title: Day8_3T3-L1

city: Tokushima-city

first: Masashi

last: Kuroda

state: Tokushima

address: 3-18-15, Kuramoto-cho

institute: Tokushima University

description: Gene expression in 3T3-L1 adipocytes 8 days after the adipogenic differentiation

hyb_protocol: 1650 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 µl containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint GE Unrestricted Microarrays (G2519F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x44K array slides (Scan Area 61x21.6 mm, Scan resolution 5 µm, Dye channel was set to Green and Green PMT was set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028282_D_F_20110531) to obtain background subtracted and spatially detrended processed signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 150 ng RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was isolated with Trizol [Quiagen] according to the manufacturer's protocol.

tag: time point

value: 8 days


title: female, p10, #1

status: Public on Apr 01 2020

type: SRA

city: Los Angeles

first: John

middle: Edward

last: van Veen

state: CA

address: 610 Charles E young Dr

department: Integrative Biology and Physiology

country: USA

institute: UCLA

library_source: transcriptomic

data_processing:
Base Calling (Illumina)
Demultiplexing (flexbar)
Genome alignment (Star)
gene level count generation (htseq-count)
Remove non protein coding genes
Genome_build: mm10
Supplementary_files_format_and_content: csv files containing gene level counts derived from unique molecular identifiers (UMIs)

molecule: total RNA

organism: Mus musculus

source_name: Ventromedial hypothalamus

extract_protocol:
Rough dissected hypothalamus was dissociated with Worthington papain dissociation kit
BD precise whole transcriptome single cell library construction
RNA-Seq (Single Cell)

tag: tissue

value: Ventromedial hypothalamus

tag: genotype

tag: Sex

value: Female

tag: age


title: Day2_3T3-L1

type: RNA

country: Japan

description: Gene expression in 3T3-L1 adipocytes just after the adipogenic differentiation

source_name: 3T3-L1 adipocytes 2 days after the adipogenic differentiation

tag: cell type

value: 2 days


title: Day20_3T3-L1

description: Gene expression in 3T3-L1 adipocytes cultured for log period of time

source_name: 3T3-L1 adipocytes 20 days after the adipogenic differentiation

value: 20 days


title: Sublingual_Fr2_rep1

city: Tokyo

first: Yue

last: Yang

state: Tokyo

institute: Tokyo medical and dental university

description: Gene expression of Sublingual mucosa CD11c-F4/80+CD206- cells

hyb_protocol: For each hybridization, 2μg of Cy3 labeled cDNA were fragmented, and hybridized at 65 °C for 17 hours to an Agilent SurePrint G3 Mouse GE v2 8x60K Microarray (Design ID: 074809).

scan_protocol: microarrays were scanned using an Agilent DNA microarray scanner.

data_processing: Intensity values of each scanned feature were quantified using Agilent feature extraction software version 11.7.1.1, which performs background subtractions. We only used features which were flagged as no errors (Detected flags) and excluded features which were not positive, not significant, not uniform, not above background, saturated, and population outliers (Compromised and Not Detected flags).

source_name: Sublingual mucosa, CD11c-F4/80+CD206-,replicate 1

label_protocol: Total RNA was amplified using Ovation Pico WTA System V2 (NuGEN Technologies, Inc.) following the manufacturer's instructions. Amplified cDNA were labeled with Cyanine 3 (Cy3) using SureTag DNA Labeling Kit (Agilent Technologies) following the manufacturer's instructions. After amplification and labeling, cDNA quantity and cyanine incorporation were determined using a Nanodrop One spectrophometer and an Agilent Bioanalyzer.

extract_protocol: Total RNA was extracted from each sample by using NucleoSpin RNA XS (Macherey-Nagel, Duren, Germany) according to the manufacturer’s instructions. RNA quantity and quality were determined using a Nanodrop One spectrophometer (Thermo Fisher Scientific Inc.).

treatment_protocol: Dorsal site of tongues from repeatedly FITC-painted mice were minced and digested in PBS with collagenase type I (400U/ml; Sigma) and DNase I (1000 U/ml, Wako) followed by incubating in a 37℃ shaker for 30 min. Fr1,Fr2 and Fr3 cells were sorted by cell sorter (MoFlo XDP, Beckman Coulter).

value: sublingual mucosa

tag: strain

value: BALB/c

tag: cell popluation


title: IRF7_3T3-L1

description: Gene expressiion in IRF7 over-expressed adipocytes

source_name: 3T3-L1 adipocytes at day 7 differentiated from precursor cells

growth_protocol: Cells were seeded

tag: infection


title: 7-058-2-3_S82

city: Lausanne

first: Gregory

last: Lefebvre

address: EPFL Scientific Parc

country: Switzerland

institute: Nestlé Institute of Health Science

data_processing:
Sequence reads are trimmed from polyA and Lexogene reference sequences using bbduk software
Sequence reads are map to reference genome using RNAStar (v2.3.0e)
Matrix of counts is ctreated from HTSeq software
Genome_build: hs_GRCh38.p2
Supplementary_files_format_and_content: Text file containing counts for each genes (rows) for each sample (columns)

organism: Homo sapiens

source_name: adipose tisue

extract_protocol: Lexogen QuantSeq - established 3' mRNA-Seq library prep protocol

tag: cid (cid1

value: baseline, cid2 :lcd, cid3 :di):CID3

tag: individual


title: 7-057-2-3_S150


title: 7-058-2-1_S152

value: baseline, cid2 :lcd, cid3 :di):CID1


title: female, p10, #2


title: 7-058-2-2_S112

value: baseline, cid2 :lcd, cid3 :di):CID2


title: male, p10, #3

value: Male


title: 7-057-2-1_S108


title: 7-056-2-3_S51


title: 7-057-2-2_S38


title: 7-056-2-2_S8


title: 7-056-2-1_S3


title: 7-055-2-1_S69


title: 7-055-2-2_S61


title: 7-055-1-1_S59


title: Wildtype Vehicle treated D14 gastric corpus

city: Houston.

first: Jason

middle: C

last: Mills

state: T

address: One Baylor Plaza

department: Gastroenterology, Medicine

institute: Baylor College of Medicine

hyb_protocol: Labelled cDNA hybridized to Affymetrix GeneChip Mouse Gene 2.0 ST Arrays according to manufacturers instructions and placed in GeneChip Hybridization Oven 620 for 18hr at 45C. Microarrays were washes and stained with Affymettrix Fluidics Station 450.

scan_protocol: Arrays were scanned with a GeneChip® Scanner 7G 3000 laser confocal slide scanner

data_processing: Microarray data data expression was process using Command Console (Affymetrix, Inc) and the raw .CEL files were analyzed using Partek Genomic Suite v7.0 (Partek Inc., St Louis, MO). Microarray CEL files were imported into Partek and normalized using RMA.

label: biotin

source_name: C57BL/6 Adult mouse injected with vehicle (saline; 14 days)

label_protocol: Total RNA was extracted and used to prepare biotinylated cDNA with Affymetrix WT plus reagent kit

growth_protocol: Mice were grown in a temperature and light controlled mouse facility; littermate controls were used when possible. Adult mice age 8-10 weeks were used.

extract_protocol: Total RNA extracted, purified by RNEasy Mini Kit, and RNA intergrity verified on Agilent Bioanalyzer

treatment_protocol: Metformin and Vehicle were administered as daily intraperitoneal injections

value: Gastric Corpus

value: WT


title: AmpkKO Metformin treated D14 gastric corpus

source_name: Atp4b-cre; Prkaa1fl/fl; Prkaa2fl/fl adult mouse injected with Metformin (300mg/kg, 14 days)

value: AmpkKO

value: mixed background generated by crossing Atp4b-cre mice (B6/FVB Background) with Prkaa1flox and prkaa2flox (B6 background)


title: Wildtype Metformin treated D14 gastric corpus

source_name: C57BL/6 Adult mouse injected with Metformin (300mg/kg, 14 days)


title: AmpkKO Vehicle treated D14 gastric corpus

source_name: Atp4b-cre; Prkaa1fl/fl; Prkaa2fl/fl adult mouse injected with vehicle (saline; 14 days)


title: 7-053-2-1_S94


title: Empty_3T3-L1

description: Gene expression in cotrol adipocytes

value: Empty-retrovirus


title: 7-052-1-3_S97


title: 7-052-1-2_S93


title: 7-052-1-2_S233


title: WT_sutured_cornea_d5

first: Shogo

last: Yamamoto

address: 4-6-1 Komaba, Megro-ku

department: Research Center for Advanced Science and Technology

institute: The University of Tokyo

description: B6 sutured cornea on day5 after the suturing

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430.2.0 Array.

scan_protocol: GeneChips Scanner 3000 (Affymetrix)

data_processing: Affymetrix GeneChip Operating Software v1.3

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA.

extract_protocol: Total RNA was extracted using RNeasy (QIAGEN) according to the manufacturer's instructions.

treatment_protocol: Eyes were enucleated from mice, and the whole cornea was separated.

value: whole cornea

tag: protocol

value: sutured

value: wild-type


title: 7-055-1-2_S72


title: WT_sutured_cornea_d7

description: B6 sutured cornea on day7 after the suturing


title: Dscr1TG_sutured_cornea_d7

description: Dscr-1 Tg sutured cornea on day7 after the suturing

value: Dscr-1 Tg


title: Shamsurgery_mouse1

city: Baltimore

first: TAKASHI

last: KAWAHARA

state: MD

address: 600 N. Wolfe Street, Marburg 148

department: Pathology

institute: The Johns Hopkins Hospital

description:
Gene expression from prostate 24 weeks after surgery
Control1

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: Normalization by Affymetrix Expression Console Software, version 1.3.1 – RMA (default settings)

label_protocol: biotin labeling using Affymetrix standard WT plus protocol

growth_protocol: C57BL/6 mice were performed vasectomy or sham surgery at the age of 16 weeks and harvested at the age of 24 weeks.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Vasectomy or sham surgery (control) were performed at the age of 16 weeks.

value: sham surgery (control)

value: lateral prostate


title: Shamsurgery_mouse2

description:
Gene expression from prostate 24 weeks after surgery
Control2


title: 7-052-1-1_S218


title: 7-051-1-1_S53


title: CTCF-ChIP-seq A2780cis cells

city: San Diego

first: Qi

last: Ma

address: 9500 Gilman Dr,

institute: UCSD

library_source: genomic

data_processing:
Reads were aligned to the hg18 human genome with bowtie2 (–very-sensitive option) and tophat. One mismatch was allowed.
Artifacts derived from clonal amplification were circumvented by considering maximal three tags from each unique genomic position as determined from the mapping data
Read counts were calculated with HOMER 3.9 considering only exonic regions of human RefSeq genes
The bedGraph and bigwig files were generated by using Homer v3.9, which the total tags are normalized to 1.00e+07.
Genome_build: hg18
Supplementary_files_format_and_content: BigWig

molecule: genomic DNA

growth_protocol: Cells  were cultured in RPMI-1640-Glutamax I (#61870-036, Life Technologies) and 10% fetal bovine serum (FBS, #FB-11, Omega Scientific) at 5% CO2 37ºC, and sub-cultured at 1:5 to 1:6 dilutions after dissociation with 0.25% trypsin. Media was changed every other day, or daily when cells reached >50-60% confluency.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10mins, and followed by glycine for 5 mins. Chromatin DNA was sheared to 200–500 bp average in size by sonication and chromatin was immunoprecipitated with antibodies. Protein G magnetic beads  were added and incubated overnight at 4°C. After washing and elution, the protein–DNA complex was reverse-crosslinked by heating at 65°C, and immunoprecipitated DNA was purified by using QIAquick Spin column.
ChIP-seq libraries were prepared using the KAPA Library Preparation Kit (KK8201)

treatment_protocol: The treatment administrated to A2780cis cells was described in the Sigma-Aldrich website as chronic exposure of the parent A27890 line to increasing concentrations of cisplatin Sigma-Aldrich (#93112517-19). Acute treatments (IC50) were administrated for 3 days, adding fresh media with drug at day 0 and after 2 days again.

