title: SW480 BZW2 SH2

city: Birmingham

first: Upender

last: Manne

state: AL

address: 1824 6th Ave South

department: Pathology

institute: The University of Alabama at Birmingham

data_processing:
The samples were sequenced using a 2x150 Paired End (PE) configuration
Image analysis and base calling were conducted by the HiSeq Control Software (HCS).
Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software.
Assembly: human GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Supplementary files format and content: tab delimited text file include normalized read counts for each sample from DESeq.

extract_protocol:
RNA from culture cells were extracted with Direct-zol RNA miniprep kit (Zymo Research)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Stable knockdowns were created using shRNA purchased from SBI (System Biosciences, Mountain View, CA). Lentiviruses for creating these stable knockdowns were created by the University of Alabama at Birmingham Vector Core. After infection of colorectal cancer celllines with lentiviruses expressing BZW2 shRNA or nontargeting shRNA, stable knockdown cell lines were generated by selection with 1µg/ml puromycin (Life Technologies).

tag: treatment

value: BZW2 shRNA


title: Melanocyte Mut P56 E5

status: Public on Mar 14 2023

type: SRA

city: Irvine

first: Maksim

middle: V

last: Plikus

state: California

address: 845 Health Sciences Road

department: Developmental and Cell Biology

country: USA

institute: University of California, Irvine

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56E5

library_source: transcriptomic

data_processing:
Pair-end RNA-seq reads were aligned using STAR_2.4.2 with parameters ‘–outFilterMismatchNmax10–outFilterMismatchNoverReadLmax 0.1–outFilter-MultimapNmax 10’ to the reference genome GRCm38/mm10. We used STAR to then convert to transcriptome-based mapping with gene annotation Gencode v.M8. Gene expression was measured using RESM/1.2.25 with expression values normalized into TPM.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include TPM values for each sample

molecule: total RNA

organism: Mus musculus

source_name: Melanocyte Mut P56

extract_protocol:
RNA libraries were prepared for sequencing using standard Illumina protocols
Smart-seq2

tag: cell type

value: Melanocytes

tag: genotype

value: Mut

tag: tissue

value: Dorsal skin

tag: age

value: Postnatal day 56


title: Melanocyte Mut P56 B11

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56B11


title: HT29 BZW2 SH2

organism: Homo sapiens

tag: cell line


title: Melanocyte Mut P56 B8

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56B8


title: Melanocyte Mut P56 B9

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56B9


title: Melanocyte Mut P56 C1

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56C1


title: SW480 SCR

value: Non targeting shRNA


title: Melanocyte Mut P56 B7

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56B7


title: Melanocyte Mut P56 B6

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56B6


title: HPSI0114ikolf2-clone1, WT [NRS_WT_R2]

city: London

first: Cristina

last: Dias

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

data_processing:
Illumina Casava software used for basecalling.
Data was processed using the nf-core/RNAseq pipeline (version 3.7) using the following parameter --aligner star_rsem.
For data upload reads mapping to the Y chromosome were removed as required by the MTA associated with the cell line using BBMap's filterbyname.sh function.
Assembly: GRCh37.75
Supplementary files format and content: Comma-delimited file containing matrix table with raw gene counts for every gene and every sample

growth_protocol: Dual SMAD inhibition: day 0 - day 12. Notch inhibition: 24 hrs on day 24.

extract_protocol:
Rneasy Micro Kit (Qiagenn 74004)
KAPA mRNA polyA HyperPrep Kit (Illumina, KR1352)

value: human induced pluripotent cells

value: WT

tag: time

value: day 24

tag: differentiation stage

value: Day 24 neuronal cultures


title: HCT116WT BZW2 SH2


title: HCT116WT SCR


title: Melanocyte Mut P56 C4

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56C4


title: Melanocyte Mut P56 B5

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56B5


title: HPSI0114ikolf2-clone1, WT [NRS_WT_R1]


title: HPSI0114ikolf2-clone1, ASCL1-KO [NRS_ASCL1_KO_R3]


title: Melanocyte Mut P56 C6

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56C6


title: HPSI0114ikolf2-clone1, ASCL1-KO [NRS_ASCL1_KO_R2]


title: HPSI0114ikolf2-clone1, ASCL1-KO [NRS_ASCL1_KO_R1]


title: Melanocyte Mut P56 B1

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56B1


title: Melanocyte Mut P56 B4

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56B4


title: HT29 SCR


title: HPSI0214i-kucg_2, WT [DAY24_KUCG2_R3]


title: Melanocyte Mut P56 A12

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56A12


title: Melanocyte Mut P56 A11

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56A11


title: Melanocyte Mut P56 A10

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56A10


title: HPSI0214i-kucg_2, WT [DAY24_KUCG2_R1]


title: Melanocyte Mut P56 B2

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56B2


title: Cal-27 PMM1-R150H mutation

type: RNA

city: Taipei

first: Wei-Min

last: Chang

state: Not Applicable

address: 128 Academia Road, Section 2, Nankang,

country: Taiwan

institute: Academia Sinica

description: Gene expression data from CX-1 cells expressing RAB3C

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 PLUS 2.0 . GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

source_name: ATCC

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Cells were cultured in 5% CO2 incubator at 37℃.

extract_protocol: Qiagene RNeasy mini kit extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Cell were selected with antibiotics for two weeks.  Stably transduced cells were use for this experiment.

value: Cal-27 Cells infected with pLenti6.3-PMM1-R150H mutation vector


title: HPSI0114ikolf2-clone1, WT [DAY24_KOLF2C1_R3]


title: HPSI0114ikolf2-clone1, WT [DAY24_KOLF2C1_R2]


title: HPSI0214i-kucg_2, WT [DAY24_KUCG2_R2]


title: Melanocyte Mut P56 A9

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56A9


title: Cal-27 empty vecotr

description: Gene expression data from CX-1 cells expressing control vector

value: Cal-27 Cells infected with pLenti6.3-control vector


title: Melanocyte Mut P56 A8

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56A8


title: SAS-CRISPR-FAS

value: SAS Cells infected with All-in-one CRISPR/Cas9 virus with sgFAS


title: Cal-27 PMM1-wildtype

value: Cal-27 Cells infected with pLenti6.3-PMM1-wildtype vector


title: Melanocyte Mut P56 B3

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56B3


title: Melanocyte Mut P56 A6

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56A6


title: HPSI0114ikolf2.1J, WT [DAY24_KOLF2.1J_R3]


title: HPSI0114ikolf2-clone1, WT [DAY24_KOLF2C1_R1]


title: HPSI0114ikolf2.1J, WT [DAY24_KOLF2.1J_R2]


title: Melanocyte Mut P56 A4

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56A4


title: Melanocyte Mut P56 A3

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56A3


title: Melanocyte Mut P56 B10

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56B10


title: HPSI0114ikolf2.1J, WT [DAY24_KOLF2.1J_R1]


title: Melanocyte Mut P56 A2

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56A2


title: Melanocyte Mut P56 A1

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56A1


title: Melanocyte Mut P56 A7

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56A7


title: HPSI0114ikolf2-clone1, WT [SMARCB1_IP_KOLF2_R3]

description:
SMARCB1.consensus_peaks.bed.gz
SMARCB1.consensus_peaks.featureCounts.txt.gz

library_source: genomic

data_processing:
Illumina Casava software used for basecalling.
Data was processed using the nf-core/ChIP pipeline (version 1.2.2) using the following parameter --min_reps_consensus 2 --single_end using --narrowPeak for ASCL1 and -broadPeak for the remainder of antibodies.
For data upload reads mapping to the Y chromosome were removed as required by the MTA associated with the cell line using BBMap's filterbyname.sh function.
Assembly: GRCh37.75
Supplementary files format and content: bed file with peak regions
Supplementary files format and content: txt files with counts for each sample and each peak region

molecule: genomic DNA

extract_protocol: KAPA Hyper Prep Kit (KapaBiosystems, KR0961)

tag: chip antibody

value: SMARCB1:Abcam ab12167


title: HPSI0114ikolf2-clone1, WT [SMARCB1_IP_KOLF2_R1]


title: Melanocyte WT P56 H11

description:
Melanocytes_WT_P56_genelist_TPM.txt
Melan WT P56H11

source_name: Melanocyte WT P56


title: Melanocyte WT P56 H12

description:
Melanocytes_WT_P56_genelist_TPM.txt
Melan WT P56H12


title: Melanocyte Mut P56 C3

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56C3


title: Melanocyte Mut P56 D9

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56D9


title: HPSI0114ikolf2-clone1, ASCL1-KO [SMARCB1_IP_ASCL1KO_KOLF2_R1]


title: HPSI0114ikolf2-clone1, ASCL1-KO [SMARCB1_IP_ASCL1KO_KOLF2_R2]


title: HPSI0114ikolf2-clone1, WT [INPUT_KOLF2_R2]

value: INPUT


title: Melanocyte WT P56 H10

description:
Melanocytes_WT_P56_genelist_TPM.txt
Melan WT P56H10


title: HPSI0114ikolf2-clone1, WT [INPUT_KOLF2_R1]


title: HPSI0114ikolf2-clone1, WT [INPUT_KOLF2_R3]


title: HPSI0114ikolf2-clone1, ASCL1-KO [INPUT_ASCL1KO_KOLF2_R3]


title: Melanocyte WT P56 H9

description:
Melanocytes_WT_P56_genelist_TPM.txt
Melan WT P56H9


title: Melanocyte WT P56 H4

description:
Melanocytes_WT_P56_genelist_TPM.txt
Melan WT P56H4


title: Melanocyte WT P56 H7

description:
Melanocytes_WT_P56_genelist_TPM.txt
Melan WT P56H7


title: HPSI0114ikolf2-clone1, WT [SMARCB1_IP_KOLF2_R2]


title: Melanocyte WT P56 H3

description:
Melanocytes_WT_P56_genelist_TPM.txt
Melan WT P56H3


title: Melanocyte WT P56 H6

description:
Melanocytes_WT_P56_genelist_TPM.txt
Melan WT P56H6


title: HPSI0114ikolf2-clone1, ASCL1-KO [INPUT_ASCL1KO_KOLF2_R1]


title: Melanocyte WT P56 H5

description:
Melanocytes_WT_P56_genelist_TPM.txt
Melan WT P56H5


title: Melanocyte WT P56 H1

description:
Melanocytes_WT_P56_genelist_TPM.txt
Melan WT P56H1


title: HPSI0114ikolf2-clone1, ASCL1-KO [SMARCB1_IP_ASCL1KO_KOLF2_R3]


title: Melanocyte WT P56 H2

description:
Melanocytes_WT_P56_genelist_TPM.txt
Melan WT P56H2


title: Melanocyte WT P56 G12

description:
Melanocytes_WT_P56_genelist_TPM.txt
Melan WT P56G12


title: HPSI0114ikolf2-clone1, ASCL1-KO [INPUT_ASCL1KO_KOLF2_R2]


title: Melanocyte WT P56 H8

description:
Melanocytes_WT_P56_genelist_TPM.txt
Melan WT P56H8


title: HPSI0114ikolf2-clone1, WT [NRS_WT_PM19276_R2]

description:
consensus_peaks.mLb.clN.bed.gz
consensus_peaks.mLb.clN.featureCounts.txt.gz

data_processing:
Illumina Casava software used for basecalling.
The nf-core/atacseq pipeline (version 1.1.0) was run with the parameter --min-reps_consensus 2.
For data upload reads mapping to the Y chromosome were removed as required by the MTA associated with the cell line using BBMap's filterbyname.sh function.
Assembly: hg19
Supplementary files format and content: bed file with peak regions
Supplementary files format and content: txt files with counts for each sample and each peak region

extract_protocol: NEBNext HiFi 2X PCR Master Mix (New England BioLabs, M0541S)


