOP CE – 4.0: Drug Treatment and Cell Lysis)

tag: tissue

value: skin

tag: cell type

value: cardiac myocytes

tag: cell line

tag: treatment time (hrs)

tag: treatment condition

value: AZA

tag: drug name

value: Azacytidine

tag: concentration

tag: well

tag: investigative unit

tag: sample id

tag: rna amount (ng)

tag: rin

tag: rna conc (ng/ul)

tag: rna volume (ul)

tag: h2o volume (ul)


title: BEV MSN05-01R-CM Rep 1 (Conv)

value: BEV

value: Bevacizmab


title: BEV MSN01-03R-CM Rep 2 (Conv)


title: AZA MSN02-04R-CM Rep 1 (Conv)


title: AZA MSN09-04R-CM Rep 2 (Conv)


title: AZA MSN01-03R-CM Rep 4 (Conv)


title: AXI MSN09-04R-CM Rep 3 (Conv)

value: AXI

value: Axitinib


title: AZA MSN01-03R-CM Rep 1 (Conv)


title: AXI MSN09-04R-CM Rep 4 (Conv)


title: AZA MSN01-03R-CM Rep 3 (Conv)


title: AZA MSN01-03R-CM Rep 2 (Conv)


title: AXI MSN09-04R-CM Rep 2 (Conv)


title: AXI MSN09-04R-CM Rep 1 (Conv)


title: AXI MSN08-13R-CM Rep 4 (Conv)


title: AXI MSN06-07R-CM Rep 4 (Conv)


title: AXI MSN08-13R-CM Rep 1 (Conv)


title: AXI MSN06-07R-CM Rep 3 (Conv)


title: AXI MSN08-13R-CM Rep 3 (Conv)


title: AXI MSN06-07R-CM Rep 1 (Conv)


title: AXI MSN05-01R-CM Rep 1 (Conv)


title: AXI MSN06-07R-CM Rep 2 (Conv)


title: AXI MSN05-01R-CM Rep 3 (Conv)


title: AXI MSN05-01R-CM Rep 2 (Conv)


title: AZA MSN05-01R-CM Rep 1 (Conv)


title: AXI MSN01-03R-CM Rep 4 (Conv)


title: AXI MSN01-03R-CM Rep 3 (Conv)


title: AXI MSN02-04R-CM Rep 1 (Conv)


title: AXI MSN01-03R-CM Rep 1 (Conv)


title: AMI MSN09-04R-CM Rep 4 (Conv)

value: AMI

value: Amiodarone


title: AMI MSN09-04R-CM Rep 3 (Conv)


title: AXI MSN01-03R-CM Rep 2 (Conv)


title: AMI MSN08-13R-CM Rep 2 (Conv)


title: AMI MSN08-13R-CM Rep 3 (Conv)


title: AXI MSN02-04R-CM Rep 2 (Conv)


title: AMI MSN08-13R-CM Rep 1 (Conv)


title: AMI MSN06-07R-CM Rep 3 (Conv)


title: AMI MSN06-07R-CM Rep 2 (Conv)


title: AMI MSN06-07R-CM Rep 1 (Conv)


title: AMI MSN05-01R-CM Rep 4 (Conv)


title: AXI MSN05-01R-CM Rep 4 (Conv)


title: AMI MSN05-01R-CM Rep 3 (Conv)


title: AMI MSN05-01R-CM Rep 2 (Conv)


title: AXI MSN08-13R-CM Rep 2 (Conv)


title: AMI MSN01-03R-CM Rep 1 (Conv)


title: AFA MSN09-04R-CM Rep 3 (Conv)

value: AFA

value: Afatinib


title: AMI MSN09-04R-CM Rep 2 (Conv)


title: AMI MSN01-03R-CM Rep 3 (Conv)


title: AMI MSN09-04R-CM Rep 1 (Conv)


title: AFA MSN09-04R-CM Rep 4 (Conv)


title: AFA MSN08-13R-CM Rep 3 (Conv)


title: AFA MSN09-04R-CM Rep 1 (Conv)


title: AFA MSN09-04R-CM Rep 2 (Conv)


title: AMI MSN01-03R-CM Rep 2 (Conv)


title: AFA MSN06-07R-CM Rep 4 (Conv)


title: AMI MSN05-01R-CM Rep 1 (Conv)


title: AFA MSN08-13R-CM Rep 2 (Conv)


title: AFA MSN08-13R-CM Rep 4 (Conv)


title: AFA MSN06-07R-CM Rep 3 (Conv)


title: AFA MSN06-07R-CM Rep 1 (Conv)


title: AMI MSN01-03R-CM Rep 4 (Conv)


title: AFA MSN05-01R-CM Rep 4 (Conv)


title: AFA MSN06-07R-CM Rep 2 (Conv)


title: AFA MSN05-01R-CM Rep 3 (Conv)


title: AFA MSN05-01R-CM Rep 1 (Conv)


title: AFA MSN02-04R-CM Rep 2 (Conv)


title: AFA MSN05-01R-CM Rep 2 (Conv)


title: AFA MSN01-03R-CM Rep 4 (Conv)


title: AFA MSN01-03R-CM Rep 2 (Conv)


title: AFA MSN01-03R-CM Rep 1 (Conv)


title: Braak_Group_0_M (sample_R90)

status: Public on Oct 28 2022

city: Oslo

first: Chiara

last: Cappelletti

address: Gaustadalléen 34

country: Norway

institute: Oslo University Hospital

description:
Paper ID: YG492
sample_R90

data_processing:
Salmon version 1.3.0 (Patro et al., 2017) was used to quantify the abundance at the transcript level with the options: (1) sequence-specific bias (--seqBias), (2) fragment-level GC bias (--gcBias), (3) –validateMapping, and (4) appropriate library type (-l ISR).
Transcript level-quantification was collapsed onto gene-level quantification using the tximport R package version 1.20.0
Read count extraction and normalization were performed using DESeq2 R package (version 1.34.0)
Assembly: GRCh38 human reference genome
Supplementary files format and content: tab-delimited text file includes DESeq2-normalized counts for each sample

source_name: frontal cortex

extract_protocol:
RNA was harvested using AllPrep® DNA/RNA/miRNA Universal kit (#80224 Qiagen). 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext Ultra RNA Library Prep Kit for Illumina following manufacturer's protocols. rRNAs were removed using the Ribo-Zero Gold kit from Illumina

value: frontal cortex

tag: Sex

value: Male

tag: braak lewy_body_stage

tag: age at_death

tag: post mortem delay


title: Braak_Group_0_F (sample_R91)

description:
Paper ID: YG497
sample_R91

tag: tissue

value: Female


title: Braak_Group_0_M (sample_R89)

description:
Paper ID: YG491
sample_R89


title: Braak_Group_1-4_F (sample_R86)

description:
Paper ID: YG485
sample_R86


title: Braak_Group_0_M (sample_R88)

description:
Paper ID: YG487
sample_R88


title: Braak_Group_1-4_F (sample_R92)

description:
Paper ID: YG498
sample_R92


title: Braak_Group_0_F (sample_R82)

description:
Paper ID: YG477
sample_R82


title: Braak_Group_0_M (sample_R83)

description:
Paper ID: YG478
sample_R83


title: Braak_Group_0_M (sample_R81)

description:
Paper ID: YG476
sample_R81


title: Braak_Group_6_F (sample_R78)

description:
Paper ID: YG471
sample_R78


title: Braak_Group_1-4_F (sample_R77)

description:
Paper ID: YG466
sample_R77


title: Braak_Group_0_F (sample_R85)

description:
Paper ID: YG484
sample_R85


title: Braak_Group_6_F (sample_R80)

description:
Paper ID: YG473
sample_R80


title: Braak_Group_0_F (sample_R79)

description:
Paper ID: YG472
sample_R79


title: Braak_Group_1-4_M (sample_R87)

description:
Paper ID: YG486
sample_R87


title: Braak_Group_0_M (sample_R75)

description:
Paper ID: YG464
sample_R75


title: Braak_Group_0_M (sample_R72)

description:
Paper ID: YG452
sample_R72


title: AFA MSN01-03R-CM Rep 3 (Conv)

tag: cell type

tag: cell line

tag: treatment time (hrs)


title: AFA MSN02-04R-CM Rep 1 (Conv)

tag: treatment condition

tag: drug name

tag: concentration


title: Braak_Group_1-4_F (sample_R71)

description:
Paper ID: YG448
sample_R71


title: Braak_Group_6_M (sample_R64)

description:
Paper ID: YG420
sample_R64


title: Braak_Group_0_M (sample_R67)

description:
Paper ID: YG432
sample_R67


title: Braak_Group_1-4_M (sample_R68)

description:
Paper ID: YG433
sample_R68


title: Braak_Group_6_M (sample_R62)

description:
Paper ID: YG400
sample_R62


title: Braak_Group_1-4_M (sample_R61)

description:
Paper ID: YG397
sample_R61


title: Braak_Group_6_M (sample_R63)

description:
Paper ID: YG402
sample_R63


title: Braak_Group_5_M (sample_R60)

description:
Paper ID: YG396
sample_R60


title: Braak_Group_0_M (sample_R59)

description:
Paper ID: YG393
sample_R59


title: Braak_Group_0_M (sample_R84)

description:
Paper ID: YG483
sample_R84


title: Braak_Group_6_M (sample_R57)

description:
Paper ID: YG388
sample_R57


title: Braak_Group_1-4_F (sample_R56)

description:
Paper ID: YG387
sample_R56


title: Braak_Group_0_F (sample_R74)

description:
Paper ID: YG459
sample_R74


title: AFA MSN08-13R-CM Rep 1 (Conv)

tag: well

tag: investigative unit

tag: sample id


title: Braak_Group_6_F (sample_R52)

description:
Paper ID: YG376
sample_R52

tag: rin


title: Braak_Group_6_M (sample_R53)

description:
Paper ID: YG383
sample_R53


title: Braak_Group_6_M (sample_R54)

description:
Paper ID: YG385
sample_R54


title: Braak_Group_0_F (sample_R48)

description:
Paper ID: YG353
sample_R48


title: Braak_Group_5_M (sample_R49)

description:
Paper ID: YG367
sample_R49


title: Braak_Group_6_F (sample_R70)

description:
Paper ID: YG435
sample_R70


title: Braak_Group_6_F (sample_R47)

description:
Paper ID: YG351
sample_R47


title: Braak_Group_6_M (sample_R58)

description:
Paper ID: YG389
sample_R58


title: Braak_Group_6_F (sample_R69)

description:
Paper ID: YG434
sample_R69


title: Braak_Group_0_F (sample_R51)

description:
Paper ID: YG373
sample_R51


title: Braak_Group_6_F (sample_R50)

description:
Paper ID: YG369
sample_R50


title: Braak_Group_1-4_F (sample_R46)

description:
Paper ID: YG347
sample_R46


title: Braak_Group_6_M (sample_R45)

description:
Paper ID: YG345
sample_R45


title: Braak_Group_6_M (sample_R44)

description:
Paper ID: YG340
sample_R44


title: Braak_Group_0_F (sample_R43)

description:
Paper ID: YG336
sample_R43


title: Braak_Group_1-4_F (sample_R40)

description:
Paper ID: YG328
sample_R40


title: Braak_Group_0_M (sample_R41)

description:
Paper ID: YG331
sample_R41


title: Braak_Group_6_M (sample_R39)

description:
Paper ID: YG321
sample_R39


title: Braak_Group_5_M (sample_R37)

description:
Paper ID: YG282
sample_R37


title: Braak_Group_1-4_F (sample_R36)

description:
Paper ID: YG276
sample_R36


title: Braak_Group_6_F (sample_R55)

description:
Paper ID: YG386
sample_R55


title: Braak_Group_0_F (sample_R38)

description:
Paper ID: YG303
sample_R38


title: Braak_Group_1-4_F (sample_R34)

description:
Paper ID: YG270
sample_R34


title: Braak_Group_6_F (sample_R35)

description:
Paper ID: YG272
sample_R35


title: Braak_Group_5_F (sample_R32)

description:
Paper ID: YG234
sample_R32


title: Braak_Group_5_M (sample_R30)

description:
Paper ID: YG196
sample_R30


title: Braak_Group_5_M (sample_R29)

description:
Paper ID: YG188
sample_R29


title: Braak_Group_5_F (sample_R26)

description:
Paper ID: YG180
sample_R26


title: Braak_Group_1-4_F (sample_R31)

description:
Paper ID: YG229
sample_R31


title: Braak_Group_6_F (sample_R24)

description:
Paper ID: YG170
sample_R24


title: Braak_Group_1-4_F (sample_R23)

description:
Paper ID: YG159
sample_R23


title: Braak_Group_1-4_F (sample_R18)

description:
Paper ID: YG138
sample_R18


title: Braak_Group_6_F (sample_R19)

description:
Paper ID: YG142
sample_R19


title: Braak_Group_5_F (sample_R21)

description:
Paper ID: YG150
sample_R21


title: Braak_Group_5_M (sample_R17)

description:
Paper ID: YG120
sample_R17


title: Braak_Group_1-4_F (sample_R28)

description:
Paper ID: YG186
sample_R28


title: Braak_Group_0_F (sample_R25)

description:
Paper ID: YG174
sample_R25


title: Braak_Group_1-4_M (sample_R15)

description:
Paper ID: YG098
sample_R15


title: Braak_Group_5_M (sample_R16)

description:
Paper ID: YG106
sample_R16


title: Braak_Group_5_M (sample_R20)

description:
Paper ID: YG143
sample_R20


title: Braak_Group_6_M (sample_R14)

description:
Paper ID: YG097
sample_R14


title: Braak_Group_5_F (sample_R12)

description:
Paper ID: YG086
sample_R12


title: Braak_Group_5_F (sample_R13)

description:
Paper ID: YG090
sample_R13


title: Braak_Group_1-4_M (sample_R10)

description:
Paper ID: YG067
sample_R10


title: Braak_Group_6_F (sample_R9)

description:
Paper ID: YG066
sample_R9


title: Braak_Group_0_F (sample_R6)

description:
Paper ID: YG047
sample_R6


title: Braak_Group_5_M (sample_R4)

description:
Paper ID: YG024
sample_R4


title: Braak_Group_5_F (sample_R2)

description:
Paper ID: YG019
sample_R2


title: Braak_Group_5_M (sample_R3)

description:
Paper ID: YG022
sample_R3


title: Braak_Group_0_M (sample_R7)

description:
Paper ID: YG050
sample_R7


title: Braak_Group_5_F (sample_R1)

description:
Paper ID: YG010
sample_R1


title: Braak_Group_1-4_M (sample_R27)

description:
Paper ID: YG184
sample_R27


title: Braak_Group_5_M (sample_R22)

description:
Paper ID: YG157
sample_R22


title: Chronic05

status: Public on Sep 20 2022

city: Philadelphia

first: Benjamin

middle: C.