tag: cell line

tag: chip antibody used for chip or oligonucletides used for chirp (chromatin isolation by rna purification)

value: Anti-CCTCF antibody Active Motif (Cat#61932; RRID:AB_2614975)


title: ApoeDscr1DKO_intact_cornea_rep2

description: intact cornea from Dscr-1-/- and ApoE-/- double null mutant mouse, biological rep2

value: intact


title: Vasectomy_mouse2

description:
Gene expression from prostate 24 weeks after surgery
Vasectomy2

value: vasectomy


title: Dscr1KO_intact_cornea_rep1

description: intact cornea from Dscr-1-/- mouse, biological rep1


title: Vasectomy_mouse1

description:
Gene expression from prostate 24 weeks after surgery
Vasectomy1


title: ApoeDscr1DKO_intact_cornea_rep1

description: intact cornea from Dscr-1-/- and ApoE-/- double null mutant mouse, biological rep1


title: 7-059-1-2_S155


title: 7-050-2-3_S78

value: baseline, cid2 :lcd, cid3 :di):CID3


title: 7-050-2-1_S173

value: baseline, cid2 :lcd, cid3 :di):CID1


title: Dscr1KO_intact_cornea_rep2

description: intact cornea from ApoE-/- mouse, biological rep2


title: 7-049-2-3_S92


title: CTCF-ChIP-seq A2780 cells


title: WT_intact_cornea_rep2

description: intact cornea from B6 mouse, biological rep2


title: ApoeKO_intact_cornea_rep2

source_name: intact cornea from ApoE-/- mouse, biological rep2

value: ApoE-/-


title: ApoeKO_intact_cornea_rep1

description: intact cornea from ApoE-/- mouse, biological rep1


title: 7-052-1-1_S106


title: WT_intact_cornea_rep1

description: intact cornea from B6 mouse, biological rep1


title: H3K27ac_A2780cis_CRISPRa_R_2

growth_protocol: Cells  were cultured in RPMI-1640-Glutamax I (#61870-036, Life Technologies) and 10% fetal bovine serum (FBS, _FB-11, Omega Scientific) at 5% CO2 37ºC, and sub-cultured at 1:5 to 1:6 dilutions after dissociation with 0.25% trypsin. Media was changed every other day, or daily when cells reached >50-60% confluency.

treatment_protocol: The treatment administrated to A2780cis cells was described in the Sigma-Aldrich website as chronic exposure of the parent A27890 line to increasing concentrations of cisplatin Sigma-Aldrich (_93112517-19). Acute treatments (IC50) were administrated for 3 days, adding fresh media with drug at day 0 and after 2 days again.

value: H3K27ac (Abcam, ab4729)


title: H3K27ac_A2780cis_CRISPRa_R_1


title: 7-049-2-2_S49

value: baseline, cid2 :lcd, cid3 :di):CID2


title: H3K27ac_A2780_CRISPRi_R_1


title: EGR1_A2780_cisplatin

value: EGR1 (Santa Cruz Biotechnology, 588, sc-110)


title: EGR1_A2780_vehicle


title: 7-048-2-2_S168


title: ISL1_A2780_cisplatin


title: 7-048-2-1_S36


title: 7-049-2-1_S155


title: 7-047-2-3_S59


title: ISL1_A2780_vehicle


title: 7-047-2-2_S122


title: 7-047-2-1_S185


title: p53_A2780_cisplatin

value: p53 (Active Motif, _39334)


title: 7-047-2-2_S26


title: 7-046-1-3_S55


title: H3K27ac_A2780cis_vehicle


title: H3K27ac_A2780cis_cisplatin


title: 7-046-1-3_S151


title: 7-045-2-3_S162


title: H3K27ac_A2780_vehicle


title: 7-048-2-3_S187


title: 7-045-2-2_S165


title: H3K4me2_A2780cis_cisplatin

value: H3K4me2 (Active Motif, 39141)


title: H3K4me2_A2780_cisplatin


title: H3K4me2_A2780cis_vehicle


title: 7-044-2-3_S25


title: H3K4me2_A2780_vehicle


title: H3K4me3_A2780_cisplatin

value: H3K4me3 (Millipore, 07-473)


title: H3K27ac_A2780_CRISPRi_R_2


title: 7-044-2-2_S173


title: H3K4me3_A2780cis_vehicle


title: 7-043-2-3_S26


title: p53_A2780_vehicle


title: 7-043-2-2_S114


title: 7-043-1-2_S109


title: 7-042-2-3_S69


title: H3K4me3_A2780_vehicle


title: H3K27ac_A2780_cisplatin


title: H3K4me3_A2780cis_cisplatin


title: 7-043-1-3_S71


title: 7-046-1-2_S113


title: U87-MG.5%hypoxia rep3

city: Chongqing

first: bao

last: liu

address: 30 Gaotanyan street

department: Institute of Medicine and Hygienic Equipment for High Altitude Region

country: China

institute: 3rd Military Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to reference gene using Bowtie2 (version 2.2.4)  and use BWA (version 0.7.10)  to reference genome hg19. Their alignment parameters change a little according different sequencing strategy：Bowtie2 parameters for PE reads: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant -p 16 -k 200; BWA parameters for PE reads: -o 1 -e 63 -i 90 -L -k 2 -l 31 -t 4 -q 10  hg19 whole genome using  Bowtie2 version 2.2.4
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated.
Identify the different expression modes of U87-MG and HEB cells response to various  hypoxia levels using STEM (short time series method) method.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Brain

extract_protocol:
Total RNA was extracted with TRIzol Reagentand quantified using a Nanodrop ND-1000 spectrophotometer.Illumina TruSeq RNA Sample Prep Kit v2 was used with 200ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HEB cells and U87-MG cells were incubated in DMEM supplemented with 10% fetal bovine serum (FBS), 2mM L-glutamine, 100U/ml penicillin and 100μg/ml streptomycin for 24h at normoxia (21% O2) and followed by 24h at normoxic or hypoxic conditions (1% O2) in hypoxic chambers (Thermo scientific) separately.

value: U87-MG cell line

value: Glioblastoma (GBM)

tag: group


title: U87-MG.5%hypoxia rep2


title: U87-MG.5%hypoxia rep1


title: U87-MG.1%hypoxia rep3


title: 7-042-2-1_S100


title: 7-040-2-3_S29


title: 7-044-2-3_S121


title: U87-MG.1%hypoxia rep2


title: 7-040-2-3_S125


title: U87-MG.1%hypoxia rep1


title: U87-MG rep3

value: tumor


title: U87-MG rep2


title: U87-MG rep1


title: HEB.5%hypoxia.rep2

value: HEB cell line

value: non-neoplastic brain cell


title: HEB.5%hypoxia.rep3


title: 7-042-2-2_S114


title: 7-040-1-2_S209


title: 7-039-2-3_S43


title: 7-039-2-3_S139


title: 7-039-2-2_S152


title: HEB.1%hypoxia.rep2


title: HEB.5%hypoxia.rep1


title: HEB.1%hypoxia.rep3


title: HEB.1%hypoxia.rep1


title: HEB rep3

value: control


title: HEB rep2


title: 7-040-2-2_S18


title: HEB rep1


title: 7-040-1-3_S126


title: 7-035-1-2_S175


title: 7-040-1-2_S63


title: 7-034-2-3_S76


title: 7-034-2-2_S121


title: 7-032-2-3_S67


title: 7-032-2-2_S19


title: 7-036-1-3_S44


title: 7-031-1-2_S142


title: 7-037-1-2_S47


title: 7-030-2-2_S133


title: PFP-Healthy-16

city: Florence

first: Giacomo

last: Bagni

address: Viale GB Morgagni 50

department: Department of Experimental and Clinical Medicine

country: Italy

institute: Università degli studi di Firenze

description:
Circulating Extracellular miRNAS expression profiling
C_PFP_41

hyb_protocol: The dried and labeled miRNA sample was resuspended in 18 ul nuclease-free water, 4.5 ul 10X GE Blocking Agent (Agilent) and 22.5 ul 2X Hi-RPM hybridization buffer (Agilent), followed by heating at 100°C for 5 minutes. Upon cooling in ice water bath for 5 mintues, the mixture was hybridized to Human miRNA Microarray based on Sanger miRbase (release 9.1). (G4471A) for 20 hours at 55°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 5 minutes at room temperature with GE Wash Buffer 1 (Agilent) and 5 minutes with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x15k Agilent- 016436 Human miRNA Microarray 1.0 G447A array  slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%)

data_processing: The scanned TIFF images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (Protocol: miRNA-v1_95_May07  Grid: 016436_D_20070426 ) to obtain background subtracted and spatially detrended Processed Signal intensities. Background-subtracted values were normalized between arrays by Quantile algorithm, included in the R package AgiMicroRna (López-Romero, P. BMC Genomics. 2011.).

source_name: Platelets-free Plasma Healthy control subject 16

label_protocol: 100 ng RNA was dephosphorylated and labeled by miRNA Complete Labeling and Hyb Kit (Agilent) according to the manufacturer's instructions.

extract_protocol: Total RNA was extracted from freshly isolated platelets-free plasma using TRIzol LS (Invitrogen S.R.L, Italy) reagent following manufacturer instructions. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) RNA samples were stored at -80°C until use.

treatment_protocol: Platelets-free plasma was obrtained from peripheral blood samples in citrate tubes via sequantial centrifugation. Plasma samples were divided in to aliquots and stored at-80°C