title: Melanocyte WT P56 G9

description:
Melanocytes_WT_P56_genelist_TPM.txt
Melan WT P56G9


title: HPSI0114ikolf2-clone1, WT [NRS_WT_PM19276_R1]


title: Melanocyte WT P56 G8

description:
Melanocytes_WT_P56_genelist_TPM.txt
Melan WT P56G8


title: HPSI0114ikolf2-clone1, WT [NP_WT_PM19276_R1]

value: day 20

value: Day 20 neural progenitors


title: Melanocyte WT P56 G11

description:
Melanocytes_WT_P56_genelist_TPM.txt
Melan WT P56G11

value: Melanocytes


title: HPSI0114ikolf2-clone1, WT [NP_WT_PM19276_R2]


title: HPSI0114ikolf2-clone1, ASCL1-KO [ASCL1_KO_PM19276_R1]


title: Melanocyte WT P56 G6

description:
Melanocytes_WT_P56_genelist_TPM.txt
Melan WT P56G6


title: Melanocyte WT P56 G7

description:
Melanocytes_WT_P56_genelist_TPM.txt
Melan WT P56G7


title: Melanocyte WT P56 G5

description:
Melanocytes_WT_P56_genelist_TPM.txt
Melan WT P56G5


title: Melanocyte WT P56 G4

description:
Melanocytes_WT_P56_genelist_TPM.txt
Melan WT P56G4


title: Melanocyte WT P56 G1

description:
Melanocytes_WT_P56_genelist_TPM.txt
Melan WT P56G1


title: Melanocyte WT P56 G2

description:
Melanocytes_WT_P56_genelist_TPM.txt
Melan WT P56G2


title: Melanocyte WT P56 G3

description:
Melanocytes_WT_P56_genelist_TPM.txt
Melan WT P56G3


title: HPSI0114ikolf2-clone1, ASCL1-KO [ASCL1_KO_PM19276_R3]


title: Melanocyte WT P56 F12

description:
Melanocytes_WT_P56_genelist_TPM.txt
Melan WT P56F12


title: WT_297

city: Baltimore

first: Jin-Young

last: Koh

state: Maryland

address: 670 W Baltimore St

department: Otorhinolaryngology-Head & Neck Surgery

institute: University of Maryland, Baltimore

library_source: transcriptomic single cell

data_processing:
The sequencing reads from fastq files were aligned to the mm10 transcriptome (GRCm38) with an index built and quantified using Kallisto pseudo-aligner. Normalized estimated counts and transcripts per kilobase million (TPM) were quantified for each cell’s transcript.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Cochlear stria vascularis

extract_protocol:
After euthanasia by CO2, the temporal bones were removed and placed into DPBS. The temporal bone was removed and opened under a dissecting microscope to access the cochlear membranous labyrinth. Once the cochlea was accessible, the stria vascularis tissue was extracted from the temporal bone and incubated for 5min at 37°C with collagenase from clostridium histolyticum solution at a working concentration of 0.3mg/500µl. The cell dissociation was completed by gently pipetting up and down. The disrupted stria vascularis tissues were placed under an inverted microscope equipped with 20x and 40x objectives and two 3D micromanipulators, each driving a pulled-glass micropipette attached to a nitrogen gas-powered Pico-Injector to control aspiration pressure. The dissociated cells were examined under the inverted microscope and were aspirated into the first pulled-glass micropipette in a slow and controlled manner then washed in fresh DPBS to remove residual collagenase solution and debris.
Nextera XT DNA sample preparation kits, including Tn5 enzymes for tagmentation, were used together with Nextera XT index kits for multiplexing. Tagmentation and amplification of adaptor-ligated fragments were carried out using half-volume reactions. For tagmentation, the input DNA was 0.125 ng. The number of amplification cycles for adaptor-ligated fragments was increased to 14. After the adaptor-ligated single-cell cDNA libraries were purified, single-cell cDNA libraries were run on the Agilent 2100 Bioanalyzer high-sensitivity DNA chips and combined in equimolar concentrations based on index balance. The concentration of pools was measured with Qubit dsDNA HS Assay Kit and Qubit 2.0 Fluorometer.

value: Stria vascularis  cells

value: Cochlear stria vascularis

tag: strain


title: WT_295


title: WT_296


title: WT_292


title: WT_291


title: WT_298


title: WT_293


title: WT_290


title: HPSI0114ikolf2-clone1, ASCL1-KO [ASCL1_KO_PM19276_R2]