last: Reiner

state: PA

address: 125 S 31st St

institute: University of Pennsylvania

data_processing:
10x Genomics Cell Ranger v3.1
Genome_build: Reference created from Ensembl Rattus_norvegicus.Rnor_6.0.101
Supplementary_files_format_and_content: Cell Ranger raw feature barcode matrix

organism: Rattus norvegicus

source_name: nucleus accumbens

extract_protocol:
Nuclei were captured with the 10x Genomics Chromium controller for 3' gene expression assay (v3.1) according to manufacturer protocols
Libraries were prepared according to 10x Genomics manufacturer protocols

tag: strain

value: Brown Norway Rat

value: frozen postmortem brain

tag: brain region

value: nucleus accumbens

tag: treatment

value: Saline yoked control

tag: molecule subtype

value: nuclear mRNA


title: Acute10

tag: Sex

value: Saline injection


title: Chronic09


title: Chronic11


title: Chronic03


title: Human Metastatic CRPC Biopsy, HMP26

status: Public on Sep 01 2022

first: Dana

last: Pe'er

address: 417 E 68th St

institute: Memorial Sloan Kettering Cancer Center

description: Analysis of HMP samples

library_source: transcriptomic single cell

data_processing:
SEQC alignment
EmptyDrops for empty droplet detection
DoubletDetection for doublet detection
sctransform for normalization
scanpy for downstream analysis
Assembly: mm38, hg38
Supplementary files format and content: counts matrices (.csv)
Supplementary files format and content: adata objects (.h5ad)
Supplementary files format and content: obs cell annotations (.csv)

source_name: Metastatic CRPC

growth_protocol: The construction and genotyping of all GEMMs has been previously described (Ku et. al 2017, Science). 7 PtR (7 mice, PbCre:Rosa26mT/mGPtenfl/flRb1fl/fl), and 13 PtRP (13 mice, PbCre: Rosa26mT/mGPtenfl/flRb1fl/flTp53fl/fl) mice analyzed were on a mixed C57BL/6:129Sv: FVB/NJ background. Organoids were cultured under standard conditions (Karthaus et al 2014. Cell).

extract_protocol:
Fresh benign and malignant GEMM and human biopsy tissue was mechanically cut using a scalpel into small pieces (~1–5 mm3). The tissue was then processed and dissociated in 5–10 mg/ml collagenase type II (Gibco) solution in adDMEM/F12+/+/+ with 10 μM Y–27632 37 dihydrochloride for 30 minutes to 2 hours on a 37oC shaking platform. This was followed by a 1 minute 0.5 M EDTA wash at room temperature, and subsequent digestion with TrypLE (Life technologies) with 10 μM Y–27632 dihydrochloride for 5–10 minutes at 37oC on a shaking platform until a single cell suspension was obtained. For human samples, if more than 10% of doublets were present (visual inspection) or there was evidence for <80% viability (hemocytometer, using 0.2% Trypan Blue), then cells were FACS–sorted for singlets and viability using a DAPI. For GEMM tissue, all cells were subsequently FACS–sorted for singlets and viability using DAPI. Organoids were isolated from basement membrane extract digested to single-cell suspension by incubating with TrypLE (Life technologies) supplemented with Y-27632 (10 μM) for 10 min at 37 °C with shaking, followed by a 2-min incubation with EDTA (1 mM), Y-27632 (10 μM) in PBS0 and a second digestion with TrypLE (Life technologies) supplemented with Y-27632 for 5 min at 37 °C with shaking. Cells were filtered and resuspended in PBS0, Y-27632 (10 μM) and BSA (0.04%) before processing further for single-cell sequencing. Cells were checked for viability using 0.2% (w/v) Trypan Blue staining (Countess II) and all sequencing experiments were performed on samples with a minimum of 80% viable cells.
Single-cell encapsulation and scRNA-seq library prep of FACS-sorted cell suspensions was performed on the Chromium instrument (10x Genomics) following the user manual (Reagent Kit 3’ v2 for organoids and GEMM or v3 for HMP samples). Each sample loaded onto the cartridge contained approximately 5,000 - 10,000 cells at a final dilution of ~500 - 1000 cells/µl. Transcriptomes of encapsulated cells were barcoded during reverse transcription and the resulting cDNA was purified with DynaBeads, followed by amplification per the user manual. Next, PCR-amplified product was fragmented, A-tailed, purified with 1.2X SPRI beads, ligated to sequencing adapters and indexed by PCR. Indexed DNA libraries were double-size purified (0.6–0.8X) with SPRI beads and sequenced on an Illumina HiSeq (R1 – 26 cycles, i7 – 8 cycles, R2 – 70 cycles or higher) to a depth of >50 million reads per sample (>13,000 reads/cell).

treatment_protocol: Six PtRP mice were castrated at 8 weeks of age for either a total of 4 weeks (3 mice, ‘Cas’), or 2 weeks followed by 2 weeks of dihydrotestosterone (DHT, ‘Cas/Reg’) addback (3 mice). DHT pellet was implanted subcutaneously. Organoids were transduced using cre expressing lentivirus followed by culturing under standard conditions.

tag: sample type

value: Human Metastatic CRPC Biopsy


title: Acute06

tag: tissue


title: Acute08


title: Human Metastatic CRPC Biopsy, HMP25

description: Analysis of HMP samples


title: Chronic07


title: Chronic01


title: Human Metastatic CRPC Biopsy, HMP20

description: Analysis of HMP samples


title: Human Metastatic CRPC Biopsy, HMP17

description: Analysis of HMP samples


title: Human Metastatic CRPC Biopsy, HMP14

description: Analysis of HMP samples

tag: tag

value: HMP14B file prefix renamed as HMP14


title: Human Metastatic CRPC Biopsy, HMP15

description: Analysis of HMP samples


title: Acute04


title: Human Metastatic CRPC Biopsy, HMP19

description: Analysis of HMP samples


title: Acute02


title: Human Metastatic CRPC Biopsy, HMP08

description: Analysis of HMP samples


title: Human Metastatic CRPC Biopsy, HMP05

description: Analysis of HMP samples


title: Human Metastatic CRPC Biopsy, HMP11_1

description: Analysis of HMP samples


title: Human Metastatic CRPC Biopsy, HMP13

description: Analysis of HMP samples

value: JZHP_3 file prefix renamed as HMP13


title: Human Metastatic CRPC Biopsy, HMP11_2

description: Analysis of HMP samples


title: Poly, IC2, TCR

status: Public on Aug 23 2022

city: Nanjing

first: Mangge

last: Zou

address: No.6 Building, Life Science TechTown, 568 Longmian Avenue Jiangning District

country: China

institute: Legend Biotech

description:
neonatally-tagged Tregs isolated from spleen, skin and colon of neontally poly I:C-treated mouse were individually hashtagged and pooled together afterwards
Poly_IC2_scTCR-seq.tar

data_processing:
Cell Ranger (v.3.0.2) was applied to align reads (mouse GRCm38/mm10 as reference genome) and to produce gene-barcode matrices for each sample. Quality control and cell clustering were performed using Seurat (version 3.1.2)
To filter out doublets and cells with low quality, cells expressing genes more than 2000, with more than 5000 counts detected, or mitochondrial genes with more than 5% of total unique molecular identifiers (UMIs) were removed from the downstream analysis. Next, gene expression levels were normalized via the NormalizeData function, and the top 2,000 variable genes were identified using the FindVariableFeatures function. To reduce the dimensions, principal component analysis (PCA) was applied to scale data with PC 1-15 and resolution 0.5.
Given that unhashtaged cells contain cells of the spleen and cells from other tissues but failed in hashtagging, we further applied an empirically filtering criteria and excluded unhashtaged cells clustered with other tissues leaving the majority of unhashtag cells clustered separately from other tissues for the further analysis. We next combined samples based on their batches and filtered out the contaminated cells, which expressed non-T cell markers including Cd19, Ncr1, Adgre1, Cd14, Itgax, Ly6g, Pdpn, Ebf1, Ebf2, Ebf3, Iglc3, Iglc2, Iglc1, Iglc4, Igkv17-127, Cd79b, Cd79a, Jchain, Lyz2, Igkv10-94, Fcer1g, Tyrobp, Ccl6, Slpi, Trdc, Gpr25, Cxcl10, Bst2, H2-Eb1, H2-Eb2, H2-Ab1, H2-Aa, Igkv10-94, Hbb-bs, Gm30211, Igkc, Apoe.
Afterward, we re-normalized the data and identified the top 2000 variable genes. Subsequently, we performed the unsupervised clustering with the same settings (PC1-15, resolution =0.5). Furtherly, we zoomed into the data of each tissue and identified the subclusters using the same PC numbers and resolution. Cell clusters were visualized using Uniform Manifold Approximation and Projection (UMAP).
To identify the differentially expressed genes for each treatment group by taking the PBS group as control, the FindMarkers function was applied with the default Wilcoxon rank sum test and P-value adjustment performed using Bonferroni correction based on the total number of genes in the tested dataset. Genes were considered differentially expressed when the logFC > 0.25, expressed in >10% of cells in the cluster, and the adjusted P-value < 0.05.
The Cell Ranger vdj pipeline was applied to assemble the TCR sequences and identify the CDR3 sequence and TCR genes. Taking the clean scRNAseq data, we further removed cells that failed in detecting both α and β chains for further analysis. A clonal size was identified by the number of cells expressing the same α and β chains.
Assembly: mm10
Supplementary files format and content: CellRanger processed fastq output yielding RMCs and gene annotation
Library strategy: TCR-seq

organism: Mus musculus

source_name: Neonatally-tagged Tregs isolated from spleen, colon and skin

growth_protocol: Newborn Foxp3EGFPCreERT2Rosa26YFP mice were intraperitoneally injected with LPS, poly I:C, or PBS, followed by three times intragastrical administrations of tamoxifen on days 2, 5, and 8 after birth. Twelve weeks post perturbation, spleen, colon and skin were harvested for lymphocyte isolation.

extract_protocol:
1. To isolate cells from the spleen , organs were disintegrated through a 30 µM cell sieve (Sysmex Partec), and splenocytes were further cleared from erythrocytes by lysis. 2.  To isolate cells from colon tissues, colons were opened longitudinally and washed with PBS to remove feces. Epithelial cells and intraepithelial lymphocytes were removed by washing with pre-digestion buffer (PBS containing 0.2% w/v BSA and 5 mM EDTA) for 30 min at 37°C. After extensive washing with PBS to get rid of the remaining EDTA, colons were cut into small pieces and digested in an HBSS medium containing 25mM HEPES, 1 mg/ml collagenase D, and 0.1 mg/ml DNase I for one hour at 37°C. Lamina propria lymphocytes were purified with a 40%/80% Percoll gradient. 3. To isolate cells from skin tissues, hair and hair follicles from the back of the animal were removed with an electric shaver and depilatory cream (Veet). The skin was separated from the dorsal surface, cut into small pieces, and digested in an HBSS medium containing 25mM HEPES, 1 mg/ml collagenase D, and 0.1 mg/ml DNase I in a GentleMACS C tube (Miltenyi Biotec) and the program ‘‘37_C_Multi_H'' for 90 minutes, followed by centrifugation and 40%/80% Percoll gradient for the enrichment of lymphocytes.
Sorted cells were uploaded onto a 10x Chromium Next GEM Chip G using reagents from the Chromium Single Cell 5' Library and Gel Bead Kit (10x Genomics) according to the manufacturer's protocol. Amplified cDNA was used for both 5' RNA-seq library generation and TCR V(D)J targeted enrichment using the Chromium Single-Cell V(D)J Enrichment Kit for Mouse T Cells (10x Genomics). 5' RNA-seq and TCR V(D)J libraries were prepared following the manufacturer's user guide (10x Genomics). Libraries were quantified by QubitTM 3.0 Fluorometer (ThermoFisher) and quality checked using 2100 Bioanalyzer with High Sensitivity DNA Kit (Agilent Technologies).
scRNA-seq libraries were sequenced on an Illumina NextSeq500 sequencer to attain approximately 141,381 ± 63,000 reads per single cell and scTCR V(D)J libraries were sequenced on an Illumina NextSeq500 sequencer to obtain approximately 63,987 ± 6,131 reads per cell. The sequencing specifications for both single-cell RNA-seq and TCR V(D)J libraries were according to the manufacturer's specification (10x Genomics).

treatment_protocol: Newborn mice (less than 24-hours-old) were carefully fixed by hand and intraperitoneally injected with 2 ug LPS or 20 ug poly I:C per gram mouse in 20 ul PBS. To label the first wave of Tregs, 100 ug tamoxifen (Sigma) dissolved in 50 ul peanut oil (Sigma) was administrated to mice on day two, day five, and day eight after birth.