tag: disease state

value: Healthy control subject

value: Platelets-free Plasma


title: PFP-Healthy-13

description:
Circulating Extracellular miRNAS expression profiling
C_PFP_38

source_name: Platelets-free Plasma Healthy control subject 13


title: PFP-Healthy-14

description:
Circulating Extracellular miRNAS expression profiling
C_PFP_39

source_name: Platelets-free Plasma Healthy control subject 14


title: PFP-Healthy-18

description:
Circulating Extracellular miRNAS expression profiling
C_PFP_43

source_name: Platelets-free Plasma Healthy control subject 18


title: PFP-Healthy-17

description:
Circulating Extracellular miRNAS expression profiling
C_PFP_42

source_name: Platelets-free Plasma Healthy control subject 17


title: PFP-Healthy-12

description:
Circulating Extracellular miRNAS expression profiling
C_PFP_36

source_name: Platelets-free Plasma Healthy control subject 12


title: 7-027-2-3_S71

value: baseline, cid2 :lcd, cid3 :di):CID3


title: 7-027-2-3_S167


title: PFP-Healthy-11

description:
Circulating Extracellular miRNAS expression profiling
C_PFP_35

source_name: Platelets-free Plasma Healthy control subject 11


title: 7-025-2-3_S35


title: 7-035-1-2_S239


title: 7-059-1-1_S186

value: baseline, cid2 :lcd, cid3 :di):CID1


title: PFP-Healthy-9

description:
Circulating Extracellular miRNAS expression profiling
C_PFP_33

source_name: Platelets-free Plasma Healthy control subject 9


title: 7-036-1-2_S68


title: PFP-Healthy-10

description:
Circulating Extracellular miRNAS expression profiling
C_PFP_34

source_name: Platelets-free Plasma Healthy control subject 10


title: 7-031-1-3_S39


title: PFP-Healthy-8

description:
Circulating Extracellular miRNAS expression profiling
C_PFP_32

source_name: Platelets-free Plasma Healthy control subject 8


title: 7-025-2-2_S9

source_name: adipose tisue


title: 7-022-2-3_S182


title: PFP-Healthy-7

description:
Circulating Extracellular miRNAS expression profiling
C_PFP_31

source_name: Platelets-free Plasma Healthy control subject 7


title: PFP-Healthy-15

description:
Circulating Extracellular miRNAS expression profiling
C_PFP_40

source_name: Platelets-free Plasma Healthy control subject 15


title: 7-021-1-3_S34


title: PFP-Healthy-5

description:
Circulating Extracellular miRNAS expression profiling
C_PFP_28

source_name: Platelets-free Plasma Healthy control subject 5


title: 7-020-2-2_S139


title: 7-020-1-2_S11


title: PFP-Healthy-4

description:
Circulating Extracellular miRNAS expression profiling
C_PFP_27

source_name: Platelets-free Plasma Healthy control subject 4


title: 7-011-2-3_S86


title: 7-019-1-2_S11


title: 7-019-1-3_S68


title: PFP-Healthy-1

description:
Circulating Extracellular miRNAS expression profiling
C_PFP_24

source_name: Platelets-free Plasma Healthy control subject 1


title: 7-008-1-3_S161


title: 7-008-1-3_S65


title: PFP-Behçet-16

description:
Circulating Extracellular miRNAS expression profiling
B_PFP_23

source_name: Platelets-free Plasma Behçet's disease patient 16

value: Behçet's disease patient


title: PFP-Behçet-14

description:
Circulating Extracellular miRNAS expression profiling
B_PFP_21

source_name: Platelets-free Plasma Behçet's disease patient 14


title: PFP-Behçet-15

description:
Circulating Extracellular miRNAS expression profiling
B_PFP_22

source_name: Platelets-free Plasma Behçet's disease patient 15


title: PFP-Healthy-3

description:
Circulating Extracellular miRNAS expression profiling
C_PFP_26

source_name: Platelets-free Plasma Healthy control subject 3


title: 6-111-1-2_S44


title: 7-005-2-3_S35


title: PFP-Behçet-12

description:
Circulating Extracellular miRNAS expression profiling
B_PFP_18

source_name: Platelets-free Plasma Behçet's disease patient 12


title: 7-037-1-3_S153


title: 6-108-1-3_S224


title: 6-108-1-3_S185


title: PFP-Behçet-13

description:
Circulating Extracellular miRNAS expression profiling
B_PFP_19

source_name: Platelets-free Plasma Behçet's disease patient 13


title: PFP-Healthy-6

description:
Circulating Extracellular miRNAS expression profiling
C_PFP_30

source_name: Platelets-free Plasma Healthy control subject 6


title: PFP-Behçet-10

description:
Circulating Extracellular miRNAS expression profiling
B_PFP_16

source_name: Platelets-free Plasma Behçet's disease patient 10


title: 6-108-1-2_S28


title: PFP-Behçet-8

description:
Circulating Extracellular miRNAS expression profiling
B_PFP_14

source_name: Platelets-free Plasma Behçet's disease patient 8


title: PFP-Behçet-9

description:
Circulating Extracellular miRNAS expression profiling
B_PFP_15

source_name: Platelets-free Plasma Behçet's disease patient 9


title: 7-020-1-2_S107


title: 6-108-1-1_S56


title: PFP-Healthy-2

description:
Circulating Extracellular miRNAS expression profiling
C_PFP_25

source_name: Platelets-free Plasma Healthy control subject 2


title: PFP-Behçet-7

description:
Circulating Extracellular miRNAS expression profiling
B_PFP_11

source_name: Platelets-free Plasma Behçet's disease patient 7


title: 6-107-2-3_S50

source_name: adipose tisue


title: 6-107-2-2_S110


title: PFP-Behçet-6

description:
Circulating Extracellular miRNAS expression profiling
B_PFP_10

source_name: Platelets-free Plasma Behçet's disease patient 6


title: 6-106-2-3_S105


title: 6-107-2-1_S3


title: 6-106-2-1_S170


title: 6-105-2-2_S8


title: PFP-Behçet-5

description:
Circulating Extracellular miRNAS expression profiling
B_PFP_9

source_name: Platelets-free Plasma Behçet's disease patient 5


title: 6-106-2-1_S74


title: 6-104-2-2_S173


title: 7-037-1-2_S143


title: 6-103-1-2_S118


title: PFP-Behçet-2

description:
Circulating Extracellular miRNAS expression profiling
B_PFP_6

source_name: Platelets-free Plasma Behçet's disease patient 2


title: 6-104-2-1_S102


title: 6-103-1-1_S119


title: PFP-Behçet-3

description:
Circulating Extracellular miRNAS expression profiling
B_PFP_7

source_name: Platelets-free Plasma Behçet's disease patient 3


title: 6-102-2-1_S199


title: 6-102-2-3_S43


title: 6-102-2-1_S130


title: 6-102-2-2_S174


title: PFP-Behçet-1

description:
Circulating Extracellular miRNAS expression profiling
B_PFP_2

source_name: Platelets-free Plasma Behçet's disease patient 1


title: 6-101-2-2_S79


title: 6-101-2-1_S144


title: 6-099-2-3_S85


title: 6-101-1-1_S111


title: 6-106-2-3_S9


title: 6-099-2-3_S181


title: 6-104-2-3_S159


title: PFP-Behçet-4

description:
Circulating Extracellular miRNAS expression profiling
B_PFP_8

source_name: Platelets-free Plasma Behçet's disease patient 4


title: 6-099-2-2_S129


title: 6-099-2-1_S54


title: 6-098-1-1_S116


title: 6-096-2-1_S58


title: 6-096-2-1_S154


title: 6-098-1-2_S48


title: PFP-Behçet-11

description:
Circulating Extracellular miRNAS expression profiling
B_PFP_17

source_name: Platelets-free Plasma Behçet's disease patient 11


title: 6-093-1-1_S84


title: 6-094-2-2_S105


title: 6-093-1-2_S50


title: 6-093-1-1_S180


title: 6-092-2-1_S161


title: 6-089-1-3_S67


title: 6-089-1-2_S92


title: 6-089-1-2_S188


title: 6-089-1-1_S114


title: smSOCS3_KO_pre_3

city: Kurume

first: Hiroki

last: Aoki

state: Fukuoka

address: 67 Asahimachi

department: Cardiovascular Research Institute

institute: Kurume University

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Mouse Gene Expression Microarray 8x60K; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. The raw signal intensities of all samples were  normalized by the quantile algorithm with the Bioconductor.

source_name: smSocs3-KO without BAPN+AngII

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

growth_protocol: To achieve the smooth muscle-specific deletion of Socs3 (smSocs3-KO), we crossed mice that were homozygous for the floxed allele of Socs3 (Socs3fl/fl) and backcrossed to C57BL/6J for three generations, with SM22-Cre mice (JAX Mice, stock # 004746) that carried a Cre recombinase transgene under control of the smooth muscle SM22 promoter. Socs3fl/fl littermate mice lacking the SM22-Cre transgene served as wild type (WT) controls.

extract_protocol: The total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega) according to the manufacturer's instructions.

treatment_protocol: As a aortic dissection model, BAPN (150 mg/kg/day) and angiotensin II (AngII; 1000 ng/kg/min) were simultaneously administered to mice with (smSocs3-KO) or without (WT) SM22-Cre transgene using osmotic minipumps (Alzet model 1002). Aortic samples were obtained with or without 3 days of BAPN+AngII infusion.

value: 129S5/SvEvBrd, C57BL6 and SJL

tag: infusion

value: without BAPN+AngII

tag: gender

value: male

value: aorta


title: smSOCS3_KO_d3_2

source_name: smSocs3-KO with BAPN+AngII

value: with BAPN+AngII

tag: tissue


title: 6-087-2-2_S52

value: baseline, cid2 :lcd, cid3 :di):CID2


title: 6-087-2-3_S110


title: 6-092-2-2_S176


title: smSOCS3_KO_d3_5


title: Dscr1KO_sutured_cornea_d5

description: Dscr-1-/- sutured cornea on day5 after the suturing

value: whole cornea

value: sutured

tag: genotype


title: smSOCS3_KO_d3_3


title: smSOCS3_WT_d3_4

source_name: WT aorta with BAPN+AngII


title: 6-087-2-1_S27


title: smSOCS3_WT_d3_3


title: smSOCS3_KO_pre_4


title: smSOCS3_WT_pre_2

source_name: WT aorta without BAPN+AngII


title: 6-086-2-3_S231


title: smSOCS3_KO_pre_1


title: smSOCS3_WT_pre_3


title: smSOCS3_WT_d3_1


title: Rapamycin20160725_2

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Mouse Gene Expression Microarray 8x60K ; Agilent Technologies) according to the manufacturer's instructions.

source_name: aorta, rapamycin

tag: treatment

value: rapamycin


title: B+A+DMSO20160627_4

source_name: aorta, beta-aminopropionitrile + angiotensin II + DMSO


title: B+A+DMSO_7

value: beta-aminopropionitrile + angiotensin II + DMSO


title: smSOCS3_WT_pre_1


title: B+A+Rapamycin20160627_3

source_name: aorta, beta-aminopropionitrile + angiotensin II + rapamycin


title: B+A+Rapamycin20160711_2

value: beta-aminopropionitrile + angiotensin II + rapamycin


title: B+A+DMSO_8


title: Rapamycin20160725_3


title: Rapamycin20160718_5


title: 6-086-2-2_S82


title: 6-086-2-3_S192


title: 6-085-2-2_S141


title: 6-085-2-1_S165


title: Pre20160725_3

source_name: aorta, DMSO

value: DMSO


title: 6-083-1-2_S95


title: 6-083-1-2_S237


title: B+A+Rapamycin20160704_3


title: 6-082-2-3_S61


title: 6-083-1-2_S191


title: 6-082-2-2_S187


title: 6-082-2-1_S56


title: 6-082-2-1_S152


title: 6-082-1-2_S31


title: 6-082-1-1_S79


title: 6-082-1-1_S175


title: 6-081-2-3_S115


title: 6-087-2-1_S123


title: 6-081-1-1_S160


title: Pre20160725_2


title: 6-079-2-3_S171


title: 6-080-1-2_S190


title: Pre20160711_2


title: 6-079-2-1_S32


title: AngII_d1_KO6

source_name: aorta, MRTF-A knockout, angiotensin II

treatment_protocol: AngII was subcutaneously infused using osmotic minipumps for 24 hours.

value: MRTF-A knockout


title: AngII_d1_WT7

source_name: aorta, wild-type, angiotensin II


title: 6-077-1-2_S125

source_name: adipose tisue


title: AngII_d1_KO7


title: AngII_d1_KO1


title: AngII_d1_WT3


title: 6-081-2-1_S16


title: 6-077-1-1_S142


title: pre_KO8

source_name: aorta, MRTF-A knockout, control


title: pre_KO6


title: pre_WT4

source_name: aorta, wild-type, control


title: pre_KO4


title: 6-079-2-2_S189


title: pre_WT5


title: 6-075-2-3_S117


title: 6-075-2-2_S85


title: SAMPLE 14_microglia_ngf_24h

city: Roma

first: Ivan

last: Arisi

address: viale Regina Elena 295

department: Bioinformatics Facility

institute: European Brain Research Institute

description: mouse microglia cells from primary cultures

hyb_protocol: One-color mixes of labelled cRNA pairs were hybridized to 8x60K whole mouse genome oligonucleotide microarray (Agilent grid ID 028005), at 65°C for 17 hours using Agilent’s Gene Expression Hybridization Kit. The hybridized microarrays were disassembled at room temperature in Agilent Gene Expression Wash Buffer 1. After the disassembly, the microarrays were washed in Gene Expression Buffer 1 for one minute at room temperature, followed by washing with Gene Expression Wash Buffer 2 for one minute at 37°C. The microarrays were then treated with acetonitrile for one minute at room temperature.

scan_protocol: Post-hybridization image acquisition was accomplished using the Agilent Scanner G2564C. Data extraction from the 20 bits TIFF images was accomplished by Agilent Feature Extraction (FE)  ver 10.7 (for raw files files * 2067_*.txt  and *0302_*.txt ) or FE version 12.0 (for raw files *0281_*.txt)  software using the standard Agilent one-color gene expression extraction protocol  (GE1_107_Sep09 for FE ver 10.7 and GE1_1200_Jun14 for FE ver 12.0).

data_processing: The “gProcessedSignal” data column of the Feature Extraction *.txt output file was used, containing the median signals corrected by spatial and multiplicative detrend. Data quality filtering was performed using Microsoft Excel, discarding features with the Feature Extraction flag gIsWellAboveBG=0 in any sample, wich is a statistical method approximately equivalent to discarding features with a Signal/Noise ratio smaller than 2.0-3.0, where Signal = (median of the spot - median spot background level) and Noise is the Standard Deviation of the median spot background. Data were normalized to the 75th percentile in Log2 scale. Data were were further filtered by excluding mRNA probes with a coefficient of variation |Dev.st/Mean |>5%  in Log2 expression values between biological replicates, across all samples, to obtain a final selection 27155 transcripts. Differentially expressed genes were selected by a combination of fold change and moderated T-test thresholds by the R-Bioconductor  tool Limma (p-value<0.05; |Log2 fold-change ratio| >0.56 equivalent to 1.5 fold in linear scale).

label_protocol: For each sample 200ng of Poly A+RNA were labelled, using Cyanine 3-CTP (Agilent) in separate labelling reactions, with the Agilent Low Imput Linear Amplification Kit and purified with Qiagen’s RNeasy mini spin columns.

growth_protocol: Primary microglial cells were derived from the brains of B6129 mice  (male and famale) at postnatal day 3-4. Cells were maintained in Dulbecco's modified Eagle's medium (DMEM/F12) containing 1% penicillin/streptomycin, 1% Glutamax and 10% FBS, in 5% CO2 pH 7.4. Microglia were separated from the mixed primary glia cultures by mild shaking, were re-suspended in DMEM/F12 with 1% penicillin/streptomycin, 1% Glutamax and 10% FBS, in 5% CO2 pH 7.4 and pleated on the supply.

extract_protocol: Total RNA was extracted at 2h, 8h, 24h after NGF adding from NGF treated and untreated cells  (controls). Total RNA was extracted  using Trizol (Invitrogen) and DNAse treated by Qiagen columns. Quality and integrity of each sample was checked using the Agilent BioAnalyzer 2100 (Agilent RNA 6000 nano kit): samples with a RNA Integrity Number (RIN) index lower than 8.0 were discarded. All the experimental steps involving the labelling, hybridization and washing of the samples were done following the one-color Agilent protocol.

treatment_protocol: Primary microglia culture cells were treated with 100 ng/ml NGF for 2, 8, 24 hours. Control samples are time-matched  untreated cells.