title: WT_287


title: Melanocyte WT P56 F11

description:
Melanocytes_WT_P56_genelist_TPM.txt
Melan WT P56F11

value: Dorsal skin

value: Postnatal day 56


title: WT_294


title: WT_288


title: Melanocyte WT P56 G10

description:
Melanocytes_WT_P56_genelist_TPM.txt
Melan WT P56G10


title: Melanocyte WT P56 F7

description:
Melanocytes_WT_P56_genelist_TPM.txt
Melan WT P56F7


title: Melanocyte WT P56 F9

description:
Melanocytes_WT_P56_genelist_TPM.txt
Melan WT P56F9


title: Melanocyte WT P56 F6

description:
Melanocytes_WT_P56_genelist_TPM.txt
Melan WT P56F6


title: WT_285


title: WT_284


title: Melanocyte WT P56 F8

description:
Melanocytes_WT_P56_genelist_TPM.txt
Melan WT P56F8


title: Melanocyte WT P56 F10

description:
Melanocytes_WT_P56_genelist_TPM.txt
Melan WT P56F10


title: Melanocyte WT P56 F5

description:
Melanocytes_WT_P56_genelist_TPM.txt
Melan WT P56F5


title: WT_283


title: Melanocyte WT P56 F4

description:
Melanocytes_WT_P56_genelist_TPM.txt
Melan WT P56F4


title: WT_286


title: WT_282


title: WT_289


title: WT_280


title: HET_279


title: WT_281


title: Melanocyte WT P56 F2

description:
Melanocytes_WT_P56_genelist_TPM.txt
Melan WT P56F2


title: Melanocyte WT P56 F3

description:
Melanocytes_WT_P56_genelist_TPM.txt
Melan WT P56F3


title: Melanocyte WT P56 F1

description:
Melanocytes_WT_P56_genelist_TPM.txt
Melan WT P56F1


title: Melanocyte WT P56 E12

description:
Melanocytes_WT_P56_genelist_TPM.txt
Melan WT P56E12


title: Melanocyte WT P56 E11

description:
Melanocytes_WT_P56_genelist_TPM.txt
Melan WT P56E11


title: HET_277


title: HET_278


title: HET_276


title: Melanocyte WT P56 E10

description:
Melanocytes_WT_P56_genelist_TPM.txt
Melan WT P56E10


title: Melanocyte WT P56 E9

description:
Melanocytes_WT_P56_genelist_TPM.txt
Melan WT P56E9


title: HET_275


title: HET_274


title: Melanocyte WT P56 E6

description:
Melanocytes_WT_P56_genelist_TPM.txt
Melan WT P56E6


title: Melanocyte WT P56 E5

description:
Melanocytes_WT_P56_genelist_TPM.txt
Melan WT P56E5


title: Melanocyte WT P56 E4

description:
Melanocytes_WT_P56_genelist_TPM.txt
Melan WT P56E4


title: Melanocyte WT P56 E3

description:
Melanocytes_WT_P56_genelist_TPM.txt
Melan WT P56E3


title: HET_272


title: HET_271


title: HET_270


title: HET_273


title: Melanocyte WT P56 D12

description:
Melanocytes_WT_P56_genelist_TPM.txt
Melan WT P56D12


title: HET_269


title: HET_268


title: Melanocyte WT P56 D10

description:
Melanocytes_WT_P56_genelist_TPM.txt
Melan WT P56D10


title: Melanocyte WT P56 E2

description:
Melanocytes_WT_P56_genelist_TPM.txt
Melan WT P56E2


title: Melanocyte WT P56 D11

description:
Melanocytes_WT_P56_genelist_TPM.txt
Melan WT P56D11


title: Melanocyte WT P56 D9

description:
Melanocytes_WT_P56_genelist_TPM.txt
Melan WT P56D9


title: HET_266


title: HET_264


title: Melanocyte WT P56 D7

description:
Melanocytes_WT_P56_genelist_TPM.txt
Melan WT P56D7


title: Melanocyte WT P56 D8

description:
Melanocytes_WT_P56_genelist_TPM.txt
Melan WT P56D8


title: HET_265


title: HET_267


title: Melanocyte WT P56 D6

description:
Melanocytes_WT_P56_genelist_TPM.txt
Melan WT P56D6


title: HET_262


title: HET_261


title: HET_263


title: Melanocyte WT P56 D4

description:
Melanocytes_WT_P56_genelist_TPM.txt
Melan WT P56D4


title: Melanocyte WT P56 D5

description:
Melanocytes_WT_P56_genelist_TPM.txt
Melan WT P56D5


title: Melanocyte WT P56 D3

description:
Melanocytes_WT_P56_genelist_TPM.txt
Melan WT P56D3


title: HET_260


title: HET_259


title: Melanocyte WT P56 D2

description:
Melanocytes_WT_P56_genelist_TPM.txt
Melan WT P56D2


title: Melanocyte WT P56 C11

description:
Melanocytes_WT_P56_genelist_TPM.txt
Melan WT P56C11


title: Melanocyte WT P56 C12

description:
Melanocytes_WT_P56_genelist_TPM.txt
Melan WT P56C12


title: Melanocyte WT P56 C10

description:
Melanocytes_WT_P56_genelist_TPM.txt
Melan WT P56C10


title: HET_258


title: HET_257


title: Melanocyte WT P56 C9

description:
Melanocytes_WT_P56_genelist_TPM.txt
Melan WT P56C9


title: HET_256


title: Melanocyte WT P56 C8

description:
Melanocytes_WT_P56_genelist_TPM.txt
Melan WT P56C8


title: Melanocyte WT P56 C7

description:
Melanocytes_WT_P56_genelist_TPM.txt
Melan WT P56C7


title: HET_255


title: HET_254


title: HET_253


title: HET_252


title: Melanocyte WT P56 C6

description:
Melanocytes_WT_P56_genelist_TPM.txt
Melan WT P56C6


title: Melanocyte WT P56 C3

description:
Melanocytes_WT_P56_genelist_TPM.txt
Melan WT P56C3


title: HET_250


title: HET_249


title: Melanocyte WT P56 C5

description:
Melanocytes_WT_P56_genelist_TPM.txt
Melan WT P56C5


title: Melanocyte WT P56 C1

description:
Melanocytes_WT_P56_genelist_TPM.txt
Melan WT P56C1


title: HET_251


title: Melanocyte WT P56 C4

description:
Melanocytes_WT_P56_genelist_TPM.txt
Melan WT P56C4


title: Melanocyte WT P56 B10

description:
Melanocytes_WT_P56_genelist_TPM.txt
Melan WT P56B10


title: Melanocyte WT P56 B12

description:
Melanocytes_WT_P56_genelist_TPM.txt
Melan WT P56B12


title: Melanocyte WT P56 B8

description:
Melanocytes_WT_P56_genelist_TPM.txt
Melan WT P56B8


title: HET_247


title: HET_248


title: HET_245


title: HET_246


title: SAS-CRISPR-Control

description: Gene expression data from CX-1 cells expressing control vector

value: SAS Cells infected with All-in-one CRISPR/Cas9 virus without sgRNA


title: Melanocyte WT P56 B7

description:
Melanocytes_WT_P56_genelist_TPM.txt
Melan WT P56B7

value: WT


title: HET_242


title: HET_243


title: Melanocyte WT P56 B6

description:
Melanocytes_WT_P56_genelist_TPM.txt
Melan WT P56B6


title: Melanocyte WT P56 B5

description:
Melanocytes_WT_P56_genelist_TPM.txt
Melan WT P56B5


title: HET_241


title: Melanocyte WT P56 B4

description:
Melanocytes_WT_P56_genelist_TPM.txt
Melan WT P56B4


title: Melanocyte WT P56 A12

description:
Melanocytes_WT_P56_genelist_TPM.txt
Melan WT P56A12


title: Melanocyte WT P56 A11

description:
Melanocytes_WT_P56_genelist_TPM.txt
Melan WT P56A11


title: KO_235


title: KO_238


title: Melanocyte WT P56 A8

description:
Melanocytes_WT_P56_genelist_TPM.txt
Melan WT P56A8


title: KO_237


title: Melanocyte WT P56 A10

description:
Melanocytes_WT_P56_genelist_TPM.txt
Melan WT P56A10


title: Melanocyte WT P56 B3

description:
Melanocytes_WT_P56_genelist_TPM.txt
Melan WT P56B3


title: KO_239


title: Melanocyte WT P56 A7

description:
Melanocytes_WT_P56_genelist_TPM.txt
Melan WT P56A7


title: HET_240


title: KO_233


title: Melanocyte WT P56 A9

description:
Melanocytes_WT_P56_genelist_TPM.txt
Melan WT P56A9


title: Melanocyte WT P56 A4

description:
Melanocytes_WT_P56_genelist_TPM.txt
Melan WT P56A4


title: KO_232


title: HET_244


title: Melanocyte WT P56 A3

description:
Melanocytes_WT_P56_genelist_TPM.txt
Melan WT P56A3


title: KO_230


title: KO_231


title: Bulge Mut P56 H11

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56H11

source_name: Bulge Mut P56

value: Bulge stem cells

value: Mut


title: Bulge Mut P56 H10

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56H10


title: KO_229


title: KO_228


title: Bulge Mut P56 H9

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56H9


title: KO_236


title: KO_227


title: Bulge Mut P56 H8

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56H8


title: KO_226


title: KO_234


title: Melanocyte WT P56 A6

description:
Melanocytes_WT_P56_genelist_TPM.txt
Melan WT P56A6


title: Bulge Mut P56 H6

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56H6


title: Bulge Mut P56 H5

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56H5


title: Melanocyte WT P56 A5

description:
Melanocytes_WT_P56_genelist_TPM.txt
Melan WT P56A5


title: Bulge Mut P56 H4

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56H4


title: KO_224


title: KO_222


title: KO_221


title: Bulge Mut P56 H3

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56H3


title: Bulge Mut P56 H2

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56H2


title: Bulge Mut P56 G11

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56G11


title: Bulge Mut P56 H1

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56H1


title: KO_220


title: WT_217


title: KO_219


title: Bulge Mut P56 G8

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56G8


title: Bulge Mut P56 G12

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56G12


title: WT_216


title: Bulge Mut P56 G10

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56G10


title: Bulge Mut P56 G9

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56G9


title: KO_218


title: WT_215


title: Bulge Mut P56 H7

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56H7


title: Bulge Mut P56 G7

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56G7


title: WT_213


title: Bulge Mut P56 G6

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56G6


title: Bulge Mut P56 G5

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56G5


title: KO_223


title: KO_225


title: WT_211


title: WT_214


title: WT_209


title: WT_212


title: Bulge Mut P56 G4

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56G4


title: Bulge Mut P56 F12

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56F12


title: WT_210


title: WT_207


title: WT_208


title: WT_206


title: Bulge Mut P56 G3

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56G3


title: Bulge Mut P56 G2

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56G2


title: Bulge Mut P56 F11

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56F11


title: Bulge Mut P56 F9

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56F9


title: WT_205


title: WT_204


title: WT_203


title: Bulge Mut P56 F10

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56F10


title: WT_201


title: Bulge Mut P56 F8

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56F8


title: Bulge Mut P56 F7

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56F7


title: Bulge Mut P56 F6

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56F6


title: WT_198


title: Bulge Mut P56 F5

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56F5


title: Bulge Mut P56 G1

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56G1


title: Bulge Mut P56 F3

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56F3


title: Bulge Mut P56 F1

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56F1


title: Bulge Mut P56 F2

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56F2


title: Bulge Mut P56 F4

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56F4


title: Bulge Mut P56 E12

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56E12


title: Bulge Mut P56 E11

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56E11


title: WT_195


title: WT_194


title: WT_193


title: WT_202


title: Bulge Mut P56 E10

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56E10


title: WT_192


title: WT_199


title: WT_191


title: NC2_3

city: Jinan

first: Mingyang

last: Li

state: --- Select One ---

address: 324 Jingwu Road, Jinan 250021, China

country: China

institute: Shandong Provincial Hospital Affiliated to Shandong First Medical University

data_processing:
Data filtering
The sequencing data was filtered with SOAPnuke [1] by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com).
RNA identification
Bowtie2[2] was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Gene Quantification Differential Expression Analysis
Expression level of gene was calculated by RSEM (v1.3.1) [3]. The heatmap was drawn by pheatmap (v1.0.8) [4] according to the gene expression difference in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5) [5] (or DEGseq[6] or PoissonDis[7])with Q value ≤ 0.05 (or FDR ≤ 0.001).
Gene Annotation
To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expression gene was performed by Phyper (https://en.wikipedia.org/wiki/Hypergeometric_distribution) based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05) [8].
Assembly: hg38
Supplementary files format and content: excel files include fpkm values and read_count for each Sample

source_name: infantile hemangioma

growth_protocol: hemangioma endothelial cells were maintained in ECM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using AG RNAex Pro. 1.0 ug of total RNA was used for the construction of sequencing libraries.
1 Sample QC
Select the corresponding testing methods for quality inspection according to the requirements of samples and products.
2 mRNA Isolation
A certain amount of RNA samples are denatured at suitable temperature to open their secondary structure, and mRNA is enriched by oligo (dT) -attached magnetic beads.
3 mRNA Fragmentation
The reaction system is configured. After reacting at the suitable temperature for a fixed period of time, RNAs are fragmented.
4 cDNA Synthesis
Prepare the first-strand synthesis reaction system, and set up the reaction program, synthesize the first- strand cDNA, prepare the second-strand synthesis reaction system, and set up the reaction program to synthesize the second-strand cDNA.
5 End Repair, Add A and Adaptor Ligation
After the reaction system and program are configured and set up, double-stranded cDNA fragments are subjected to end-repair, and then a single ‘A’ nucleotide is added to the 3’ ends of the blunt fragments. The reaction system and program for adaptor ligation are subsequently configured and set up to ligate adaptors with the cDNAs.
6 PCR
The PCR reaction system and program are configured and set up to amplify the product.
7 Library QC
The corresponding library quality control protocol will be selected depending upon product requirements.
8 Circularization
Single-stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single-stranded cyclized products are produced, while uncyclized linear DNA molecules are digested.
9 Sequencing
Single-stranded circle DNA molecules are replicated via rolling cycle amplification, and a DNA nanoball (DNB) which contain multiple copies of DNA is generated. Sufficient quality DNBs are then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS).

treatment_protocol: Sample1-6 have no other treatment.Sample7-9 were transfected with negative control lentivirus. Sample10-12 were transfected with OTUB1-knockdown lentivirus

value: infantile hemangioma

value: hemangioma endothelial cells


title: OTUB1 sh3_2

value: OTUB1 knockdown

value: transfected with OTUB1-knockdown lentivirus


title: NC2_2

value: transfected with negative control lentivirus


title: WT_200


title: OTUB1 sh3_1


title: WT_190


title: WT_197


title: Bulge Mut P56 E8

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56E8


title: proliferating IH6(NC1_3)


title: WT_196


title: proliferating IH5(NC1_2)


title: proliferating IH3(LV_3)


title: proliferating IH4(NC1_1)


title: WT_189


title: Bulge Mut P56 E7

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56E7


title: Bulge Mut P56 E6

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56E6


title: Bulge Mut P56 E9

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56E9


title: proliferating IH2(LV_2)


title: OTUB1 sh3_3


title: Bulge Mut P56 E4

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56E4


title: WT_187


title: WT_188


title: Normal_central 9

city: Los Angeles

first: Vasu

last: Punj

state: CA

address: Biggy Street

institute: USC

description: Barcode: ACAGTG

data_processing:
Illumina Casava1.7 software (illumina)  used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCH37  using  Bowtie 1.
Exon and intron boundaries were marked and coding regions were excluded.  Reads were quantified as sequence tags in each library separately and normalized as reads per million (RPM).  Differential expression was calculated at a significance of p<0.05 after Benjamini and Hochberg correction using a one way ANOVA or t-test.To further rank differentially expressed miRNAs, the data was shifted to log2 values and fold change was calculated.
microRNA was excluded if it had 0 reads in all samples.
Genome_build: GRCH37 and annotations were obtained from various ncRNA databases like Gencode v19 (human genome) and mirBase 20.
Supplementary_files_format_and_content: TXT file (File1_Vasu_Normalized RPM values_ miRNAseq_Mehrnoosh.txt) include RPM values for each Sample.

growth_protocol: Human corneas received from NDRI  within 24 hours of donor death were 8.5 mm-trephined into central and limbal components and immediately snap freeze and kept at –80 degree

extract_protocol:
Total RNA including low molecular weight (LMW) RNA was extracted using mirVanaTM miRNA kit (Thermo Fisher Scientific, Waltham, MA) from human central and limbal corneas.
Illumina TruSeq™ Small RNA Library Prep kit per the manufacturer’s protocol was used toconstruct libraries as recommended by manufcaturer.  In brief, adapters were ligated to both ends of the RNA, transcripts were reverse transcribed, and then cDNA was PCR amplified with indexed primers to enable multiplexing samples for sequencing.  Libraries between 145-160 base pairs long were purified from gel. Libraries were pooled in equimolar concentration for each experiment  and clustered on a single-end flow cell using an Illumina c-bot. The library-clustered flow cell was sequenced on the Illumina GAIIx, 1x36 bp sequencing chemistry.

tag: disease state

value: Normal

value: Corneal Central tissue


title: Normal_central 8

description: Barcode: TGACCA


title: Normal_Limbus 9

description: Barcode: CCGTCC

value: Corneal Limbal tissue


title: NC2_1


title: Bulge Mut P56 E5

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56E5


title: WT_186


title: Normal_central 3

description: Barcode: ACAGTG


title: Bulge Mut P56 E2

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56E2


title: Normal_Limbus 3

description: Barcode: CCGTCC


title: WT_185


title: WT_184


title: Normal_Limbus 8

description: Barcode: ATGTCA


title: Normal_central 27

description: Barcode: TTAGGC


title: Bulge Mut P56 E1

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56E1


title: Normal_central 1

description: Barcode: TGACCA


title: proliferating IH1(LV_1)