tag: genetic background

value: spleen, colon and skin

tag: cell type

value: neonatally tagged Tregs (YFP+ Tregs)

tag: dataset type

value: combined scRNAseq with scTCR-seq

value: Neonatal PolyI:C-treatment


title: Poly, IC1, TCR

description:
neonatally-tagged Tregs isolated from spleen, skin and colon of neontally poly I:C-treated mouse were individually hashtagged and pooled together afterwards
Poly_IC1_scTCR-seq.tar


title: LPS2, TCR

description:
neonatally-tagged Tregs isolated from spleen, skin and colon of neontally LPS-treated mouse were individually hashtagged and pooled together afterwards
LPS2_scTCR-seq.tar

value: Neonatal LPS-treatment


title: Braak_Group_5_M (sample_R76)

description:
Paper ID: YG465
sample_R76

value: frontal cortex

tag: braak lewy_body_stage

tag: age at_death

tag: post mortem delay


title: LPS1, TCR

description:
neonatally-tagged Tregs isolated from spleen, skin and colon of neontally LPS-treated mouse were individually hashtagged and pooled together afterwards
LPS1_scTCR-seq.tar


title: PBS2, TCR

description:
neonatally-tagged Tregs isolated from spleen, skin and colon of neontally PBS-treated mouse were individually hashtagged and pooled together afterwards
PBS2_scTCR-seq.tar

value: Neonatal PBS-treatment


title: PBS1, TCR

description:
neonatally-tagged Tregs isolated from spleen, skin and colon of neontally PBS-treated mouse were individually hashtagged and pooled together afterwards
PBS1_scTCR-seq.tar


title: LPS2, HTO

description:
neonatally-tagged Tregs isolated from spleen, skin and colon of neontally LPS-treated mouse were individually hashtagged and pooled together afterwards
LPS2_filtered_feature_bc_matrix_scRNAseq.tar

library_source: other

data_processing:
Cell Ranger (v.3.0.2) was applied to align reads (mouse GRCm38/mm10 as reference genome) and to produce gene-barcode matrices for each sample. Quality control and cell clustering were performed using Seurat (version 3.1.2)
To filter out doublets and cells with low quality, cells expressing genes more than 2000, with more than 5000 counts detected, or mitochondrial genes with more than 5% of total unique molecular identifiers (UMIs) were removed from the downstream analysis. Next, gene expression levels were normalized via the NormalizeData function, and the top 2,000 variable genes were identified using the FindVariableFeatures function. To reduce the dimensions, principal component analysis (PCA) was applied to scale data with PC 1-15 and resolution 0.5.
Given that unhashtaged cells contain cells of the spleen and cells from other tissues but failed in hashtagging, we further applied an empirically filtering criteria and excluded unhashtaged cells clustered with other tissues leaving the majority of unhashtag cells clustered separately from other tissues for the further analysis. We next combined samples based on their batches and filtered out the contaminated cells, which expressed non-T cell markers including Cd19, Ncr1, Adgre1, Cd14, Itgax, Ly6g, Pdpn, Ebf1, Ebf2, Ebf3, Iglc3, Iglc2, Iglc1, Iglc4, Igkv17-127, Cd79b, Cd79a, Jchain, Lyz2, Igkv10-94, Fcer1g, Tyrobp, Ccl6, Slpi, Trdc, Gpr25, Cxcl10, Bst2, H2-Eb1, H2-Eb2, H2-Ab1, H2-Aa, Igkv10-94, Hbb-bs, Gm30211, Igkc, Apoe.
Afterward, we re-normalized the data and identified the top 2000 variable genes. Subsequently, we performed the unsupervised clustering with the same settings (PC1-15, resolution =0.5). Furtherly, we zoomed into the data of each tissue and identified the subclusters using the same PC numbers and resolution. Cell clusters were visualized using Uniform Manifold Approximation and Projection (UMAP).
To identify the differentially expressed genes for each treatment group by taking the PBS group as control, the FindMarkers function was applied with the default Wilcoxon rank sum test and P-value adjustment performed using Bonferroni correction based on the total number of genes in the tested dataset. Genes were considered differentially expressed when the logFC > 0.25, expressed in >10% of cells in the cluster, and the adjusted P-value < 0.05.
The Cell Ranger vdj pipeline was applied to assemble the TCR sequences and identify the CDR3 sequence and TCR genes. Taking the clean scRNAseq data, we further removed cells that failed in detecting both α and β chains for further analysis. A clonal size was identified by the number of cells expressing the same α and β chains.
Assembly: mm10
Supplementary files format and content: CellRanger processed fastq output yielding RMCs and gene annotation

molecule: protein


title: Human Metastatic CRPC Biopsy, HMP16

description: Analysis of HMP samples

value: JZHP_4 file prefix renamed as HMP16


title: LPS1, HTO

description:
neonatally-tagged Tregs isolated from spleen, skin and colon of neontally LPS-treated mouse were individually hashtagged and pooled together afterwards
LPS1_filtered_feature_bc_matrix_scRNAseq.tar


title: Poly, IC1, HTO

description:
neonatally-tagged Tregs isolated from spleen, skin and colon of neontally poly I:C-treated mouse were individually hashtagged and pooled together afterwards
Poly_IC1_filtered_feature_bc_matrix_scRNAseq.tar


title: Poly, IC2, GEX

description:
neonatally-tagged Tregs isolated from spleen, skin and colon of neontally poly I:C-treated mouse were individually hashtagged and pooled together afterwards
Poly_IC2_filtered_feature_bc_matrix_scRNAseq.tar


title: LPS2, GEX


title: AMI MSN08-13R-CM Rep 4 (Conv)

value: skin

value: cardiac myocytes

tag: cell line

tag: treatment time (hrs)

tag: treatment condition

value: AMI

tag: drug name

value: Amiodarone

tag: concentration

tag: well

tag: investigative unit

tag: rna amount (ng)

tag: rna conc (ng/ul)

tag: rna volume (ul)

tag: h2o volume (ul)


title: Poly, IC2, HTO

tag: genetic background

tag: tissue

tag: treatment


title: PBS1, GEX

description:
neonatally-tagged Tregs isolated from spleen, skin and colon of neontally PBS-treated mouse were individually hashtagged and pooled together afterwards
PBS1_filtered_feature_bc_matrix_scRNAseq.tar

tag: cell type

tag: dataset type


title: LPS1, GEX


title: PBS2, HTO

description:
neonatally-tagged Tregs isolated from spleen, skin and colon of neontally PBS-treated mouse were individually hashtagged and pooled together afterwards
PBS2_filtered_feature_bc_matrix_scRNAseq.tar


title: Poly, IC1, GEX


title: Human Metastatic CRPC Biopsy, HMP04

description: Analysis of HMP samples

tag: sample type


title: PBS1, HTO


title: lib17422

status: Public on Aug 10 2022

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

institute: Benaroya Research Institute

data_processing:
Base calls were processed to FASTQs on BaseSpace (Illumina).
Reads were processed using workflows managed on the Galaxy platform; reads were trimmed by 1 base at the 3’ end, and then trimmed from both ends until base calls had a minimum quality score of at least 30 (Galaxy FASTQ Trimmer tool v1.0.0)
FastqMcf (v1.1.2, https://benthamopen.com/ ABSTRACT/TOBIOIJ-7-1) was used to remove any remaining adapter sequence.
Reads were aligned by STAR1 2.4.2a to GRCh38
Gene counts were generated using HTSeq-count (v0.4.1). Quality metrics were compiled from PICARD (v1.134, http://broadinstitute.github.io/picard/), FASTQC (v0.11.3, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), Samtools (v1.2)30, and HTSeq-count (v0.4.1).
Genome_build: GRCh38
Supplementary_files_format_and_content: Processed data is in .csv format. Each row is a gene, each column is a sample.

source_name: CD154+ CD4 T-cells

extract_protocol:
A total of 100 sorted pTeff cells were sorted directly into reaction buffer from the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara), and reverse transcription was performed followed by PCR amplification to generate full length amplified cDNA.
Sequencing libraries were constructed using the NexteraXT DNA sample preparation kit with unique dual indexes (Illumina) to generate Illumina-compatible barcoded libraries.
Libraries were pooled and quantified using a Qubit® Fluorometer (Life Technologies). Sequencing of pooled libraries was carried out on a HiSeq 2500 sequencer (Illumina) with paired-end 53-base reads and a target depth of 5 million reads per sample.

treatment_protocol: Peanut-reactive CD4+ T effector (pTeff) cells were tracked using the CD154 up-regulation assay(29, 30). Briefly, 10-20 x 106 freshly isolated PBMCs in culture medium at a concentration of 10 x 106 cells/ml were stimulated with a pooled library of 20-mer peptides derived from Ara h 1, Ara h 2, Ara h 3, Ara h 6, and Ara h 8 peanut-allergic components and 1 µg/ml of anti-CD40 blocking mAb (clone HB14, Miltenyi Biotec, Auburn, CA). After 14 hours stimulation at 37°C, cells were harvested and labeled with PE-Conjugated anti-CD154 mAb for 10 minutes at 4°C. Cells were then washed, labeled with anti-PE magnetic beads and enriched by using a magnetic column, according to the manufacturer’s instructions (Miltenyi Biotec, Bergisch Gladbach, Germany).

tag: donorid

tag: age

tag: sort group

value: memory CD4 T cell

tag: study group

value: Control


title: lib17420


title: lib17418


title: lib17421


title: lib17416

value: Peanut Allergic


title: lib17414


title: lib17419


title: lib17415


title: lib17413


title: PBS2, GEX


title: Normal lung 2

status: Public on Aug 17 2022

type: RNA

city: Madrid

first: Corina

last: Lorz

state: Madrid

address: Avda. Complutense 40

country: Spain

institute: Ciemat (Centro de Investigaciones Energeticas Mediambientales y Tecnologicas)

description: Gene expression data from normal lung

hyb_protocol: Following fragmentation, 3.5 ug of ssDNA were hybridized on Mouse Gene 2.0 ST Chip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station according to the manufacturer's instructions.

scan_protocol: GeneChips were scanned using the Affymetrix system.

data_processing: The data were analyzed with RMA using Gene Expression Console.

label: biotin

source_name: Normal lung

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Extraction of total RNA was performed with miRNeasy Mini Kit Qiagen according to the manufacturer's instructions.

value: normal lung


title: PSC tumor 3

description: Gene expression data from Lung tumor from Naphthalene + Ad5-CMVCre treated Trp53F/F; PtenF/Fmouse

value: tumor (lung)


title: lib17412


title: Normal lung 1

description: Gene expression data from normal lung


title: PSC tumor 2

source_name: Lung tumor from Naphthalene + Ad5-CMVCre treated Trp53F/F; PtenF/Fmouse


title: ADC tumor 2

description: Gene expression data from Lung tumor from Ad5-CMVCre treated Trp53F/F; PtenF/Fmouse


title: lib17411


title: lib17410


title: PSC tumor 5

description: Gene expression data from Lung tumor from  Ad5-CMVCre treated Trp53F/F; PtenF/Fmouse


title: lib17408


title: Normal lung 4

description: Gene expression data from normal lung


title: lib17407


title: ADC tumor 5

description: Gene expression data from Lung tumor from Naphthalene + Ad5-K5Cre treated Trp53F/F; PtenF/Fmouse

source_name: Lung tumor from Naphthalene + Ad5-K5Cre treated Trp53F/F; PtenF/F mouse


title: ADC tumor 3

source_name: Lung tumor from Ad5-CMVCre treated Trp53F/F; PtenF/Fmouse


title: Normal lung 3

description: Gene expression data from normal lung


title: lib17405


title: lib17404


title: PSC tumor 4


title: lib17409


title: lib17403


title: lib17406


title: Normal lung 5

description: Gene expression data from normal lung


title: ADC tumor 1


title: PSC tumor 6


title: ADC tumor 7

description: Gene expression data from Lung tumor from Ad5-K5Cre treated Trp53F/F; PtenF/Fmouse

source_name: Lung tumor from Ad5-K5Cre treated Trp53F/F; PtenF/F mouse


title: PSC tumor 1


title: lib17401


title: Normal lung 6

description: Gene expression data from normal lung


title: ADC tumor 6


title: lib17400


title: ADC tumor 4


title: lib14199


title: lib14201


title: 35_Alpha_V_CPG_2395_2 [lib41831]

status: Public on Jul 29 2022

data_processing:
Base calls were processed to FASTQs on BaseSpace (Illumina).
Reads were processed using workflows managed on the Galaxy platform; reads were trimmed by 1 base at the 3’ end, and then trimmed from both ends until base calls had a minimum quality score of at least 30 (Galaxy FASTQ Trimmer tool v1.0.0)
FastqMcf (v1.1.2) was used to remove any remaining adapter sequence.
Reads were aligned by bowtie and TopHat v1.4.0 to GRCh38
Gene counts were generated using HTSeq-count (v0.4.1). Quality metrics were compiled from PICARD (v1.134, http://broadinstitute.github.io/picard/), FASTQC (v0.11.3, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), Samtools (v1.2)30, and HTSeq-count (v0.4.1).
Assembly: GRCh38
Supplementary files format and content: Processed data is in .csv format. Each row is a gene, each column is a sample.

source_name: HBL1  cell line

extract_protocol:
The indicated populations were isolated by flow cytometry, and after stimulation cells were resuspended in SMARTer v4 lysis reagents (Clontech). Cells were lysed and cDNA was synthesized. For the cell lines, stimulated or unstimulated cells were used for RNA extraction with QIAGEN RNeasy Mini kit and cDNA synthesized from this.
After amplification, sequencing libraries were prepared using the Nextera XT DNA Library Preparation Kit (Illumina).
Barcoded libraries were pooled and quantified using a Qubit® Fluorometer (Life Technologies). Single-read sequencing of the pooled libraries was carried out on a HiSeq2500 sequencer (Illumina) for 74 cycles, using TruSeq v3, and SBS kits (Illumina). Target read depths were ~5-10 million raw reads per sample.