tag: Sex

value: pooled male and female

tag: age

value: postnatal day 3-4

value: brain

value: primary microglia cells

tag: treated with

value: 100 ng/ml NGF for 24 hrs


title: SAMPLE 13_microglia_ngf_24h

tag: strain

tag: cell type


title: SAMPLE 12_microglia_ctr_24h

value: none (untreated)


title: SAMPLE 9_microglia_ctr_24h


title: AngII_d1_WT2


title: SAMPLE 11_microglia_ctr_24h


title: SAMPLE 8_microglia_ngf_8h

value: 100 ng/ml NGF for 8 hrs


title: 6-075-2-1_S188

tag: cid (cid1

value: baseline, cid2 :lcd, cid3 :di):CID1


title: SAMPLE 7_microglia_ngf_8h


title: SAMPLE 6_microglia_ctr_8h


title: SAMPLE 10_microglia_ctr_24h


title: pre_WT2

value: aorta


title: 6-074-1-2_S79

value: baseline, cid2 :lcd, cid3 :di):CID2

tag: individual


title: 6-073-1-3_S86

value: baseline, cid2 :lcd, cid3 :di):CID3


title: 6-073-1-2_S45


title: 6-074-1-1_S20


title: 6-073-1-1_S131


title: 36h_actTreg_OX40 agonist rep2

city: Paris

first: Benoit

last: Salomon

address: 8 rue de la Croix-Jarry

department: Inserm DR6

country: France

institute: BioPark

data_processing:
Quality of raw data has been evaluated with FastQC
Poor quality sequences has been trimmed or removed with Trimmomatic software to retain only good quality paired reads with following parameters : cutoff: '20' leading: '10' minlen: '50' slidingwindow: '4' trailing: '10'
Star v2.5.3a has been used to align reads on  reference genome using standard options
Quantification of gene and isoform abundances has been done with rsem 1.2.28
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files including expecting counts, TPM and FPKM

source_name: Foxp3 Treg

growth_protocol: Purified Foxp3/GFP+ Tregs were stimulated for 18h or 36h with coated anti-CD3 and anti-CD28 mAbs in 96-well falt plates in RPMI 1640; glutamax and 10% fetal bovine serum with mouse IL-2 (10 ng/ml, Peprotech)

extract_protocol:
RNA was extracted using the NucleoSpin RNA XS kit from Machery-Nagel
SMART-Seq v4 Ultra Low Input RNA kit TAKARA

treatment_protocol: Tregs were costimulated with TNC-sc(mu)TNF80 (STAR2, 12 ng/ml) or anti-4-1BB mAb (10 µg/ml, 3H3, BioXCell) or TL1A (12 ng/ml) or OX40L (100 ng/ml, AdipoGen).

tag: knock-in

value: Treg

tag: agonist

tag: time point

value: 2.5 month-old


title: 6-072-2-1_S61


title: 36h_actTreg_OX40 agonist rep3


title: 36h_actTreg_OX40 agonist rep1


title: 36h_actTreg_DR3 agonist rep3


title: Perinatal cardiomyocyte maturation reference

first: Suraj

last: Kannan

address: 720 Rutland Avenue Ross 954

department: Cardiology

institute: Johns Hopkins University

data_processing:
For the RNA-seq data generated in this manuscript, we mapped raw reads to the mouse genome GRCm38 from Ensembl concatenated with ERCC spike-in references. We mapped reads using zUMIs (version > 2.4) with default settings and barcodes provided as a list. By default, zUMIs uses STAR in a two-pass mapping format, and featureCounts through Rsubread to tabulate counts and UMI tables.
R1:Cell Barcode+UMI
R2:i7 Tag
R3: cDNA Read
Genome_build: GRCm38_r92
Supplementary_files_format_and_content: For each study, we provide both the 3’ reads as well as the collapsed UMIs (output from zUMIs). We provide with both ensembl genes (as output by zUMIs) as well as with gene symbol. In addition, we provide a metadata table for each cell.

source_name: Cardiomyocytes

growth_protocol: To generate mice for our reference dataset, we crossed aMHC-cre (Jackson Laboratory, Stock No. 011038) with mTmG (Jackson Laboratory, Stock No. 007676) mice. Both mice have C57BL/6J congenic background. All animals were maintained compliant to protocols by the Johns Hopkins Animal Care and Use Committee.

extract_protocol:
For isolation of CMs from e14-p4 timepoints, we used the neonatal cardiomyocyte isolation kit from Miltenyi Biotec in conjunction with the gentleMACS Dissociator. For later timepoints, Langendorff perfusion was performed based on established literature protocols using collagenase and protease. We used a horizontal (i.e. non-hanging) Langendorff apparatus with a chamber filled with perfusion buffer. To perform isolation, we first performed isofluorane anaesthesia on non-heparinized mice. Mice were observed until clearly anaesthetized and unresponsive to toe pinch, and subsequently euthanized by cervical dislocation. The heart was then rapidly excised from the chest and cannulated to the Langendorff apparatus. We flowed digestion buffer for 9 minutes at 1.5 mL/min. Subsequently, the ventricle was excised and minced. We filtered isolated cells through a 100 µM screen to eliminate large tissue chunks, spun down at 800 RPM for 1 minute (Eppendorf centrifuge 5702), and resuspended cells in 10 mL Tyrode’s buffer. All cells were isolated using LP-FACS, as outlined in Kannan et al. (Circ Res 2019).
We performed sequencing using the mcSCRB-seq protocol. The protocol has been described at protocols.io at dx.doi.org/10.17504/protocols.io.p9kdr4w. Pooled libraries were sequenced on one mid-output lanes of the Illumina NextSeq500 with 16 base pair barcode read, 8 base pair i7 index read, and 66 base pair cDNA read design.

tag: strain/background

value: aMHC-cre x mTmG

value: Cardiomyocyte


title: 6-072-2-1_S157


title: 36h_actTreg_DR3 agonist rep2


title: 6-071-1-3_S160


title: 36h_actTreg_DR3 agonist rep1


title: 36h_actTreg_4-1BB agonist rep2


title: 6-070-1-1_S14


title: 36h_actTreg_TNFR2 agonist rep3


title: 6-068-2-2_S52


title: 6-070-1-2_S149


title: 6-068-2-1_S50


title: SAMPLE 5_microglia_ctr_8h


title: SAMPLE 3_microglia_ngf_2h

value: 100 ng/ml NGF for 2 hrs


title: SAMPLE 4_microglia_ngf_2h


title: 36h_actTreg_4-1BB agonist rep3


title: SAMPLE 2_microglia_ctr_2h


title: 6-067-2-1_S53


title: 6-065-2-3_S161


title: 36h_actTreg_TNFR2 agonist rep2


title: 36h_actTreg_TNFR2 agonist rep1


title: 6-067-2-2_S80


title: 6-073-1-1_S207


title: 36h_actTreg_4-1BB agonist rep1


title: 6-065-2-2_S23


title: 36h_actTreg_ctrl rep3


title: SAMPLE 1_microglia_ctr_2h


title: 36h_actTreg_ctrl rep2


title: 6-064-2-3_S108


title: 6-064-2-1_S102


title: 18h_actTreg_OX40 agonist rep2


title: 6-065-2-1_S187


title: 36h_actTreg_ctrl rep1


title: 6-063-1-2_S52


title: 6-063-1-2_S148


title: 6-063-1-1_S26


title: 6-061-1-3_S36


title: 18h_actTreg_OX40 agonist rep1


title: 18h_actTreg_DR3 agonist rep3


title: 18h_actTreg_DR3 agonist rep1


title: 18h_actTreg_4-1BB agonist rep3


title: 6-061-1-2_S20


title: 18h_actTreg_4-1BB agonist rep1


title: 6-061-1-1_S226


title: 6-060-1-3_S141


title: 18h_actTreg_ctrl rep3


title: 18h_actTreg_TNFR2 agonist rep3


title: 6-061-1-1_S90


title: 6-060-1-2_S150


title: 18h_actTreg_ctrl rep2


title: 6-059-1-3_S63


title: 18h_actTreg_ctrl rep1


title: resting Treg rep3


title: 6-059-1-2_S117


title: 6-060-1-1_S10


title: 6-059-1-1_S38


title: resting Treg rep2


title: 6-061-1-3_S223


title: 6-057-2-3_S34


title: 6-057-2-2_S177


title: 6-061-1-2_S116


title: 18h_actTreg_TNFR2 agonist rep2


title: NFI-dKO_Input_Rep2

city: New York

first: Hanseul

state: NY

address: 1230 York Avenue

institute: Rockefeller University

description: Input DNA

data_processing:
Alignment: Sequence reads were obtained and mapped to the mouse genome (mm10, build 38) using the Bowtie program (Version 0.1.2.7). Unique reads mapped to a single genomic location (allowing two mismatches) were kept for peak identification.
Peak detection was performed with the software MACS (Version 1.4.2) with input as controls.
tdf files were created using IGVtools with 25bp windows with no extension to reads.
Genome_build: mm10
Supplementary_files_format_and_content: tdf files; enrichment values in 25bp windows

source_name: Mouse back skin

extract_protocol:
Mouse hair follicle stem cells were purified from Sox9-CreER;NFIBfl/fl;NFIXfl/fl and WT littermate mice at P70 2nd telogen.
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibodies (H3K4me1, Abcam, #ab8895; H3K27ac, Abcam, #ab4729; H3K27me3, Millipore, #07-449).  Libraries were prepared according to a ChIPmentation protocol (Schmidl et. al., Nature Methods, 2015 ). Briefly, immunoprecitiated nucleosomes on beads were tagmented by Tagmentation enzyme from the Nextera DNA Sample Prep Kit (Illumina). Follwoing tagmentation, the beads were washed and DNA elution, reerse cross-linking, DNA purification, and PCR amplification were performed. During PCR amplification, each sample were barcoded by different adaptor primers for illumina sequencing. Sequencing libraries were pooled and sequenced on the NextSeq 500 instrument with 37/38 cycles paried end high-output mode.

value: male

value: back skin

tag: sorting markers

value: DAPI (neg), Sca-1 (neg), integrina6  (pos), CD34 (pos), YFP (pos)

tag: chip antibody

value: none; input


title: 6-057-2-1_S128


title: resting Treg rep1


title: WT_K27ac_Rep2

description: Chromatin IP against H3K27ac

value: DAPI (neg), Sca-1 (neg), integrina6  (pos), CD34 (pos)

value: H3K27ac (Abcam, #ab4729)


title: 6-056-2-2_S40


title: 6-056-2-1_S153


title: 6-056-1-3_S94


title: WT_K4me1_Rep2

description: Chromatin IP against H3K4me1

value: H3K4me1 (Abcam, #ab8895)


title: WT_Input_Rep2

description: Input DNA


title: 6-056-1-3_S240


title: ntregWT1

city: Esch-sur-Alzette

first: Rashi

last: Halder

address: 7, Avenue des Hauts-Fourneaux

country: Luxembourg

institute: Luxembourg Center for Systems Biomedicine

data_processing:
Illumina bcl2fastq (v 2.18.0.12)
Sequenced reads were mapped using Star (v 2.5.2b) and gene counts were calculated using featureCounts finction of subread package (v 1.5.2)
Genome_build: mm10
Supplementary_files_format_and_content: gene count file generated from featureCounts

source_name: sorted T-regulatory cells from mouse

extract_protocol:
RNA was isolated using a NucleoSpin RNA Kit according to the manufacturer's protocol (Macherey-Nagel, #740 955 250)
RNA sequencing libraries were prepared using TruSeq Stranded mRNA Library Prep Kit (Cat. no. RS-122-2101)
Stranded mRNA-Seq

value: 8 weeks

value: sorted T-regulatory cells

value: WT


title: ntregWT3


title: ntregWT2


title: 6-056-1-1_S33

value: baseline, cid2 :lcd, cid3 :di):CID1


title: ntregKO4

value: Gclc mutant


title: 6-055-2-3_S83

value: baseline, cid2 :lcd, cid3 :di):CID3


title: NFI-dKO_K27ac_Rep2

description: Chromatin IP against H3K27ac


title: NFI-dKO_K4me1_Rep2

description: Chromatin IP against H3K4me1


title: 6-056-2-3_S123


title: 6-054-2-3_S189


title: itregWT3

source_name: induced Tregs from mouse

value: induced Tregs


title: ntregKO2


title: 6-054-2-1_S71


title: itregWT2


title: 6-055-2-1_S81


title: ntregKO1


title: 6-053-2-1_S109


title: itregsKO4


title: 6-053-2-3_S35


title: itregsKO2


title: 6-048-2-2_S21

value: baseline, cid2 :lcd, cid3 :di):CID2


title: itregsKO1


title: 6-056-1-2_S32


title: 6-048-2-2_S202


title: male, p10, #2

source_name: Ventromedial hypothalamus

value: Ventromedial hypothalamus

value: Male


title: female, p10, #3

value: Female


title: male, p10, #1


title: 6-047-1-1_S137


title: 6-053-2-2_S121


title: itregWT1


title: 6-046-2-3_S187


title: 6-046-2-1_S67


title: 6-046-2-1_S163


title: 6-045-1-1_S153


title: NOD-ICAM-2

city: Muenster

first: Michael

last: Heming

address: Albert-Schweitzer-Campus 1, Bldg A1

department: Department of Neurology with Institute of Translational Neurology

country: Germany

institute: University Hospital Muenster

description:
mouse_barcodes.tsv
mouse_features.tsv
mouse_matrix.mtx.gz
8

data_processing:
Raw bcl files were de-multiplexed using the cellranger mkfastq pipeline (cellranger v3.0.2)
Subsequent reads alignments and transcript counting was done individually for each sample using the cellranger count pipeline with standard parameters
The cellranger aggr pipeline was employed, to generate a single cell-barcode matrix containing all the samples without normalization
Genome_build: mm10, Rattus_norvegicus.Rnor_6.0.dna.toplevel
Supplementary_files_format_and_content: Standard cellranger output format

