title: N01_C05R26 Non-diabetic human islet single cell

description:
N01_C05R26
counts.csv


title: LKR10Pool04_T0

status: Public on Nov 11 2021

type: SRA

city: San Francisco

first: David

last: Simpson

state: California

address: 1550 4th Street

country: USA

institute: UCSF

library_source: genomic

data_processing:
Library strategy: shRNAseq
Original fastq files for each GAIIx run were composed of 30-60 multiplexed samples. Each fastq was split by a barcode identifier using the FASTX-toolkit barcode_splitter.pl script
Count files were created in R (v. 3.1.1) using the edgeR package (v. 3.6.8) processHairpinReads function with no mismatches or shifting allowed, shRNAs with no counts were filtered out and all shRNAs were given an extra count to avoid dividing by zero counts
Analysis of shRNA abundance was performed in edgeR using a time-course design and generalized linear models to compare the initial (T0) and final (T1) timepoints of the untreated cells and the the final timepoints of untreated and cisplatin treated cells and a likelihood ratio test (using the glmLRT function) was used to report log2 fold change scores and significance.
Genome_build: no alignment necessary
Supplementary_files_format_and_content: tab delimited text files containing either counts for each shRNA (*.Counts.txt) or log2 fold change and likelihood ratio scores for each shRNA (*Analysis.txt)

molecule: genomic DNA

organism: Mus musculus

source_name: primary murine lung tumor organoids

growth_protocol: Primary lung tumor cells isolated from the KRAS/P53/YFP GEMM were depleted for CD45, CD31, and TER119, and 2x10^6 cells were spinfected with lentiviral shRNA libraries (100 shRNA/pool at an MOI <0.5) and seeded in equal parts Matrigel and 2x SCM (DMEM;F12, 10% FBS, and supplemented with N2 supplement, BPE, 10 ng/mL EGF, 10ng/mL FGF, and antibiotic/antimycotic) and overlayed with 1x SCM to grow into primary tumor spheres.

extract_protocol:
Genomic DNA was extracted using the Qiagen DNeasy Blood & Tissue kit
Lentiviral pLKO shRNA vectors were amplified using PCR with ExTaq, and each sample was given direct barcodes for multiplexing and Illumina compatible adapters using a secondary PCR step

treatment_protocol: Primary tumor spheres were selected with 1ug/mL Puromycin from 24h-72 hours in culture. After 96 hours, cells were treated with 1µM Cisplatin. After 7 days in culture, the first timepoint was collected as genomic DNA from 50% of cells, and the remaining 50% of cells were re-seeeded to form secondary spheres which were collected as genomic DNA after day 7 as secondary spheres.

tag: tissue

value: primary murine lung tumor organoids

tag: timepoint

tag: replicate

tag: strain


title: LKR10Pool04_T1


title: N01_C05R25 Non-diabetic human islet single cell

city: Tucson

first: Hongxu

last: Ding

state: AZ

address: The University of Arizona

institute: University of Arizona

description:
N01_C05R25
counts.csv

library_source: transcriptomic

data_processing:
After demultiplexing, the resulting raw reads were aligned to hg19 reference genome by Bowtie2-2.2.6.
Aligned reads were sorted and indexed by samtools-1.2
Counts matrix was measured with R package GenomicFeatures (1.24.5),  GenomicAlignments (1.8.4) and TxDb.Hsapiens.UCSC.hg19.knownGene (3.2.2)
Samples annotated as living singlets were kept in the counts matrix
Genome_build: hg19, UCSC annotation from R package TxDb.Hsapiens.UCSC.hg19.knownGene (3.2.2)
Supplementary_files_format_and_content: comma separated file including counts matrix

molecule: polyA RNA

organism: Homo sapiens

source_name: Isolated single cells from normal human islets

extract_protocol:
Automated Fludigm C1 800 chip standard protocol
Nextera XT Library kit standard protocol