tag: cell line

value: HBL1  cell line

value: HBL1 Cells

tag: stimulation

value: 3hr CPG (ODN 2395)


title: 39_CtlCrispr_(ATGguide_no_cas9)_CPG_2395 [lib41835]


title: 36_Alpha_V_CPG_2395_3 [lib41832]


title: 37_CtlCrispr_(ATGguide_no_cas9)_NoStim [lib41833]

value: No stim


title: 29_Alpha_V_NoStim_2 [lib41825]


title: 27_ATG7_CPG_2395_3 [lib41823]


title: 31_Alpha_V_CPG_2006_1 [lib41827]

value: 3hr CPG (ODN 2006)


title: 34_Alpha_V_CPG_2395_1 [lib41830]


title: 33_Alpha_V_CPG_2006_3 [lib41829]


title: 32_Alpha_V_CPG_2006_2 [lib41828]


title: 30_Alpha_V_NoStim_3 [lib41826]


title: 25_ATG7_CPG_2395_1 [lib41821]


title: 26_ATG7_CPG_2395_2 [lib41822]


title: 28_Alpha_V_NoStim_1 [lib41824]


title: 24_ATG7_CPG_2006_3 [lib41820]


title: lib17402


title: 19_ATG7_NoStim_1 [lib41815]


title: 21_ATG7_NoStim_3 [lib41817]


title: 17_ATG5_CPG_2395_2 [lib41813]


title: 16_ATG5_CPG_2395_1 [lib41812]


title: 22_ATG7_CPG_2006_1 [lib41818]


title: 15_ATG5_CPG_2006_3 [lib41811]


title: 23_ATG7_CPG_2006_2 [lib41819]


title: 18_ATG5_CPG_2395_3 [lib41814]


title: lib17398


title: 20_ATG7_NoStim_2 [lib41816]


title: 38_CtlCrispr_(ATGguide_no_cas9)_CPG_2006 [lib41834]


title: 14_ATG5_CPG_2006_2 [lib41810]


title: 13_ATG5_CPG_2006_1 [lib41809]


title: 12_ATG5_NoStim_3 [lib41808]


title: 11_ATG5_NoStim_2 [lib41807]


title: 8_HBL1_par_CPG_2395_2 [lib41804]


title: 9_HBL1_par_CPG_2395_3 [lib41805]


title: 5_HBL1_par_CPG_2006_2 [lib41801]


title: 6_HBL1_par_CPG_2006_3 [lib41802]


title: 7_HBL1_par_CPG_2395_1 [lib41803]


title: 2_HBL1_par_NoStim_2 [lib41798]


title: 1_HBL1_par_NoStim_1 [lib41797]


title: Memory 3h CPG 2395 [lib29827]

source_name: Tonsil

value: Tonsil

value: Memory B cells


title: Na√Øve 3h IgM +CD40 [lib29824]

value: Naive B cells

value: 3h IgM+ CD40


title: Transitional 3h  CPG 2395 [lib29826]

value: Transitional B cells


title: Transitional no stim [lib29816]


title: GC 3h CPG 2006 [lib29818]

value: Germinal center B cells


title: Na√Øve 3h CPG 2006 [lib29821]


title: GC-3h CPG 2395 [lib29819]


title: Na√Øve 3h CPG 2395 [lib29822]


title: 14_Memory_3h_CPG2395 [lib29296]


title: GC -3h R848 [lib29820]


title: Na√Øve 3h R848 [lib29823]


title: 13_Memory_3h_CPG2006 [lib29295]


title: Na√Øve no stim [lib29815]


title: GC no stim [lib29814]


title: Memory no stim [lib29817]


title: 12_Transitional_3h_CPG2395 [lib29294]


title: 11_Transitional_3h_CPG2006 [lib29293]


title: 10_ATG5_NoStim_1 [lib41806]


title: 10_Naive_3h_IgM [lib29292]

value: 3h IgM


title: 9_Naive_3h_CPG2395 [lib29291]


title: 3_HBL1_par_NoStim_3 [lib41799]


title: 4_HBL1_par_CPG_2006_1 [lib41800]


title: Transitional 3h CPG 2006 [lib29825]


title: 7_GC-3h_IgM [lib29289]


title: 4_Memory_nostim [lib29286]


title: 3_Transitional_nostim [lib29285]


title: 5_GC_3h_CPG2006 [lib29287]


title: 6_GC_3h_CPG2395 [lib29288]


title: 2_Naive_nostim [lib29284]


title: 1_GC_nostim [lib29283]


title: 13_Memory_3h_CPG [lib29282]

value: 3h CPG


title: 11_Transitional_3h_CPG [lib29280]


title: 9_Na√Øve_3h_R848 [lib29278]


title: 7_GC-3h_IgM [lib29276]


title: 5_GC_3h_CPG [lib29274]


title: 4_Memory_nostim [lib29273]


title: 1_GC_nostim [lib29270]


title: 3_Transitional_nostim [lib29272]


title: 14_Memory_3h_R848 [lib27737]


title: 13_Memory_3h_CPG [lib27736]


title: 2_Na√Øve_nostim [lib29271]


title: 11_Trans_3h_CPG [lib27734]


title: 10_Naive_3h_IgM [lib27733]


title: 12_Trans_3h_R848 [lib27735]


title: 8_Naive_3h_CPG [lib27731]


title: 8_Naive_3h_CPG2006 [lib29290]


title: 9_Naive_3h_R848 [lib27732]


title: 6_GC_3h_R848 [lib27729]


title: 7_3h_IgM [lib27730]


title: 3_Trans_NoStim [lib27726]


title: 4_Memory_NoStim [lib27727]


title: 12_Transitional_3h_R848 [lib29281]


title: 2_Naive_NoStim [lib27725]


title: Stim_R848_Mem_B10 [lib23395]

value: Memory 3h R848


title: 5_GC_3h_CPG [lib27728]


title: 10_Na√Øve_3h_IgM [lib29279]


title: Stim_IgMplusCD40_GC_B8 [lib23393]

value: GC 3h IgM+CD40


title: 1_GC_NoStim [lib27724]


title: 6_GC-3h_R848 [lib29275]


title: Stim_CPG_Mem_B9 [lib23394]

value: Memory 3h CPG


title: Stim_R848_GC_B7 [lib23392]

value: GC 3h R848


title: Stim_CPG_GC_B6 [lib23391]

value: GC 3h CPG


title: 8_Na√Øve_3h_CPG [lib29277]


title: Stim_IgMplusCD40_BCRstim_Naive_B3 [lib23388]

value: Naive 3h IgM+ CD40 (BCR stim)


title: Stim_R848_TLR7_Naive_B2 [lib23387]

value: Naive 3h R848 (TLR7 ligand)


title: NoStim_GC_A3 [lib23384]

value: No stim


title: NoStim_Trans_A2 [lib23383]


title: XPB1027216348.CD3CD28.Treg.CBLB.KO

status: Public on Jul 19 2022

data_processing:
Base calls were processed to FASTQs on BaseSpace (Illumina).
Reads were processed using workflows managed on the Galaxy platform; reads were trimmed by 1 base at the 3’ end, and then trimmed from both ends until base calls had a minimum quality score of at least 30 (Galaxy FASTQ Trimmer tool v1.0.0)
FastqMcf (v1.1.2, https://benthamopen.com/ ABSTRACT/TOBIOIJ-7-1) was used to remove any remaining adapter sequence.
Reads were aligned by STAR1 2.4.2a to GRCh38.91
Gene counts were generated using HTSeq-count (v0.4.1). Quality metrics were compiled from PICARD (v1.134, http://broadinstitute.github.io/picard/), FASTQC (v0.11.3, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), Samtools (v1.2)30, and HTSeq-count (v0.4.1).
Assembly: GRCh38.91
Supplementary files format and content: Processed data is in .csv format. Each row is a gene, each column is a sample.

source_name: blood

growth_protocol: PBMC were isolated from human peripheral blood by centrifugation over Ficoll-Hypaque gradients. CD4+ T cells were isolated via negative selection using the CD4+ T cell isolation kit (Miltenyi Biotec)

extract_protocol:
In one Treg suppression assay, edited cells and iTregs were co-cultured at 1:1 and activated with human T-activator CD3/CD28 Dynabeads at 1:28 for 24 hours, 1000 CBLB-KO GFP+BFP+ or AAVS1-/-GFP+BFP+ cells were sorted to do bulk RNAseq via a FACS AriaII (n=4).
Reverse transcription was performed followed by PCR amplification to generate full-length amplified cDNA.  Sequencing libraries were constructed using a modified protocol of the Nextera XT DNA Sample Preparation Kit (Illumina) to generate Illumina-compatible barcoded libraries
Libraries were pooled and quantified using a Qubit Fluorometer (Life Technologies).  Dual-index, single-read sequencing of the pooled libraries was carried out on a HiSeq 2500 sequencer (Illumina) with 58-base reads, using HiSeq v4 Cluster and SBS Kits (Illumina) with a target depth of 5 million reads per sample.

treatment_protocol: At day 4, CD4+ T cells were transfected with CBLB CRISPR/Cas9 RNP and cultured at a 96-well U bottom plate. 40µl of GFP or BFP AAV (20% of volume) was added to each designated well immediately after electroporation. In the case of both the GFP-AAV and BFP-AAV being added, 20µl of each was added. Single guide RNA (sgRNA) targeted the 2nd exon of CBLB gene were designed according to online CRISPR/Cas9 database (IDT and Synthego). Chemically modified sgRNA (supplementary table1) (Synthergo) and spyFi-Cas9 Nuclease (Aldervron) were assembled at a ratio of 1.2:1. 2.5ug of complexed CBLB CRISPR/Cas9 RNPs and 10ul of CD4+ T cells (final concentration 30x106 cells/mL) were mixed and electroporated at 1400V, 10ms, 3 pulses in a Neon tip using the Neon Transfection System (Thermo Fisher Scientific). AAVs targeted the same CBLB gene locus or designated AAVS1 or CCR5 gene locus were designed and constructed in the viral core of Seattle children’s research institute (SCRI) (Sup Figure1A). After Rep amplification the AAV genome flanked by AAV tails is packaged into AAV serotype6 Capsid and transduced into T cells.

value: CBLB-KO

tag: donor


title: Stim_R848_Trans_B5 [lib23390]

value: Tonsil

value: Transitional 3h R848


title: Stim_CPG_TLR9_Naive_B1 [lib23386]

value: Naive B cells

value: Naive 3h CPG (TLR9 ligand)


title: NoStim_Naive_A1 [lib23382]


title: XPB1027216348.CD3CD28.Treg.AAVS1.KO


title: XPB1027216348.NO.AAVS1.KO


title: XPB456224218.CD3CD28.Treg.CBLB.KO


title: XPB1027216348.NO.CBLB.KO


title: XPB456224218.NO.AAVS1.KO


title: XPB456224218.NO.CBLB.KO


title: XPB456224218.CD3CD28.AAVS1.KO


title: XPB468589631.CD3CD28.Treg.AAVS1.KO


title: XPB468589631.CD3CD28.CBLB.KO


title: XPB468589631.NO.CBLB.KO


title: XPB468589631.CD3CD28.Treg.CBLB.KO


title: XPB456224218.CD3CD28.Treg.AAVS1.KO


title: XPB468589631.CD3CD28.AAVS1.KO


title: XPB610745444.CD3CD28.Treg.CBLB.KO


title: XPB610745444.NO.CBLB.KO


title: NoStim_Mem_A4 [lib23385]

value: Memory B cells


title: XPB610745444.CD3CD28.Treg.AAVS1.KO


title: XPB468589631.NO.AAVS1.KO


title: XPB610745444.CD3CD28.CBLB.KO


title: Stim_CPG_Trans_B4 [lib23389]

value: Transitional B cells

value: Transitional 3h CPG


title: XPB610745444.NO.AAVS1.KO


title: XPB1027216348.CD3CD28.CBLB.KO


title: XPB1027216348.CD3CD28.AAVS1.KO


title: 301_NoStimCD4_N

status: Public on Jun 27 2022

source_name: CD4 Naive

extract_protocol:
Full-length cDNA was prepared from 500-1000 cells using half-volume SMART-SeqV4 reactions (Clontech, Mountain View, CA).
Sequencing libraries were constructed using the NexteraXT DNA sample preparation kit with unique dual indexes (Illumina) to generate Illumina-compatible barcoded libraries.
Libraries were pooled and quantified using a Qubit® Fluorometer (Life Technologies). Sequencing of pooled libraries was carried out on a HiSeq 2500 sequencer (Illumina) with paired-end 53-base reads and a target depth of 5 million reads per sample.

treatment_protocol: Primary human CD3+ T cells treated with (20ng/mL) or without (0ng/mL) IL-6 for 4 hours at 37°C.