source_name: PNS

extract_protocol:
Sciatic nerves and the brachial nerve plexus were dissected from intracardial PBS perfused the mice. Nerves were first mechanically dissociated. Cells were then isolated by combining enzymatic digestion (Trypsin, Collagenase II, Hyaluronidase and Pronase) with myelin depletion and flow cytometry-based cell sorting (Calcein-AM, Zombi NIR, DAPI). Rats sciatic nerves were isolated and enzymatically digested in Collagenase/Dispase and DNase I. Cells were centrifuged on a 30%/70% Percoll gradient and the mononuclear interphase was collected. No sorting was performed.
Single cell suspensions were loaded onto the Chromium Single Cell Controller using the Chromium Single Cell 3' Library & Gel Bead Kit v2 (both from 10X Genomics) chemistry following the manufacturer’s instructions. Sample processing and library preparation was performed according to manufacturer instructions using AMPure XP beads (Beckman Coulter). Sequencing was either carried out on a local Illumina Nextseq 500 using the High-Out 75 cycle kit with a 26-8-0-57 read setup or commercially (Microanaly, China) on a NovaSeq 6000 using the 300 cycle kit with paired end 150 read setup. All the samples were sequenced with a sequencing depth >50,000 reads per cell
ScRNA-seq

tag: genetic background


title: 6-046-2-2_S115


title: NOD-ctrl2-2

description:
mouse_barcodes.tsv
mouse_features.tsv
mouse_matrix.mtx.gz
6

value: NOD control


title: NOD-ICAM-1

description:
mouse_barcodes.tsv
mouse_features.tsv
mouse_matrix.mtx.gz
7


title: NOD-ICAM-3

description:
mouse_barcodes.tsv
mouse_features.tsv
mouse_matrix.mtx.gz
9


title: 6-044-2-1_S48


title: 6-044-2-2_S193


title: NOD-ctrl1

description:
mouse_barcodes.tsv
mouse_features.tsv
mouse_matrix.mtx.gz
4


title: NOD-ctrl2-1

description:
mouse_barcodes.tsv
mouse_features.tsv
mouse_matrix.mtx.gz
5


title: 6-044-1-2_S32


title: Tet2KO RP RNA-seq 2

city: St Louis

first: Grant

middle: A

last: Challen

state: MO

address: 660 Euclid Avenue

department: Medicine

institute: Washington University School of Medicine

data_processing:
For RNA-seq reads were aligned to the Ensembl release 76 top-level assembly with STAR version 2.0.4
For RNA-seq gene counts were derived with  htseq-count v0.8.0
RNA-seq quantification, normalization, and differnetial gene expression as performed using EdgeR release 3.9
Supplementary_files_format_and_content: RNA-Seq: tab-delimited file with raw gene counts
For ATAC-seq reads were aligned to mm10 using BWA mem.
Duplicate reads were filtered out with Picard tools.
Addiciontal ATAC-seq read filtering and then peak calling was performed with deepTools and MACS2 via SnakePipes.
Differential chromatin accessibility was determined using reads filterd for short fragment lengths, a mean of 150bp. These bam files were downsampled to contain the same number of reads. A consensus peak set was determined by intersecting all narrowPeak files. The number of reads per peak for each sample was calculated with Subread featureCounts. EdgeR was used to perform differential read density of each consensus peak.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files for ATAC_seq and a table of counts for exon transcripts for RNA-seq

source_name: Restricted Progenitor

extract_protocol:
For RNA-seq, HSCs (Lin-, cKit+, Sca1+, CD150+, CD48-) and Rps (Lin-, cKit+, Sca1+, C-150- CD48+) were sorted from a pooled sample of 2 male and 2 female 8-week old mice HSCs were purified from three or four biological replicates (composed of pooled WBM from three male and three female mice) of either Vav-CRE: Dnmt3a+/+; Tet2+/+ or Vav-CRE:Dnmt3afl/fl or + or Vav-CRE:Tet2fl/fl  mice.  Total RNA was isolated from the samples using the NucleoSpin RNA XS kit
For RNA-seq, the SMARTer Ultra Low RNA kit (Clontech) was used to prepare the libraries from 3-5ng of total RNA.
For ATAC-seq, HSCs (Lin-, cKit+, Sca1+, CD150+, CD48-),MPPs ( Lin-, cKit+, Sca1+, C-150-, CD48-) and Rps (Lin-, cKit+, Sca1+, C-1-0+, CD+8-) were sorted from a pooled sample of 2 male and 2 female 8-week old mice HSCs were purified from three or four biological replicates (composed of pooled WBM from three male and three female mice) of either Vav-CRE: Dnmt3a+/+; Tet2+/+ or Vav-CRE:Dnmt3afl/fl or + or Vav-CRE:Tet2fl/fl  mice.
For ATAC-Seq, NEBNext High-Fidelity 2X PCR Master MIX (NEB M0541L) along with Nextera custom primers were used for library amplification of the ATAC DNA(5-7 cycles of PCR as determined by qPCR).  Libraries were again purified with Ampure XP beads and run on an Illumina Hiseq 3000 (PE2X150) or NovaSeq(PE2x150).

tag: cre-driver

value: Vav

value: Restricted Progenitor


title: Tet2KO RP RNA-seq 4

tag: genotype


title: Tet2KO RP RNA-seq 3


title: 6-047-1-2_S192


title: 6-044-1-1_S47


title: 6-043-2-3_S55


title: 6-047-1-3_S40


title: 6-043-2-1_S41


title: Tet2KO RP RNA-seq 1


title: Control RP RNA-seq 4

value: Wild-type


title: 6-042-1-3_S162


title: Pooled P10_P15_P20_normal_toned

city: Boston

first: Brian

last: Kalish

state: MA

address: 220 Longwood Ave

department: Neurobiology

institute: Boston Children's Hospital

description:
Single nucleus RNA-seq.
Single cell isolation by InDrops.

data_processing:
Transcripts were processed according to the pipeline in Macosko et al. (2015). Briefly, this pipeline was used to build a custom transcriptome from Ensembl GRCm38 genome and GRCm38.84 annotation using Bowtie 1.1.1, after filtering the annotation gtf file (gencode.v17.annotation.gtf filtered for feature_type="gene", gene_type="protein_coding" and gene_status="KNOWN"). Read quality control and mapping against this transcriptome were performed. Unique molecular identifiers (UMIs) were used to link sequence reads back to individual captured molecules. All steps of the pipeline were run using default parameters unless explicitly stated.
Genome_build: GRCm38
Supplementary_files_format_and_content: *tsv: Tab-separated text files include transcript counts.

source_name: Auditory cortex

extract_protocol:
Frozen tissue was thawed in 500 uL Buffer HB (0.25M sucrose, 25mM KCl, 5mM MgCl2, 20mM Tricine-KOH pH 7.8, 0.15mM spermine tetrahydrochloride, 0.5mM spermidine trihydrochloride, 1mM DTT). The tissue was transferred to a 2 mL dounce. 500ul 5% IGEPAL CA-630 (Sigma) and 1 mL HB were added to the tissue and the tissue was homogenized with a tight pestle 10-15 times. The sample was transferred to a 15 mL tube and total solution brought to 9 mL with HB. In a Corex tube, 1 mL 30% iodixanol layered on top of 1 mL 40% iodixanol. The 9 mL sample was layered on top of the iodixanol cushion. The sample was spun at 10,000 xg for 18 minutes. 1 mL of sample at the 30-40% iodixanol interface was collected. After counting nuclear with a hemocytometer, the sample was diluted to 100,000 nuclear/mL with 30% iodixanol (with RNAsin) and subjected to single nuclear droplet encapsulation with InDrops.
Individual cells were captured and barcoded using the inDrops platform as previously described. Briefly, single-cell suspensions were fed into a microfluidic device that packaged the cells with barcoded hydrogel microspheres and reverse transcriptase/lysis reagents. After cell encapsulation, primers were photo-released by UV exposure. Two libraries of approximately 3000 cells each were collected for each sample. Indexed libraries were pooled and sequenced on a NextSeq 500 (Illumina).

tag: developmental stage

value: mixed sample (non-demultiplexed)

tag: tissue

value: Auditory cortex

tag: treatment


title: Control RP RNA-seq 2

tag: age


title: 6-043-2-2_S34


title: 6-042-1-1_S156


title: 6-042-1-2_S178


title: Control RP RNA-seq 1

tag: strain


title: 6-040-2-2_S124


title: Control RP RNA-seq 3

tag: cell type


title: 6-040-2-1_S39

tag: cid (cid1


title: Tet2KO HSC RNA-seq 4

source_name: Hematopoietic Stem Cell

value: Hematopoietic stem cell


title: Tet2KO HSC RNA-seq 3


title: 6-039-2-3_S27

tag: individual


title: Tet2KO HSC RNA-seq 1


title: 6-040-2-3_S135


title: Dnmt3aKO HSC RNA-seq 4


title: Dnmt3aKO HSC RNA-seq 2


title: Dnmt3aKO HSC RNA-seq 1


title: 6-035-1-2_S22


title: 6-035-1-1_S122


title: Control HSC RNA-seq 3


title: Control HSC RNA-seq 2


title: 6-032-2-2_S96


title: 6-032-2-3_S91


title: 6-032-2-1_S64


title: NFI-dKO_K27me3

description: Chromatin IP against H3K27me3.

data_processing:
Alignment: Sequence reads were obtained and mapped to the mouse genome (mm10, build 38) using the Bowtie program (Version 0.1.2.7). Unique reads mapped to a single genomic location (allowing two mismatches) were kept for peak identification.
Peak detection was performed with the software MACS (Version 1.4.2) with input as controls.
tdf files were created using IGVtools with 25bp windows with no extension to reads.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: tdf files; enrichment values in 25bp windows.

extract_protocol:
Mouse hair follicle stem cells were purified from Sox9-CreER;NFIBfl/fl;NFIXfl/fl and WT littermate mice at P70 2nd telogen.
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibodies (H3K4me1, Abcam, #ab8895; H3K27ac, Abcam, #ab4729; H3K27me3, Millipore, #07-449). Libraries were prepared according to a ChIPmentation protocol (Schmidl et. al., Nature Methods, 2015 ). Briefly, immunoprecipitated nucleosomes on beads were tagmented by Tagmentation enzyme from the Nextera DNA Sample Prep Kit (Illumina). Following tagmentation, the beads were washed and DNA elution, reverse cross-linking, DNA purification, and PCR amplification were performed. During PCR amplification, each sample were barcoded by different adaptor primers for Illumina sequencing. Sequencing libraries were pooled and sequenced on the NextSeq 500 instrument with 37/38 cycles paired end high-output mode.

tag: Sex

value: Hair follicle stem cells

value: DAPI (neg), Sca-1 (neg), integrina6 (pos), CD34 (pos), YFP (pos)


title: 6-031-2-3_S123

data_processing:
Sequence reads are trimmed from polyA and Lexogene reference sequences using bbduk software
Sequence reads are map to reference genome using RNAStar (v2.3.0e)
Matrix of counts is ctreated from HTSeq software
Genome_build: hs_GRCh38.p2
Supplementary_files_format_and_content: Text file containing counts for each genes (rows) for each sample (columns)

extract_protocol: Lexogen QuantSeq - established 3' mRNA-Seq library prep protocol


title: Tet2KO HSC RNA-seq 2


title: 6-039-2-2_S130


title: 6-031-2-1_S40

value: baseline, cid2 :lcd, cid3 :di):CID1


title: 6-027-2-2_S113


title: 6-031-2-2_S34


title: NFI-dKO_K27ac

description: Chromatin IP against H3K27ac.


title: WT_K27me3

description: Chromatin IP against H3K27me3.

value: DAPI (neg), Sca-1 (neg), integrina6 (pos), CD34 (pos)


title: NFI-dKO_K4me1

description: Chromatin IP against H3K4me1.


title: 6-027-2-1_S13


title: NFI-dKO_Input

description: Input DNA


title: WT_K27ac

description: Chromatin IP against H3K27ac.


title: 6-035-1-3_S190

value: baseline, cid2 :lcd, cid3 :di):CID3


title: 6-025-2-3_S28


title: Control HSC RNA-seq 4


title: 6-025-2-2_S1


title: WT_K4me1

description: Chromatin IP against H3K4me1.


title: 6-025-2-1_S57


title: dKO_2_H9

description: processed data file: NFI_scRNA_TPM.txt

data_processing:
Alignment: Sequence reads were obtained and mapped to the mouse genome (mm10) using the Bowtie2 program (version 2.2.9).
The expression values of each gene were quantified as transcript per million (TPM) using RSEM (v1.2.30).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: NFI_scRNA_TPM.txt: Tab-delimited text file includes TPM values for each Sample.

extract_protocol:
Single bulge hair follicle stem cells were FACS-purified, collected into 96 well plates containing lysis buffer and stored in -80oC.
Single cells were lyzed by incubating at 72oC for 3 min. Reverse transcription reaction and whole transcriptome amplification were performed according to Smart-seq2 protocol. The amplified cDNA libraries were purified by Ampure XP beads (Beckman Coulter), and tagmentation reaction was performed by Illumina Nextera XT DNA Library Prep Kit. The libraries were pooled and sequenced on Illumina Nextseq 500 with high-output 38/37cycles paired-end mode.