title: WT_183


title: Normal_Limbus 27

description: Barcode: AGTTCC


title: WT_182


title: Bulge Mut P56 D12

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56D12


title: Bulge Mut P56 D11

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56D11


title: Normal_central 24

description: Barcode: CGATGT


title: Normal_central 11

description: Barcode: TTAGGC


title: Normal_Limbus 11

description: Barcode: AGTTCC


title: Bulge Mut P56 E3

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56E3


title: WT_181


title: Normal_Limbus 24

description: Barcode: AGTCAA


title: Bulge Mut P56 D10

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56D10


title: WT_180


title: Normal_Limbus 23

description: Barcode: CTTGTA


title: Bulge Mut P56 D9

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56D9


title: Normal_central 23

description: Barcode: ATCACG


title: Normal_central 22

description: Barcode: CGATGT


title: Bulge Mut P56 D7

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56D7


title: WT_178


title: Normal_Limbus 1

description: Barcode: ATGTCA


title: Normal_central 21

description: Barcode: ATCACG


title: DM2_central 7

description: Barcode: GGCTAC

value: type II diabetes


title: Normal_Limbus 22

description: Barcode: AGTCAA


title: WT_177

value: Stria vascularis  cells


title: Bulge Mut P56 D6

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56D6


title: DM2_Limbus 7

description: Barcode: GTTTCG


title: WT_176

value: Cochlear stria vascularis


title: DM1_central 5

description: Barcode: GATCAG

value: type I diabetes


title: DM2_central 6

description: Barcode: TAGCTT


title: WT_175


title: DM1_Limbus 5

description: Barcode: GTGAAA


title: DM2_Limbus 2

description: Barcode: GTCCGC


title: DM2_Limbus 6

description: Barcode: GTGGCC


title: Bulge Mut P56 D4

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56D4

value: Dorsal skin

value: Postnatal day 56


title: DM2_central 2

description: Barcode: ACTTGA


title: WT_174


title: Bulge Mut P56 D8

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56D8


title: Bulge Mut P56 D3

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56D3


title: Normal_Limbus 21

description: Barcode: CTTGTA


title: WT_173


title: DM1_Limbus 14

description: Barcode: CGTACG


title: Bulge Mut P56 C12

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56C12


title: DM1_Limbus 12

description: Barcode: GTGGCC


title: Bulge Mut P56 D5

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56D5


title: Bulge Mut P56 D2

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56D2


title: Bulge Mut P56 D1

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56D1


title: WT_171


title: WT_169


title: WT_170


title: DM1_central 12

description: Barcode: GATCAG


title: Bulge Mut P56 C11

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56C11


title: DM2_central 11

description: Barcode: ACTTGA


title: DM2_central 10

description: Barcode: CAGATC


title: DM2_Limbus 11

description: Barcode: GTGAAA


title: DM2_Limbus 10

description: Barcode: CGTACG


title: WT_179


title: WT_168


title: DM1_Limbus 31

description: Barcode: GTCCGC


title: Bulge Mut P56 C10

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56C10


title: DM1_Limbus 13

description: Barcode: GTTTCG


title: Bulge Mut P56 C9

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56C9


title: WT_172


title: DM1_central 31

description: Barcode: GCCAAT


title: WT_167


title: Bulge Mut P56 C8

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56C8


title: DM1_central 14

description: Barcode: GGCTAC


title: DM1_Limbus 30

description: Barcode: GTAGAG


title: DM1_central 30

description: Barcode: CAGATC


title: DM2_central 18

description: Barcode: GCCAAT


title: DM1_central 13

description: Barcode: TAGCTT


title: WT_166


title: WT_165


title: DM2_Limbus 18

description: Barcode: GTAGAG


title: WT_164


title: Bulge Mut P56 C4

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56C4


title: Bulge Mut P56 C3

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56C3


title: WT_162


title: Bulge Mut P56 C2

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56C2


title: WT_161


title: Bulge Mut P56 C1

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56C1


title: WT_163


title: WT_160


title: WT_159


title: BEC_AsthmaHDM_DAY4-DJ61

city: Zurich

first: Ge

last: Tan

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich

country: Switzerland

institute: University of Zurich

hyb_protocol: Samples were processed for HuGene 1.0 array  following the manufacturers instructions (Affymetrix).

scan_protocol: The arrays were scanned by the high-resolution scanner of GeneChip Scanner (Affymetrix)

data_processing: Raw data were normalized using justRMA() from affy R package.

source_name: BEC

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

extract_protocol: Total RNA was extracted with the use of RNAeasy Mini kit (Qiagen) according to manufacturers instructions.

treatment_protocol: Control individuals and patients with asthma were inoculated intranassaly with 100 TCID50 of rhinovirus A16. Bronchial brushings from around two weeks before (day -14) and four days after infection (day 4) were collected.

tag: group

value: AsthmaHDM

tag: donor


title: BEC_AsthmaHDM_DAY4-DJ67


title: Bulge Mut P56 B11

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56B11

value: Bulge stem cells


title: Bulge Mut P56 C6

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56C6

value: Mut


title: BEC_AsthmaHDMNeg_DAY4-DJ126

value: AsthmaHDMNeg


title: Bulge Mut P56 C5

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56C5


title: BEC_AsthmaHDM_DAY4-DJ75


title: BEC_AsthmaHDM_DAY4-DJ121


title: BEC_AsthmaHDM_DAY4-DJ86


title: BEC_Healthy_DAY4-DJ56

value: Healthy


title: BEC_AsthmaHDM_DAY4-DJ136


title: Bulge Mut P56 B10

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56B10


title: BEC_AsthmaHDMNeg_DAY4-DJ125


title: WT_158


title: WT_157


title: Bulge Mut P56 B9

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56B9


title: Bulge Mut P56 B12

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56B12


title: WT_156


title: BEC_AsthmaHDMNeg_DAY4-DJ73


title: BEC_AsthmaHDM_DAY4-DJ92


title: BEC_AsthmaHDM_DAY4-DJ148


title: Bulge Mut P56 B8

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56B8


title: BEC_AsthmaHDM_DAY4-DJ129


title: BEC_Healthy_DAY4-DJ47


title: WT_155


title: Bulge Mut P56 B7

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56B7


title: BEC_Healthy_DAY4-DJ101


title: WT_154


title: Bulge Mut P56 B6

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56B6


title: Bulge Mut P56 B5

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56B5


title: WT_153


title: BEC_AsthmaHDMNeg_DAY4-DJ134


title: BEC_AsthmaHDM_DAY4-DJ139


title: BEC_Healthy_DAY4-DJ81


title: BEC_AsthmaHDM_DAY4-DJ113


title: BEC_AsthmaHDM_DAY4-DJ144


title: Bulge Mut P56 B4

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56B4


title: WT_152


title: BEC_Healthy_DAY4-DJ114


title: BEC_Healthy_DAY14-DJ101


title: WT_151


title: BEC_AsthmaHDM_DAY14-DJ61


title: BEC_AsthmaHDMNeg_DAY4-DJ60


title: BEC_AsthmaHDM_DAY14-DJ75


title: WT_150


title: Bulge Mut P56 B3

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56B3


title: Bulge Mut P56 B2

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56B2


title: WT_149


title: Bulge Mut P56 B1

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56B1


title: WT_148


title: BEC_Healthy_DAY14-DJ56


title: OB_GAS_4

city: Worcester

first: Travis

middle: E.

last: Faust

state: MA

address: 366 Plantation Street

department: Neurobiology

institute: University of Massachusetts Chan Medical School

description:
CountsAndCellMetadata_Coverslip_4.csv
GAS_4 sample is at positions > 4500 Y

hyb_protocol: Tissue was washed and hybridized for 15 minutes with the first hybridization buffer containing readout probes associated with the first round of imaging as well as the reagents for DAPI and polyT staining.

scan_protocol: MERFISH imaging was performed as previously described (Moffitt et al., 2018) with parameters files provided by Vizgen. Briefly, the sample was loaded into a flow chamber connected to the Vizgen Alpha Instrument. First, a low-resolution mosaic image was acquired (405 nm channel) with a low magnification objective (10x). Then the objective was switched to a high magnification objective (60x) and seven 1.5 μm z-stack images of each field of view position were generated in 749 nm, 638 nm and 546 nm channels. A single image of the fiducial beads on the surface of the coverslip was acquired and used as a spatial reference (477 nm channel). After each round of imaging, the readout probes were extinguished, and the sample was hybridized with the next set of readout probes. This process was repeated until combinatorial FISH was completed.

data_processing:
Raw data were decoded using the MERlin pipeline (Vizgen, v0.1.6 ) using the relevant library codebook. Cell boundaries were segmented in each FOV using a seeded watershed algorithm using DAPI signal as the seed and poly-T signal as the watershed channel. The volume, X position, and Y position of these cell boundaries, as well as the probe counts within each cell boundary, were output to CountsAndCellMetadata.csv files for further analysis.   MERFISH data was analyzed in RStudio using Seurat and custom-made scripts as previously described (Feinberg et al 2022).  Cell segmentations with volume < 50µm3 or < 10 unique transcripts were first excluded. Cell gene expression data of each cell was then normalized to that cell’s volume and the total transcript count of that cell, then scaled. To correct for global differences in total transcript counts between coverslips (each containing 1 GAS sample and 1 PBS sample), we performed ComBat batch correction (sva 3.38.0). To identify individual cell types, we performed principle component analysis was performed using the entire probe library (391 transcripts) as the variable features, followed by linear dimensional reduction. Clusters were manually annotated based on the spatial distribution of the cells in the tissue and the expression cell type-specific marker genes. Because of imperfections in cell boundary segmentation, a small fraction of cells expressed cell type markers for multiple cell types. Clusters composed of these “hybrid” cells were removed from the analysis, and UMAP embedding and clustering analysis were iteratively repeated until all “hybrid” clusters were removed. Nearest neighbor analysis of microglial distance to T cells was calculated based the X, Y coordinates of the centers of the cell segmentations using a custom python script.
CountsAndCellMetadata.csv files contain matrices of cell IDs as rows, genes and metadata as columns. Matrix contains raw counts of detected transcripts. Volume metadata is provided in cubic microns. X and Y metadata are provided in microns.

source_name: Olfactory bulb

label_protocol: Tissue on coverslips was fixed for 15 minutes at room temperature in 4% paraformaldehyde in PBS, followed by three washes with PBS. Tissue was then permeabilized in 70% ethanol for 24 hours. After a wash with Formamide Wash Buffer  (30% formamide in 2X saline sodium citrate (SSC)), the MERFISH library mix was added and allowed to hybridize to occur for 48 hours. Sample was then washed and incubated at 47°C with Formamide Wash Buffer twice  and then the tissue was embedded in a polyacrylamide gel followed by incubation with tissue clearing solution (2X SSC, 2% SDS, 0.5% v/v Triton X-100, and proteinase K 1:100) overnight at 37°C.

extract_protocol: After perfusion with cold PBS, brains were embedded in OCT for sectioning onto specialized coverslips. 10 microns coronal sections of the olfactory bulb (around bregma 4.28) were collected for analysis by MERFISH

treatment_protocol: Brains were isolated from P53 mice following five repeated inoculations with either a suspension of Group A Streptococcus or with vehicle (PBS), and profiled at 24 hours post-inoculation.

tag: Sex

value: Female

value: Olfactory bulb

value: GAS inoculation

tag: timepoint

value: 24 hours after fifth inoculation


title: BEC_Healthy_DAY4-DJ116


title: OB_PBS_4

description:
CountsAndCellMetadata_Coverslip_4.csv
PBS_4 sample is at positions < 4500 Y

value: PBS inoculation


title: OB_GAS_3

description:
CountsAndCellMetadata_Coverslip_3.csv
GAS_3 sample is at positions < 7000 Y


title: Bulge Mut P56 A12

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56A12


title: Bulge Mut P56 A11

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56A11


title: OB_PBS_3

description:
CountsAndCellMetadata_Coverslip_3.csv
PBS_3 sample is at positions > 7000 Y


title: WT_147


title: BEC_AsthmaHDM_DAY14-DJ67


title: OB_GAS_2

description:
CountsAndCellMetadata_Coverslip_2.csv
GAS_2 sample is at positions >7000 Y


title: BEC_Healthy_DAY14-DJ48


title: BEC_AsthmaHDM_DAY14-DJ86


title: WT_146


title: Bulge Mut P56 A10

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56A10


title: BEC_AsthmaHDMNeg_DAY14-DJ126


title: BEC_AsthmaHDM_DAY14-DJ121


title: WT_145


title: BEC_AsthmaHDM_DAY14-DJ148


title: Bulge Mut P56 A9

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56A9


title: BEC_Healthy_DAY14-DJ116


title: WT_144


title: OB_PBS_2

description:
CountsAndCellMetadata_Coverslip_2.csv
PBS_2 sample is at positions <5600 Y


title: BEC_AsthmaHDMNeg_DAY14-DJ125


title: OB_GAS_1

description:
CountsAndCellMetadata_Coverslip_1.csv
GAS_1 sample is at positions <7000 Y