value: CD4 Naive

tag: genotype

value: A/A

value: 0 ng

tag: time

value: 4 hours

tag: draw id

tag: Sex

value: M


title: 304_StimCD4_N

value: 20 ng


title: XPB610745444.CD3CD28.AAVS1.KO


title: 280_StimCD4_N

value: F


title: XPB456224218.CD3CD28.CBLB.KO


title: 292_StimCD4_N


title: 274_StimCD4_N


title: 289_NoStimCD4_N


title: 271_NoStimCD4_N


title: 277_NoStimCD4_N


title: 262_StimCD4_N


title: 259_NoStimCD4_N


title: 247_NoStimCD4_N


title: 175_NoStim_CD4N


title: 163_NoStim_CD4N


title: 154_Stim_CD4N


title: 151_NoStim_CD4N


title: 133_NoStim_CD4N


title: 166_Stim_CD4N


title: 124_Stim_CD4N


title: 136_Stim_CD4N


title: 52_StimCD4_N


title: 121_NoStim_CD4N


title: 40_StimCD4_N


title: 28_StimCD4_N


title: 49_NoStimCD4_N


title: 37_NoStimCD4_N


title: 4_StimCD4_N


title: 1_NoStimCD4_N


title: 276_StimCD8_N

source_name: CD8 Naive

value: CD8 Naive


title: 13_NoStimCD4_N


title: 25_NoStimCD4_N


title: 275_StimCD4_Me

source_name: CD4 Memory

value: CD4 Memory


title: 272_NoStimCD4_Me


title: 273_NoStimCD8_N


title: 250_StimCD4_N


title: 252_StimCD8_N


title: 178_Stim_CD4N


title: 248_NoStimCD4_Me


title: 249_NoStimCD8_N


title: 251_StimCD4_Me


title: 126_Stim_CD8N


title: 125_Stim_CD4Me


title: 122_NoStim_CD4Me


title: 54_StimCD8_N


title: 123_NoStim_CD8N


title: 53_StimCD4_Me


title: 51_NoStimCD8_N


title: 50_NoStimCD4_Me


title: 294_StimCD8_N


title: 293_StimCD4_Me


title: 291_NoStimCD8_N


title: 16_StimCD4_N


title: 264_StimCD8_N


title: 290_NoStimCD4_Me


title: 261_NoStimCD8_N


title: 260_NoStimCD4_Me


title: 168_Stim_CD8N


title: 165_NoStim_CD8N


title: 167_Stim_CD4Me


title: 164_NoStim_CD4Me


title: 137_Stim_CD4Me


title: 30_StimCD8_N


title: 138_Stim_CD8N


title: 134_NoStim_CD4Me


title: 135_NoStim_CD8N


title: 29_StimCD4_Me


title: 26_NoStimCD4_Me


title: 6_StimCD8_N


title: 5_StimCD4_Me


title: 27_NoStimCD8_N


title: 306_StimCD8_N


title: 2_NoStimCD4_Me


title: 302_NoStimCD4_Me


title: 303_NoStimCD8_N


title: 263_StimCD4_Me


title: 282_StimCD8_N


title: 305_StimCD4_Me


title: 279_NoStimCD8_N


title: 278_NoStimCD4_Me


title: 180_Stim_CD8N


title: 179_Stim_CD4Me


title: 177_NoStim_CD8N


title: 176_NoStim_CD4Me


title: 155_Stim_CD4Me


title: 152_NoStim_CD4Me


title: 156_Stim_CD8N


title: 42_StimCD8_N


title: 41_StimCD4_Me


title: 38_NoStimCD4_Me


title: 3_NoStimCD8_N


title: 39_NoStimCD8_N


title: 18_StimCD8_N


title: T3008.Control.LAD2.RV

status: Public on Jun 22 2022

source_name: LAD2 MCs; cultured with Healthy Control AECs

extract_protocol:
Following infection of AECs with HRV16 for 48 hours, RNA was extracted from the AECs and LAD2 MCs using a RNAqueous™-Micro Total RNA Isolation Kit (ThermoFisher/Life Technologies).
Using 1ug total RNA with a RNA integrity number (RIN) ≥8, polyadenylated RNA (primarily mRNA) was selected and purified using oligo-dT conjugated magnetic beads. cDNA libraries were then constructed for each sample using the TruSeq Stranded mRNA Sample Prep Kit (Illumina, #RS-122-2103). Final cDNA libraries were analyzed for size distribution using an Agilent Bioanalyzer (DNA 1000 kit, Agilent # 5067-1504), quantitated by qPCR (KAPA Library Quant Kit, KAPA Biosystems # KK4824), then normalized to 2 nM in preparation for sequencing.
Libraries were pooled and quantified using a Qubit® Fluorometer (Life Technologies). Sequencing of pooled libraries was carried out on a HiSeq 2500 sequencer (Illumina) with paired-end 53-base reads and a target depth of 5 million reads per sample.

treatment_protocol: AEC ALI organotypic cultures were differentiated in PneumaCult™-ALI Medium (Stemcell™ Technologies) on 12 mm 0.4 µm permeable polyester membrane transwell inserts (Corning®). LAD2 MCs at a concentration of 0.5 x 106 cells/mL were added to the basolateral chamber in a 1:1 mixture of LAD2 MC medium and PneumaCult™-ALI Medium. Either 100 µl of HRV16 at a MOI of 1:1 suspended in Hank’s Balanced Salt Solution (HBSS) (100 µg/ml) or 100 µl HBSS (vehicle control) were added to the apical surface of AECs for 48 hours.

value: LAD2 MCs

tag: treatment exposure

value: AECs treated with HRV16

tag: aec donor_id

tag: aec donor_phenotype

value: Healthy Control

tag: sex of_aec_donor

value: Male

tag: libid


title: 15_NoStimCD8_N

tag: cell type


title: 14_NoStimCD4_Me


title: 17_StimCD4_Me


title: 281_StimCD4_Me


title: T3004.Control.LAD2.RV

value: Female


title: T392.Control.LAD2.RV


title: T389.Control.LAD2.RV


title: T385.Control.LAD2.RV


title: T391.Control.LAD2.RV


title: T383.Control.LAD2.RV


title: T388.Control.LAD2.RV


title: T384.Control.LAD2.RV


title: 153_NoStim_CD8N


title: T171.Asthma.LAD2.RV

source_name: LAD2 MCs; cultured with Asthmatic AECs

value: Asthma


title: T167.Asthma.LAD2.RV


title: T166.Asthma.LAD2.RV


title: T164.Asthma.LAD2.RV


title: T137.Asthma.LAD2.RV


title: T117.Asthma.LAD2.RV


title: T161.Asthma.LAD2.RV


title: T3008.Control.LAD2

value: AECs treated with Vehicle Control


title: T150.Asthma.LAD2.RV


title: T3004.Control.LAD2


title: T391.Control.LAD2


title: T170.Asthma.LAD2.RV


title: T388.Control.LAD2


title: T389.Control.LAD2


title: T384.Control.LAD2


title: T397.Control.LAD2


title: T397.Control.LAD2.RV


title: T392.Control.LAD2


title: T385.Control.LAD2


title: T383.Control.LAD2


title: T174.Asthma.LAD2.RV


title: T161.Asthma.LAD2


title: T166.Asthma.LAD2


title: T174.Asthma.LAD2


title: T164.Asthma.LAD2


title: T171.Asthma.LAD2


title: T150.Asthma.LAD2


title: T167.Asthma.LAD2


title: T137.Asthma.LAD2


title: T3008.Control.AEC.LAD.RV

source_name: AECs, Healthy Control; cultured with LAD2 MCs

value: AEC


title: T3004.Control.AEC.LAD.RV


title: T397.Control.AEC.LAD.RV


title: T117.Asthma.LAD2


title: T391.Control.AEC.LAD.RV


title: T392.Control.AEC.LAD.RV


title: T388.Control.AEC.LAD.RV


title: T384.Control.AEC.LAD.RV


title: T385.Control.AEC.LAD.RV


title: T174.Asthma.AEC.LAD.RV

source_name: AECs, Asthma; cultured with LAD2 MCs


title: T170.Asthma.AEC.LAD.RV


title: T389.Control.AEC.LAD.RV


title: T167.Asthma.AEC.LAD.RV


title: T164.Asthma.AEC.LAD.RV


title: T171.Asthma.AEC.LAD.RV


title: T383.Control.AEC.LAD.RV


title: T166.Asthma.AEC.LAD.RV


title: T150.Asthma.AEC.LAD.RV


title: T170.Asthma.LAD2


title: T137.Asthma.AEC.LAD.RV


title: T161.Asthma.AEC.LAD.RV


title: T148.Asthma.AEC.LAD.RV


title: T392.Control.AEC.LAD


title: T3008.Control.AEC.LAD


title: T117.Asthma.AEC.LAD.RV


title: T391.Control.AEC.LAD


title: T397.Control.AEC.LAD


title: T388.Control.AEC.LAD


title: T384.Control.AEC.LAD


title: T385.Control.AEC.LAD


title: T389.Control.AEC.LAD


title: T171.Asthma.AEC.LAD


title: T174.Asthma.AEC.LAD


title: T170.Asthma.AEC.LAD


title: T167.Asthma.AEC.LAD


title: T164.Asthma.AEC.LAD


title: T117.Asthma.AEC.LAD


title: T137.Asthma.AEC.LAD


title: T161.Asthma.AEC.LAD


title: T397.Control.AEC.Alone.RV

source_name: AECs, Healthy Control; cultured alone


title: T389.Control.AEC.Alone.RV


title: T3004.Control.AEC.Alone.RV


title: T385.Control.AEC.Alone.RV


title: T150.Asthma.AEC.LAD


title: T3004.Control.AEC.LAD


title: T3008.Control.AEC.Alone.RV


title: T384.Control.AEC.Alone.RV


title: T392.Control.AEC.Alone.RV


title: T170.Asthma.AEC.Alone.RV

source_name: AECs, Asthma; cultured alone


title: T174.Asthma.AEC.Alone.RV


title: T388.Control.AEC.Alone.RV


title: T383.Control.AEC.Alone.RV


title: T383.Control.AEC.LAD


title: T164.Asthma.AEC.Alone.RV


title: T150.Asthma.AEC.Alone.RV


title: T148.Asthma.AEC.Alone.RV


title: T171.Asthma.AEC.Alone.RV


title: T166.Asthma.AEC.Alone.RV


title: T167.Asthma.AEC.Alone.RV


title: T391.Control.AEC.Alone.RV


title: T161.Asthma.AEC.Alone.RV


title: T166.Asthma.AEC.LAD


title: T3004.Control.AEC.Alone


title: T397.Control.AEC.Alone


title: T391.Control.AEC.Alone


title: T392.Control.AEC.Alone


title: T389.Control.AEC.Alone


title: T388.Control.AEC.Alone


title: T385.Control.AEC.Alone


title: T384.Control.AEC.Alone


title: T383.Control.AEC.Alone


title: T174.Asthma.AEC.Alone


title: T171.Asthma.AEC.Alone


title: T170.Asthma.AEC.Alone


title: T167.Asthma.AEC.Alone


title: T164.Asthma.AEC.Alone


title: T161.Asthma.AEC.Alone


title: T166.Asthma.AEC.Alone


title: T137.Asthma.AEC.Alone.RV


title: T148.Asthma.AEC.Alone


title: T137.Asthma.AEC.Alone


title: T117.Asthma.AEC.Alone


title: 48h_WT_Cont

status: Public on May 25 2022

city: Ulju-gun

first: Wonhyo

last: Lee

state: Ulsan

address: Unist-gil 50

department: Biological Sciences

country: South Korea

institute: UNIST

description: Prdx1 +/+ tMCAO 48h contralateral hemisphere

data_processing:
The single cell RNA libraries constructed by 10x Single Cell chip A kit are sequenced by llumina HiSeq2500 Instrument
Illumina fastq files are aligned on mm10 reference genome by Cell ranger
barcode, feature, and matrix file which are output file of Cell ranger are imported to R with Read10x function of Seurat  package
10x data are converted to seurat object CreateSeuratObject function of seurat package
Multiplet data are eliminated by doubletFinder package
Genome_build: mm10
Supplementary_files_format_and_content: Matrix file of barcodes and genes which shows gene expression of each single cells.

source_name: brain hemisphere

extract_protocol:
The brain hemisphere was removed after cold PBS transcardial perfusion, and tissues were cut into pieces and transferred to the gentleMACSTM C tubes (Miltenyi Biotec) containing the Adult Brain Dissociation kit mouse and rat (Miltenyi Biotec, 130-107-677) enzyme mixture. The brain tissue dissociated with gentleMACSTM program 37°C _ABDK_1 with run 30 min incubations on the MACSmix tube rotator. The supernatant was aspirated, the pellet was resuspended in 8ml of 40% Percoll (GE Healthcare) and overlaid on the top of 4ml of 80% Percoll. The myelin debris was removed using Percoll separation. The gradient is centrifuged at 2200rpm for 20 min without brake at 22°C. Cells were collected 40% to 80% interface and washed with PBS and stained with Zombie NIRTM Fixable viability kit (Biolegend, 423106). The cells were washed by PBS for two times.
BD FACS Aria III (BD Biosciences) was used for sorting brain single live cells. Each cell suspension was subjected to 3′ single-cell RNA sequencing using Single Cell A Chip Kit, Single Cell 3′ Library and Gel Bead Kit V2, and i7 Multiplex Kit (10x Genomics) with a cell recovery target of 9000, following the manufacturer’s instructions

treatment_protocol: C57B6L/J male mice, aged 8-9 weeks Prdx1+/+, Prdx1-/- mice36, and weighing 20−24g, were used for focal brain ischemia experiments. There was no significant difference in weight and age between Prdx1+/+ mice and any Prdx1-/- mice groups. We used a transient (60 min) middle cerebral artery occlusion (tMCAO) model induced through an intraluminal suture (Doccol, 701956PK5Re) under anesthesia with 1.5% isoflurane (SomnosuiteR, Kent Scientific). The method of inducing this tMCAO model 10-20% reduction in cerebral blood flow was confirmed by Laser Doppler Flowmetry (LDF, Primed 3000 system). The rectal temperature was maintained at 37±0.5°C during surgery using a heating pad system. 60 min after MCAO, the brain blood flow was reperfused by the withdrawal of the intraluminal suture.