value: DAPI (neg), Sca-1 (neg), integrina6 (pos), YFP (pos)


title: dKO_2_H8

description: processed data file: NFI_scRNA_TPM.txt


title: 6-020-2-3_S97


title: 6-020-2-2_S151

value: baseline, cid2 :lcd, cid3 :di):CID2


title: dKO_2_H7

description: processed data file: NFI_scRNA_TPM.txt


title: dKO_2_H5

description: processed data file: NFI_scRNA_TPM.txt


title: dKO_2_H6

description: processed data file: NFI_scRNA_TPM.txt


title: 6-016-1-2_S49


title: dKO_2_H3

description: processed data file: NFI_scRNA_TPM.txt


title: dKO_2_H2

description: processed data file: NFI_scRNA_TPM.txt


title: dKO_2_H1

description: processed data file: NFI_scRNA_TPM.txt


title: 6-014-1-1_S148


title: 6-014-1-2_S27


title: 6-009-1-2_S7


title: 6-013-2-2_S1


title: WT_Input

description: Input DNA


title: dKO_2_G8

description: processed data file: NFI_scRNA_TPM.txt


title: 6-009-1-1_S4


title: dKO_2_G7

description: processed data file: NFI_scRNA_TPM.txt


title: dKO_2_H12

description: processed data file: NFI_scRNA_TPM.txt


title: 6-008-1-2_S38


title: 6-016-1-1_S144


title: dKO_2_H4

description: processed data file: NFI_scRNA_TPM.txt


title: 6-008-1-1_S16


title: 6-002-1-2_S25


title: 6-020-2-1_S180


title: dKO_2_G4

description: processed data file: NFI_scRNA_TPM.txt


title: dKO_2_G5

description: processed data file: NFI_scRNA_TPM.txt


title: 6-002-1-1_S8


title: dKO_2_G2

description: processed data file: NFI_scRNA_TPM.txt


title: dKO_2_G6

description: processed data file: NFI_scRNA_TPM.txt


title: dKO_2_G3

description: processed data file: NFI_scRNA_TPM.txt


title: 6-009-1-3_S30


title: dKO_2_H10

description: processed data file: NFI_scRNA_TPM.txt


title: dKO_2_G12

description: processed data file: NFI_scRNA_TPM.txt


title: dKO_2_G10

description: processed data file: NFI_scRNA_TPM.txt


title: 5-099-2-3_S229


title: 5-100-1-1_S18


title: 18h_actTreg_TNFR2 agonist rep1

tag: knock-in

value: Treg

tag: agonist

value: 2.5 month-old


title: 5-099-2-1_S78


title: dKO_2_F8

description: processed data file: NFI_scRNA_TPM.txt

value: Male


title: 5-100-1-2_S164


title: dKO_2_G1

description: processed data file: NFI_scRNA_TPM.txt


title: 5-097-1-1_S7


title: 18h_actTreg_4-1BB agonist rep2

tag: time point


title: dKO_2_F7

description: processed data file: NFI_scRNA_TPM.txt

tag: sorting markers


title: 5-097-2-1_S99


title: dKO_2_F6

description: processed data file: NFI_scRNA_TPM.txt


title: dKO_2_G11

description: processed data file: NFI_scRNA_TPM.txt


title: 5-097-2-1_S204


title: 5-097-2-2_S175


title: 5-100-1-3_S174


title: 5-096-2-3_S8


title: 5-096-2-3_S104


title: dKO_2_F1

description: processed data file: NFI_scRNA_TPM.txt


title: dKO_2_F3

description: processed data file: NFI_scRNA_TPM.txt


title: dKO_2_F12

description: processed data file: NFI_scRNA_TPM.txt


title: dKO_2_F5

description: processed data file: NFI_scRNA_TPM.txt


title: dKO_2_F2

description: processed data file: NFI_scRNA_TPM.txt


title: 5-096-2-2_S67


title: 5-096-2-1_S136


title: 5-095-2-3_S64


title: dKO_2_F11

description: processed data file: NFI_scRNA_TPM.txt


title: dKO_2_F10

description: processed data file: NFI_scRNA_TPM.txt


title: 5-095-2-2_S18


title: 5-095-2-1_S95


title: dKO_2_E6

description: processed data file: NFI_scRNA_TPM.txt


title: 5-094-2-3_S55


title: dKO_2_E5

description: processed data file: NFI_scRNA_TPM.txt


title: dKO_2_E4

description: processed data file: NFI_scRNA_TPM.txt


title: dKO_2_E12

description: processed data file: NFI_scRNA_TPM.txt


title: dKO_2_E2

description: processed data file: NFI_scRNA_TPM.txt


title: 5-094-2-1_S73


title: dKO_2_E3

description: processed data file: NFI_scRNA_TPM.txt


title: 5-094-1-2_S71


title: 5-094-1-3_S70


title: 5-094-1-1_S107


title: dKO_2_E11

description: processed data file: NFI_scRNA_TPM.txt


title: dKO_2_E10

description: processed data file: NFI_scRNA_TPM.txt


title: 5-092-1-3_S27


title: 5-093-1-1_S98


title: 5-093-2-1_S28


title: 5-092-1-1_S111


title: dKO_2_D7

description: processed data file: NFI_scRNA_TPM.txt


title: dKO_2_D8

description: processed data file: NFI_scRNA_TPM.txt


title: 5-092-1-2_S89


title: dKO_2_E8

description: processed data file: NFI_scRNA_TPM.txt


title: 5-095-2-3_S160


title: dKO_2_D5

description: processed data file: NFI_scRNA_TPM.txt


title: dKO_2_D3

description: processed data file: NFI_scRNA_TPM.txt


title: 5-091-1-3_S184


title: 5-091-1-2_S146


title: 5-094-2-2_S139


title: dKO_2_D2

description: processed data file: NFI_scRNA_TPM.txt


title: 5-091-1-1_S104


title: dKO_2_D1

description: processed data file: NFI_scRNA_TPM.txt


title: 5-090-2-1_S128


title: dKO_2_D12

description: processed data file: NFI_scRNA_TPM.txt


title: 5-089-1-1_S10


title: dKO_2_D11

description: processed data file: NFI_scRNA_TPM.txt


title: 5-088-2-1_S185


title: dKO_2_D10

description: processed data file: NFI_scRNA_TPM.txt


title: 5-088-2-3_S2


title: dKO_2_D6

description: processed data file: NFI_scRNA_TPM.txt


title: dKO_2_C9

description: processed data file: NFI_scRNA_TPM.txt


title: dKO_2_C8

description: processed data file: NFI_scRNA_TPM.txt


title: 5-087-2-2_S140


title: dKO_2_C6

description: processed data file: NFI_scRNA_TPM.txt


title: dKO_2_C7

description: processed data file: NFI_scRNA_TPM.txt


title: 5-086-2-3_S35


title: 5-087-2-1_S149


title: dKO_2_C5

description: processed data file: NFI_scRNA_TPM.txt


title: dKO_2_C4

description: processed data file: NFI_scRNA_TPM.txt


title: 5-086-2-2_S14


title: 5-085-1-2_S15


title: 5-086-2-1_S181


title: dKO_2_C3

description: processed data file: NFI_scRNA_TPM.txt


title: dKO_2_C2

description: processed data file: NFI_scRNA_TPM.txt


title: dKO_2_C1

description: processed data file: NFI_scRNA_TPM.txt


title: 5-084-1-3_S216


title: 5-085-1-1_S135


title: dKO_2_C12

description: processed data file: NFI_scRNA_TPM.txt


title: 5-084-1-3_S129


title: dKO_2_C11

description: processed data file: NFI_scRNA_TPM.txt


title: 5-084-1-2_S141


title: 5-084-1-1_S42


title: 5-088-1-1_S139


title: dKO_2_B4

description: processed data file: NFI_scRNA_TPM.txt

value: DAPI (neg), Sca-1 (pos), integrina6 (pos), YFP (pos)