value: inlet cells


title: N01_C05R24 Non-diabetic human islet single cell

description:
N01_C05R24
counts.csv


title: LKR10Pool03_T1


title: N01_C05R23 Non-diabetic human islet single cell

description:
N01_C05R23
counts.csv


title: N01_C05R22 Non-diabetic human islet single cell

description:
N01_C05R22
counts.csv


title: LKR10Pool03_T0


title: N01_C05R21 Non-diabetic human islet single cell

description:
N01_C05R21
counts.csv


title: LKR10Pool02_T1


title: N01_C05R20 Non-diabetic human islet single cell

description:
N01_C05R20
counts.csv


title: N01_C05R19 Non-diabetic human islet single cell

description:
N01_C05R19
counts.csv


title: LKR10Pool01_T1


title: LKR10Pool02_T0


title: CisplatinPool25_T1_Rep3


title: N01_C05R16 Non-diabetic human islet single cell

description:
N01_C05R16
counts.csv


title: CisplatinPool25_T1_Rep2


title: N01_C05R17 Non-diabetic human islet single cell

description:
N01_C05R17
counts.csv


title: CisplatinPool25_T1_Rep1


title: N01_C05R14 Non-diabetic human islet single cell

description:
N01_C05R14
counts.csv


title: N01_C05R15 Non-diabetic human islet single cell

description:
N01_C05R15
counts.csv


title: N01_C05R18 Non-diabetic human islet single cell

description:
N01_C05R18
counts.csv


title: N01_C05R13 Non-diabetic human islet single cell

description:
N01_C05R13
counts.csv


title: N01_C05R12 Non-diabetic human islet single cell

description:
N01_C05R12
counts.csv


title: N01_C05R11 Non-diabetic human islet single cell

description:
N01_C05R11
counts.csv


title: CisplatinPool24_T1_Rep3


title: CisplatinPool24_T1_Rep2


title: N01_C05R10 Non-diabetic human islet single cell

description:
N01_C05R10
counts.csv


title: LKR10Pool01_T0


title: CisplatinPool24_T0_Rep3


title: N01_C05R09 Non-diabetic human islet single cell

description:
N01_C05R09
counts.csv


title: N01_C05R07 Non-diabetic human islet single cell

description:
N01_C05R07
counts.csv


title: CisplatinPool24_T0_Rep2


title: N01_C05R08 Non-diabetic human islet single cell

description:
N01_C05R08
counts.csv


title: N01_C05R06 Non-diabetic human islet single cell

description:
N01_C05R06
counts.csv


title: CisplatinPool24_T0_Rep1


title: LKR10Pool06_T1


title: CisplatinPool23_T1_Rep2


title: CisplatinPool23_T1_Rep3


title: LKR10Pool10_T1


title: N01_C05R04 Non-diabetic human islet single cell

description:
N01_C05R04
counts.csv


title: N01_C05R03 Non-diabetic human islet single cell

description:
N01_C05R03
counts.csv


title: CisplatinPool23_T1_Rep1


title: CisplatinPool25_T0_Rep3


title: CisplatinPool23_T0_Rep2


title: CisplatinPool25_T0_Rep1


title: CisplatinPool23_T0_Rep3


title: CisplatinPool23_T0_Rep1


title: N01_C05R01 Non-diabetic human islet single cell

description:
N01_C05R01
counts.csv


title: CisplatinPool24_T1_Rep1


title: N01_C05R02 Non-diabetic human islet single cell

description:
N01_C05R02
counts.csv


title: N01_C04R40 Non-diabetic human islet single cell

description:
N01_C04R40
counts.csv


title: CisplatinPool22_T1_Rep2


title: N01_C04R39 Non-diabetic human islet single cell

description:
N01_C04R39
counts.csv


title: CisplatinPool22_T1_Rep3


title: CisplatinPool22_T0_Rep3


title: CisplatinPool22_T1_Rep1


title: N01_C04R38 Non-diabetic human islet single cell

description:
N01_C04R38
counts.csv


title: N01_C04R36 Non-diabetic human islet single cell

description:
N01_C04R36
counts.csv


title: N01_C05R05 Non-diabetic human islet single cell

description:
N01_C05R05
counts.csv


title: CisplatinPool22_T0_Rep1


title: N01_C04R35 Non-diabetic human islet single cell

description:
N01_C04R35
counts.csv


title: CisplatinPool22_T0_Rep2


title: CisplatinPool21_T1_Rep3


title: N01_C04R33 Non-diabetic human islet single cell

description:
N01_C04R33
counts.csv


title: CisplatinPool21_T1_Rep2


title: N01_C04R32 Non-diabetic human islet single cell

description:
N01_C04R32
counts.csv


title: N01_C04R31 Non-diabetic human islet single cell

description:
N01_C04R31
counts.csv


title: CisplatinPool21_T0_Rep3


title: CisplatinPool21_T0_Rep2


title: N01_C04R30 Non-diabetic human islet single cell

description:
N01_C04R30
counts.csv


title: CisplatinPool21_T1_Rep1


title: N01_C04R29 Non-diabetic human islet single cell

description:
N01_C04R29
counts.csv


title: N01_C04R28 Non-diabetic human islet single cell

description:
N01_C04R28
counts.csv


title: CisplatinPool20_T1_Rep3


title: N01_C04R37 Non-diabetic human islet single cell

description:
N01_C04R37
counts.csv


title: N01_C04R26 Non-diabetic human islet single cell

description:
N01_C04R26
counts.csv


title: N01_C04R27 Non-diabetic human islet single cell

description:
N01_C04R27
counts.csv


title: N01_C04R25 Non-diabetic human islet single cell

description:
N01_C04R25
counts.csv


title: N01_C04R34 Non-diabetic human islet single cell

description:
N01_C04R34
counts.csv


title: CisplatinPool20_T1_Rep2


title: CisplatinPool20_T0_Rep3


title: CisplatinPool20_T1_Rep1


title: CisplatinPool20_T0_Rep1


title: N01_C04R22 Non-diabetic human islet single cell

description:
N01_C04R22
counts.csv


title: CisplatinPool19_T1_Rep3


title: N01_C04R21 Non-diabetic human islet single cell

description:
N01_C04R21
counts.csv


title: CisplatinPool20_T0_Rep2


title: CisplatinPool19_T1_Rep2


title: N01_C04R20 Non-diabetic human islet single cell

description:
N01_C04R20
counts.csv


title: CisplatinPool19_T1_Rep1


title: CisplatinPool19_T0_Rep3


title: N01_C04R18 Non-diabetic human islet single cell

description:
N01_C04R18
counts.csv


title: CisplatinPool19_T0_Rep2


title: CisplatinPool19_T0_Rep1


title: CisplatinPool21_T0_Rep1


title: N01_C04R16 Non-diabetic human islet single cell

description:
N01_C04R16
counts.csv


title: CisplatinPool18_T1_Rep3


title: N01_C04R17 Non-diabetic human islet single cell

description:
N01_C04R17
counts.csv


title: N01_C04R14 Non-diabetic human islet single cell

description:
N01_C04R14
counts.csv


title: CisplatinPool18_T1_Rep1


title: N01_C04R15 Non-diabetic human islet single cell

description:
N01_C04R15
counts.csv


title: CisplatinPool18_T1_Rep2


title: N01_C04R24 Non-diabetic human islet single cell

description:
N01_C04R24
counts.csv


title: N01_C04R13 Non-diabetic human islet single cell

description:
N01_C04R13
counts.csv


title: CisplatinPool18_T0_Rep3


title: N01_C04R23 Non-diabetic human islet single cell

description:
N01_C04R23
counts.csv


title: CisplatinPool18_T0_Rep1


title: N01_C04R11 Non-diabetic human islet single cell

description:
N01_C04R11
counts.csv


title: N01_C04R12 Non-diabetic human islet single cell

description:
N01_C04R12
counts.csv


title: N01_C04R08 Non-diabetic human islet single cell

description:
N01_C04R08
counts.csv


title: N01_C04R19 Non-diabetic human islet single cell

description:
N01_C04R19
counts.csv


title: N01_C04R10 Non-diabetic human islet single cell

description:
N01_C04R10
counts.csv


title: CisplatinPool18_T0_Rep2


title: CisplatinPool17_T1_Rep3


title: N01_C04R09 Non-diabetic human islet single cell

description:
N01_C04R09
counts.csv


title: N01_C04R07 Non-diabetic human islet single cell

description:
N01_C04R07
counts.csv


title: CisplatinPool17_T1_Rep2


title: N01_C04R05 Non-diabetic human islet single cell

description:
N01_C04R05
counts.csv


title: N01_C04R06 Non-diabetic human islet single cell

description:
N01_C04R06
counts.csv


title: CisplatinPool17_T0_Rep1


title: N01_C04R04 Non-diabetic human islet single cell

description:
N01_C04R04
counts.csv


title: CisplatinPool16_T1_Rep3


title: N01_C04R03 Non-diabetic human islet single cell

description:
N01_C04R03
counts.csv


title: CisplatinPool16_T1_Rep2


title: N01_C04R02 Non-diabetic human islet single cell

description:
N01_C04R02
counts.csv


title: CisplatinPool16_T1_Rep1


title: N01_C03R39 Non-diabetic human islet single cell

description:
N01_C03R39
counts.csv


title: N01_C03R40 Non-diabetic human islet single cell

description:
N01_C03R40
counts.csv


title: CisplatinPool16_T0_Rep3


title: CisplatinPool16_T0_Rep1


title: CisplatinPool15_T1_Rep3


title: CisplatinPool16_T0_Rep2


title: N01_C03R38 Non-diabetic human islet single cell

description:
N01_C03R38
counts.csv


title: CisplatinPool17_T1_Rep1


title: N01_C03R36 Non-diabetic human islet single cell

description:
N01_C03R36
counts.csv


title: N01_C03R37 Non-diabetic human islet single cell

description:
N01_C03R37
counts.csv


title: CisplatinPool17_T0_Rep3


title: N01_C03R34 Non-diabetic human islet single cell

description:
N01_C03R34
counts.csv


title: CisplatinPool17_T0_Rep2


title: N01_C03R32 Non-diabetic human islet single cell

description:
N01_C03R32
counts.csv


title: CisplatinPool15_T1_Rep2


title: N01_C03R31 Non-diabetic human islet single cell

description:
N01_C03R31
counts.csv


title: CisplatinPool15_T0_Rep2


title: CisplatinPool15_T0_Rep3


title: CisplatinPool15_T0_Rep1


title: N01_C03R30 Non-diabetic human islet single cell

description:
N01_C03R30
counts.csv


title: CisplatinPool14_T1_Rep3


title: CisplatinPool14_T1_Rep2


title: CisplatinPool14_T1_Rep1


title: CisplatinPool25_T0_Rep2


title: N01_C04R01 Non-diabetic human islet single cell

description:
N01_C04R01
counts.csv


title: CisplatinPool14_T0_Rep3


title: N01_C03R29 Non-diabetic human islet single cell

description:
N01_C03R29
counts.csv


title: CisplatinPool14_T0_Rep1


title: N01_C03R26 Non-diabetic human islet single cell

description:
N01_C03R26
counts.csv


title: CisplatinPool14_T0_Rep2


title: CisplatinPool13_T1_Rep3


title: CisplatinPool15_T1_Rep1


title: N01_C03R27 Non-diabetic human islet single cell

description:
N01_C03R27
counts.csv


title: N01_C03R35 Non-diabetic human islet single cell

description:
N01_C03R35
counts.csv


title: N01_C03R28 Non-diabetic human islet single cell

description:
N01_C03R28
counts.csv


title: N01_C03R24 Non-diabetic human islet single cell

description:
N01_C03R24
counts.csv


title: CisplatinPool13_T1_Rep1


title: CisplatinPool13_T1_Rep2


title: N01_C03R33 Non-diabetic human islet single cell

description:
N01_C03R33
counts.csv


title: N01_C03R23 Non-diabetic human islet single cell

description:
N01_C03R23
counts.csv


title: CisplatinPool13_T0_Rep3


title: N01_C03R22 Non-diabetic human islet single cell

description:
N01_C03R22
counts.csv


title: CisplatinPool13_T0_Rep2


title: N01_C03R21 Non-diabetic human islet single cell

description:
N01_C03R21
counts.csv


title: CisplatinPool13_T0_Rep1


title: N01_C03R19 Non-diabetic human islet single cell

description:
N01_C03R19
counts.csv


title: N01_C03R20 Non-diabetic human islet single cell

description:
N01_C03R20
counts.csv


title: N01_C03R18 Non-diabetic human islet single cell

description:
N01_C03R18
counts.csv


title: CisplatinPool12_T1_Rep1


title: CisplatinPool12_T0_Rep3


title: N01_C03R17 Non-diabetic human islet single cell

description:
N01_C03R17
counts.csv


title: CisplatinPool12_T1_Rep3


title: CisplatinPool12_T1_Rep2


title: N01_C03R15 Non-diabetic human islet single cell

description:
N01_C03R15
counts.csv


title: CisplatinPool12_T0_Rep2


title: N01_C03R25 Non-diabetic human islet single cell

description:
N01_C03R25
counts.csv


title: N01_C03R14 Non-diabetic human islet single cell

description:
N01_C03R14
counts.csv


title: CisplatinPool11_T1_Rep3


title: N01_C03R13 Non-diabetic human islet single cell

description:
N01_C03R13
counts.csv


title: N01_C03R16 Non-diabetic human islet single cell

description:
N01_C03R16
counts.csv


title: CisplatinPool12_T0_Rep1


title: CisplatinPool11_T1_Rep1


title: CisplatinPool11_T1_Rep2


title: CisplatinPool11_T0_Rep3


title: N01_C03R09 Non-diabetic human islet single cell

description:
N01_C03R09
counts.csv


title: CisplatinPool11_T0_Rep1


title: N01_C03R08 Non-diabetic human islet single cell

description:
N01_C03R08
counts.csv


title: CisplatinPool11_T0_Rep2


title: N01_C03R10 Non-diabetic human islet single cell

description:
N01_C03R10
counts.csv


title: CisplatinPool10_T1_Rep3


title: N01_C03R06 Non-diabetic human islet single cell

description:
N01_C03R06
counts.csv


title: CisplatinPool10_T0_Rep3


title: CisplatinPool10_T1_Rep1


title: N01_C03R07 Non-diabetic human islet single cell

description:
N01_C03R07
counts.csv