tag: strain

tag: tissue

value: contralateral hemisphere

value: WT


title: 24h_WT_Cont

description: Prdx1 +/+ tMCAO 24h contralateral hemisphere


title: 24h_WT_Ipsil

description: Prdx1 +/+ tMCAO 24h ipsillateral hemisphere

value: ipsillateral hemisphere


title: T3008.Control.AEC.Alone

tag: age


title: Stable Vitiligo PtG lesional

status: Public on May 20 2022

city: Baltimore

first: Jessica

last: Shiu

state: MD

address: 655 W Baltimore St

department: Pediatrics

institute: University of Maryland School of Medicine

description:
10x genomics
PtG
barcodes appended with '-1' are: non-lesional tissue
barcodes appended with '-2' are: lesional tissue

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Each library was aligned to an indexed hg38 genome using Cell Ranger Count
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: skin

extract_protocol:
All procedures were conducted according to an approved institutional review board protocol of the University of California, Irvine (HS No. 2018-4362), with written informed consent obtained from all patients. The donor skin sites were cleaned with ethanol wipes and 5 suction blisters (1cm diameter) were created by applying a standard suction blister device. We unroofed the blisters and used half for melanocyte-keratinocyte transplant procedure(67). The rest of the blisters were incubated in trypsin for 15 minutes at 37°C, followed by mechanical separation and centrifugation at 1000 rpm for 10 minutes at 4°C to pellet cells. Cells were washed with 0.04% UltraPure BSA:PBS buffer, gently re-suspended in the same buffer, and filtered through a 70mm mesh strainer to create a single cell suspension. Cells were washed and viability was calculated using trypan blue
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics).

value: skin

value: Suction Blisters

value: Single cell suspension

value: Lesional

tag: treatment


title: 48h_WT_Ipsil

description: Prdx1 +/+ tMCAO 48h ipsillateral hemisphere


title: T150.Asthma.AEC.Alone


title: Stable Vitiligo PtG nonlesional

tag: cell line

value: Nonlesional


title: T117.Asthma.AEC.Alone.RV


title: Stable Vitiligo PtF nonlesional

description:
10x genomics
PtF
barcodes appended with '-1' are: non-lesional tissue
barcodes appended with '-2' are: lesional tissue


title: Stable Vitiligo PtE nonlesional

description:
10x genomics
PtE
barcodes appended with '-1' are: non-lesional tissue
barcodes appended with '-2' are: lesional tissue


title: Stable vitiligo PtF lesional


title: Stable Vitiligo PtD nonlesional

description:
10x genomics
PtD
barcodes appended with '-1' are: non-lesional tissue
barcodes appended with '-2' are: lesional tissue


title: Stable Vitiligo PtC nonlesional

description:
10x genomics
PtC
barcodes appended with '-1' are: non-lesional tissue
barcodes appended with '-2' are: lesional tissue


title: Stable Vitiligo PtC lesional


title: Stable Vitiligo PtA nonlesional

description:
10x genomics
PtA
barcodes appended with '-1' are: non-lesional tissue
barcodes appended with '-2' are: lesional tissue


title: MV4;11_MS40N1_rep2, RNA-Seq

status: Public on May 15 2022

city: Chapel Hill

first: Gang Greg

last: Wang

state: NORTH CAROLINA

address: 405 West Drive

department: UNC Lineberger Comprehensive Cancer Center; Department of Biochemistry and Biophysics

institute: University of North Carolina at chapel hill

data_processing:
All reads were mapped to the human genome (hg19) using the BWA alignment software. Unique reads mapped to a single best-matching location with no more than two mismatches were kept using Samtools. We filtered out reads with a mapping quality score of < 20 for downstream analysis.
Then the quantification was done by salmon (ver 0.14.1). Different expression analysis was done using DESeq2.
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited matrix of gene level count estimates

source_name: MV4;11 cells

growth_protocol: MV4;11 cells were grown in RPMI1640 base medium plus 10% FBS and 1% antibiotics.

extract_protocol:
RNA was extracted by using Qiagen RNeasy Mini Kit. Illumina Truseq sample prep kit v2 was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: For compound treatment studies, MV4;11 cells were treated with 0.5 µM of MS40, pomalidomide or MS40N1, relative to DMSO, for 4 days. For the WDR5 knockdown (KD) experiments, MV4;11 cells stably transduced with a doxycycline-inducible WDR5-targeted shRNA (sh#47) or empty vector (shEV) were treated with 0.5 µg/mL of doxycycline (Dox) for four days.

tag: agent


title: MV4;11_MS40N1_rep1, RNA-Seq


title: MV4;11_pomal._rep2, RNA-Seq

value: pomalidomide


title: MV4;11_pomal._rep1, RNA-Seq


title: MV4;11_MS40_rep2, RNA-Seq


title: MV4;11_DMSO_rep1, RNA-Seq

value: DMSO


title: MV4;11_DMSO_rep2, RNA-Seq


title: MV4;11_MS40_rep1, RNA-Seq


title: MV4;11_sh#47_rep2, RNA-Seq

tag: shRNA


title: MV4;11_shEV_rep2, RNA-Seq

value: shEV


title: MV4;11_sh#47_rep1, RNA-Seq


title: MV4;11_shEV_rep1, RNA-Seq


title: MV4;11_DMSO_MLL1-SPIKE-IN

library_source: genomic

data_processing:
All reads were mapped to the human genome (hg19) and drosophila genome(dm3) using the BWA alignment software. Unique reads mapped to a single best-matching location with no more than two mismatches were kept, which were then subject to removal of reads generated by PCR-caused duplicates using the Picard and Samtools. We also filtered out reads with a mapping quality score less than 20 for downstream analysis.
Profiles of ChIP-Seq read densities were displayed in the Integrative Genomics Viewer (IGV, Broad Institute).
The MACS2 software was used for peak identification with data from input as controls and default parameters.
Genome_build: hg19/dm3
Supplementary_files_format_and_content: bigWig

molecule: genomic DNA

organism:
Drosophila melanogaster
Homo sapiens

source_name: MV4;11 cells; added with fly S2 cells

extract_protocol:
Chromatin lysates were prepared from the sonicated nuclei, followed by addition with a fixed amount of sonicated, clarified chromatin of the Drosophila S2 cells across all samples; protein-DNA complexes were isolated with antibodies against H3K4me2 (Millipore 07-030) or MLL1 (Bethyl A300-086A), combined with those against fly-specific H2Av (Active Motif 39715).
Libraries were prepared for deep sequencing using standard Illumina protocols.

treatment_protocol: For ChIP-seq experiments, MV4;11 cells were treated with DMSO and 0.5 μM of MS40 for 4 days and collected.

tag: antibody used

value: Anti-MLL1 (Bethyl Laboratories A300-086A) and Histone H2Av antibody (Active Motif 39715 )

tag: time point

value: 4 days


title: MV4;11_MS40_MLL1-SPIKE-IN


title: Stable Vitiligo PtE lesional

tag: genotype


title: hTSC, CUT&RUN, IgG

status: Public on Apr 15 2022

city: London

first: Miguel

middle: R

last: Branco

address: 4 Newark Street

country: United Kingdom

institute: Blizard Institute

data_processing:
Adaptors and low-quality base calls were trimmed using Trim Galore v0.6.5 with default parameters.
Trimmed reads were mapped to hg38 using bowtie2 v2.4.1 with default paramaters. Reads with MAPQ<2 were removed.
Peaks were called using SEACR v1.2 with normalisation to IgG and relaxed mode.
BigWig tracks were generated using the bamCoverage function of deepTools2.0, with CPM normalisation and 100 bp bin size.
Assembly: hg38
Supplementary files format and content: Bigwig tracks
Supplementary files format and content: Peaks, bed format
Library strategy: CUT&RUN

source_name: hTSC CT29

growth_protocol: Human trophoblast stem cells were grown on plates coated either with 5–10 µg/mL collagen IV or 0.5 µg/mL iMatrix 511. Medium comprised DMEM/F12 supplemented with 1% KSR, 0.5% Penicillin-Streptomycin, 0.15% BSA, 1% ITS-X supplement, 200 µM L-ascorbic acid, 2.5 µM Y27632, 5 µM A83-01, 2 µM CHIR99021, 50 ng/ml EGF and 0.8 mM valproic acid.

extract_protocol:
Cells were bound to BioMagPlus Concanavalin A coated magnetic beads and incubated overnight with primary antibodies, then washed and incubated with pA-Mnase followed by digestion (100mM CaCl2) and reaction arrest in digitonin/EGTA STOP buffer. DNA was extracted using phenol/chloroform.
Libraries were constructed with the NEBNext Ultra II DNA Library Prep Kit.

value: hTSC CT29

value: Human trophoblast stem cells

tag: antibody

value: Rabbit IgG (Santa Cruz sc-2027)


title: MV4;11_DMSO_MLL1-INPUT

value: n/a (input)


title: MV4;11_DMSO_H3K4me2-INPUT


title: MV4;11 cell_DMSO_H3K4me2-SPIKE-IN

value: Anti-H3K4me2 (Millipore 07-030) and Anti-H2Av antibody (Active Motif 39715 )


title: hTSC, CUT&Tag, H3K4me3, rep 2

data_processing:
Adaptors and low-quality base calls were trimmed using Trim Galore v0.6.5 with default parameters.
Trimmed reads were mapped to hg38 using bowtie2 v2.4.1 with default paramaters. Reads with MAPQ<2 were removed.
Peaks were called using SEACR v1.2 with normalisation to IgG and relaxed mode.
BigWig tracks were generated using the bamCoverage function of deepTools2.0, with CPM normalisation and 100 bp bin size.
Assembly: hg38, mm10
Supplementary files format and content: Bigwig tracks
Supplementary files format and content: Peaks, bed format
Library strategy: CUT&Tag

source_name: hTSC CT27

extract_protocol:
Cells were bound to BioMagPlus Concanavalin A coated magnetic beads and incubated overnight with primary antibodies. Samples were washed and incubated with secondary antibody (Guinea Pig anti-Rabbit IgG ABIN101961) for 1 hr, then washed and incubated with pA-Tn5 loaded with Illumina NEXTERA adapters, followed by tagmentation. Adapter-ligated DNA was released with proteinase K and phenol/chloroform extracted.
NEXTERA-tagmented libraries were amplified using NEBNext HiFi 2x PCR Master mix.

treatment_protocol: EVT differentiation was performed in matrigel, in DMEM/F12 supplemented with 0.1 mM 2-mercaptoethanol, 0.5% Penicillin-Streptomycin, 0.3% BSA, 1% ITS-X, 100 ng/ml NRG1, 7.5 μM A83-01, 2.5 μM Y27632 and 4% KSR. NRG1 was exlcuded from the medium from day 3, and KSR from day 6. Cells were collected on day 8.

value: hTSC CT27

value: anti-H3K4me3 (Diagenode C15410003)


title: Stable Vitiligo PtD lesional

value: skin


title: hTSC, CUT&RUN, H3K9me3

value: anti-H3K9me3 (Diagenode C15410193)


title: Stable Vitiligo PtA lesional

value: Suction Blisters

value: Single cell suspension


title: hTSC, CUT&Tag, H3K4me3, rep 1


title: hTSC, CUT&RUN, H3K27me3

value: anti-H3K27me3 (Diagenode C15410195)


title: Liver transcriptome of Patient_97

status: Public on Apr 05 2022

city: Tokyo

first: Hayato

last: Nakagawa

address: 7-3-1 Hongo Bunkyo-ku

country: Japan

institute: The University of Tokyo

data_processing:
Raw sequencing reads were aligned to human reference genome (GRCh38) by STAR, and gene-level read counts were calculated by RSEM.
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Liver

extract_protocol:
RNA was extracted from liver biopsy samples using ISOGEN with Spin Column (Nippon Gene).
Illumina TruSeq Stranded Total RNA LT Sample Prep Kit (Gold) was used with 500ng of total RNA for the construction of sequencing libraries. RNA-Seq libraries were prepared for sequencing using standard Illumina protocols.