title: WT_143


title: Bulge Mut P56 A8

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56A8


title: OB_PBS_1

description:
CountsAndCellMetadata_Coverslip_1.csv
PBS_1 sample is at positions >7000 Y


title: Bulge Mut P56 A7

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56A7


title: Bulge Mut P56 A6

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56A6


title: BEC_Healthy_DAY14-DJ47


title: KO_142


title: Bulge Mut P56 A5

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56A5


title: KO_140


title: Low_TB_4

city: guangzhou

first: wen

middle: zhao

last: wei

address: No. 1838, Guangzhou Avenue North, Baiyun District, Guangzhou

department: Department of Oncology,

institute: Nanfang Hospital, Southern Medical University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes count values for each Sample

source_name: Subcutaneous tumor

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Subcutaneous tumor

tag: tumor burden

value: LTB


title: Low_TB_5


title: BEC_AsthmaHDM_DAY14-DJ92


title: Low_TB_3


title: BEC_AsthmaHDM_DAY14-DJ136


title: Bulge Mut P56 A4

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56A4


title: KO_139

value: Stria vascularis  cells


title: Bulge Mut P56 A3

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56A3


title: Bulge Mut P56 A2

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56A2


title: KO_138

value: Cochlear stria vascularis


title: Low_TB_2


title: BEC_AsthmaHDMNeg_DAY14-DJ73


title: BEC_AsthmaHDMNeg_DAY14-DJ60


title: High_TB_5

value: HTB


title: BEC_Healthy_DAY14-DJ114


title: KO_141


title: BEC_AsthmaHDMNeg_DAY14-DJ134


title: KO_136


title: High_TB_4


title: KO_135


title: BEC_Healthy_DAY14-DJ81


title: Bulge WT P56 H11

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56H11

source_name: Bulge WT P56

value: WT

value: Dorsal skin


title: High_TB_3


title: BEC_AsthmaHDM_DAY14-DJ139

value: AsthmaHDM


title: Bulge WT P56 H10

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56H10

value: Bulge stem cells

value: Postnatal day 56


title: Bulge WT P56 H9

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56H9


title: KO_134


title: Low_TB_1


title: BEC_AsthmaHDM_DAY14-DJ129


title: KO_132


title: KO_137


title: High_TB_1


title: Bulge WT P56 H8

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56H8


title: KO_133


title: Bulge Mut P56 A1

description:
Bulge_stem_cells_Mut_P56_genelist_TPM.txt
B Mut P56A1

value: Mut


title: KO_131


title: Bulge WT P56 H7

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56H7


title: BEC_AsthmaHDM_DAY14-DJ113


title: Bulge WT P56 H12

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56H12


title: Bulge WT P56 H6

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56H6


title: Cre_pos_rep3

first: Patrick

last: Sheehan

address: 364 Plantation Ave.

institute: University of Massachusetts Medical School

data_processing:
Basecalls and demultiplexing was performed with Illumina’s RTA 1.9 software and the reads were aligned to the Mus musculus Ensembl release 76 GRCm38 primary assembly with STAR version 2.5.1a.  Gene counts were quantitated with Subread:featureCount version 1.4.6-p5.
All gene counts were then imported into the R/Bioconductor package EdgeR and TMM normalization size factors were calculated to adjust the samples for differences in library size.  Ribosomal genes were removed and only genes expressed greater than one count-per-million in at least four samples were kept for further analysis. The adjusted TMM size factors and the matrix of counts were then imported into the R/Bioconductor package Limma. Weighted likelihoods were then calculated for all samples and the count matrix was transformed to moderated log 2 counts-per-million with Limma’s voomWithQualityWeights.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include CPM values for each Sample

source_name: cortical tissue

extract_protocol:
Cortical tissue was submerged in Trizol reagent (Invitrogen/ThermoFisher) and mechanically dissociated using a bead homogenizer. Chloroform extraction was performed, and the supernatant was collected and mRNA was isolated using Ambion PureLink RNA iolation kit (ThermoFisher), following the manufacturers instructions.
Library preparation was performed with 10ng of total RNA for samples with a Bioanalyzer RIN score greater than 8.0. ds-cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) per manufacturer's protocol.

value: 4 Months

value: cortical tissue


title: Bulge WT P56 H5

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56H5


title: Cre_pos_rep5


title: KO_129


title: Cre_pos_rep4


title: Cre_pos_rep2


title: High_TB_2


title: BEC_AsthmaHDM_DAY14-DJ144


title: KO_130


title: Bulge WT P56 H4

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56H4


title: KO_127


title: KO_128


title: Bulge WT P56 H3

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56H3


title: Cre_neg_rep5


title: HPSI0114ikolf2-clone1_ASCL1ko_DAPT [ASCL1ko_DAPT_TAN2457A27]

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg19
Supplementary files format and content: Tab-separated values files and matrix files

growth_protocol: Dual SMAD inhibition: day 0 - day 12.

extract_protocol:
On the day of harvest, adherent cell cultures cells were washed twice with DPBS then incubated at 37˚C in accutase (Sigma-Aldrich, A6964) and manually dissociated by pipetting with a P1000. 2 volumes of DMEM F-12 were added and cells passed through a 40µm cell strainer to achieve a single-celled suspension before counting on a NucleoCounter NC-200. 1.5 x 106 cells were then centrifuged at 255 x gg for 2mins. The pellet was resuspended in 750mml of 0.22µm-filtered 1% BSA in DPBS for a theoretical concentration of 2000 cells/mml. This suspension was then counted. 10,000 cells were loaded onto the Chromium X (10x Genomics) to generate single-celled Gel Beads-in-Emulsion (GEMs) for library preparation. Dual index Chromium Single Cell 3' v3.1 Chemistry was used according to manufacturer’s instructions, using 11 cycles for the cDNA amplification and 14 cycles for the library PCR. Libraries were then sequenced on a NovaSeq 6000 (Illumina).
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics). Briefly, single-cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

treatment_protocol: Notch inhibition: 24 hrs on day 24.

value: human induced pluripotent cells

value: DAPT

tag: treatment length

value: day 24


title: KO_126


title: HPSI0114ikolf2-clone1_WT_DAPT [WT_DAPT_TAN2457A26]

description: 10x Genomics

tag: treatment


title: KO_125

tag: cell type


title: Cre_neg_rep4

tag: genotype


title: Bulge WT P56 H2

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56H2

tag: tissue


title: Bulge WT P56 H1

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56H1

tag: age


title: BEC_Healthy_DAY4-DJ48

value: Healthy


title: HPSI0114ikolf2-clone1_WT [WT_neg_TAN2457A25]

description: 10x Genomics

tag: cell line


title: Cre_neg_rep3


title: Cre_neg_rep2


title: KO_124


title: Bulge WT P56 G12

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56G12


title: Bulge WT P56 G11

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56G11


title: Cre_neg_rep1


title: KO_123


title: HPSI0114ikolf2-clone1_ASCL1ko_DAPT [ASCL1ko_DAPT_TAN2457A24]

description: 10x Genomics

tag: time


title: HPSI0114ikolf2-clone1_ASCL1ko_DAPT [ASCL1ko_DAPT_TAN2457A23]

description: 10x Genomics


title: KO_121


title: WT_122


title: Cre_pos_rep1


title: Bulge WT P56 G10

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56G10


title: KO_120


title: Bulge WT P56 G8

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56G8


title: HPSI0114ikolf2-clone1_WT_DAPT [WT_DAPT_TAN2457A21]

description: 10x Genomics


title: KO_119


title: F1_pre-cDC1_2

city: Saint Louis

first: Tiantian

last: Liu

state: MO

address: 660 S. Euclid Ave.

department: Pathology and Immunology

institute: Washington University in St. Louis

data_processing:
The adaptor sequences were removed by Trimmomatic program: java -jar trimmomatic-0.39.jar PE -threads 30 -phred33 samplename_R1.fastq.gz samplename_R2.fastq.gz -baseout samplename.fastq.gz ILLUMINACLIP:Truseq3.PE.fa:2:15:4:4:true LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:25  The trimmed reads were aligned and mapped to the mouse reference genome (GRCm38/mm10) by Bowtie2 software version 2.2.5: bowtie2 -p 30 --dovetail --phred33 -x mm10 -1 samplename_1P.fastq.gz -2 samplename_2P.fastq.gz > samplename.sam  Duplicated reads are discarded using 'make tag directory' of Homer software package (version 4.9) with the parameter -tbp 1: makeTagDirectory samplename.tags samplename.sam -fragLength given -tbp 1  Data were visualized with the 'makeUCSCfile' of Homer: makeUCSCfile samplename.tags -o auto -fragLength given -tbp 1 -fsize 5e7
Assembly: mm10
Supplementary files format and content: bedGraph files were generated with Homer software package using the "makeUCSCfile" command

source_name: bone marrow progenitor cells

extract_protocol: 1 million fresh sort purified cells were adsorbed to activated Concanavalin A (ConA) beads, permeabilized with 0.01% digitonin, and incubated with 0.5 mg rabbit-anti-BATF3 antibody overnight at 4 °C. After antibody binding, the targete-DNA complex is cleaved by the Protein A/Protein G-Micrococcal Nuclease (pAG-MNase) for 2 hours at 4 °C. 0.05ng E. coli Spike-in DNA was added before releasing CUT&RUN fragments at 37°C for 10 min. The CUT&RUN enriched DNA is purified from the supernatant.  Libraries were prepared with a NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs) and cleaned-up with AMPureXP.  OTHER: CUT&RUN

value: pre-cDC1 progenitor

tag: chip or cut&run antibody

value: Rabbit anti-BATF3 antibody


title: F1_pre-cDC2_2

value: pre-cDC2 progenitor


title: 32het_pre-cDC2_2


title: Bulge WT P56 G6

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56G6


title: HPSI0114ikolf2-clone1_WT [WT_neg_TAN2457A19]

description: 10x Genomics


title: Bulge WT P56 G7

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56G7


title: KO_118

value: Stria vascularis  cells

value: Cochlear stria vascularis


title: Csf2 ΔCD4 (CW026)

city: New York

first: Charlotte

middle: Remy

last: Wayne

state: NY

address: 650 W 168th Street, BB310

department: Neurology

institute: Columbia University Irving Medical Center

description: single-cell RNA sequencing

data_processing:
cellranger-5.0.1
Assembly: mm10-2020-A
Supplementary files format and content: Unfiltered feature-barcode matrix

extract_protocol:
Miltenyi neural dissociation kit (P) used to dissociate the tissue into a single cell suspension. Following myelin removal, samples were stained with CD31 FITC, CD11b PE-Cy7, DRAQ5 and propidium iodide, and live nucleated CD31+ or CD11b+ cells were collected by FACS for single-cell RNA sequencing
10x Genomics Chromium 3’ v3 chemistry

value: Olfactory bulb

value: Csf2 fl/fl CD4-CreERT2

value: GAS inoculation, 4'OH-Tamoxifen


title: Bulge WT P56 G5

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56G5

value: Bulge stem cells

value: WT

value: Dorsal skin


title: KO_116


title: KO_115


title: Csf2 fl/fl (CW025)

description: single-cell RNA sequencing

value: Csf2 fl/fl


title: HPSI0114ikolf2-clone1_WT_DAPT [WT_DAPT_TAN2457A22]

description: 10x Genomics


title: Bulge WT P56 G9

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56G9

value: Postnatal day 56


title: Bulge WT P56 G4

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56G4


title: HPSI0114ikolf2-clone1, WT, DMSO [48h_DMSO_R3]

value: human induced pluripotent cells

value: DMSO

tag: differentiation stage

value: Day 24 neuronal cultures


title: PBS (CW023)