title: N01_C03R05 Non-diabetic human islet single cell

description:
N01_C03R05
counts.csv


title: CisplatinPool10_T0_Rep2


title: CisplatinPool10_T1_Rep2


title: N01_C03R04 Non-diabetic human islet single cell

description:
N01_C03R04
counts.csv


title: N01_C03R12 Non-diabetic human islet single cell

description:
N01_C03R12
counts.csv


title: CisplatinPool09_T1_Rep3


title: N01_C03R02 Non-diabetic human islet single cell

description:
N01_C03R02
counts.csv


title: CisplatinPool10_T0_Rep1


title: N01_C03R01 Non-diabetic human islet single cell

description:
N01_C03R01
counts.csv


title: CisplatinPool09_T1_Rep2


title: CisplatinPool09_T1_Rep1


title: N01_C02R39 Non-diabetic human islet single cell

description:
N01_C02R39
counts.csv


title: CisplatinPool09_T0_Rep3


title: N01_C02R37 Non-diabetic human islet single cell

description:
N01_C02R37
counts.csv


title: CisplatinPool09_T0_Rep1


title: N01_C02R36 Non-diabetic human islet single cell

description:
N01_C02R36
counts.csv


title: CisplatinPool08_T1_Rep3


title: CisplatinPool09_T0_Rep2


title: N01_C02R35 Non-diabetic human islet single cell

description:
N01_C02R35
counts.csv


title: N01_C03R03 Non-diabetic human islet single cell

description:
N01_C03R03
counts.csv


title: N01_C02R38 Non-diabetic human islet single cell

description:
N01_C02R38
counts.csv


title: CisplatinPool08_T0_Rep3


title: CisplatinPool08_T0_Rep1


title: N01_C02R40 Non-diabetic human islet single cell

description:
N01_C02R40
counts.csv


title: CisplatinPool08_T1_Rep2


title: CisplatinPool08_T1_Rep1


title: N01_C02R30 Non-diabetic human islet single cell

description:
N01_C02R30
counts.csv


title: N01_C02R33 Non-diabetic human islet single cell

description:
N01_C02R33
counts.csv


title: N01_C02R34 Non-diabetic human islet single cell

description:
N01_C02R34
counts.csv


title: N01_C02R29 Non-diabetic human islet single cell

description:
N01_C02R29
counts.csv


title: CisplatinPool07_T1_Rep3


title: CisplatinPool08_T0_Rep2


title: N01_C02R31 Non-diabetic human islet single cell

description:
N01_C02R31
counts.csv


title: CisplatinPool07_T1_Rep1


title: CisplatinPool07_T1_Rep2


title: N01_C02R25 Non-diabetic human islet single cell

description:
N01_C02R25
counts.csv


title: N01_C02R27 Non-diabetic human islet single cell

description:
N01_C02R27
counts.csv


title: N01_C02R28 Non-diabetic human islet single cell

description:
N01_C02R28
counts.csv


title: CisplatinPool07_T0_Rep2


title: N01_C02R26 Non-diabetic human islet single cell

description:
N01_C02R26
counts.csv


title: CisplatinPool07_T0_Rep3


title: N01_C02R32 Non-diabetic human islet single cell

description:
N01_C02R32
counts.csv


title: N01_C03R11 Non-diabetic human islet single cell

description:
N01_C03R11
counts.csv


title: N01_C02R24 Non-diabetic human islet single cell

description:
N01_C02R24
counts.csv


title: CisplatinPool07_T0_Rep1


title: N01_C02R22 Non-diabetic human islet single cell

description:
N01_C02R22
counts.csv


title: CisplatinPool06_T1_Rep1


title: N01_C02R21 Non-diabetic human islet single cell

description:
N01_C02R21
counts.csv


title: CisplatinPool06_T1_Rep3


title: N01_C02R23 Non-diabetic human islet single cell

description:
N01_C02R23
counts.csv


title: CisplatinPool06_T1_Rep2


title: CisplatinPool06_T0_Rep3


title: N01_C02R19 Non-diabetic human islet single cell

description:
N01_C02R19
counts.csv


title: N01_C02R17 Non-diabetic human islet single cell

description:
N01_C02R17
counts.csv


title: N01_C02R20 Non-diabetic human islet single cell

description:
N01_C02R20
counts.csv


title: CisplatinPool06_T0_Rep1


title: CisplatinPool05_T1_Rep2


title: CisplatinPool06_T0_Rep2


title: N01_C02R15 Non-diabetic human islet single cell

description:
N01_C02R15
counts.csv


title: N01_C02R18 Non-diabetic human islet single cell

description:
N01_C02R18
counts.csv


title: CisplatinPool05_T1_Rep3


title: CisplatinPool05_T0_Rep3


title: CisplatinPool05_T0_Rep2


title: N01_C02R16 Non-diabetic human islet single cell

description:
N01_C02R16
counts.csv


title: N01_C02R12 Non-diabetic human islet single cell

description:
N01_C02R12
counts.csv


title: N01_C02R14 Non-diabetic human islet single cell

description:
N01_C02R14
counts.csv


title: CisplatinPool04_T1_Rep3


title: CisplatinPool04_T1_Rep2


title: N01_C02R11 Non-diabetic human islet single cell

description:
N01_C02R11
counts.csv


title: N01_C02R09 Non-diabetic human islet single cell

description:
N01_C02R09
counts.csv


title: CisplatinPool04_T1_Rep1


title: N01_C02R10 Non-diabetic human islet single cell

description:
N01_C02R10
counts.csv


title: CisplatinPool05_T0_Rep1


title: N01_C02R03 Non-diabetic human islet single cell

description:
N01_C02R03
counts.csv


title: N01_C02R07 Non-diabetic human islet single cell

description:
N01_C02R07
counts.csv


title: CisplatinPool04_T0_Rep1


title: CisplatinPool03_T1_Rep3


title: N01_C02R06 Non-diabetic human islet single cell

description:
N01_C02R06
counts.csv


title: N01_C02R05 Non-diabetic human islet single cell

description:
N01_C02R05
counts.csv


title: N01_C02R13 Non-diabetic human islet single cell

description:
N01_C02R13
counts.csv


title: CisplatinPool04_T0_Rep2


title: N01_C02R04 Non-diabetic human islet single cell

description:
N01_C02R04
counts.csv


title: CisplatinPool03_T1_Rep2


title: N01_C02R08 Non-diabetic human islet single cell

description:
N01_C02R08
counts.csv


title: CisplatinPool03_T0_Rep3


title: CisplatinPool03_T1_Rep1


title: N01_C02R02 Non-diabetic human islet single cell

description:
N01_C02R02
counts.csv


title: N01_C02R01 Non-diabetic human islet single cell

description:
N01_C02R01
counts.csv


title: CisplatinPool03_T0_Rep2


title: N01_C01R40 Non-diabetic human islet single cell

description:
N01_C01R40
counts.csv


title: CisplatinPool04_T0_Rep3


title: CisplatinPool02_T1_Rep3


title: N01_C01R37 Non-diabetic human islet single cell

description:
N01_C01R37
counts.csv


title: N01_C01R39 Non-diabetic human islet single cell

description:
N01_C01R39
counts.csv


title: N01_C01R38 Non-diabetic human islet single cell

description:
N01_C01R38
counts.csv


title: N01_C01R36 Non-diabetic human islet single cell

description:
N01_C01R36
counts.csv


title: CisplatinPool02_T1_Rep1


title: CisplatinPool02_T0_Rep2


title: CisplatinPool03_T0_Rep1


title: CisplatinPool02_T1_Rep2


title: CisplatinPool02_T0_Rep3


title: N01_C01R34 Non-diabetic human islet single cell

description:
N01_C01R34
counts.csv


title: N01_C01R32 Non-diabetic human islet single cell

description:
N01_C01R32
counts.csv


title: CisplatinPool02_T0_Rep1


title: N01_C01R35 Non-diabetic human islet single cell

description:
N01_C01R35
counts.csv


title: CisplatinPool01_T0_Rep3


title: CisplatinPool01_T1_Rep2


title: CisplatinPool01_T0_Rep2


title: N01_C01R31 Non-diabetic human islet single cell

description:
N01_C01R31
counts.csv


title: CisplatinPool01_T1_Rep1


title: CisplatinPool01_T1_Rep3


title: N01_C01R30 Non-diabetic human islet single cell

description:
N01_C01R30
counts.csv


title: N01_C01R29 Non-diabetic human islet single cell

description:
N01_C01R29
counts.csv


title: N01_C01R28 Non-diabetic human islet single cell

description:
N01_C01R28
counts.csv


title: N01_C01R27 Non-diabetic human islet single cell

description:
N01_C01R27
counts.csv


title: N01_C01R24 Non-diabetic human islet single cell

description:
N01_C01R24
counts.csv


title: N01_C01R23 Non-diabetic human islet single cell

description:
N01_C01R23
counts.csv


title: UntreatedPool25_T0_Rep1


title: N01_C01R21 Non-diabetic human islet single cell

description:
N01_C01R21
counts.csv


title: UntreatedPool25_T0_Rep3


title: UntreatedPool25_T0_Rep2


title: N01_C01R26 Non-diabetic human islet single cell

description:
N01_C01R26
counts.csv


title: UntreatedPool25_T1_Rep2


title: N01_C01R25 Non-diabetic human islet single cell

description:
N01_C01R25
counts.csv


title: UntreatedPool25_T1_Rep3


title: CisplatinPool01_T0_Rep1


title: N01_C01R22 Non-diabetic human islet single cell

description:
N01_C01R22
counts.csv


title: UntreatedPool24_T1_Rep3


title: UntreatedPool25_T1_Rep1


title: N01_C01R19 Non-diabetic human islet single cell

description:
N01_C01R19
counts.csv


title: UntreatedPool24_T1_Rep2


title: UntreatedPool24_T1_Rep1


title: N01_C01R16 Non-diabetic human islet single cell

description:
N01_C01R16
counts.csv


title: N01_C01R20 Non-diabetic human islet single cell

description:
N01_C01R20
counts.csv


title: UntreatedPool24_T0_Rep3


title: UntreatedPool23_T1_Rep3


title: UntreatedPool24_T0_Rep2


title: N01_C01R18 Non-diabetic human islet single cell

description:
N01_C01R18
counts.csv


title: UntreatedPool24_T0_Rep1


title: N01_C01R15 Non-diabetic human islet single cell

description:
N01_C01R15
counts.csv


title: UntreatedPool23_T0_Rep3


title: N01_C01R12 Non-diabetic human islet single cell

description:
N01_C01R12
counts.csv


title: N01_C01R11 Non-diabetic human islet single cell

description:
N01_C01R11
counts.csv


title: UntreatedPool23_T0_Rep1


title: UntreatedPool22_T1_Rep3


title: N01_C01R17 Non-diabetic human islet single cell

description:
N01_C01R17
counts.csv


title: N01_C01R10 Non-diabetic human islet single cell

description:
N01_C01R10
counts.csv


title: UntreatedPool22_T1_Rep2


title: N01_C01R09 Non-diabetic human islet single cell

description:
N01_C01R09
counts.csv


title: UntreatedPool22_T1_Rep1


title: UntreatedPool23_T1_Rep1


title: N01_C01R07 Non-diabetic human islet single cell

description:
N01_C01R07
counts.csv


title: N01_C01R06 Non-diabetic human islet single cell

description:
N01_C01R06
counts.csv


title: UntreatedPool22_T0_Rep2


title: N01_C01R13 Non-diabetic human islet single cell

description:
N01_C01R13
counts.csv


title: N01_C01R08 Non-diabetic human islet single cell

description:
N01_C01R08
counts.csv


title: UntreatedPool23_T1_Rep2


title: N01_C01R05 Non-diabetic human islet single cell

description:
N01_C01R05
counts.csv


title: UntreatedPool21_T1_Rep3


title: UntreatedPool22_T0_Rep1


title: UntreatedPool21_T1_Rep1


title: CisplatinPool05_T1_Rep1


title: UntreatedPool21_T1_Rep2


title: N01_C01R03 Non-diabetic human islet single cell

description:
N01_C01R03
counts.csv


title: N01_C01R02 Non-diabetic human islet single cell

description:
N01_C01R02
counts.csv


title: N01_C01R14 Non-diabetic human islet single cell

description:
N01_C01R14
counts.csv


title: N01_C01R33 Non-diabetic human islet single cell

description:
N01_C01R33
counts.csv


title: N01_C01R01 Non-diabetic human islet single cell

description:
N01_C01R01
counts.csv


title: UntreatedPool21_T0_Rep3


title: UntreatedPool23_T0_Rep2


title: UntreatedPool21_T0_Rep2


title: UntreatedPool21_T0_Rep1


title: UntreatedPool20_T1_Rep3


title: UntreatedPool22_T0_Rep3


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_h7

description: HsMm.csv

data_processing:
After demultiplexing, UMIs from the barcode read (8nt) were concatenated onto the 5’ part of corresponding mappable reads using a custom Python script.
The concatenated mappable reads were aligned and mapped using the STAR 2.5.1a with option --quantMode TranscriptomeSAM so that output alignments are translated into transcript coordinates for downstream analysis, and --clip5pNbases 8 so that the UMI sequences are not mapped. All other options for STAR are set as default.
Specifically, for mix-species experiments, the concatenated mappable reads were aligned and mapped using the STAR 2.5.1a with option --outFilterMultimapNmax 1 so that only reads that uniquely mapped are considered.
The mapped transcripts per gene and mapped reads per gene were quantified using a custom Python script. When measuring mapped transcripts per gene, we use hamming distance threshold 1, which means only if the hamming distance between two UMIs is greater than 1, then they are considered from different transcripts.
Genome_build: UCSC hg38 for HEK293 RNA-Seq and scRNA-Seq, and U87 scRNA-Seq.
Genome_build: Concatenated UCSC hg38 and mm10 for U87-3T3 cell mixture scRNA-Seq profiles.
Supplementary_files_format_and_content: comma separated file including umi matrix, counts matrix and cross-species matrix.