title: 5-084-1-1_S138


title: dKO_2_B8

description: processed data file: NFI_scRNA_TPM.txt


title: 5-083-2-2_S166


title: dKO_2_B5

description: processed data file: NFI_scRNA_TPM.txt


title: dKO_2_B3

description: processed data file: NFI_scRNA_TPM.txt


title: dKO_2_B2

description: processed data file: NFI_scRNA_TPM.txt


title: 5-082-1-3_S72


title: dKO_2_B12

description: processed data file: NFI_scRNA_TPM.txt


title: dKO_2_B1

description: processed data file: NFI_scRNA_TPM.txt


title: 5-082-1-2_S166


title: 5-081-2-1_S96


title: dKO_2_B10

description: processed data file: NFI_scRNA_TPM.txt


title: dKO_2_B11

description: processed data file: NFI_scRNA_TPM.txt


title: 5-081-2-1_S192


title: 5-080-1-3_S123


title: 5-082-1-1_S176


title: 5-080-1-1_S20


title: dKO_2_A8

description: processed data file: NFI_scRNA_TPM.txt


title: dKO_2_A7

description: processed data file: NFI_scRNA_TPM.txt


title: dKO_2_A6

description: processed data file: NFI_scRNA_TPM.txt


title: dKO_2_A5

description: processed data file: NFI_scRNA_TPM.txt


title: 5-079-2-3_S111


title: dKO_2_A4

description: processed data file: NFI_scRNA_TPM.txt


title: 18h_actTreg_DR3 agonist rep2


title: dKO_2_A2

description: processed data file: NFI_scRNA_TPM.txt


title: 5-079-2-1_S159


title: 5-078-1-1_S140


title: 5-083-2-1_S113


title: 5-077-2-1_S149


title: 5-077-1-2_S59


title: dKO_2_A11

description: processed data file: NFI_scRNA_TPM.txt


title: 5-077-2-2_S19


title: dKO_2_A12

description: processed data file: NFI_scRNA_TPM.txt


title: dKO_2_A1

description: processed data file: NFI_scRNA_TPM.txt


title: dKO_2_A10

description: processed data file: NFI_scRNA_TPM.txt


title: 5-078-1-2_S115


title: 5-077-1-2_S155


title: 5-076-2-3_S48


title: dKO_1_H9

description: processed data file: NFI_scRNA_TPM.txt


title: 5-076-2-1_S93


title: 5-074-2-3_S64


title: 5-077-1-1_S173


title: dKO_1_H7

description: processed data file: NFI_scRNA_TPM.txt


title: 5-076-2-2_S5


title: 5-074-2-2_S132


title: dKO_1_H2

description: processed data file: NFI_scRNA_TPM.txt


title: dKO_1_H6

description: processed data file: NFI_scRNA_TPM.txt


title: dKO_1_H3

description: processed data file: NFI_scRNA_TPM.txt


title: dKO_1_H5

description: processed data file: NFI_scRNA_TPM.txt


title: 5-074-2-1_S183


title: 5-073-2-3_S29


title: dKO_1_H12

description: processed data file: NFI_scRNA_TPM.txt


title: dKO_1_H1

description: processed data file: NFI_scRNA_TPM.txt


title: dKO_1_G9

description: processed data file: NFI_scRNA_TPM.txt


title: 5-073-1-3_S117


title: dKO_1_H11

description: processed data file: NFI_scRNA_TPM.txt


title: dKO_1_G8

description: processed data file: NFI_scRNA_TPM.txt


title: 5-072-2-3_S31


title: 5-072-2-3_S244


title: 5-073-1-1_S133


title: dKO_1_G7

description: processed data file: NFI_scRNA_TPM.txt


title: 5-072-2-1_S17


title: dKO_1_G5

description: processed data file: NFI_scRNA_TPM.txt


title: 5-071-1-2_S2


title: dKO_1_G3

description: processed data file: NFI_scRNA_TPM.txt


title: dKO_1_G1

description: processed data file: NFI_scRNA_TPM.txt


title: dKO_1_G2

description: processed data file: NFI_scRNA_TPM.txt


title: 5-070-1-1_S73


title: dKO_1_G12

description: processed data file: NFI_scRNA_TPM.txt


title: 5-068-2-2_S4


title: 5-069-2-1_S181


title: dKO_1_G4

description: processed data file: NFI_scRNA_TPM.txt


title: 5-068-2-1_S113


title: dKO_1_G10

description: processed data file: NFI_scRNA_TPM.txt


title: dKO_1_F9

description: processed data file: NFI_scRNA_TPM.txt


title: 5-073-2-1_S26


title: 5-068-1-2_S105


title: dKO_1_H10

description: processed data file: NFI_scRNA_TPM.txt


title: 5-067-2-2_S69


title: dKO_1_G6

description: processed data file: NFI_scRNA_TPM.txt


title: dKO_1_F8

description: processed data file: NFI_scRNA_TPM.txt


title: 5-068-1-1_S171


title: dKO_1_F7

description: processed data file: NFI_scRNA_TPM.txt


title: 5-067-2-2_S165


title: dKO_1_F5

description: processed data file: NFI_scRNA_TPM.txt


title: 5-067-2-1_S92


title: dKO_1_F6

description: processed data file: NFI_scRNA_TPM.txt


title: 5-066-2-3_S91


title: dKO_1_F4

description: processed data file: NFI_scRNA_TPM.txt


title: 5-071-1-3_S38


title: 5-070-1-3_S101


title: 5-066-2-1_S45


title: dKO_1_G11

description: processed data file: NFI_scRNA_TPM.txt


title: 5-065-2-1_S184


title: dKO_1_F2

description: processed data file: NFI_scRNA_TPM.txt


title: 5-064-2-1_S123


title: dKO_1_F11

description: processed data file: NFI_scRNA_TPM.txt


title: 5-063-2-3_S96


title: 5-064-2-2_S164


title: dKO_1_F1

description: processed data file: NFI_scRNA_TPM.txt


title: dKO_1_F12

description: processed data file: NFI_scRNA_TPM.txt


title: dKO_1_F10

description: processed data file: NFI_scRNA_TPM.txt


title: 5-063-2-3_S198


title: 5-063-2-1_S51


title: dKO_1_E8

description: processed data file: NFI_scRNA_TPM.txt


title: dKO_1_E9

description: processed data file: NFI_scRNA_TPM.txt


title: 5-063-2-2_S171


title: dKO_1_E6

description: processed data file: NFI_scRNA_TPM.txt


title: 5-063-1-2_S168


title: dKO_1_E7

description: processed data file: NFI_scRNA_TPM.txt


title: 5-063-1-2_S72


title: 5-062-2-2_S21


title: dKO_1_E5

description: processed data file: NFI_scRNA_TPM.txt


title: 5-063-1-1_S82


title: dKO_1_E4

description: processed data file: NFI_scRNA_TPM.txt


title: dKO_1_F3

description: processed data file: NFI_scRNA_TPM.txt


title: dKO_1_E2

description: processed data file: NFI_scRNA_TPM.txt


title: dKO_1_E3

description: processed data file: NFI_scRNA_TPM.txt


title: 5-062-2-1_S153


title: 5-064-2-2_S217


title: 5-060-2-1_S32


title: 5-059-2-2_S186


title: dKO_1_E12

description: processed data file: NFI_scRNA_TPM.txt


title: dKO_1_E10

description: processed data file: NFI_scRNA_TPM.txt


title: dKO_1_E11

description: processed data file: NFI_scRNA_TPM.txt


title: 5-057-2-2_S127


title: 5-057-2-1_S37


title: dKO_1_D8

description: processed data file: NFI_scRNA_TPM.txt


title: 5-056-2-3_S84


title: dKO_1_D7

description: processed data file: NFI_scRNA_TPM.txt


title: 5-055-2-3_S171


title: 5-055-2-2_S165


title: dKO_1_D4

description: processed data file: NFI_scRNA_TPM.txt


title: 5-056-2-1_S152


title: dKO_1_D6

description: processed data file: NFI_scRNA_TPM.txt


title: dKO_1_D5

description: processed data file: NFI_scRNA_TPM.txt


title: 5-055-2-1_S159


title: dKO_1_D3

description: processed data file: NFI_scRNA_TPM.txt


title: 5-054-2-1_S3


title: 5-054-2-2_S24


title: dKO_1_E1

description: processed data file: NFI_scRNA_TPM.txt


title: dKO_1_D1

description: processed data file: NFI_scRNA_TPM.txt


title: 5-052-2-2_S170


title: dKO_1_D12

description: processed data file: NFI_scRNA_TPM.txt


title: 5-053-1-1_S77


title: dKO_1_D11

description: processed data file: NFI_scRNA_TPM.txt


title: 5-059-2-1_S77


title: 5-052-2-1_S39


title: dKO_1_D10

description: processed data file: NFI_scRNA_TPM.txt


title: 5-057-2-3_S101


title: 5-052-2-1_S135


title: dKO_1_D9

description: processed data file: NFI_scRNA_TPM.txt


title: 5-050-2-1_S175


title: dKO_1_C9

description: processed data file: NFI_scRNA_TPM.txt


title: 5-049-2-1_S186


title: dKO_1_C8

description: processed data file: NFI_scRNA_TPM.txt


title: 5-048-2-3_S2


title: dKO_1_C6

description: processed data file: NFI_scRNA_TPM.txt


title: dKO_1_D2

description: processed data file: NFI_scRNA_TPM.txt


title: 5-048-2-1_S172


title: 5-047-2-1_S45


title: dKO_1_C3

description: processed data file: NFI_scRNA_TPM.txt


title: dKO_1_C4

description: processed data file: NFI_scRNA_TPM.txt


title: 5-046-2-2_S44


title: dKO_1_C1

description: processed data file: NFI_scRNA_TPM.txt


title: dKO_1_C12

description: processed data file: NFI_scRNA_TPM.txt


title: 5-046-2-1_S23


title: 5-045-2-1_S147


title: 5-044-2-2_S77


title: 5-044-2-3_S57


title: 5-044-2-3_S153


title: dKO_1_C10

description: processed data file: NFI_scRNA_TPM.txt


title: dKO_1_B8

description: processed data file: NFI_scRNA_TPM.txt


title: 5-043-1-2_S57


title: dKO_1_C7

description: processed data file: NFI_scRNA_TPM.txt


title: dKO_1_B9

description: processed data file: NFI_scRNA_TPM.txt


title: 5-048-2-1_S76


title: dKO_1_C5

description: processed data file: NFI_scRNA_TPM.txt


title: 5-044-2-1_S6


title: dKO_1_B7

description: processed data file: NFI_scRNA_TPM.txt


title: dKO_1_B5

description: processed data file: NFI_scRNA_TPM.txt


title: 5-043-1-1_S10


title: dKO_1_B6

description: processed data file: NFI_scRNA_TPM.txt


title: dKO_1_B4

description: processed data file: NFI_scRNA_TPM.txt


title: 5-046-2-2_S140


title: 5-042-2-1_S78


title: dKO_1_B3

description: processed data file: NFI_scRNA_TPM.txt


title: 5-042-2-2_S122


title: 5-041-1-3_S129


title: 5-040-2-3_S99


title: dKO_1_B1

description: processed data file: NFI_scRNA_TPM.txt


title: dKO_1_B12

description: processed data file: NFI_scRNA_TPM.txt


title: dKO_1_B11

description: processed data file: NFI_scRNA_TPM.txt


title: dKO_1_C11

description: processed data file: NFI_scRNA_TPM.txt


title: dKO_1_C2

description: processed data file: NFI_scRNA_TPM.txt


title: dKO_1_B10

description: processed data file: NFI_scRNA_TPM.txt


title: 5-040-2-1_S5


title: 5-043-2-2_S168


title: 5-040-2-2_S80


title: 5-039-1-1_S46


title: dKO_1_B2

description: processed data file: NFI_scRNA_TPM.txt


title: dKO_1_A9

description: processed data file: NFI_scRNA_TPM.txt


title: dKO_1_A7

description: processed data file: NFI_scRNA_TPM.txt


title: 5-038-1-3_S159


title: 5-038-1-2_S166


title: dKO_1_A6

description: processed data file: NFI_scRNA_TPM.txt


title: 5-037-1-3_S53


title: 5-038-1-1_S169


title: dKO_1_A5

description: processed data file: NFI_scRNA_TPM.txt


title: dKO_1_A2

description: processed data file: NFI_scRNA_TPM.txt


title: 5-036-2-3_S50


title: dKO_1_A3

description: processed data file: NFI_scRNA_TPM.txt


title: dKO_1_A1

description: processed data file: NFI_scRNA_TPM.txt


title: 5-036-2-2_S53


title: 5-036-2-1_S53


title: dKO_1_A12

description: processed data file: NFI_scRNA_TPM.txt


title: 5-036-2-2_S205


title: dKO_1_A10

description: processed data file: NFI_scRNA_TPM.txt


title: dKO_1_A11

description: processed data file: NFI_scRNA_TPM.txt


title: 5-032-2-3_S230


title: dKO_1_A8

description: processed data file: NFI_scRNA_TPM.txt


title: 5-032-2-3_S114


title: 5-032-2-3_S18


title: 5-032-2-2_S145


title: cKO_3_H7

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_3_H8

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_3_H9

description: processed data file: NFI_scRNA_TPM.txt


title: 5-031-2-3_S185


title: dKO_1_A4

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_3_H6

description: processed data file: NFI_scRNA_TPM.txt


title: 5-037-1-3_S149


title: cKO_3_H5

description: processed data file: NFI_scRNA_TPM.txt


title: 5-031-2-2_S151


title: cKO_3_H4

description: processed data file: NFI_scRNA_TPM.txt


title: 5-031-2-1_S122


title: 5-031-1-3_S186


title: cKO_3_H3

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_3_H1

description: processed data file: NFI_scRNA_TPM.txt


title: 5-031-1-2_S145


title: 5-031-1-1_S77


title: 5-034-2-1_S111


title: cKO_3_H11

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_3_H12

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_3_H10

description: processed data file: NFI_scRNA_TPM.txt


title: 5-029-1-2_S144


title: 5-028-1-3_S156


title: cKO_3_G9

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_3_G8

description: processed data file: NFI_scRNA_TPM.txt


title: 5-028-1-1_S71


title: cKO_3_G7

description: processed data file: NFI_scRNA_TPM.txt


title: 5-026-2-2_S142


title: cKO_3_G6

description: processed data file: NFI_scRNA_TPM.txt


title: 5-024-1-3_S133


title: 5-028-1-2_S77


title: cKO_3_G4

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_3_G5

description: processed data file: NFI_scRNA_TPM.txt


title: 5-024-1-1_S7


title: cKO_3_G3

description: processed data file: NFI_scRNA_TPM.txt


title: 5-023-2-1_S63


title: 5-025-2-3_S166


title: 5-021-1-3_S188


title: cKO_3_G2

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_3_F9

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_3_G10

description: processed data file: NFI_scRNA_TPM.txt


title: 5-020-2-1_S136


title: cKO_3_F8

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_3_G11

description: processed data file: NFI_scRNA_TPM.txt


title: 5-020-1-3_S37


title: cKO_3_F6

description: processed data file: NFI_scRNA_TPM.txt


title: 5-020-1-2_S165


title: cKO_3_F4

description: processed data file: NFI_scRNA_TPM.txt


title: 5-020-1-1_S156


title: cKO_3_F5

description: processed data file: NFI_scRNA_TPM.txt


title: 5-019-2-1_S89


title: cKO_3_F3

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_3_F2

description: processed data file: NFI_scRNA_TPM.txt


title: 5-018-2-3_S146


title: 5-018-2-1_S55


title: 5-019-2-1_S185


title: 5-017-2-1_S68


title: 5-017-2-1_S164


title: 5-021-1-1_S20


title: 5-016-2-2_S45


title: 5-021-1-2_S180


title: 5-016-2-2_S141


title: cKO_3_E9

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_3_F11

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_3_F12

description: processed data file: NFI_scRNA_TPM.txt


title: 5-016-2-1_S105


title: cKO_3_F10

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_3_E8

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_3_E7

description: processed data file: NFI_scRNA_TPM.txt


title: 5-015-2-2_S37


title: cKO_3_E6

description: processed data file: NFI_scRNA_TPM.txt


title: 5-015-2-2_S133


title: cKO_3_E5

description: processed data file: NFI_scRNA_TPM.txt


title: 5-015-2-1_S107


title: 5-015-1-3_S5


title: cKO_3_F1

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_3_E3

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_3_E2

description: processed data file: NFI_scRNA_TPM.txt


title: 5-041-1-1_S162


title: 5-014-2-3_S113


title: 5-015-1-2_S135


title: 5-013-2-3_S248


title: cKO_3_E1

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_3_E12

description: processed data file: NFI_scRNA_TPM.txt


title: 5-013-2-3_S128


title: 5-013-2-1_S31


title: 5-012-1-3_S72


title: cKO_3_D7

description: processed data file: NFI_scRNA_TPM.txt


title: 5-012-1-2_S125


title: cKO_3_D6

description: processed data file: NFI_scRNA_TPM.txt