description: single-cell RNA sequencing

extract_protocol:
Miltenyi neural dissociation kit (P) used to dissociate the tissue into a single cell suspension. Following myelin removal, samples were stained with DRAQ5 and propidium iodide, and live nucleated cells were collected by FACS for single-cell RNA sequencing
10x Genomics Chromium 3’ v3 chemistry

tag: strain

value: PBS inoculation


title: Bulge WT P56 G3

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56G3


title: KO_117


title: HPSI0114ikolf2-clone1, WT [48h_WT_R1]

value: day 24


title: GAS (CW024)

description: single-cell RNA sequencing

value: GAS inoculation


title: KO_114


title: HPSI0114ikolf2-clone1_WT [WT_neg_TAN2457A20]

description: 10x Genomics


title: KO_113


title: 32het_pre-cDC1_2

value: pre-cDC1 progenitor

value: Rabbit anti-BATF3 antibody


title: HPSI0114ikolf2-clone1, WT [48h_WT_R2]


title: HPSI0114ikolf2-clone1, WT, DMSO [48h_DMSO_R2]


title: KO_112

value: Stria vascularis  cells

value: Cochlear stria vascularis


title: Csf2 fl/fl (CW021)

description: single-cell RNA sequencing

value: Olfactory bulb


title: HPSI0114ikolf2-clone1, WT [48h_WT_R3]


title: HPSI0114ikolf2-clone1, WT, DMSO [48h_DMSO_R1]


title: WT_111


title: GAS (NALT) (CW020)

description: single-cell RNA sequencing

source_name: Nasal associate lymphoid tissue and olfactory epithelium

extract_protocol:
Miltenyi neural dissociation kit (P) used to dissociate the tissue into a single cell suspension. Samples were stained with CD11b PE-Cy7, DRAQ5 and propidium iodide, and live CD11b+ cells were collected by FACS for single-cell RNA sequencing
10x Genomics Chromium 3’ v3 chemistry


title: Bulge WT P56 F12

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56F12

extract_protocol:
RNA libraries were prepared for sequencing using standard Illumina protocols
Smart-seq2


title: HPSI0114ikolf2-clone1, WT, BRM014 [48h_BRM014_R3]

extract_protocol:
Rneasy Micro Kit (Qiagenn 74004)
KAPA mRNA polyA HyperPrep Kit (Illumina, KR1352)


title: HPSI0114ikolf2-clone1, WT, BRM014 [48h_BRM014_R2]


title: Bulge WT P56 G2

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56G2


title: Csf2 ΔCD4 (CW022)

description: single-cell RNA sequencing

value: Csf2 fl/fl CD4-CreERT2

value: GAS inoculation, 4'OH-Tamoxifen


title: RORγt (CW018)

description: single-cell RNA sequencing

value: ROR{gamma}t-/-


title: WT_110


title: HPSI0114ikolf2-clone1, WT [WT_H3K27ac_R3]

description:
H3K27ac.consensus_peaks.bed.gz
H3K27ac.consensus_peaks.featureCounts.txt.gz

value: WT

tag: chip antibody

value: H3K27ac:Abcam ab4729


title: IL-17A mAb (CW016)

description: single-cell RNA sequencing

value: GAS inoculation, α-IL-17A mAb


title: HPSI0114ikolf2-clone1, WT, BRM014 [48h_BRM014_R1]

value: human induced pluripotent cells


title: KO_108


title: KO_107


title: IL-17A mAb (CW017)

description: single-cell RNA sequencing


title: WT_109


title: Bulge WT P56 F8

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56F8

value: Bulge stem cells

value: Dorsal skin

value: Postnatal day 56


title: Bulge WT P56 G1

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56G1


title: Bulge WT P56 F7

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56F7


title: Isotype mAb (CW015)

description: single-cell RNA sequencing

value: GAS inoculation, Isotype control mAb


title: KO_106


title: HPSI0114ikolf2-clone1, WT [WT_H3K27ac_R1]

value: day 24

value: Day 24 neuronal cultures


title: Bulge WT P56 F11

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56F11


title: PBS (CW014)

description: single-cell RNA sequencing

value: PBS inoculation


title: PBS (NALT) (CW019)

description: single-cell RNA sequencing

value: Nasal associate lymphoid tissue and olfactory epithelium


title: Bulge WT P56 F5

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56F5


title: RORγt (CW013)

description: single-cell RNA sequencing

value: GAS inoculation


title: WT_104

value: Stria vascularis  cells

value: Cochlear stria vascularis


title: Bulge WT P56 F9

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56F9


title: HPSI0114ikolf2-clone1, WT [WT_H3K27ac_Input_R2]

value: INPUT


title: Bulge WT P56 F4

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56F4


title: IL-17A mAb (CW012)

description: single-cell RNA sequencing

value: Olfactory bulb


title: Bulge WT P56 F3

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56F3

value: WT


title: HPSI0114ikolf2-clone1, WT [WT_H3K27ac_Input_R1]


title: WT_103


title: HPSI0114ikolf2-clone1, WT [WT_H3K27ac_R2]

value: H3K27ac:Abcam ab4729


title: HPSI0114ikolf2-clone1, WT, DMSO [DMSO_ASCL1_R3]

description:
ASCL1.consensus_peaks.bed.gz
ASCL1.consensus_peaks.featureCounts.txt.gz

value: DMSO

value: ASCL1:Abcam ab74065


title: KO_105


title: Isotype mAb (CW011)

description: single-cell RNA sequencing


title: Bulge WT P56 F2

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56F2

value: Bulge stem cells


title: Bulge WT P56 F1

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56F1

value: Dorsal skin


title: HPSI0114ikolf2-clone1, WT, DMSO [DMSO_ASCL1_R2]

value: human induced pluripotent cells


title: WT_102


title: Bulge WT P56 F10

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56F10

value: Postnatal day 56


title: RORγt (CW010)

description: single-cell RNA sequencing

value: ROR{gamma}t-/-


title: HPSI0114ikolf2-clone1, WT, DMSO [DMSO_ASCL1_R1]

value: day 24

value: Day 24 neuronal cultures


title: KO_100


title: GAS (CW009)

description: single-cell RNA sequencing


title: Bulge WT P56 E12

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56E12


title: WT_099


title: GAS (CW008)

description: single-cell RNA sequencing


title: HPSI0114ikolf2-clone1, WT [WT_H3K27ac_Input_R3]


title: HPSI0114ikolf2-clone1, WT, DMSO [DMSO_ASCL1_Input_R3]


title: GAS (NALT) (CW007)

description: single-cell RNA sequencing

extract_protocol:
Miltenyi neural dissociation kit (P) used to dissociate the tissue into a single cell suspension. Samples were stained with DRAQ5 and propidium iodide, and live nucleated cells were collected by FACS for single-cell RNA sequencing
10x Genomics Chromium 3’ v3 chemistry

value: Nasal associate lymphoid tissue and olfactory epithelium


title: HPSI0114ikolf2-clone1, WT, DMSO [DMSO_ASCL1_Input_R2]

extract_protocol: KAPA Hyper Prep Kit (KapaBiosystems, KR0961)


title: WT_098


title: Bulge WT P56 E10

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56E10


title: KO_101


title: WT_097


title: Bulge WT P56 E9

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56E9


title: KO_096


title: HPSI0114ikolf2-clone1, WT, DMSO [DMSO_ASCL1_Input_R1]


title: GAS (CW005)

description: single-cell RNA sequencing

data_processing:
cellranger-4.0.0
Assembly: mm10-2020-A
Supplementary files format and content: Unfiltered feature-barcode matrix

value: GAS inoculation


title: PBS (NALT) (CW006)

description: single-cell RNA sequencing

value: PBS inoculation


title: Bulge WT P56 E8

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56E8


title: PBS (CW004)

description: single-cell RNA sequencing


title: KO_095

value: Stria vascularis  cells

value: Cochlear stria vascularis


title: HPSI0114ikolf2-clone1, WT, BRM014 [BRM_ASCL1_R1]


title: Microglia_24h_GMCSF_2

description:
bulk RNA sequencing
DESeq2_kallisto_ControlvsGM-CSF_CW100_CW101_CW102_vs_CW109_CW110_CW111-DEG_list.csv

data_processing:
RTA (Illumina) for base calling
bcl2fastq2 (v2.19) for converting FASTQ, adaptor trimming
kallisto (v0.44.0)
DESeq2 for differential expression
pseudoalignment to a kallisto index from mouse transcriptomes GRCm38
Assembly: GRCm38
Supplementary files format and content: csv files of differential expression between control and cytokine-treated conditions

source_name: forebrains

extract_protocol:
TRIzol RNA extraction
TruSeq Stranded mRNA kit (Illumina)

value: forebrains

value: Primary microglia

value: Granulocyte-macrophage colony-stimulating factor (100 ng/mL) for 24 hours


title: HPSI0114ikolf2-clone1, WT, BRM014 [BRM_ASCL1_R2]

value: WT


title: Microglia_24h_GMCSF_3


title: Bulge WT P56 E11

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56E11

data_processing:
Pair-end RNA-seq reads were aligned using STAR_2.4.2 with parameters ‘–outFilterMismatchNmax10–outFilterMismatchNoverReadLmax 0.1–outFilter-MultimapNmax 10’ to the reference genome GRCm38/mm10. We used STAR to then convert to transcriptome-based mapping with gene annotation Gencode v.M8. Gene expression was measured using RESM/1.2.25 with expression values normalized into TPM.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include TPM values for each sample


title: Bulge WT P56 E7

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56E7


title: Bulge WT P56 E6

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56E6


title: WT_093

extract_protocol:
After euthanasia by CO2, the temporal bones were removed and placed into DPBS. The temporal bone was removed and opened under a dissecting microscope to access the cochlear membranous labyrinth. Once the cochlea was accessible, the stria vascularis tissue was extracted from the temporal bone and incubated for 5min at 37°C with collagenase from clostridium histolyticum solution at a working concentration of 0.3mg/500µl. The cell dissociation was completed by gently pipetting up and down. The disrupted stria vascularis tissues were placed under an inverted microscope equipped with 20x and 40x objectives and two 3D micromanipulators, each driving a pulled-glass micropipette attached to a nitrogen gas-powered Pico-Injector to control aspiration pressure. The dissociated cells were examined under the inverted microscope and were aspirated into the first pulled-glass micropipette in a slow and controlled manner then washed in fresh DPBS to remove residual collagenase solution and debris.
Nextera XT DNA sample preparation kits, including Tn5 enzymes for tagmentation, were used together with Nextera XT index kits for multiplexing. Tagmentation and amplification of adaptor-ligated fragments were carried out using half-volume reactions. For tagmentation, the input DNA was 0.125 ng. The number of amplification cycles for adaptor-ligated fragments was increased to 14. After the adaptor-ligated single-cell cDNA libraries were purified, single-cell cDNA libraries were run on the Agilent 2100 Bioanalyzer high-sensitivity DNA chips and combined in equimolar concentrations based on index balance. The concentration of pools was measured with Qubit dsDNA HS Assay Kit and Qubit 2.0 Fluorometer.