organism:
Homo sapiens
Mus musculus

source_name: Single cell from U87-3T3 cell mixture

extract_protocol:
published scPLATE-Seq protocol
published scPLATE-Seq protocol

tag: cell line

value: U87 and 3T3


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_h8

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_h9

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_h6

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_h4

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_h3

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_h2

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_h5

description: HsMm.csv


title: UntreatedPool20_T0_Rep3


title: UntreatedPool20_T1_Rep1


title: UntreatedPool20_T0_Rep1


title: N01_C01R04 Non-diabetic human islet single cell

description:
N01_C01R04
counts.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_h1

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_h11

description: HsMm.csv


title: UntreatedPool19_T1_Rep1


title: UntreatedPool19_T0_Rep3


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_h10

description: HsMm.csv


title: UntreatedPool19_T1_Rep2


title: UntreatedPool19_T0_Rep1


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_g8

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_g7

description: HsMm.csv


title: UntreatedPool20_T1_Rep2


title: UntreatedPool20_T0_Rep2


title: UntreatedPool18_T1_Rep3


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_h12

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_g6

description: HsMm.csv


title: UntreatedPool18_T1_Rep1


title: UntreatedPool18_T1_Rep2


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_g5

description: HsMm.csv


title: UntreatedPool18_T0_Rep2


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_g9

description: HsMm.csv


title: UntreatedPool17_T1_Rep3


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_g12

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_g3

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_g11

description: HsMm.csv


title: UntreatedPool17_T1_Rep2


title: UntreatedPool19_T1_Rep3


title: UntreatedPool19_T0_Rep2


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_g10

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_g2

description: HsMm.csv


title: UntreatedPool17_T1_Rep1


title: UntreatedPool17_T0_Rep3


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_g1

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_f9

description: HsMm.csv


title: UntreatedPool17_T0_Rep1


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_f8

description: HsMm.csv


title: UntreatedPool18_T0_Rep3


title: UntreatedPool16_T1_Rep3


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_g4

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_f7

description: HsMm.csv


title: UntreatedPool17_T0_Rep2


title: UntreatedPool18_T0_Rep1


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_f6

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_f4

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_f5

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_f12

description: HsMm.csv


title: UntreatedPool16_T1_Rep1


title: UntreatedPool16_T0_Rep3


title: UntreatedPool15_T1_Rep3


title: UntreatedPool16_T0_Rep2


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_f3

description: HsMm.csv


title: UntreatedPool16_T0_Rep1


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_f10

description: HsMm.csv


title: UntreatedPool15_T1_Rep1


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_e9

description: HsMm.csv


title: UntreatedPool15_T1_Rep2


title: UntreatedPool15_T0_Rep3


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_f1

description: HsMm.csv


title: UntreatedPool15_T0_Rep2


title: UntreatedPool16_T1_Rep2


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_e8

description: HsMm.csv


title: UntreatedPool15_T0_Rep1


title: UntreatedPool14_T1_Rep3


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_e6

description: HsMm.csv


title: UntreatedPool14_T1_Rep2


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_f2

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_e4

description: HsMm.csv


title: UntreatedPool14_T1_Rep1


title: UntreatedPool14_T0_Rep3


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_e5

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_e3

description: HsMm.csv


title: UntreatedPool14_T0_Rep2


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_e2

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_f11

description: HsMm.csv


title: UntreatedPool13_T1_Rep3


title: UntreatedPool14_T0_Rep1


title: UntreatedPool13_T1_Rep2


title: UntreatedPool13_T1_Rep1


title: UntreatedPool13_T0_Rep3


title: UntreatedPool13_T0_Rep1


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_d9

description: HsMm.csv


title: UntreatedPool12_T1_Rep3


title: UntreatedPool13_T0_Rep2


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_d8

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_d7

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_d6

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_e7

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_d5

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_d4

description: HsMm.csv


title: UntreatedPool12_T1_Rep1


title: UntreatedPool12_T0_Rep3


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_e12

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_e11

description: HsMm.csv


title: UntreatedPool12_T0_Rep1


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_d3

description: HsMm.csv


title: UntreatedPool12_T0_Rep2


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_e10

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_d12

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_d1

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_e1

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_d10

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_d11

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_d2

description: HsMm.csv


title: UntreatedPool11_T1_Rep2


title: UntreatedPool11_T0_Rep3


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_c9

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_c8

description: HsMm.csv


title: UntreatedPool12_T1_Rep2


title: UntreatedPool11_T0_Rep1


title: UntreatedPool11_T0_Rep2


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_c7

description: HsMm.csv


title: UntreatedPool10_T1_Rep3


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_c6

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_c5

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_c4

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_c3

description: HsMm.csv


title: UntreatedPool11_T1_Rep3


title: UntreatedPool10_T1_Rep1


title: UntreatedPool10_T1_Rep2


title: UntreatedPool09_T1_Rep3


title: UntreatedPool11_T1_Rep1


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_c2

description: HsMm.csv


title: UntreatedPool10_T0_Rep3


title: UntreatedPool10_T0_Rep1


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_c11

description: HsMm.csv


title: UntreatedPool10_T0_Rep2


title: UntreatedPool09_T1_Rep2


title: UntreatedPool09_T1_Rep1


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_c12

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_c10

description: HsMm.csv


title: UntreatedPool09_T0_Rep3


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_b9

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_c1

description: HsMm.csv


title: UntreatedPool09_T0_Rep2


title: UntreatedPool09_T0_Rep1


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_b8

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_b6

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_b5

description: HsMm.csv


title: UntreatedPool08_T1_Rep2


title: UntreatedPool08_T1_Rep1


title: UntreatedPool08_T1_Rep3


title: UntreatedPool08_T0_Rep3


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_b4

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_b3

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_b2

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_b10

description: HsMm.csv


title: UntreatedPool07_T1_Rep2


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_b11

description: HsMm.csv


title: UntreatedPool07_T1_Rep3


title: UntreatedPool08_T0_Rep1


title: UntreatedPool08_T0_Rep2


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_a9

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_b1

description: HsMm.csv


title: UntreatedPool07_T0_Rep3


title: UntreatedPool07_T1_Rep1


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_a8

description: HsMm.csv


title: UntreatedPool07_T0_Rep2


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_a6

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_b7

description: HsMm.csv


title: UntreatedPool06_T1_Rep2


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_a7

description: HsMm.csv


title: UntreatedPool06_T1_Rep1


title: UntreatedPool06_T0_Rep2


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_a3

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_a4

description: HsMm.csv


title: UntreatedPool06_T1_Rep3


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_a2

description: HsMm.csv


title: UntreatedPool06_T0_Rep3


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_b12

description: HsMm.csv


title: UntreatedPool06_T0_Rep1


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_a12

description: HsMm.csv


title: UntreatedPool05_T1_Rep3


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_a11

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_h9

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_a1

description: HsMm.csv


title: UntreatedPool05_T1_Rep1


title: UntreatedPool05_T0_Rep3


title: UntreatedPool05_T0_Rep2


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_a5

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_h7

description: HsMm.csv


title: UntreatedPool04_T1_Rep3


title: UntreatedPool05_T1_Rep2


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and Silane U87_3T3_SC_C4_a10

description: HsMm.csv


title: UntreatedPool07_T0_Rep1


title: UntreatedPool04_T1_Rep1


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_h6

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_h4

description: HsMm.csv


title: UntreatedPool04_T1_Rep2


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_h5

description: HsMm.csv


title: UntreatedPool05_T0_Rep1


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_h3

description: HsMm.csv


title: UntreatedPool04_T0_Rep1


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_h11

description: HsMm.csv


title: UntreatedPool03_T1_Rep3


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_h8

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_h10

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_h12

description: HsMm.csv


title: UntreatedPool03_T1_Rep2


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_h1

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_h2

description: HsMm.csv


title: UntreatedPool03_T1_Rep1


title: UntreatedPool03_T0_Rep3


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_g7

description: HsMm.csv


title: UntreatedPool03_T0_Rep2


title: UntreatedPool03_T0_Rep1


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_g8

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_g5

description: HsMm.csv


title: UntreatedPool02_T1_Rep3


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_g6

description: HsMm.csv


title: UntreatedPool04_T0_Rep3


title: UntreatedPool02_T1_Rep2


title: UntreatedPool04_T0_Rep2


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_g2

description: HsMm.csv


title: UntreatedPool02_T0_Rep3


title: UntreatedPool02_T1_Rep1


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_g3

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_g4

description: HsMm.csv


title: UntreatedPool02_T0_Rep2


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_g12

description: HsMm.csv


title: UntreatedPool01_T1_Rep3


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_g11

description: HsMm.csv


title: UntreatedPool01_T1_Rep2


title: UntreatedPool02_T0_Rep1


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_g10

description: HsMm.csv


title: UntreatedPool01_T1_Rep1


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_g1

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_g9

description: HsMm.csv


title: UntreatedPool01_T0_Rep3


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_f9

description: HsMm.csv


title: UntreatedPool01_T0_Rep2


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_f8

description: HsMm.csv


title: UntreatedPool01_T0_Rep1


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_f7

description: HsMm.csv


title: mPFC saline rep9

city: Torino

first: Aurora

last: Savino

state: Piemonte

address: via Nizza, 52

country: Italy

institute: Università di Torino

data_processing:
Reads were mapped to the Rattus norvegicus rn6 reference assembly using Hisat2.
Gene counts were computed using the htseq-count tool from the HTSeq package and the ncbi RefSeq gtf file.
Genome_build: rn6 (Rnor_6.0)
Supplementary_files_format_and_content: Raw_gene_counts_matrix.txt: Matrix table with raw gene counts for every gene and every sample.