title: 5-012-1-1_S126


title: cKO_3_E10

description: processed data file: NFI_scRNA_TPM.txt


title: 5-009-1-3_S95


title: cKO_3_D8

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_3_E11

description: processed data file: NFI_scRNA_TPM.txt


title: 5-008-1-3_S95


title: cKO_3_D9

description: processed data file: NFI_scRNA_TPM.txt


title: 5-011-1-1_S22


title: cKO_3_D5

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_3_D4

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_3_D3

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_3_E4

description: processed data file: NFI_scRNA_TPM.txt


title: 5-007-2-1_S66


title: cKO_3_D2

description: processed data file: NFI_scRNA_TPM.txt


title: 5-007-2-3_S62


title: 5-006-2-3_S172


title: 5-006-2-2_S104


title: 5-006-2-1_S99


title: cKO_3_D11

description: processed data file: NFI_scRNA_TPM.txt


title: 5-006-2-1_S3


title: 5-005-2-3_S33


title: cKO_3_D12

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_3_C9

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_3_C8

description: processed data file: NFI_scRNA_TPM.txt


title: 5-005-2-1_S138


title: cKO_3_C7

description: processed data file: NFI_scRNA_TPM.txt


title: 5-004-2-1_S93


title: 5-003-2-3_S187


title: 5-004-1-2_S155


title: 5-003-2-2_S206


title: cKO_3_C6

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_3_C3

description: processed data file: NFI_scRNA_TPM.txt


title: 5-003-2-2_S102


title: cKO_3_C5

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_3_C4

description: processed data file: NFI_scRNA_TPM.txt


title: 5-003-1-3_S133


title: cKO_3_C1

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_3_C12

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_3_C11

description: processed data file: NFI_scRNA_TPM.txt


title: 5-003-1-2_S84


title: 4-105-2-1_S146


title: cKO_3_D1

description: processed data file: NFI_scRNA_TPM.txt


title: 4-104-2-1_S119


title: cKO_3_B9

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_3_B8

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_3_C10

description: processed data file: NFI_scRNA_TPM.txt


title: 4-104-2-1_S23


title: 4-104-1-3_S119


title: cKO_3_B7

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_3_B6

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_3_B5

description: processed data file: NFI_scRNA_TPM.txt


title: 4-104-1-1_S12


title: 4-103-1-1_S83


title: 4-102-2-1_S115


title: cKO_3_B3

description: processed data file: NFI_scRNA_TPM.txt


title: 4-103-2-1_S143


title: cKO_3_B4

description: processed data file: NFI_scRNA_TPM.txt


title: 4-101-2-1_S49


title: 4-099-2-2_S105


title: 4-097-2-3_S73


title: cKO_3_B2

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_3_B1

description: processed data file: NFI_scRNA_TPM.txt


title: 4-097-2-2_S166


title: cKO_3_B11

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_3_B10

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_3_A8

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_3_B12

description: processed data file: NFI_scRNA_TPM.txt


title: 4-097-1-3_S246


title: 4-097-1-3_S192


title: cKO_3_A7

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_3_A6

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_3_A9

description: processed data file: NFI_scRNA_TPM.txt


title: 4-097-1-1_S47


title: cKO_3_A4

description: processed data file: NFI_scRNA_TPM.txt


title: 4-094-2-3_S69


title: 4-096-2-1_S15


title: 4-093-2-3_S30


title: cKO_3_A1

description: processed data file: NFI_scRNA_TPM.txt


title: 4-093-2-2_S241


title: cKO_3_A12

description: processed data file: NFI_scRNA_TPM.txt


title: 4-097-2-1_S64


title: cKO_3_A11

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_3_A10

description: processed data file: NFI_scRNA_TPM.txt


title: 4-093-2-1_S165


title: cKO_2_E8

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_2_E9

description: processed data file: NFI_scRNA_TPM.txt


title: 4-092-2-1_S179


title: 4-088-1-1_S29


title: 4-095-2-1_S171


title: cKO_2_E6

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_2_E7

description: processed data file: NFI_scRNA_TPM.txt


title: 4-081-2-1_S30


title: cKO_2_E5

description: processed data file: NFI_scRNA_TPM.txt


title: 4-082-1-2_S76


title: cKO_3_A5

description: processed data file: NFI_scRNA_TPM.txt


title: 4-084-2-1_S92


title: cKO_2_E3

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_2_E4

description: processed data file: NFI_scRNA_TPM.txt


title: 4-094-2-1_S120


title: 4-079-2-1_S85


title: cKO_3_A2

description: processed data file: NFI_scRNA_TPM.txt


title: 4-074-2-1_S37


title: 4-074-2-1_S195


title: 4-093-2-2_S127


title: 4-075-1-2_S151


title: cKO_2_E2

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_2_E1

description: processed data file: NFI_scRNA_TPM.txt


title: 4-092-2-2_S83


title: cKO_2_E12

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_2_E11

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_2_E10

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_2_D9

description: processed data file: NFI_scRNA_TPM.txt


title: 4-073-2-1_S158


title: cKO_2_D8

description: processed data file: NFI_scRNA_TPM.txt


title: 4-073-2-1_S62


title: 4-072-2-1_S134


title: 4-072-2-1_S38


title: 4-069-1-1_S88


title: cKO_2_D3

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_2_D4

description: processed data file: NFI_scRNA_TPM.txt


title: 4-068-2-1_S136


title: 4-069-2-2_S124


title: cKO_2_D7

description: processed data file: NFI_scRNA_TPM.txt


title: 4-069-1-2_S155


title: cKO_2_D2

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_2_D5

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_2_D1

description: processed data file: NFI_scRNA_TPM.txt


title: 4-067-1-1_S135


title: cKO_2_D12

description: processed data file: NFI_scRNA_TPM.txt


title: 4-068-1-1_S103


title: 4-066-1-2_S208


title: 4-066-1-1_S70


title: 4-073-2-2_S121


title: cKO_2_D11

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_2_C6

description: processed data file: NFI_scRNA_TPM.txt


title: 4-064-2-1_S66


title: 4-063-2-1_S137


title: 4-065-2-1_S184


title: 4-063-2-1_S41


title: cKO_2_C4

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_2_C3

description: processed data file: NFI_scRNA_TPM.txt


title: 4-072-2-2_S62


title: 4-062-1-2_S61


title: cKO_2_C2

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_2_B8

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_2_C11

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_2_B9

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_2_C10

description: processed data file: NFI_scRNA_TPM.txt


title: 4-059-2-2_S168


title: 4-060-2-1_S83


title: cKO_2_B7

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_2_D10

description: processed data file: NFI_scRNA_TPM.txt


title: 4-062-1-1_S108


title: cKO_2_C9

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_2_B5

description: processed data file: NFI_scRNA_TPM.txt


title: 4-059-2-1_S18


title: 4-058-2-1_S11


title: cKO_2_B12

description: processed data file: NFI_scRNA_TPM.txt


title: 4-058-1-1_S59


title: cKO_2_B10

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_2_C5

description: processed data file: NFI_scRNA_TPM.txt


title: 4-057-1-1_S154


title: cKO_2_A9

description: processed data file: NFI_scRNA_TPM.txt


title: 4-054-2-3_S25


title: 4-054-2-2_S20


title: 4-054-1-3_S5


title: cKO_2_A6

description: processed data file: NFI_scRNA_TPM.txt


title: 4-054-1-3_S101


title: 4-059-2-3_S179


title: cKO_2_A5

description: processed data file: NFI_scRNA_TPM.txt


title: 4-061-1-1_S46


title: cKO_2_A2

description: processed data file: NFI_scRNA_TPM.txt


title: 4-052-1-2_S81


title: cKO_2_A1

description: processed data file: NFI_scRNA_TPM.txt


title: 4-049-2-3_S121


title: cKO_2_A12

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_2_A10

description: processed data file: NFI_scRNA_TPM.txt


title: 4-049-2-1_S89


title: cKO_2_A11

description: processed data file: NFI_scRNA_TPM.txt


title: 4-048-2-1_S51


title: 4-047-1-1_S12


title: cKO_1_H9

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_1_H8

description: processed data file: NFI_scRNA_TPM.txt


title: 4-047-1-2_S143


title: cKO_2_A7

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_1_H6

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_1_H5

description: processed data file: NFI_scRNA_TPM.txt


title: 4-047-1-1_S108


title: cKO_2_A4

description: processed data file: NFI_scRNA_TPM.txt


title: 4-054-1-2_S130


title: cKO_1_H4

description: processed data file: NFI_scRNA_TPM.txt


title: 4-046-1-1_S5


title: 4-042-2-2_S33


title: 4-043-2-1_S70


title: 4-045-1-1_S138


title: cKO_1_H2

description: processed data file: NFI_scRNA_TPM.txt


title: 4-050-2-1_S191


title: cKO_1_H12

description: processed data file: NFI_scRNA_TPM.txt


title: 4-042-2-2_S129


title: cKO_1_H11

description: processed data file: NFI_scRNA_TPM.txt


title: 4-042-2-1_S62


title: 4-047-2-1_S149


title: cKO_1_H10

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_1_H7

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_1_G9

description: processed data file: NFI_scRNA_TPM.txt


title: 4-041-2-2_S167


title: 4-041-2-1_S44


title: cKO_1_G8

description: processed data file: NFI_scRNA_TPM.txt


title: 4-040-1-2_S126


title: 4-037-2-2_S9


title: cKO_1_G7

description: processed data file: NFI_scRNA_TPM.txt


title: 4-040-1-3_S21


title: cKO_1_G6

description: processed data file: NFI_scRNA_TPM.txt


title: 4-037-2-1_S177


title: cKO_1_G5

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_1_H3

description: processed data file: NFI_scRNA_TPM.txt


title: 4-034-2-3_S184


title: cKO_1_G3

description: processed data file: NFI_scRNA_TPM.txt


title: 4-033-2-1_S157


title: 4-034-2-1_S2


title: cKO_1_G12

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_1_G2

description: processed data file: NFI_scRNA_TPM.txt


title: 4-032-2-2_S17


title: cKO_1_G11

description: processed data file: NFI_scRNA_TPM.txt


title: 4-032-2-1_S118


title: 4-029-2-2_S111


title: 4-030-1-1_S29


title: 4-028-2-3_S107


title: cKO_1_F8

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_1_F6

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_1_F9

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_1_G10

description: processed data file: NFI_scRNA_TPM.txt


title: 4-028-2-2_S73


title: cKO_1_F5

description: processed data file: NFI_scRNA_TPM.txt


title: 4-035-2-1_S58


title: cKO_1_G4

description: processed data file: NFI_scRNA_TPM.txt


title: 4-028-2-2_S169


title: cKO_1_F4

description: processed data file: NFI_scRNA_TPM.txt


title: 4-028-2-1_S43


title: 4-027-2-1_S154


title: cKO_1_F3

description: processed data file: NFI_scRNA_TPM.txt


title: 4-026-2-2_S142


title: cKO_1_F12

description: processed data file: NFI_scRNA_TPM.txt


title: 4-027-2-2_S11


title: cKO_1_F1

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_1_F11

description: processed data file: NFI_scRNA_TPM.txt


title: 4-022-2-1_S99


title: 4-026-2-1_S182


title: cKO_1_G1

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_1_F10

description: processed data file: NFI_scRNA_TPM.txt


title: 4-019-2-1_S74


title: 4-018-2-1_S55


title: cKO_1_E9

description: processed data file: NFI_scRNA_TPM.txt


title: 4-018-1-1_S37


title: cKO_1_E5

description: processed data file: NFI_scRNA_TPM.txt


title: 4-017-1-1_S98


title: cKO_1_E7

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_1_E8

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_1_F2

description: processed data file: NFI_scRNA_TPM.txt


title: 4-016-1-1_S127


title: cKO_1_E4

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_1_E1

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_1_E2

description: processed data file: NFI_scRNA_TPM.txt


title: 4-015-2-3_S131


title: 4-015-2-1_S116


title: 4-014-2-3_S153


title: cKO_1_E3

description: processed data file: NFI_scRNA_TPM.txt


title: 4-015-2-2_S62


title: 4-014-2-1_S14


title: 4-014-2-2_S6


title: cKO_1_E12

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_1_E11

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_1_D8

description: processed data file: NFI_scRNA_TPM.txt


title: 4-014-2-1_S110


title: cKO_1_D9

description: processed data file: NFI_scRNA_TPM.txt


title: 4-011-2-3_S17


title: cKO_1_D6

description: processed data file: NFI_scRNA_TPM.txt


title: 4-012-1-1_S109


title: cKO_1_D7

description: processed data file: NFI_scRNA_TPM.txt


title: 4-008-2-1_S50


title: cKO_1_D5

description: processed data file: NFI_scRNA_TPM.txt


title: 4-007-2-2_S23


title: cKO_1_D3

description: processed data file: NFI_scRNA_TPM.txt


title: 4-007-2-1_S55


title: cKO_1_D11

description: processed data file: NFI_scRNA_TPM.txt


title: 4-004-2-1_S48


title: cKO_1_D10

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_1_C9

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_1_C8

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_1_C5

description: processed data file: NFI_scRNA_TPM.txt


title: 4-003-1-3_S23


title: 4-003-1-1_S127


title: 4-002-2-2_S42


title: 4-004-1-1_S106


title: 4-003-1-1_S31


title: cKO_1_C1

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_1_C12

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_1_C11

description: processed data file: NFI_scRNA_TPM.txt


title: 4-002-2-1_S52


title: 4-010-2-1_S99


title: cKO_1_C10

description: processed data file: NFI_scRNA_TPM.txt


title: 3-112-2-1_S119


title: cKO_1_B9

description: processed data file: NFI_scRNA_TPM.txt


title: 3-118-1-1_S232


title: 3-118-1-1_S170


title: 3-107-2-2_S24


title: cKO_1_D2

description: processed data file: NFI_scRNA_TPM.txt


title: 3-107-2-1_S116


title: cKO_1_B5

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_1_B8

description: processed data file: NFI_scRNA_TPM.txt


title: 3-105-2-1b_S243


title: 3-105-2-1b_S10


title: cKO_1_B2

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_1_B1

description: processed data file: NFI_scRNA_TPM.txt


title: 3-104-2-1_S213


title: 3-104-2-1_S104


title: 3-103-2-1b_S234


title: cKO_1_C2

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_1_B11

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_1_B12

description: processed data file: NFI_scRNA_TPM.txt


title: cKO_1_A2

description: processed data file: NFI_scRNA_TPM.txt