title: HPSI0114ikolf2-clone1, WT, BRM014 [BRM_ASCL1_Input_R3]

value: INPUT


title: Microglia_24h_GMCSF_1


title: HPSI0114ikolf2-clone1, WT, BRM014 [BRM_ASCL1_Input_R2]


title: Bulge WT P56 E4

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56E4

value: Bulge stem cells


title: WT_092


title: Bulge WT P56 E5

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56E5

value: Dorsal skin


title: WT_091


title: HPSI0114ikolf2-clone1, WT, BRM014 [BRM_ASCL1_Input_R1]

value: human induced pluripotent cells


title: Microglia_24h_IL17a_3

description:
bulk RNA sequencing
DESeq2_kallisto_ControlvsIL17A_CW100_CW101_CW102_vs_CW106_CW107_CW108-DEG_list.csv

value: Interleukin 17 (100 ng/mL) for 24 hours


title: Bulge WT P56 E3

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56E3

value: Postnatal day 56


title: HPSI0114ikolf2-clone1, WT, BRM014 [BRM_ASCL1_R3]

value: day 24

value: ASCL1:Abcam ab74065


title: Microglia_24h_IL17a_1


title: HPSI0114ikolf2-clone1, WT [ASCL1_D20_Input_R3]

value: day 20

value: Day 20 neural progenitors


title: Microglia_24h_IL17a_2


title: Bulge WT P56 E2

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56E2


title: KO_090


title: WT_088


title: Bulge WT P56 E1

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56E1


title: KO_094


title: WT_089


title: Bulge WT P56 D12

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56D12


title: WT_087


title: HPSI0114ikolf2-clone1, WT [ASCL1_D20_ChIP_R3]

description:
day20_ASCL1.consensus_peaks.bed.gz
day20_ASCL1.consensus_peaks.featureCounts.txt.gz


title: Bulge WT P56 D11

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56D11


title: Microglia_24h_IFNg_1

description:
bulk RNA sequencing
DESeq2_kallisto_ControlvsIFNg_CW100_CW101_CW102_vs_CW103_CW104_CW105-DEG_list.csv

value: Interferon gamma (100 ng/mL) for 24 hours


title: HPSI0114ikolf2-clone1, WT [ASCL1_D20_Input_R1]


title: Bulge WT P56 D10

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56D10


title: HPSI0114ikolf2-clone1, WT [ASCL1_D20_ChIP_R2]


title: HPSI0114ikolf2-clone1, WT [ASCL1_D20_ChIP_R1]


title: Bulge WT P56 D9

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56D9


title: Microglia_24h_Vehicle_2

description: bulk RNA sequencing

value: No treatment


title: KO_085

value: Stria vascularis  cells

value: Cochlear stria vascularis


title: HPSI0114ikolf2-clone1, WT [ASCL1_D20_Input_R2]


title: WT_084


title: Microglia_24h_IFNg_3

value: forebrains

value: Primary microglia


title: HPSI0114ikolf2-clone1, WT [WT_PM21132_R3]

description:
consensus_peaks.mLb.clN.bed.gz
consensus_peaks.mLb.clN.featureCounts.txt.gz

extract_protocol: NEBNext HiFi 2X PCR Master Mix (New England BioLabs, M0541S)

value: WT

value: Day 24 neuronal cultures


title: WT_083


title: HPSI0114ikolf2-clone1, WT [WT_PM21132_R2]


title: Bulge WT P56 D8

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56D8

value: Bulge stem cells


title: Microglia_24h_Vehicle_1

description: bulk RNA sequencing


title: WT_082


title: HPSI0114ikolf2-clone1, WT [WT_PM21132_R1]


title: KPC1 PDAC tumors treated with Vehicle [V3]

first: Marcus

last: Ruscetti

address: 364 Plantation Street, LRB-613, LRB-613

department: MCCB

institute: Umass Chan Medical School

data_processing:
150-bp Paired-end reads were aligned to the mouse reference genome GRCm38.p6 (Ensembl, version 101) using STAR (version2.5.3a) (Dobin et al., 2013) with the following option setting: --outFilterMultimapNmax --outFilterScoreMinOverLread  0.15 --outFilterMatchNminOverLread  0.15  --alignSJoverhangMin 8  --twopassMode Basic  --alignSJDBoverhangMin 1  --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.1  --seedSearchStartLmax 50 --seedSearchStartLmaxOverLread 0.15 --alignIntronMin 20  --alignIntronMax 1000000  --alignMatesGapMax 1000000  --outFilterType BySJout --limitSjdbInsertNsj  2000000. A gene-by-sample count matrix was generated using featureCounts (subread version 1.6.2) (Liao et al., 2014) with the following option settings: -p  -d 25 -D 1000 -s 0  -F GTF -g gene_id -t exon. All downstream statistical analyses were done using the R (version 4.1.0) programming language (Ihaka and Gentleman, 1996). Briefly, entries of genes with extremely low expression were first removed from the gene-by-sample count matrix. Differential gene analysis was performed using DESeq2 (version 1.32.0) (Love et al., 2014) in consideration of surrogate variables for hidden variations, which were identified using svaseq  (sva version3.40.0)(Leek, 2014). Genes with absolute values of log2 (fold change) greater than one and p-values less than 0.05, which were corrected for multiple testing using the Benjamini-Hochberg procedure (Benjamini and Hochberg, 1995), were considered as significantly differentially expressed genes (DEGs).
Assembly: GRCm38.p6
Supplementary files format and content: A .txt file containing a gene-by-sample raw count matrix with Ensembl gene ID as row and sample name as column.

source_name: Pancreas

growth_protocol: To generate PDAC tumors, 5x104 KrasG12D/+;Trp53R172H/wt (KPCmut) PDAC cells expressing luciferase and GFP (LUC-GFP) were transplanted into the pancreas of 8-10 week old C57BL/6 female mice. Mice were monitored for tumor development by ultrasound on a VEVO3100 system before being randomized into various study cohorts.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen)
RNA library is formed by polyA capture, RNA fragmentation by hydrolysis,  reverse transcription, end-repair, adapter ligation, amplification and size-selectioni by following the instructions of TruSeq RNA Library Prep Kit v2 low sample protocol

treatment_protocol: Mice were treated with vehicle or trametinib (1 mg/kg body weight) and palbociclib (100 mg/kg body weight) (T/P) per os for 4 consecutive days followed by 3 days off treatment, and/or GCV (50 mg/kg body weight) by daily IP injection.

value: Pancreas

value: PDAC

value: KRASG12D;P53 R172H

value: Vehicle


title: KPC1 PDAC tumors treated with Vehicle [V4]


title: Microglia_24h_IFNg_2


title: Bulge WT P56 D6

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56D6

value: Dorsal skin

value: Postnatal day 56


title: HPSI0114ikolf2-clone1, WT, DMSO [DMSO_PM21132_R3]

value: human induced pluripotent cells

value: DMSO

value: day 24


title: KO_086


title: KPC1 PDAC tumors treated with Vehicle [V2]


title: Bulge WT P56 D5

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56D5


title: WT_081


title: Microglia_24h_Vehicle_3

description: bulk RNA sequencing

value: No treatment


title: KO_080

value: Stria vascularis  cells


title: HPSI0114ikolf2-clone1, WT, DMSO [DMSO_PM21132_R2]


title: KO_079

value: Cochlear stria vascularis


title: Bulge WT P56 D3

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56D3


title: Bulge WT P56 D4

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56D4


title: HPSI0114ikolf2-clone1, WT, DMSO [DMSO_PM21132_R1]


title: KPC1 PDAC tumors treated with T/P + GCV [TPGCV5]

value: T/P + GCV


title: KO_078


title: Bulge WT P56 D7

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56D7


title: KPC1 PDAC tumors treated with T/P + GCV [TPGCV4]


title: KO_077


title: Bulge WT P56 D2

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56D2


title: HPSI0114ikolf2-clone1, WT, BRM014 [BRM014_PM21132_R2]


title: Bulge WT P56 D1

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56D1


title: KPC1 PDAC tumors treated with T/P + GCV [TPGCV3]


title: HPSI0114ikolf2-clone1, WT, BRM014 [BRM014_PM21132_R1]


title: WT_076


title: Bulge WT P56 C12

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56C12


title: WT_075


title: WT_074


title: KPC1 PDAC tumors treated with T/P + GCV [TPGCV1]


title: Bulge WT P56 C11

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56C11


title: MD1353

city: New Delhi

first: Sunil

middle: Kumar

last: Saini

state: Delhi

address: Ansari Marg

department: Department of Biophysics

country: India

institute: AIIMS, New Delhi

data_processing:
All samples were processed using an mRNA-seq pipeline implemented by Novogene Co., Ltd.
Original image data file from high- throughput sequencing Illumina platform was transformed to sequenced reads (called raw reads) by CASAVA base recognition (base calling).
Raw reads were trimmed to remove reads with adaptor contamination, remove reads when uncertain nucleotides constitute more than 10 percent of either read (N > 10%) and remove reads when low quality nucleotides (base quality less than 5) constitute more than 50 percent of the read.
Quality control of reads demonstrated a Q20(%) score of > 97.5 and an error rate < 0.03% for all the samples. The trimmed reads were mapped to human genome.
STAR software was used to accomplish the mapping. Abundance of transcripts were determined as Fragments Per Kilobase of transcript sequence per Millions base pairs (FPKM)
Genome_build: Homo Sapiens(GRCh38/hg38)
Supplementary_files_format_and_content: raw counts

source_name: Gastrocnemius muscle

extract_protocol:
Muscle tissue was collected, snap-frozen in liquid nitrogen and stored at −80°C until analysis. Total RNA from calf muscle tissues was isolated using Tri Reagent (Sigma #93289)
RNA-Seq analysis was performed using Novogene in-house protocol on the Illumina NovaSeq platform (HWI-ST1276) with paired-end 150bp sequencing strategy
RNA library is formed by polyA capture and reverse transcription of cDNA.

value: calf skeletal muscle

tag: disease state

value: Non-PAD individual

tag: progression status

value: Non-PAD

value: Male

tag: race

value: White


title: L15258

value: Individual  having PAD with progression

value: PAD progression

tag: Sex


title: KPC1 PDAC tumors treated with T/P + GCV [TPGCV2]

value: Pancreas

value: PDAC

value: KRASG12D;P53 R172H


title: WT_073


title: Bulge WT P56 C10

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56C10

value: Bulge stem cells

value: WT

value: Dorsal skin

value: Postnatal day 56


title: KPC1 PDAC tumors treated with T/P [TP5]

value: T/P


title: Bulge WT P56 C9

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56C9


title: Bulge WT P56 C8

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56C8


title: KPC1 PDAC tumors treated with T/P [TP4]


title: KPC1 PDAC tumors treated with Vehicle [V1]

value: Vehicle


title: WT_071

value: Stria vascularis  cells

value: Cochlear stria vascularis


title: KPC1 PDAC tumors treated with T/P [TP3]


title: WT_072


title: MD1369

value: calf skeletal muscle

value: Non-PAD individual

value: Black


title: Bulge WT P56 C6

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56C6


title: KO_053


title: KPC1 PDAC tumors treated with T/P [TP2]


title: Bulge WT P56 C5

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56C5


title: P317691

value: Male


title: KPC1 PDAC tumors treated with T/P [TP1]


title: WT_052


title: P286974

value: Individual  having PAD with no progression

value: PAD no progression


title: Bulge WT P56 C4

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56C4


title: R34342

value: Individual  having PAD with progression

value: PAD progression


title: T14805

description: Only R2 file is available for this sample.