molecule: total RNA

organism: Rattus norvegicus

source_name: mPFC

growth_protocol: Male Sprague-Dawley rats obtained from Harlan (Indianapolis, IN) were aged 6-8 weeks (180-200 g) at the start of treatment. Animals were housed individually for seven days before treatment, during which time they were handled for 15 min each day. During treatment, rats were individually housed in translucent home cages, allowed free access to food and water, and kept on a 12:12 h light/dark cycle.

extract_protocol:
4 μg of total extracted RNA were subjected to poly(A) selection.
Sample libraries were prepared with Illumina mRNA sample preparation kits.

treatment_protocol: Rats were injected (i.p.) with either sterile saline, or LSD (0.16 mg/kg) every other day for 90 days.

value: Sprague-Dawley

tag: gender

value: male

value: medial prefrontal cortex

tag: treatment

value: Saline


title: mPFC saline rep10


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_f6

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_f5

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_f4

description: HsMm.csv


title: mPFC saline rep7


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_f2

description: HsMm.csv


title: mPFC saline rep6


title: mPFC saline rep8


title: mPFC saline rep5


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_f12

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_f10

description: HsMm.csv


title: mPFC saline rep2


title: mPFC saline rep1


title: mPFC saline rep3


title: mPFC LSD rep10

value: LSD


title: mPFC LSD rep9


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_e9

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_f3

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_f1

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_e7

description: HsMm.csv


title: mPFC saline rep4


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_f11

description: HsMm.csv


title: mPFC LSD rep7


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_e5

description: HsMm.csv


title: mPFC LSD rep6


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_e8

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_e4

description: HsMm.csv


title: mPFC LSD rep8


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_e6

description: HsMm.csv


title: mPFC LSD rep5


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_e3

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_e2

description: HsMm.csv


title: mPFC LSD rep4


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_e12

description: HsMm.csv


title: mPFC LSD rep2


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_e10

description: HsMm.csv


title: mPFC LSD rep3


title: mPFC LSD rep1


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_e11

description: HsMm.csv


title: 50od

city: Santander

first: Lucio

last: Di Filippo

state: Cantabria

address: PCTCAN - Cl. Albert Einstein, 22

country: Spain

institute: IBBTEC

description: Pool of PCR products

data_processing:
Library strategy: Amplicon sequencing
CRISPResso Analysis of genome editing outcomes.
Either wild-type or integrated donor sequences are used as reference.
Genome_build: NM_145383.2 ; NM_214221.1
Supplementary_files_format_and_content: *_CRISPResso_quantification_of_editing_frequency.txt: CRISPResso quantification of editing frequency.
Supplementary_files_format_and_content: HITI_INDEL.fasta: CRISPRESSO Amplicons Reference.
Supplementary_files_format_and_content: HITI_INDEL_guides.txt: CRISPRESSO sgRNA Reference.

source_name: retina

extract_protocol:
Genomic DNA was extracted from frozen mouse and pig retina. 150 bp regions flanking the on-target sits of mRho/pRHO gRNAs were amplified by PCR. PCR products were pooled and used for library construction.
10 ng of PCR products were used as input for the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina.

treatment_protocol: gRNA-treated mouse and pig retina.

value: retina

tag: genotype

value: wild type


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_d9

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_d8

description: HsMm.csv


title: 49os

description: Pool of PCR products


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_d6

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_d7

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_d5

description: HsMm.csv


title: pool_2084

description: Pool of PCR products

data_processing:
CRISPResso Analysis of genome editing outcames
Genome_build: GRCm39/mm39
Supplementary_files_format_and_content: Quantification of editing frequency as determined by the percentage and number of unmodified and modified reads; fasta of amplicons used as reference; txt file of amplicone guides

source_name: liver

extract_protocol:
Genomic DNA was extracted from frozen retina and liver samples. 150 bp regions flanking the on target and off-target sites of mRho and mAlb gRNA were amplified by PCR, pooled and used for library construction.
10 ng of PCR products were used as input for the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina
OTHER: Amplicon sequencing

treatment_protocol: gRNA- and scramble-treated retina and liver.

tag: tissue.

value: liver


title: pool_2086

description: Pool of PCR products


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_d4

description: HsMm.csv


title: pool_2067

description: Pool of PCR products


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_d2

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_d3

description: HsMm.csv


title: pool_2073

description: Pool of PCR products


title: pool_2191

description: Pool of PCR products


title: pool_5_50os

description: Pool of PCR products


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_d12

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_d11

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_d10

description: HsMm.csv


title: MDXT1CD: MDX_T1_Cisplatin_Rep4

data_processing:
Library strategy: shRNAseq
Original fastq file from the MiSeq was composed of 32 multiplexed samples. Each fastq was split by a barcode identifier using the FASTX-toolkit barcode_splitter.pl script
Count files were created in R (v. 3.1.1) using the edgeR package (v. 3.6.8) processHairpinReads function with no mismatches or shifting allowed, shRNAs with no counts were filtered out and all shRNAs were given an extra count to avoid dividing by zero counts
Analysis of shRNA abundance was performed in edgeR using a time-course design and generalized linear models to compare the initial (T0) and final (T1) timepoints of the untreated cells and the the final timepoints of untreated and cisplatin treated cells and a likelihood ratio test (using the glmLRT function) was used to report log2 fold change scores and significance.
Genome_build: no alignment necessary
Supplementary_files_format_and_content: tab delimited text files containing either counts for each shRNA (*.counts.txt) or log2 fold change and likelihood ratio scores for each shRNA (*Analysis.txt)

source_name: primary murine lung tumor derived xenograft

growth_protocol: The murine derived xenograft (MDX) line was created by serial passaging of a single cell suspension of primary tumor cells from the KP mouse model by i.p. injection into the flanks of NOD scid IL2Rgnull (NSG) mice, analogous to PDX generation methods. After growth in NGS mice, primary xenografts were dissociated into single cells and spinfected with the lentiviral shRNA pool,then re-injected directly into NSG mice without selection or attachment on plastic dishes after spinfection. LKR10 cells were grown in DMEM, 10% FBS, and Pen/Strep/Glutamine.

extract_protocol:
Genomic DNA was extracted using the Qiagen DNeasy Blood & Tissue kit
Lentiviral pLKO shRNA vectors were amplified using PCR with ExTaq, and each sample was given direct barcodes for multiplexing and Illumina compatible adapters using a secondary PCR step.

treatment_protocol: Samples (1e6 cells) were taken for gDNA after passaging once in NGS flanks, and again after re-growing in NGS mice and treating with 3 weekly doses of 7mg/kg cisplatin. In parallel, gDNA was taken from LKR10 cells at identical timepoints before and after cisplatin treatment (10µM cisplatin) for comparison.


title: pool_1_47os

description: Pool of PCR products


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_e1

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_d1

description: HsMm.csv


title: MDXT1CB: MDX_T1_Cisplatin_Rep2

value: primary murine lung tumor derived xenograft


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_c8

description: HsMm.csv


title: MDXT1CA: MDX_T1_Cisplatin_Rep1


title: MDXT1UD: MDX_T1_Untreated_Rep4


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_c6

description: HsMm.csv


title: pool_3_49os

description: Pool of PCR products


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_c5

description: HsMm.csv


title: MDXT1CC: MDX_T1_Cisplatin_Rep3


title: MDXT1UA: MDX_T1_Untreated_Rep1


title: MDXT1UC: MDX_T1_Untreated_Rep3


title: MDXT1UB: MDX_T1_Untreated_Rep2


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_c3

description: HsMm.csv


title: MDXT0CD: MDX_T0_Cisplatin_Rep4


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_c2

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_c12

description: HsMm.csv


title: pool_2_48os

description: Pool of PCR products


title: pool_4_48od

description: Pool of PCR products


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_c9

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_c10

description: HsMm.csv


title: MDXT0CA: MDX_T0_Cisplatin_Rep1


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_c4

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_b9

description: HsMm.csv


title: MDXT0UB: MDX_T0_Untreated_Rep2


title: MDXT0UC: MDX_T0_Untreated_Rep3


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_b8

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_c1

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_c7

description: HsMm.csv


title: MDXT0UA: MDX_T0_Untreated_Rep1


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_b7

description: HsMm.csv


title: 2DT1C2D: LKR10_T1_Cisplatin_Rep4

source_name: LKR10 cell line

value: LKR10 cell line


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_b5

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_b6

description: HsMm.csv


title: MDXT0CB: MDX_T0_Cisplatin_Rep2


title: 2DT1C2C: LKR10_T1_Cisplatin_Rep3


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_c11

description: HsMm.csv


title: 2DT1C1D: LKR10_T1_Cisplatin_Rep2


title: 2DT1U2B: LKR10_T1_Untreated_Rep4


title: 2DT1C1C: LKR10_T1_Cisplatin_Rep1


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_b4

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_b2

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_b12

description: HsMm.csv


title: 2DT1U2A: LKR10_T1_Untreated_Rep3


title: 2DT1U1B: LKR10_T1_Untreated_Rep2


title: MDXT0UD: MDX_T0_Untreated_Rep4


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_b11

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_b10

description: HsMm.csv


title: 2DT1U1A: LKR10_T1_Untreated_Rep1


title: 2DT0C2D: LKR10_T0_Cisplatin_Rep4


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_a9

description: HsMm.csv


title: 2DT0C1D: LKR10_T0_Cisplatin_Rep2


title: 2DT0C2C: LKR10_T0_Cisplatin_Rep3


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_a7

description: HsMm.csv


title: 2DT0C1C: LKR10_T0_Cisplatin_Rep1


title: 2DT0U2B: LKR10_T0_Untreated_Rep4


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_b1

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_a6

description: HsMm.csv


title: 2DT0U2A: LKR10_T0_Untreated_Rep3


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_a5

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_a4

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_b3

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_a3

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_a12

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_a11

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_a10

description: HsMm.csv


title: Ecoli DNA input library  [MPPRA]

city: St. Louis

first: SIQI

last: ZHAO

state: MO

address: Campus Box 8232 4515 McKinley Ave.