tag: disease state

value: NAFLD

value: liver

tag: Sex

value: M

tag: fibrosis stage

tag: nafld activity score


title: Liver transcriptome of Patient_98

value: F


title: Liver transcriptome of Patient_9


title: Liver transcriptome of Patient_94


title: Liver transcriptome of Patient_93


title: Liver transcriptome of Patient_95


title: Liver transcriptome of Patient_92


title: Liver transcriptome of Patient_8


title: MV4;11_MS40_H3K4me2-SPIKE-IN

value: 4 days


title: Liver transcriptome of Patient_89


title: Liver transcriptome of Patient_87


title: Liver transcriptome of Patient_88


title: Liver transcriptome of Patient_86


title: Liver transcriptome of Patient_85


title: Liver transcriptome of Patient_82


title: Liver transcriptome of Patient_71


title: Liver transcriptome of Patient_72


title: Liver transcriptome of Patient_79


title: Liver transcriptome of Patient_69


title: Liver transcriptome of Patient_70


title: Liver transcriptome of Patient_77


title: Liver transcriptome of Patient_7


title: Liver transcriptome of Patient_65


title: Liver transcriptome of Patient_64


title: Liver transcriptome of Patient_96


title: Liver transcriptome of Patient_90


title: Liver transcriptome of Patient_61


title: Liver transcriptome of Patient_63


title: Liver transcriptome of Patient_67


title: Liver transcriptome of Patient_59


title: Liver transcriptome of Patient_5


title: Liver transcriptome of Patient_57


title: Liver transcriptome of Patient_73


title: Liver transcriptome of Patient_84


title: Liver transcriptome of Patient_68


title: Liver transcriptome of Patient_56


title: Liver transcriptome of Patient_81


title: Liver transcriptome of Patient_53


title: Liver transcriptome of Patient_50


title: Liver transcriptome of Patient_75


title: Liver transcriptome of Patient_58


title: Liver transcriptome of Patient_48


title: Liver transcriptome of Patient_44


title: Liver transcriptome of Patient_39


title: Liver transcriptome of Patient_37


title: Liver transcriptome of Patient_43


title: Liver transcriptome of Patient_36


title: Liver transcriptome of Patient_35


title: Liver transcriptome of Patient_33


title: Liver transcriptome of Patient_34


title: Liver transcriptome of Patient_27


title: Liver transcriptome of Patient_26


title: Liver transcriptome of Patient_28


title: Liver transcriptome of Patient_32


title: Liver transcriptome of Patient_25


title: Liver transcriptome of Patient_55


title: Liver transcriptome of Patient_29


title: Liver transcriptome of Patient_2


title: Liver transcriptome of Patient_24


title: Liver transcriptome of Patient_1


title: Liver transcriptome of Patient_14


title: Liver transcriptome of Patient_18


title: Liver transcriptome of Patient_19


title: Liver transcriptome of Patient_12


title: Liver transcriptome of Patient_13


title: Liver transcriptome of Patient_127


title: Liver transcriptome of Patient_126


title: Liver transcriptome of Patient_45


title: Liver transcriptome of Patient_125


title: Liver transcriptome of Patient_42


title: Liver transcriptome of Patient_40


title: Liver transcriptome of Patient_123


title: Liver transcriptome of Patient_124


title: Liver transcriptome of Patient_122


title: Liver transcriptome of Patient_121


title: Liver transcriptome of Patient_11


title: Liver transcriptome of Patient_116


title: Liver transcriptome of Patient_23


title: Liver transcriptome of Patient_115


title: Liver transcriptome of Patient_110


title: Liver transcriptome of Patient_111


title: Liver transcriptome of Patient_114


title: Liver transcriptome of Patient_10


title: Liver transcriptome of Patient_108


title: Liver transcriptome of Patient_107


title: Liver transcriptome of Patient_109


title: Liver transcriptome of Patient_106


title: Liver transcriptome of Patient_103


title: Liver transcriptome of Patient_102


title: U9_scRNA-seq

status: Public on Mar 31 2022

city: Houston

first: Angela

middle: H

last: Ting

state: Tx

address: 1881 East Road

department: Epigenetics and Molecular Carcinogenesis

institute: The University of Texas MD Anderson Cancer Center

data_processing:
cellranger 4.0.0 was used to demultiplex and map the raw sequencing data
The downstream analysis was performed using Seurat 3.2.1 on R 3.6.2
Genome_build: GRCh38-2020A (pre-built GRCh38 genome reference provided by 10X Genomics)
Supplementary_files_format_and_content: Normalized gene count for every gene and every cell (where raw counts were divided by total transcipts per cell and expressed as transcripts per 10000)

molecule: polyA RNA

source_name: human ureter

extract_protocol:
10x Chromium Next GEM Single Cell 3ʹ Kit v3.1
barcoded single cell RNA seq libraries were prepared for each sample and subjected to 150 base paired-end sequencing on Illumina NovaSeq. Each sample library was loaded on 4 lanes of flowcell generating 4 sets of fastq files

value: normal

value: human ureter


title: Liver transcriptome of Patient_101


title: U10_scRNA-seq


title: U8_scRNA-seq


title: Liver transcriptome of Patient_105


title: U6_scRNA-seq


title: Liver transcriptome of Patient_119


title: U2_scRNA-seq


title: Liver transcriptome of Patient_104


title: U3_scRNA-seq


title: Sorted fibroblasts (CD45/CD31/YFP negative) from KPC;YFP tumor [739-pri-fibroblasts]

status: Public on Mar 19 2022

first: Kalluri

last: Lab

state: Texas

address: 1901 East Rd

institute: UT MD Anderson Cancer Center

description:
Mouse pancreatic tumor single-cell RNA-seq
Sample name: 739-pri-fibroblasts
Each biological sample includes 3 Fastq files named starting with "Sample name"

data_processing:
Raw sequencing data from the Illumina platform were converted into Fastq files
Fastq files from the Illumina platform were aligned to the reference genome mm10 using the 10X Genomics Cell Ranger Pipeline
After the alignment, a matrix file containing the cell barcode identity and gene values was exported by the 10X Genomics Cell Ranger Pipeline
Matrix files for the samples were then processed and analyzed by Seurat R software
Assembly: mm10
Supplementary files format and content: Processed data are in the CSV matrix format. All samples combined matrix CSV file as processed data was provided, while individual mouse/sample can be identified by the barcode.

source_name: Mouse pancreatic tumor

growth_protocol: KPC;YFP (LSL-KrasG12D;LSL-P53R172H;Pdx1-Cre;LSL-YFP) and KPC;YFP;aSMA-RFP (LSL-KrasG12D;LSL-P53R172H;Pdx1-Cre;LSL-YFP;aSMA-RFP) mice were housed under standard housing conditions.

extract_protocol:
Single-cell barcoding and library preparation were performed using the 10X Genomics’ Chromium controller and Single Cell 3’ Reagent Kits v2 according to the manufacturer’s instructions.
Following capture and lysis, cDNA was synthesized and amplified to construct Illumina sequencing libraries using the 10X Chromium v2 according to the manufacturer’s instructions.

treatment_protocol: All mice were housed under standard housing conditions at MDACC animal facilities, without any treatment.

value: KPC;YFP

tag: detailed genotype

value: Mouse pancreatic tumor

value: Sorted fibroblasts (CD45/CD31/YFP negative) from total tumor mixture


title: Liver transcriptome of Patient_112


title: U7_scRNA-seq


title: U1_scRNA-seq


title: U5_scRNA-seq


title: Liver transcriptome of Patient_128


title: KPC;YFP tumor live sorted  [739-PriTumor-all]

description:
Mouse pancreatic tumor single-cell RNA-seq
Sample name: 739-PriTumor-all
Each biological sample includes 3 Fastq files named starting with "Sample name"

tag: cell type

value: Total tumor mixture with various cell types


title: KPC;YFP tumor live sorted  [177B-pri-all]

description:
Mouse pancreatic tumor single-cell RNA-seq
Sample name: 177B-pri-all
Each biological sample includes 3 Fastq files named starting with "Sample name"


title: Sorted fibroblasts (CD45/CD31/YFP negative) from KPC;YFP tumor [468B-Fibro]

description:
Mouse pancreatic tumor single-cell RNA-seq
Sample name: 468B-Fibro
Each biological sample includes 3 Fastq files named starting with "Sample name"


title: KPC;YFP tumor live sorted  [591-KPL-All]

description:
Mouse pancreatic tumor single-cell RNA-seq
Sample name: 591-KPL-All
Each biological sample includes 12 Fastq files named starting with "Sample name"


title: KPC;YFP tumor live sorted  [468B-All]

description:
Mouse pancreatic tumor single-cell RNA-seq
Sample name: 468B-All
Each biological sample includes 3 Fastq files named starting with "Sample name"


title: Sorted fibroblasts (aSMA-RFP positive) from KPC;YFP;aSMA-RFP tumor [377D-RFP]

description:
Mouse pancreatic tumor single-cell RNA-seq
Sample name: 377D-RFP
Each biological sample includes 3 Fastq files named starting with "Sample name"

value: KPC;YFP;aSMA-RFP

value: Sorted aSMA-RFP fibroblasts from total tumor mixture


title: Sorted fibroblasts (CD45/CD31/YFP negative) from KPC;YFP tumor [314B-Fibro]

description:
Mouse pancreatic tumor single-cell RNA-seq
Sample name: 314B-Fibro
Each biological sample includes 3 Fastq files named starting with "Sample name"


title: Sorted fibroblasts (CD45/CD31/YFP negative) from KPC;YFP;aSMA-RFP tumor [377D-Fibro]

description:
Mouse pancreatic tumor single-cell RNA-seq
Sample name: 377D-Fibro
Each biological sample includes 3 Fastq files named starting with "Sample name"


title: KPC;YFP;aSMA-RFP tumor live sorted all cells [377D-All]

description:
Mouse pancreatic tumor single-cell RNA-seq
Sample name: 377D-All
Each biological sample includes 3 Fastq files named starting with "Sample name"


title: KPC;YFP tumor live sorted  [314B-All]

description:
Mouse pancreatic tumor single-cell RNA-seq
Sample name: 314B-All
Each biological sample includes 3 Fastq files named starting with "Sample name"


title: KPC;YFP tumor live sorted  [0286-All]

description:
Mouse pancreatic tumor single-cell RNA-seq
Sample name: 0286-All
Each biological sample includes 12 Fastq files named starting with "Sample name"


title: MPRA plasmid rep 5

status: Public on Feb 28 2022

description:
CMS_OL12_Counts_20200827.txt
CMS_OL12_NormCounts_20200827.txt

data_processing:
Reads from the sequencing of the mpra∆orf library were merged into single amplicons using Flash v1.2.7 (flags: -r150, -f 220, -s 10)
Amplicon sequences were kept if the 5’ adapter matched with a levenshtein distance of 3 or less and 2 bp at the edges of both the 5’ and internal constant sequences matched perfectly. Oligo sequences from the passing reads were then mapped back to the expected oligo sequences using BWA mem version 0.7.9a (flags: -L 100 -k 8 -O 5)
Alignment scores were calculated as matching bases divided by the expected oligo size and reads with alignment scores of less than  0.95 were discarded.
Remaining oligo/barcode pairs were then merged and barcodes attributable to multiple oligo sequences were marked as conflicting and removed from further analysis.
Genome_build: GRCh37
Supplementary_files_format_and_content: counts; normalized counts

source_name: Jurkat T cells

growth_protocol: Jurkat T cells Cells were grown at 37 °C maintaining cultures between 1x10^5 and 1x10^6 cells per mL.

extract_protocol:
Total RNA was extracted from cells using QIAGEN Maxi RNeasy (QIAGEN, 75162) following the manufacturer’s protocol including the on-column DNase digestion. A second DNase treatment was performed on the purified RNA using 5 μL of Turbo DNase (Life Technologies, AM2238) with buffer, in 750 μL of total volume for 1 h at 37 °C. The digestion was stopped with the addition of 7.5 μL 10% SDS and 75 μL of 0.5 M EDTA followed by a 5-min incubation at 70 °C. The total reaction was then used for pulldown of GFP mRNA.
First-strand cDNA was synthesized from the DNase-treated GFP mRNA with SuperScript III. Single-stranded cDNA was purified by SPRI and eluted in 30 μL EB. To minimize amplification bias during the creation of cDNA tag sequencing libraries, samples were amplified by qPCR to estimate relative concentrations of GFP cDNA using 1 μL of sample in a 10 μL PCR reaction containing 5 μL Q5 NEBNext master mix, 1.7 μL SYBR Green I diluted 1:10,000 (Life Technologies, S-7567) and 0.5 μM of TruSeq_Universal_Adapter and MPRA_Illumina_GFP_F primers. Samples were amplified with the following qPCR conditions: 95 °C for 20 s, 40 cycles (95 °C for 20 s, 65 °C for 20 s, 72 °C for 30 s), 72 °C for 2 min. The number of cycles for sample amplification was 1−n (the number of cycles it took for each sample to pass the threshold) from the qPCR. To add Illumina sequencing adapters, 10 μL of cDNA samples and mpra:minP:gfp plasmid control (diluted to the qPCR cycle range of the samples) were amplified using the reaction conditions from the qPCR scaled to 50 μL, excluding SYBR Green I. Amplified cDNA was SPRI purified and eluted in 40 μL of EB. To determine oligo/barcode combinations within the MPRA pool, Illumina libraries were prepared from the plasmid library by performing five separate amplifications with 200 ng of plasmid in a 100 μL Q5 NEBNext PCR reaction.  Amplified material was SPRI purified using a 0.6 × bead/sample ratio and eluted with 30 μL of EB. Sequencing indexes were then attached using 20 μL of the eluted product and the same reaction conditions as for the tag-seq protocol, except the number of enrichment cycles was lowered to 5. Samples were molar pooled and sequenced using 2 × 150 bp chemistry on an Illumina NextSeq 550.

tag: source

value: plasmid library


title: Pool 1

description: 10X Genomics single-cell RNA-seq and feature barcode data. Contains WT cells from M1, M2, and M3 and Bach2-18del cells from M4 and M5.

data_processing:
Base-calling was performed automatically with Illumina RTA (v. 1.18.66.3).
For each flowcell, libraries were demultiplexed using bcl2fastq; unassigned reads were processed with a custom script to recover reads with missing base calls in the index sequences. All unambiguously demultiplexed reads for each sample were combined for downstream processing.
Reads were aligned to the genome, collapsed to UMIs, and counts per gene ID were estimated using 10X Cell Ranger count (v. 6.1.1).
Barcodes were called as cells or background using default settings in 10X Cell Ranger (v. 6.1.1).
Genome_build: GRCm38
Supplementary_files_format_and_content: Sparse matrix HDF5 file with UMI counts per barcode per gene ID, and table of read characteristics for each UMI / barcode combination

source_name: spleen

extract_protocol:
Cells were loaded onto a 10X Genomics GemCode Single-Cell Instrument per manufacturer instructions for nanodroplet single-cell capture, cell lysis, mRNA rtPCR, and cDNA barcoding within droplets.
Per manufacturer instructions, droplet emulsions were broken, cDNA was amplified, and libraries were generated using enzymatic fragmentation.

treatment_protocol: CD8 T-cells freshly isolated from blood were sorted.