value: Non-PAD


title: Bulge WT P56 C3

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56C3

value: Bulge stem cells


title: WT_050


title: KPC1 PDAC tumors treated with GCV [GCV5]

value: Pancreas

value: PDAC

value: KRASG12D;P53 R172H

value: GCV


title: WT_051


title: KPC1 PDAC tumors treated with GCV [GCV4]


title: R25672


title: Bulge WT P56 C2

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56C2

value: WT

value: Dorsal skin

value: Postnatal day 56


title: P286737

value: calf skeletal muscle

value: White


title: Bulge WT P56 C1

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56C1


title: Bulge WT P56 F6

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56F6


title: R47078


title: KPC1 PDAC tumors treated with GCV [GCV3]


title: Bulge WT P56 B12

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56B12


title: WT_049

value: Stria vascularis  cells

value: Cochlear stria vascularis


title: KPC1 PDAC tumors treated with GCV [GCV1]


title: WT_047


title: WT_048


title: Bulge WT P56 B11

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56B11


title: R23755

value: Female


title: KPC1 PDAC tumor cells treated with T/P in vitro [KPC1 TP4]

description: KPC1 TP4

data_processing:
Paired-end reads were aligned to the mouse reference genome GRCm38 (Ensembl, version 101) using bwa mem (version 0.7.17) (Li and Durbin, 2009) after quality assurance with FastQC (version 0.11.5) (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Alignment files in the SAM format were first sorted by coordinates and converted into the BAM format using SAMtools (version 1.9) (Li et al., 2009). Subsequently, PCR duplicates were removed from the BAM files using MarkDuplicates command of the Picard tools (version 2.9.0) (https://broadinstitute.github.io/picard/). The resulting BAM files were name sorted using SAMtools again. Peaks per condition were called using Genrich (version 0.6) (https://github.com/jsh58/Genrich) with name-sorted, de-duplicated BAM files of all biological replicates for a given condition as input and a q-value cutoff of 0.05. Given that H3K27me3 modification are widespread across inactive gene regions, peaks with sizes less than 1 kb were filtered out. Consensus peaks-by-sample count matrix were determined using DiffBind (version 3.6.1) (Ross-Innes et al., 2012). Differential peak analysis was conducted using DEseq2 (version 1.32.0) (Love et al., 2014) with hidden variations adjusted for using svaseq sva version3.40.0) (Leek, 2014). Peaks with absolute values of log2 (shrunken fold change) greater than one and p-values less than 0.05, which were corrected for multiple testing using the Benjamini-Hochberg procedure (Benjamini and Hochberg, 1995), were considered as significantly differential peaks.
Assembly: GRCm38.p6
Supplementary files format and content: .bigwig files containing the genome-wide read coverage per sample
Supplementary files format and content: .narrowPeak files containing peaks of size greater than 1 kb called by Genrich with a q-value cutoff of 0.05
Supplementary files format and content: .txt file containing a consensus peak-by-sample count matrix, with peak ID (chromosome:peakStart:peakEnd) as rownames and sample names as column names.
Library strategy: CUT&Tag sequencing for H3K27me3

source_name: pancreas

extract_protocol:
CUT&Tag was performed largely as described in Kaya-Okur et.al. (Nature Protocols, 2020). FACS sorted GFP+ tumor cells from transplanted PDAC tumors or trypsinized cells in culture were counted and 100,000 cells were washed and resuspended in wash buffer (20 mM HEPES pH 7.5; 150 mM NaCl; 0.5 mM Spermidine; 1× Protease inhibitor cocktail) and used for CUT&Tag. 10 µL of activated Concanavalin A coated magnetic beads (Polysciences) were added per sample and incubated at room temperature for 15 min. Bead-bound cells were resuspended in 100 µL Dig-wash Buffer (20 mM HEPES pH 7.5; 150 mM NaCl; 0.5 mM Spermidine; 0.05% Digitonin; 1× Protease inhibitor cocktail) containing 2 mM EDTA and 1ul of H3K27me3 antibody (ThermoFisher, MA5-11198). The mixture was incubated overnight at 4 °C for antibodies to bind. After pulling beads to the side of the tube using a magnetic rack and removal of unbound primary antibody, beads were resuspended in 100ul Dig-wash Buffer containing 1ul of Guinea Pig anti-Rabbit antibody (Antibodies-Online ABIN101961) and incubated for 30 mins at RT. Cells were washed 3 times with Dig-wash and then incubated with a 1:50 dilution of pA-Tn5 adapter complex in Dig-med (0.05% Digitonin, 20 mM HEPES, pH 7.5, 300 mM NaCl, 0.5 mM Spermidine, 1X Protease inhibitor cocktail) at RT for 1 hr. Cells were washed thrice in Dig-med Buffer and then resuspended in 300 µL Dig-med Buffer containing 10 mM MgCl2 and incubated at 37 °C for 1 h to activate tagmentation. To stop tagmentation, 10 µL of 0.5 M EDTA, 3 µL of 10% SDS and 1 µL of 20 mg/mL Proteinase K was added to each tube, which were incubated at 55 °C for 1 hour. DNA was extracted by performing one phenol:chloroform extraction followed by ethanol precipitation. The DNA pellet was resuspended in 22 µL of 10 mM Tris pH 8.
CUT&Tag libraries were amplified by mixing 21 µL of tagmented DNA with 2µL each of (10 µM) barcoded i5 and i7 primers, using a different combination for each sample. 25 µL NEBNext HiFi 2× PCR Master mix (NEB) was added, and PCR was performed using the following cycling conditions: 72 °C for 5 min (gap filling); 98 °C for 30 s; 17 cycles of 98 °C for 10 s and 63 °C for 30 s; final extension at 72 °C for 1 min and holding at 4 °C. 1.1× volumes of Ampure XP beads (Beckman Coulter) were incubated with libraries for 10 min room temperature to clean up the PCR reaction. Bead bound DNA was purified by washing twice with 80% ethanol and eluting in 20 µL 10 mM Tris pH 8.0.

value: pancreas

value: T/P

tag: library type

value: CUT&Tag sequencing for H3K27me3


title: WT_046


title: Bulge WT P56 B10

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56B10


title: KPC1 PDAC tumor cells treated with T/P in vitro [KPC1 TP2]

description: KPC1 TP2


title: R29063

value: Individual  having PAD with no progression

value: PAD no progression


title: WT_045


title: Bulge WT P56 B9

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56B9

value: Bulge stem cells


title: KPC1 PDAC tumor cells treated with T/P in vitro [KPC1 TP1]

description: KPC1 TP1

value: PDAC


title: KPC1 PDAC tumor cells treated with vehicle in vitro [KPC1 V4]

description: KPC1 V4

value: KRASG12D;P53 R172H

value: Vehicle


title: Bulge WT P56 B8

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56B8

value: WT


title: MD1335

value: Non-PAD individual

value: Non-PAD


title: WT_043


title: MD1150

value: calf skeletal muscle

value: Black


title: Bulge WT P56 B7

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56B7

value: Dorsal skin

value: Postnatal day 56


title: KPC1 PDAC tumors treated with GCV [GCV2]

value: Pancreas

value: GCV


title: P345288

value: Female


title: L12464

value: Individual  having PAD with progression

value: PAD progression


title: KPC1 PDAC tumor cells transplanted into pancreas (PIP) treated with T/P [PIP TP5]

description: PIP TP5

value: pancreas

value: T/P

value: CUT&Tag sequencing for H3K27me3


title: KPC1 PDAC tumor cells transplanted into pancreas (PIP) treated with T/P [PIP TP4]

description: PIP TP4

value: PDAC

value: KRASG12D;P53 R172H


title: L10522

value: Individual  having PAD with no progression

value: PAD no progression


title: WT_041

value: Stria vascularis  cells

value: Cochlear stria vascularis


title: Bulge WT P56 B5

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56B5

value: Bulge stem cells

value: WT


title: WT_040


title: Bulge WT P56 B4

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56B4

value: Dorsal skin

value: Postnatal day 56


title: KPC1 PDAC tumor cells transplanted into pancreas (PIP) treated with T/P [PIP TP3]

description: PIP TP3


title: WT_044


title: MD1245

description: Only R1 file is available for this sample.

value: calf skeletal muscle

value: Non-PAD individual

value: Non-PAD

value: Black


title: R75233

value: Individual  having PAD with progression

value: PAD progression

value: Female


title: Bulge WT P56 B6

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56B6


title: WT_038


title: KPC1 PDAC tumor cells transplanted into pancreas (PIP) treated with T/P [PIP TP1]

description: PIP TP1

value: pancreas

value: PDAC

value: T/P

value: CUT&Tag sequencing for H3K27me3


title: KPC1 PDAC tumor cells transplanted into pancreas (PIP) treated with vehicle [PIP V5]

description: PIP V5

value: KRASG12D;P53 R172H

value: Vehicle


title: KPC1 PDAC tumor cells treated with vehicle in vitro [KPC1 V1]

description: KPC1 V1


title: Bulge WT P56 B3

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56B3

value: Bulge stem cells


title: KPC1 PDAC tumor cells transplanted into pancreas (PIP) treated with vehicle [PIP V3]

description: PIP V3


title: WT_042

value: Stria vascularis  cells

value: Cochlear stria vascularis


title: Bulge WT P56 B1

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56B1

value: WT

value: Dorsal skin

value: Postnatal day 56


title: WT_036


title: WT_037


title: KPC1 PDAC tumor cells transplanted into pancreas (PIP) treated with vehicle [PIP V2]

description: PIP V2


title: WT_035


title: Bulge WT P56 A11

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56A11


title: WT_034


title: Bulge WT P56 A10

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56A10


title: WT_033


title: Bulge WT P56 A9

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56A9


title: Bulge WT P56 A8

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56A8


title: WT_032


title: 32het_pre-cDC2

data_processing:
The adaptor sequences were removed by Trimmomatic program: java -jar trimmomatic-0.39.jar PE -threads 30 -phred33 samplename_R1.fastq.gz samplename_R2.fastq.gz -baseout samplename.fastq.gz ILLUMINACLIP:Truseq3.PE.fa:2:15:4:4:true LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:25
The trimmed reads were aligned and mapped to the mouse reference genome (GRCm38/mm10) by Bowtie2 software version 2.2.5: bowtie2 -p 30 --dovetail --phred33 -x mm10 -1 samplename_1P.fastq.gz -2 samplename_2P.fastq.gz > samplename.sam
Duplicated reads are discarded using 'make tag directory' of Homer software package (version 4.9) with the parameter -tbp 1: makeTagDirectory samplename.tags samplename.sam -fragLength given -tbp 1
Data were visualized with the 'makeUCSCfile' of Homer: makeUCSCfile samplename.tags -o auto -fragLength given -tbp 1 -fsize 5e7
Assembly: mm10
Supplementary files format and content: bedGraph files were generated with Homer software package using the "makeUCSCfile" command.

growth_protocol: BM cells were isolated from Irf8 +32+/- and +32/+41 compound heterozygous mice and CD3-, CD19-, B220-, CD105-, TER-119-, Ly-6G-, TCRb-, CD11b- and IL-7Ra-expressing lineage-committed cells were depleted. Pre-cDC1 and pre-cDC2 progenitors were sort purified.

extract_protocol:
1 million fresh sort purified cells were adsorbed to activated Concanavalin A (ConA) beads, permeabilized with 0.01% digitonin, and incubated with 0.5 mg rabbit-anti-BATF3 antibody overnight at 4 °C. After antibody binding, the targete-DNA complex is cleaved by the Protein A/Protein G-Micrococcal Nuclease (pAG-MNase) for 2 hours at 4 °C. 0.05ng E. coli Spike-in DNA was added before releasing CUT&RUN fragments at 37°C for 10 min. The CUT&RUN enriched DNA is purified from the supernatant.
Libraries were prepared with a NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs) and cleaned-up with AMPureXP.
OTHER: CUT&RUN

treatment_protocol: Irf8 +32+/- and +32/+41 compound heterozygous mice were injected once daily, intraperitoneally, with 15 mg recombinant Flt-3L-Ig (BE0098; Bio X Cell) for eight consecutive days to expand pre-cDC1 and pre-cDC2 progenitor cell numbers.

value: pre-cDC2 progenitor

value: Rabbit anti-BATF3 antibody


title: F1_pre-cDC1

value: pre-cDC1 progenitor


title: F1_pre-cDC2


title: WT_031

data_processing:
The sequencing reads from fastq files were aligned to the mm10 transcriptome (GRCm38) with an index built and quantified using Kallisto pseudo-aligner. Normalized estimated counts and transcripts per kilobase million (TPM) were quantified for each cell’s transcript.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files


title: Bulge WT P56 A5

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56A5


title: Bulge WT P56 B2

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56B2


title: 32het_pre-cDC1


title: Bulge WT P56 A12

description:
Bulge_stem_cells_WT_P56_genelist_TPM.txt
B WT P56A12


title: KPC1 PDAC tumor cells transplanted into pancreas (PIP) treated with vehicle [PIP V1]

description: PIP V1