department: Genetics

institute: Washington University in St. Louis

description: Demultiplexed barcodes

data_processing:
Library strategy: Massively Parallel Reporter Assay
scRNA-seq data was processed with Cell Ranger 6.0.1; Barcodes were extracted by fuzzy match the 8 bp before and after the barcode region, wrong length barcodes were removed. Barcodes attached to wrong cell barcode determiend by Cell Ranger were removed.
Genome_build: hg38
Supplementary_files_format_and_content: bulk RNA-seq and DNA-seq counts are stored in bulk_abundance.csv; single-cell RNA-seq processed expression using Cell Ranger is stored in .mtx.gz files. scMPRA barcodes counts per cell are storedd in pBC_exp.csv

organism: Escherichia coli

source_name: Bacterial culture

growth_protocol: K562 cells were cultured using a medium consisting of Iscove’s Modified Dulbecco’s Medium (IMDM) + 10% Fetal Bovine Serum (FBS) + 1% non-essential amino acids + 1% pen/strep at 37 C with 5% of CO2. HEK293 cells were cultured using a medium consisting of Eagle’s Minimum Essential Medium (EMEM) + 10% Fetal Bovine Serum (FBS) + 1% pen/strep at 37 C with 5% of CO2.

extract_protocol:
To estimate the library complexity, we sequenced the DNA library using a nested PCR-based Illumina library preparation protocol. Briefly, we first used Q5 polymerase (New England BioLabs M0515) to amplify the region containing the 2 barcodes with SCARED P17 (5’-GACGAGCTCTATAAGTAATCTAGA-3’) and SCARED P18 (5’-TTTTCTAGGTCTCTGGTCGA-3’). The total reaction volume is 50ul with 50ng of plasmids with 10uM of primer each. The annealing temperature is 61 C with an extension time of 10s. 25 cycles of amplification were done. The product was then purified with the Monarch PCR&DNA Cleanup kit (New England BioLabs T1030L), and eluted with 20 ul of ddH2O. For the second PCR (SCARED P19: 5’-GGACGAGCTCTATAAGTAATCTAGA-3’, SCARED P20: 5’-GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT-3’), a 25 ul reaction was set up with 0.25 ul product from the previous step, the annealing temperature is 61 C, and the extension time is 10s, a total of 10 cycles was done. The PCR product was cleaned up using the Monarch PCR&DNA Cleanup kit. For the last PCR to add the P5 and P7 Illumina adapters (P5: 5’-AATGATACGGCGACCACCGAGATCTACACACCCGCACACTCTTTCCCTACACGACGCT-3’, P7:5’-CAAGCAGAAGACGGCATACGAGATAAGTTGACAGTGACTGGAGTTCAGACGTG-3’), a reaction with 25 ul of total volume was set up with 2 ul of cleaned product from PCR2, a total of 10 cycles of PCR was done.
scRNA-seq and scMPRA are extracted using 10X protocol
Bulk RNA was extracted using Qiagen RNeasy kit

tag: cell line background


title: 2DT0U1A: LKR10_T0_Untreated_Rep1


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_h9

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_h8

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_a1

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_h7

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_h6

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_a8

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_h5

description: HsMm.csv


title: F1648 Input merged

city: Goettingen

first: Lukas

last: Krauß

state: Lower Saxony

address: Robert-Koch-Straße 40

department: Surgery-Department

country: Germany

institute: University Medicine Göettingen

data_processing:
ChIP-seq, data was analyzed with the nf-core chipseq pipeline v1.2.2 (Ewels PA, Peltzer A, Fillinger S, Patel H, Alneberg J, Wilm A, et al. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020;38:276–8) with the following parameter settings: --macs_pvalue 0.005 and --broad_cutoff 0.005. Input Samples were merged prior to analysis. Bam and peak files were then imported into R v4.1.0 and analyzed with DiffBind v 3.2.4 (Parameters: normalize=DBA_NORM_LIB, summits = 350, method=DBA_DESEQ2) (Ross-Innes CS, Stark R, Teschendorff AE, Holmes KA, Ali HR, Dunning MJ, et al. Differential oestrogen receptor binding is associated with clinical outcome in breast cancer. Nature. 2012;481:389–93.;Brown RS and G. DiffBind: Differential binding analysis of ChIPSeq peak data. http://bioconductor.org/ [Internet]. Available from: http://bioconductor.org/packages/release/bioc/vignettes/DiffBind/inst/doc/DiffBind.pdf).
Peaks were annotated with ChIPSeeker (Parameter: annoDb="org.Mm.eg.db") (Yu G, Wang L-G, He Q-Y. ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization. Bioinformatics. 2015;31:2382–3.). For downstream analysis peaks located within 3 kb around the TSS of a gene and a FDR below or equal to 0.05 were selected. These genes were intersected with significant genes from the RNAseq analysis and resulting gene lists were used as input for pathway analysis with EnrichR within the Hallmark gene set collection. Motif Enrichment analysis of ChIP-peaks was performed using Homer (Heinz S, Benner C, Spann N, Bertolino E, Lin YC, Laslo P, et al. Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities. Mol Cell. 2010;38:576–89) with the following parameters: findMotifsGenome.pl <peak/BED file> mm10 <output directory> -size 50.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files

source_name: murine PDAC cells

extract_protocol:
10 million cross-linked cells per sample were lysed in 5 Aliquots in Lysis Buffer I on ice for 10 min, spun down and supernatant was removed. Next, pellet was resuspended Lysis Buffer II on ice for 10 min, spun down and supernatant was removed. Then, the pellet was resupended in 300 µl Shearing Buffer and incubated on ice for 10 min and sonicated in a Bioruptor Plus TPX microtubes using a Bioruptor device to shear the chromatin to an average size of 100–500 base pairs long. After successful size check, sonicated chromatin was precleared with blocked Dynabeads 5% of precleared sample was used for Input. Then of sonicated chromatin was incubated overnight at on a rotating wheel with Hdac2 antibody. The next day, blocked beads were added to antibody-bound chromation and incubated at 4°C for 2 hours. Next, beads were washed twice with 1ml Low Salt Wash Buffer. Low-binding Eppendorf tubes were changed after first wash. Then, beads were washed with High Salt Wash Buffer. Next, beads were washed with LiCl Wash Buffer. Then, 1x TE-buffer was added and beads were placed on a magnet and supernatant was aspirated completely. For crosslink reversal of immunoprecipitated DNA beads were resuspended in ChIP Elution Buffer. Input sampes were diluted with Chip Elution Buffer. Next RNAse A was added and Samples and Input Chromatin were incubated at 37°C for 30 min. Afterwards, Proteinase was added and beads or Input Chromatin were incubated at 55°C for 1h and then incubated at 65°C for 8h for decrosslinking. Afterwards beads were separated from supernatant using a magnet and supernatant was collected in a new tube. Elution buffer was added to the beads and incubated for one minute and then elution buffer was combined with supernatant. Proteinase K was added to eluates and incubated at 55°C for 1 h. For DNA Purification, Ampure Beads were added to the decrosslinked Chromatin samples. Entire Volume was then mixed for at least 10 times and beads and DNA was incubated at room temperature for 10 min. Afterwards tubes were placed on a magnet and supernatant was removed. Next, Beads were washed with 80% Ethanol twice. Beads were then dried for 5 minutes before adding Elution buffer. Beads were incubated for 5 minutes and Eluate was collected in a new tube. Eluate concentrations were determined using Qubid HS DNA Assay.
Purified DNA was used as input for library preparation with NEBNext Ultra II DNA Library Prep Kit for Illumina and processed according to the manufacturer´s instructions. Libraries were quality controlled by Qubit and Agilent DNA Bioanalyzer analysis. The library was sequenced on a NextSeq 500 (Illumina) with 76 cycles for the cDNA in read1 and 16 cycles for the barcodes and UMIs in read2.

treatment_protocol: Cells were treated with ETOH (Vehicle) or 4-OHT for 8 days to induce Hdac2 knockout prior to Chromation Immunprecipitation

tag: cell type

value: murine PDAC cells (Kras G12D)

tag: hdac2 status

value: mixed

tag: chip antibody


title: F1648 EtOH_Hdac2 rep2

value: proficient

value: Hdac2 (Cell Signaling, HDAC2 (D6S5P) Rabbit mAb #57156)

value: EtOH (Vehicle)


title: F1648 4OHT_Hdac2 rep1

value: deficient


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_h4

description: HsMm.csv

value: U87 and 3T3


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_h2

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_h3

description: HsMm.csv


title: F1648 4OHT_Hdac2 rep2


title: D-Cre+ RAPA

city: Rotterdam

first: Ype

last: Elgersma

address: Doctor Molewaterplein 40

department: Neuroscience

country: Netherlands

institute: Erasmus MC

data_processing:
CutAdapt (Galaxy Version 1.16.5) was used to trim reads of low sequencing quality (threshold of 20), filtering out reads with a read length <50 nucleotides (mouse)
Alignment with STAR algorithm (Galaxy Version 2.7.2b), Transcript assembly was guided by the reference annotation file Gencode version M24
Feature Counts tool (Galaxy Version 1.6.4+galaxy1) to assess counts per gene
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Murine adult hippocampus

extract_protocol:
RNA was extracted from  mice on four different time points during epileptogenesis: day 4, day 6, day 8, and day 13. Mice were anaesthetized with isoflurane before decapitation. The hippocampi were isolated and immediately homogenized in Trizol (15596-026, Invitrogen). Total RNA was isolated using the PureLink RNA Mini Kit (12183018A, Thermo Scientific) according to manufacturer’s instructions.
Stranded total RNA libraries were prepared using the Illumina TruSeq Stranded Total RNA LT kit (with Ribo-Zero Gold Human/Mouse/Rat).