tag: strain

value: C57BL/6 WT and Bach218del

tag: tissue

value: spleen

value: OTI CD8 T-cells

value: VSV-OVA


title: Sorted fibroblasts (CD45/CD31/YFP negative) from KPC;YFP tumor [177B-Fibroblasts]

description:
Mouse pancreatic tumor single-cell RNA-seq
Sample name: 177B-Fibroblasts
Each biological sample includes 3 Fastq files named starting with "Sample name"


title: U4_scRNA-seq

tag: age


title: KPC;YFP tumor live sorted  [0892-All]

description:
Mouse pancreatic tumor single-cell RNA-seq
Sample name: 0892-All
Each biological sample includes 12 Fastq files named starting with "Sample name"


title: MPRA plasmid rep 4


title: MPRA plasmid rep 3


title: MPRA mRNA rep 3

source_name: plasmid library

value: ATCC TIB-152


title: MPRA mRNA rep 2


title: MPRA plasmid rep 1


title: HEK-R2-HEK-C_S188

data_processing:
CRISPResso (version 2.0.29)68 was used to count the genotypes of each of the base editor-induced mutations present within the sequencing data associated with each FACS sorting bin.
The read counts and genotypes for each sorting bin and the unsorted cells as output by CRIPSResso, were input into R, and MAUDE (version 0.99.3)69 was used to infer the expression levels of genotype, separately for each experiment.
Here, we assumed that 10.5% of the cells were sorted into each of the sorting bins, which was the approximate number observed to fall into each bin during the experiments. We used MAUDE's 'findGuideHitsAllScreens' function to identify the mean expression associated with each genotype (treating genotypes as MAUDE "guides"), using default parameters.
The statistical effect of rs72928038 base edits compared to WT on BACH2 expression were calculated using a paired (by experiment) one-sided Student's t-test with unequal variance.
Genome_build: GRCh37
Supplementary_files_format_and_content: Allele frequency table

extract_protocol:
rs72928038 region amplicon libraries were prepared by nested PCR of each sample, splitting each into two 50 μL reactions (25 μL NEBNext Master Mix, 2.5 μL 10 μM BACH2_gDNAamp_F and 2.5 10 μM BACH2_gDNAamp_R, and 20 μL of reverse-crosslinked sample), program: 98 °C for 30 s, 23 cycles of 98 °C for 15 s, 65 °C for 30 s, 72 °C for 1 min, then 72 °C for 2 min, followed by 1.5X Ampure XP cleanup, and elution in 25 μL EB.
A second 50 μL PCR was performed to add Nextera adapters (25 μL NEBNext Master Mix, 2.5 μL 10 μM BACH2_gseq_F and 2.5 10 μM BACH2_gseq_R, and 20 μL of Ampure-cleaned PCR1), program: 98 °C for 30 s, 6 cycles of 98 °C for 15 s, 64 °C for 30 s, 72 °C for 30 s, then 72 °C for 2 min, followed by 1.5X Ampure XP cleanup, and elution in 25 μL EB. A final 50 μL PCR to add Nextera barcodes and sequencing adapters was then performed (25 μL NEBNext Master Mix, 2.5 μL of mixed 10 μM barcoded Nextera_F and Nextera_R, and 22.5 μL Ampure-cleaned PCR2) for 6 cycles; program: 98 °C for 30 s, 25 cycles of 98 °C for 15 s, 62 °C for 15 s, 72 °C for 16 s, then 72 °C for 2 min. The libraries were then quantified by Qubit and TapeStation, mixed at equimolar ratios, PhiX (Illumina, FC-110-3001) was added at 20%, and samples were sequenced aiming to get >1,000,000 reads per bin, on either an Illumina Nextseq 550 or MiSeq.

tag: locus

value: safe harbor control

tag: replicate

tag: sort bin


title: HEK-R2-HEK-D_S189


title: HEK-R2-HEK-A_S186


title: MPRA plasmid rep 2


title: HEK-R2-NS_S142

value: Not sorted


title: MPRA mRNA rep 1


title: HEK-R2-HEK-NS_S190


title: HEK-R2-HEK-B_S187


title: HEK-R2-B_S139


title: HEK-R2-D_S141


title: HEK-R1-HEK-NS_S185


title: HEK-R1-HEK-D_S184


title: HEK-R1-HEK-C_S183


title: HEK-R1-HEK-B_S182


title: HEK-R1-HEK-A_S181


title: Pool 2

description: 10X Genomics single-cell RNA-seq and feature barcode data. Contains WT cells from M4 and M5 and Bach2-18del cells from M1, M2, and M3.

tag: treatment


title: HEK-R2-C_S140


title: HEK-R1-D_S136


title: HEK-R1-A_S133


title: HEK-R1-B_S134


title: HEK-R1-NS_S137


title: HEK-HEK92-NS_S180


title: HEK-HEK92-C_S156


title: HEK-HEK92-D_S168


title: HEK-HEK92-B_S144


title: HEK-HEK91-D_S108


title: HEK-HEK91-NS_S120


title: HEK-HEK92-A_S132


title: HEK-HEK91-A_S167


title: HEK-HEK62D_S143


title: HEK-R2-A_S138


title: HEK-HEK91-B_S179


title: HEK-HEK62-A_S107


title: HEK-HEK62-NS_S155


title: HEK-HEK62-C_S131


title: HEK-HEK62-B_S119


title: HEK-C2-HEK-C_S176


title: HEK-C2-HEK-NS_S178


title: HEK-C2-HEK-B_S175


title: HEK-C2-NS_S130


title: HEK-C2-HEK-D_S177


title: HEK-R1-C_S135


title: HEK-C2-B_S127


title: HEK-C2-D_S129


title: HEK-C2-C_S128


title: HEK-C1-HEK-B_S170


title: HEK-C1-HEK-D_S172


title: HEK-C1-HEK-C_S171


title: HEK-C1-HEK-NS_S173


title: HEK-HEK91-C_S191


title: HEK-C1-NS_S125


title: HEK-C1-B_S122


title: HEK-C1-C_S123


title: HEK-C1-A_S121


title: HEK-B2-HEK-NS_S166


title: HEK-C1-D_S124


title: HEK-C2-HEK-A_S174


title: HEK-B2-HEK-D_S165


title: HEK-C1-HEK-A_S169


title: HEK-B2-HEK-A_S162


title: HEK-B2-HEK-B_S163


title: HEK-B2-C_S116


title: HEK-B1-HEK-NS_S161


title: HEK-B2-A_S114


title: HEK-B2-D_S117


title: HEK-B2-NS_S118


title: HEK-B1-HEK-D_S160


title: HEK-B1-HEK-A_S157


title: Oligo/barcode pairings

organism: Escherichia coli

source_name: Escherichia coli

value: Endura ElectroCompetent  E. coli


title: HEK-B1-HEK-B_S158


title: HEK-B1-NS_S113


title: HEK-B1-C_S111


title: HEK-B2-HEK-C_S164


title: HEK-B1-A_S109


title: HEK-B1-B_S110


title: HEK-B1-D_S112


title: HEK-A2-HEK-NS_S154


title: HEK-B2-B_S115


title: HEK-A2-HEK-C_S152


title: HEK-A2-HEK-A_S150


title: HEK-A2-NS_S106


title: HEK-A2-HEK-D_S153


title: HEK-C2-A_S126


title: HEK-A2-C_S104


title: HEK-A2-HEK-B_S151


title: HEK-A2-B_S103


title: HEK-A1-HEK-NS_S149


title: HEK-A1-HEK-D_S148


title: HEK-B1-HEK-C_S159


title: HEK-A2-A_S102


title: HEK-A1-HEK-C_S147


title: HEK-A1-HEK-A_S145


title: HEK-A1-C_S99


title: HEK-A2-D_S105


title: HEK-A1-HEK-B_S146


title: HEK-A1-NS_S101


title: HEK-A1-B_S98


title: HEK-A1-D_S100


title: HEK-A1-A_S97


title: BACH2-R2-HEK-NS_S94


title: BACH2-R2-HEK-B_S91


title: BACH2-R2-HEK-D_S93


title: BACH2-R2-NS_S46


title: BACH2-R2-D_S45


title: BACH2-R2-C_S44


title: BACH2-R2-HEK-A_S90


title: BACH2-R2-A_S42


title: BACH2-R1-HEK-NS_S89


title: BACH2-R1-HEK-C_S87


title: BACH2-R1-HEK-D_S88


title: BACH2-R1-HEK-A_S85


title: BACH2-R1-NS_S41


title: BACH2-R1-HEK-B_S86


title: BACH2-R1-D_S40


title: BACH2-R1-C_S39


title: BACH2-R1-B_S38


title: BACH2-HEK92-D_S72


title: BACH2-HEK92-C_S60


title: BACH2-R1-A_S37


title: BACH2-HEK92-NS_S84


title: BACH2-HEK92-B_S48


title: BACH2-HEK92-A_S36


title: BACH2-HEK91-D_S12


title: BACH2-HEK91-NS_S24


title: BACH2-R2-B_S43


title: BACH2-HEK91-B_S83


title: BACH2-HEK62-NS_S59


title: BACH2-HEK62-C_S35


title: BACH2-R2-HEK-C_S92


title: BACH2-C2-HEK-NS_S82


title: BACH2-HEK62D_S47


title: BACH2-HEK62-B_S23


title: BACH2-C2-HEK-D_S81


title: BACH2-HEK62-A_S11


title: BACH2-C2-HEK-C_S80


title: BACH2-C2-HEK-B_S79


title: BACH2-C2-HEK-A_S78


title: BACH2-C2-NS_S34


title: BACH2-C2-C_S32


title: BACH2-C2-D_S33


title: BACH2-C1-HEK-D_S76


title: BACH2-C2-A_S30


title: BACH2-C2-B_S31


title: BACH2-C1-HEK-C_S75


title: BACH2-HEK91-A_S71


title: BACH2-C1-NS_S29


title: BACH2-C1-D_S28


title: BACH2-C1-HEK-B_S74


title: BACH2-C1-C_S27


title: BACH2-HEK91-C_S95


title: BACH2-C1-HEK-A_S73


title: BACH2-C1-B_S26


title: BACH2-C1-A_S25


title: BACH2-B2-HEK-C_S68


title: BACH2-B2-HEK-B_S67


title: BACH2-B2-HEK-D_S69


title: BACH2-B2-HEK-A_S66


title: BACH2-B2-D_S21


title: BACH2-B2-C_S20


title: BACH2-B2-B_S19


title: BACH2-B2-HEK-NS_S70


title: BACH2-B2-A_S18


title: BACH2-B1-HEK-B_S62


title: BACH2-B1-HEK-A_S61


title: BACH2-B2-NS_S22


title: BACH2-B1-D_S16


title: BACH2-B1-C_S15


title: BACH2-B1-B_S14


title: BACH2-A2-HEK-NS_S58


title: BACH2-A2-HEK-C_S56


title: BACH2-A2-D_S9


title: BACH2-A2-HEK-D_S57


title: BACH2-A2-HEK-B_S55


title: BACH2-A2-NS_S10


title: BACH2-A2-HEK-A_S54


title: BACH2-C1-HEK-NS_S77


title: BACH2-A2-A_S6


title: BACH2-A2-B_S7


title: BACH2-A1-HEK-B_S50


title: BACH2-A1-HEK-D_S52


title: BACH2-A1-HEK-NS_S53


title: BACH2-B1-HEK-D_S64


title: BACH2-A1-HEK-A_S49


title: BACH2-A1-HEK-C_S51


title: BACH2-A1-C_S3


title: BACH2-A1-B_S2


title: BACH2-A1-NS_S5


title: BACH2-A1-A_S1


title: BACH2-B1-HEK-C_S63


title: BACH2-B1-A_S13


title: CD8 Naïve T cells of wildtype control, replicate3 [WT_forKO_CD8_Na_rep3]

data_processing:
library strategy: Bulk RNA Barcoding and sequencing (BRB-seq)
Reads were demultiplexed by BRBseqTools (v1.3.1)
Reads were mapped using STAR (v2.7.6a, --outFilterMultimapNmax 1)
Mapped reads were counted by BRBseqTools (v1.3.1).
Genome_build: GRCh38
Supplementary_files_format_and_content: counts

source_name: CD8 Naïve T cells of wildtype control

extract_protocol:
CD4 and CD8 Naive T cells were sorted from spleen using antibodies against CD8a, CD19, CD4, CD3e, CD62L, CD45R/B220, CD44, and CD16.
Total RNA from sorted cells was isolated by using RNeasy plus micro (QIAGEN, 74034). 50 ng for each sample was used for the reverse transcription with barcoded primer BU3 followed by the purification, second strand synthesis and tagmentation following the original BRB-seq protocol (Alpern et al., 2019 Genome Biology) but using AMPure XP for purification.

value: CD8 Naive T cells

tag: strain/genotype


title: CD8 Naïve T cells of wildtype control, replicate2 [WT_forKO_CD8_Na_rep2]


title: BACH2-A2-C_S8


title: CD8 Naïve T cells of wildtype control, replicate1 [WT_forKO_CD8_Na_rep1]


title: BACH2-A1-D_S4


title: CD4 Naïve T cells of wildtype control, replicate3 [WT_forKO_CD4_Na_rep3]

source_name: CD4 Naïve T cells of wildtype control

value: CD4 Naive T cells


title: CD4 Naïve T cells of wildtype control, replicate2 [WT_forKO_CD4_Na_rep2]


title: CD8 Naïve T cells of Bach2<18del>, replicate3 [KO_CD8_Na_rep3]

source_name: CD8 Naïve T cells of Bach2<18del>


title: CD8 Naïve T cells of Bach2<18del>, replicate2 [KO_CD8_Na_rep2]


title: CD4 Naïve T cells of Bach2<18del>, replicate3 [KO_CD4_Na_rep3]

source_name: CD4 Naïve T cells of Bach2<18del>


title: CD4 Naïve T cells of Bach2<18del>, replicate1 [KO_CD4_Na_rep1]


title: CD4 Naïve T cells of Bach2<18del>, replicate2 [KO_CD4_Na_rep2]


title: BACH2-B1-HEK-NS_S65