value: Tsc1f/f-Tg (Camk2a-CreERT2+)

value: Tamoxifen

tag: drug

value: 10 mg/kg rapamycin

value: Tsc1 gene deletion

tag: time

value: Sacrificed at Day 13 after Tamoxifen injection start / Tsc1 gene deletion, daily Rapamycin treatment from Day 4

value: hippocampus


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_h11

description: HsMm.csv


title: 2DT0U1B: LKR10_T0_Untreated_Rep2


title: C-Cre+ RAPA


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_h10

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 12xSMRT, 12xNextera and SPRI U87_3T3_SC_C3_a2

description: HsMm.csv


title: F1648 EtOH_Hdac2 rep1


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_h1

description: HsMm.csv


title: B-Cre+ RAPA


title: A-Cre+ RAPA


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_g9

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_g7

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_g8

description: HsMm.csv


title: B-Cre+ Day13

value: Sacrificed at Day 13 after Tamoxifen injection start / Tsc1 gene deletion


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_g6

description: HsMm.csv


title: C-Cre+ Day13


title: A-Cre+ Day13


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_g5

description: HsMm.csv


title: D-Cre+ Day8

value: Sacrificed at Day 8 after Tamoxifen injection start / Tsc1 gene deletion


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_g4

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_g3

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_h12

description: HsMm.csv


title: A-Cre+ Day8


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_g2

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_g12

description: HsMm.csv


title: C-Cre+ Day8


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_g10

description: HsMm.csv


title: D-Cre+ Day6

value: Sacrificed at Day 6 after Tamoxifen injection start / Tsc1 gene deletion


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_g11

description: HsMm.csv


title: A-Cre+ Day6


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_f9

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_g1

description: HsMm.csv


title: D-Cre+ Day13


title: D-Cre+ Day4

value: Sacrificed at Day 4 after Tamoxifen injection start / Tsc1 gene deletion


title: C-Cre+ Day4


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_f8

description: HsMm.csv


title: A-Cre+ Day4


title: B-Cre+ Day4


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_f5

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_f4

description: HsMm.csv


title: C-Cre-

value: control

value: Sacrificed at Day 8 after Tamoxifen injection start, no gene deletion


title: B-Cre+ Day8


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_f3

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_f2

description: HsMm.csv


title: B-Cre-


title: A-Cre-


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_f12

description: HsMm.csv


title: C-Cre+ Day6


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_f11

description: HsMm.csv


title: K562 cell barcodes rep2 [scMPPRA]

description: Demultiplexed barcodes

data_processing:
Library strategy: single cell Massively Parallel Reporter Assay
scRNA-seq data was processed with Cell Ranger 6.0.1; Barcodes were extracted by fuzzy match the 8 bp before and after the barcode region, wrong length barcodes were removed. Barcodes attached to wrong cell barcode determiend by Cell Ranger were removed.
Genome_build: hg38
Supplementary_files_format_and_content: bulk RNA-seq and DNA-seq counts are stored in bulk_abundance.csv; single-cell RNA-seq processed expression using Cell Ranger is stored in .mtx.gz files. scMPRA barcodes counts per cell are storedd in pBC_exp.csv

source_name: Cell culture

extract_protocol:
We harvested both K562 and HEK293 cells 24 hours after transfection, then followed the cell preparation protocol of 10X genomics. We used the 10X V3.1 chromium kit for our single-cell RNA-seq protocol. All PCRs were performed on an Invitrogen PCR machine.  We targeted 2000 cells per replicate for each experiment for the mixed cell experiment. We targeted 2500 cells per replicate for the K562 substrate experiment. We followed the 10X protocol (https://support.10xgenomics.com/single-cell-gene-expression/library-prep/doc/user-guide-chromium-single-cell-3-reagent-kits-user-guide-v31-chemistry) with 12 cycles of cDNA amplification. To amplify the Capture-Sequence captured reads. 0.25 μl of 100 uM SCARED P32 (5’-GTCAGATGTGTATAAGAGACAG-3’) was added to the cDNA amplification mix. For step 2.2, we modify the clean-up protocol by saving both the beads and supernatents and for the supernatents, we use a final concentration of 1.2X beads to pull down the DNA fragments. We then take 25% of both the 0.6X and 1.2X pull down products for the next step of PCR. To construct the illumina sequencing library, we used a 3-step nested PCR strategy. Briefly, we first used Q5 (New England BioLabs M0515) polymerase to amplify the region containing the 2 barcodes with SCARED P17 and SCARED P18. We pooled 8 PCR reactions, each with 50 μl of total volume, with 10 cycles to reduce possible jackpotting.  The annealing temperature is 61°C with an extension time of 10s. The product was then purified with the Monarch PCR&DNA Cleanup kit (New England BioLabs T1030L), and eluted with 20 μl of ddH2O. For the second PCR using the following 3 primers (SCARED P21: 5’-GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTGGACGAGCTCTATAAGTAATCT-3’, CAS PC2: 5’-CGAGATCTACACTCGTCGGCAGCGTCAGATGTGTATAAGAGACAG-3’, CAS PP2: 5’-ATCTACACTCTTTCCCTACACGACGCTCTTC-3’ ), we pulled 8 PCR reactions, each with 50 μl of total volume, with 10 cycles to reduce possible jackpotting , the annealing temperature is 61°C, and the extension time is 10s, a total of 10 cycles was done. The PCR product was cleaned up using the Monarch PCR&DNA Cleanup kit (New England BioLabs T1030L). For the last PCR to add the P5 and P7 Illumina adapters (CAS P48: 5’-CAAGCAGAAGACGGCATACGAGATNNNNNNNN[index]GTGACTGGAGTTCAGAC-3’, CAS PP4: 5’-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACA-3’, CAS PC4: 5’-AATGATACGGCGACCACCGAGATCTACACTCGTCG-3’), we pulled 8 PCR reactions, each with 50 μl of total volume, with 10 cycles to reduce possible jackpotting, a total of 10 cycles of PCR was done. The transcriptome is generated using the 10X Dual-Index Set TT expression kit (https://support.10xgenomics.com/single-cell-gene-expression/index/doc/technical-note-chromium-next-gem-single-cell-3-v31-dual-index-libraries).
scRNA-seq and scMPRA are extracted using 10X protocol
Bulk RNA was extracted using Qiagen RNeasy kit


title: B-Cre+ Day6


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_f10

description: HsMm.csv


title: Mixed cell barcodes rep1 [scMPPRA]

description: Demultiplexed barcodes


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_f7

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_f1

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_e9

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_e8

description: HsMm.csv


title: K562 single-cell transcriptome rep2 [scRNA-seq]

description: single cell trnascriptome

data_processing:
scRNA-seq data was processed with Cell Ranger 6.0.1; Barcodes were extracted by fuzzy match the 8 bp before and after the barcode region, wrong length barcodes were removed. Barcodes attached to wrong cell barcode determiend by Cell Ranger were removed.
Genome_build: hg38
Supplementary_files_format_and_content: bulk RNA-seq and DNA-seq counts are stored in bulk_abundance.csv; single-cell RNA-seq processed expression using Cell Ranger is stored in .mtx.gz files. scMPRA barcodes counts per cell are storedd in pBC_exp.csv

extract_protocol:
The transcriptome is generated using the 10X Dual-Index Set TT expression kit
scRNA-seq and scMPRA are extracted using 10X protocol
Bulk RNA was extracted using Qiagen RNeasy kit


title: D-Cre-


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_e7

description: HsMm.csv


title: Mixed cell single-cell transcriptome rep2 [scRNA-seq]

description: single cell trnascriptome


title: K562 single-cell transcriptome rep1 [scRNA-seq]

description: single cell trnascriptome


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_f6

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_e6

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_e5

description: HsMm.csv


title: Mixed cell single-cell transcriptome rep1 [scRNA-seq]

description: single cell trnascriptome


title: HEK293 bulk barcodes  rep2 [MPPRA]

description: Demultiplexed barcodes

extract_protocol:
For both K562 cells and HEK293 cells, we harvested the cells after transfection at 24 hours, and proceeded to extract total mRNA with Qiagen RNeasy kit. The reverse transcription was done with Superscript IV Reverse Transcriptase (Invitrogen 18090010). The final sequencing library was constructed using a nested PCR strategy. Briefly, we first used Q5 (New England BioLabs M0515) polymerase to amplify the region containing the 2 barcodes with SCARED P17 and SCARED P18. The total reaction volume is 50μl with 50ng of backbone with 2.5 μl of 10uM primer each. The annealing temperature is 61°C with an extension time of 10s. 25 cycles of amplification was done. The product was then purified with the Monarch PCR&DNA Cleanup kit (New England BioLabs T1030L), and eluted with 20 μl of ddH2O. For the second PCR using primers SCARED P19 and SCARED p20, a 25 μl reaction was set up with 0.25 μl product from the previous step, the annealing temperature is 61°C, and the extension time is 10s, a total of 10 cycles was done. The PCR product was cleaned up using the Monarch PCR&DNA Cleanup kit (New England BioLabs T1030L). For the last PCR to add the P5 and P7 Illumina adapters, a reaction with 25 μl of total volume was set up with 2 μl of cleaned product from PCR2, a total of 10 cycles of PCR was done. The sequencing library was sequenced on an Illumina Mi-seq machine with other samples pooled in the same lane.
scRNA-seq and scMPRA are extracted using 10X protocol
Bulk RNA was extracted using Qiagen RNeasy kit


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_e4

description: HsMm.csv


title: HEK293 bulk barcodes rep1 [MPPRA]

description: Demultiplexed barcodes


title: K562 bulk barcodes rep2 [MPPRA]

description: Demultiplexed barcodes


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_e3

description: HsMm.csv


title: K562 cell barcodes rep1 [scMPPRA]

description: Demultiplexed barcodes


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_e2

description: HsMm.csv


title: K562 bulk barcodes rep1 [MPPRA]

description: Demultiplexed barcodes


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_e11

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_e12

description: HsMm.csv


title: Mixed cell barcodes rep2 [scMPPRA]

description: Demultiplexed barcodes


title: Sample_4

city: Smithfield

first: Matt

last: Field

address: 14-88 Macgregor Road

country: Australia

institute: James Cook University

data_processing:
Transcriptome data were analysed using a modified version of an existing variant detection pipeline consisting of software STAR aligner, samtools and consensusDE.
Reads were first aligned to human reference genome GRCh38 using STAR with the gene model set to ensembl v95 annotation and quantmode set to GeneCounts.
Count data was fed to ConsensusDE and grouped by heterozygous or homozygous VANGL1 deletions
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include CPM values for each sample.

source_name: PBMC

extract_protocol:
FACs live/dead negative selection
Conducted by AGRF (Brisbane) using the Illumina TruSeq stranded mRNA kit and the NextSeq 500

value: Total PBMC

tag: zygosity

value: Homozygous


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_e10

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_e1

description: HsMm.csv


title: Sample_3

value: Heterozygous


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_d8

description: HsMm.csv


title: Sample_2


title: Sample_6


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_d9

description: HsMm.csv


title: Sample_1


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_d7

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_d5

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_d6

description: HsMm.csv


title: MDXT0CC: MDX_T0_Cisplatin_Rep3

value: primary murine lung tumor derived xenograft


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_d4

description: HsMm.csv

value: U87 and 3T3


title: siTASOR+siCNOT1_2

city: Paris

first: Roy

last: MATKOVIC

state: Select One

address: 22, Rue Mechain

department: Infection Immunity and Inflammation

country: France

institute: Institut Cochin

data_processing:
Trimmed PE reads were mapped against the human reference genome, hg38 (Gencode and gene annotation version 29) using STAR (version 2.7.5c) as described in Doblin et al., Bioinformatics, 2013.
The parameters used for the mapping were as follows: --outFilterMultimapNmax 1000 (1000 alignments allowed per read-pair), --alignSJoverhangMin 8 (minimum overhang for unannotated junctions).
Genome_build: hg38
Supplementary_files_format_and_content: bigWig files

source_name: HeLa cells

growth_protocol: Cells were cultured in DMEM medium, from ThermoFisher, containing 10% heat-inactivated fetal bovine serum (FBS, Dominique Dutscher), 1,000 units.ml−1 penicillin, 1,000µg.ml−1 streptomycin.

extract_protocol:
RNA extraction was performed using a standard TRIZOL/Phenol/Chloroform protocol. RNAs resolubilised in 20µL of RNase Free water were then passed through an RNA purification column (from the Macherey Nagel Ref:740955.250 kit) and subjected to rDNAse digestion from the purification kit.
Libraries were prepared using the NEB Ultra II protocol (stranded polyA+ RNA-seq) and sequenced with an Illumina NextSeq 500 as 2x75 bp paired-ends (PE)

treatment_protocol: Cells were transfected  for 72h with siRNAs targeting Mock, or TASOR or CNOT1 or both TASOR and CNOT1 expressions using Dharmafect 1 (Horizon Discovery)

value: Cervical cancer cell line

value: HeLa

tag: knockdown


title: siTASOR+siCNOT1_1


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_d3

description: HsMm.csv


title: siCNOT1+siCtrl_2


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_d2

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_d12

description: HsMm.csv


title: siCNOT1+siCtrl_1


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_d11

description: HsMm.csv


title: siTASOR+siCtrl_3

value: siTASOR+siCtrl


title: siTASOR+siCtrl_2


title: siTASOR+siCtrl_1


title: Sample_5


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_d10

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_d1

description: HsMm.csv


title: siTASOR+siCNOT1_3


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_c9

description: HsMm.csv


title: siCtrl_2

value: siCtrl


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_c8

description: HsMm.csv


title: siCtrl_1


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_c7

description: HsMm.csv


title: siCtrl_3


title: U87 scRNA-Seq U87_SC_h9

description: umi0.csv, umi1.csv, counts.csv

source_name: Single cell from cultured U87 cells


title: U87 scRNA-Seq U87_SC_h8

description: umi0.csv, umi1.csv, counts.csv


title: siCNOT1+siCtrl_3


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_c5

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_c2

description: HsMm.csv


title: U87 scRNA-Seq U87_SC_h7

description: umi0.csv, umi1.csv, counts.csv


title: U87 scRNA-Seq U87_SC_h5

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_c3

description: HsMm.csv


title: U87 scRNA-Seq U87_SC_h4

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_c12

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_c4

description: HsMm.csv


title: U87 scRNA-Seq U87_SC_h3

description: umi0.csv, umi1.csv, counts.csv


title: U87 scRNA-Seq U87_SC_h12

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_c11

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_c10

description: HsMm.csv


title: U87 scRNA-Seq U87_SC_h2

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_c1

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_b9

description: HsMm.csv


title: U87 scRNA-Seq U87_SC_h10

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_c6

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_b8

description: HsMm.csv


title: U87 scRNA-Seq U87_SC_h1

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_b6

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_b7

description: HsMm.csv


title: U87 scRNA-Seq U87_SC_g7

description: umi0.csv, umi1.csv, counts.csv


title: U87 scRNA-Seq U87_SC_g6

description: umi0.csv, umi1.csv, counts.csv


title: U87 scRNA-Seq U87_SC_g9

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_b3

description: HsMm.csv


title: U87 scRNA-Seq U87_SC_g8

description: umi0.csv, umi1.csv, counts.csv


title: U87 scRNA-Seq U87_SC_g5

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_b4

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_b10

description: HsMm.csv


title: U87 scRNA-Seq U87_SC_g2

description: umi0.csv, umi1.csv, counts.csv


title: U87 scRNA-Seq U87_SC_g11

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_a7

description: HsMm.csv


title: U87 scRNA-Seq U87_SC_h6

description: umi0.csv, umi1.csv, counts.csv


title: U87 scRNA-Seq U87_SC_g4

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_b2

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_a5

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_a6

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_a4

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_b12

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_a2

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_b11

description: HsMm.csv


title: U87 scRNA-Seq U87_SC_g12

description: umi0.csv, umi1.csv, counts.csv


title: U87 scRNA-Seq U87_SC_h11

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_a11

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_a12

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_b1

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_a9

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_a1

description: HsMm.csv


title: U87 scRNA-Seq U87_SC_f11

description: umi0.csv, umi1.csv, counts.csv


title: U87 scRNA-Seq U87_SC_f10

description: umi0.csv, umi1.csv, counts.csv


title: U87 scRNA-Seq U87_SC_g10

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_a8

description: HsMm.csv


title: U87 scRNA-Seq U87_SC_g1

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2h7

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_b5

description: HsMm.csv


title: U87 scRNA-Seq U87_SC_e9

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2h5

description: HsMm.csv


title: U87 scRNA-Seq U87_SC_e8

description: umi0.csv, umi1.csv, counts.csv


title: U87 scRNA-Seq U87_SC_f9

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2h4

description: HsMm.csv


title: U87 scRNA-Seq U87_SC_f8

description: umi0.csv, umi1.csv, counts.csv


title: U87 scRNA-Seq U87_SC_f7

description: umi0.csv, umi1.csv, counts.csv


title: U87 scRNA-Seq U87_SC_f6

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2h3

description: HsMm.csv


title: U87 scRNA-Seq U87_SC_e5

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_a3

description: HsMm.csv


title: U87 scRNA-Seq U87_SC_f5

description: umi0.csv, umi1.csv, counts.csv


title: U87 scRNA-Seq U87_SC_g3

description: umi0.csv, umi1.csv, counts.csv


title: U87 scRNA-Seq U87_SC_e2

description: umi0.csv, umi1.csv, counts.csv


title: U87 scRNA-Seq U87_SC_f4

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2h1

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2h10

description: HsMm.csv


title: U87 scRNA-Seq U87_SC_e10

description: umi0.csv, umi1.csv, counts.csv


title: U87 scRNA-Seq U87_SC_f3

description: umi0.csv, umi1.csv, counts.csv


title: U87 scRNA-Seq U87_SC_f2

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2g6

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_a10

description: HsMm.csv


title: U87 scRNA-Seq U87_SC_d8

description: umi0.csv, umi1.csv, counts.csv


title: U87 scRNA-Seq U87_SC_f12

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2h9

description: HsMm.csv


title: U87 scRNA-Seq U87_SC_e12

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2h8

description: HsMm.csv


title: U87 scRNA-Seq U87_SC_f1

description: umi0.csv, umi1.csv, counts.csv


title: U87 scRNA-Seq U87_SC_d7

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2h6

description: HsMm.csv


title: U87 scRNA-Seq U87_SC_e7

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2g3

description: HsMm.csv


title: U87 scRNA-Seq U87_SC_e6

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2h2

description: HsMm.csv


title: U87 scRNA-Seq U87_SC_e4

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2h12

description: HsMm.csv


title: U87 scRNA-Seq U87_SC_d4

description: umi0.csv, umi1.csv, counts.csv


title: U87 scRNA-Seq U87_SC_e3

description: umi0.csv, umi1.csv, counts.csv


title: U87 scRNA-Seq U87_SC_e11

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2g12

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2g8

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2g9

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2h11

description: HsMm.csv


title: U87 scRNA-Seq U87_SC_e1

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2g7

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2g5

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2f9

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2g4

description: HsMm.csv


title: U87 scRNA-Seq U87_SC_d11

description: umi0.csv, umi1.csv, counts.csv


title: U87 scRNA-Seq U87_SC_d6

description: umi0.csv, umi1.csv, counts.csv


title: U87 scRNA-Seq U87_SC_d5

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2f8

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2g2

description: HsMm.csv


title: U87 scRNA-Seq U87_SC_d9

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2f6

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2g11

description: HsMm.csv


title: U87 scRNA-Seq U87_SC_c9

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2g10

description: HsMm.csv


title: U87 scRNA-Seq U87_SC_d12

description: umi0.csv, umi1.csv, counts.csv


title: U87 scRNA-Seq U87_SC_d2

description: umi0.csv, umi1.csv, counts.csv


title: U87 scRNA-Seq U87_SC_c5

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2f3

description: HsMm.csv


title: U87 scRNA-Seq U87_SC_d3

description: umi0.csv, umi1.csv, counts.csv


title: U87 scRNA-Seq U87_SC_c6

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2f2

description: HsMm.csv


title: U87 scRNA-Seq U87_SC_d10

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2f7

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2f4

description: HsMm.csv


title: U87 scRNA-Seq U87_SC_c7

description: umi0.csv, umi1.csv, counts.csv


title: U87 scRNA-Seq U87_SC_d1

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2f5

description: HsMm.csv


title: U87 scRNA-Seq U87_SC_c8

description: umi0.csv, umi1.csv, counts.csv


title: U87 scRNA-Seq U87_SC_c4

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2g1

description: HsMm.csv


title: U87 scRNA-Seq U87_SC_c2

description: umi0.csv, umi1.csv, counts.csv


title: U87 scRNA-Seq U87_SC_c3

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2f10

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2f11

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2e9

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2f1

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2f12

description: HsMm.csv


title: U87 scRNA-Seq U87_SC_c12

description: umi0.csv, umi1.csv, counts.csv