title: CAP41-C11


title: CAP41-C18

status: Public on Jan 02 2019

type: SRA

city: Lausanne

first: Federico

last: Santoni

address: rue du Bugnon, 7

country: Switzerland

institute: CHUV

description:
Single cell fibroblast
ASE_gene_cell_ind.csv

library_source: transcriptomic

data_processing:
Genome sequencing: For each individual,we used the Burrows- Wheeler Aligner (BWA mem v.0.7.10) to align the sequencing reads (fastq) to the human reference genome (GRCh37/hg19). We used SAMtools v.1.4 to remove paired-end duplicates and pile up the remaining reads. BCFtools v.1.4 was used to call the SNVs and Annovar (2016Feb01) for the annotation. SNVs with quality score <100 where excluded from the analysis.
Single cell RNA-seq: RNA sequences were mapped with GEM. Uniquely mapping reads were extracted by filtering for mapping quality (MQ>=150). An in-house algorithm was used to quantify RPKM expression using GENCODE v26. Cells with less than 1 million uniquely mapped reads were excluded from further analysis
Allele specific expression: For each gene on the X chromosome, the aggregate monoallelic ratio (AR) per cell was calculated by averaging the allelic ratio of the reads covering the respective heterozygous sites (AR = sum of number of reads from the active X allele / total SNV reads; 0≤AR≤1). Since we do not have the availability of parental genotype for all the individuals, we designed an algorithm to estimate the active X allele per site based on the assumption that the active X allele is, on average, more transcribed than the inactive X. We validated this assumption comparing the prediction of our algorithm with the phasing of twins’ X alleles based on parental information (more details in Methods S1). According to this metric, inactivated genes cluster around AR=1 while known escapees appear as been uniformly distributed between 0.5≤AR≤0.95 (linear phase of the cumulative distribution, Figure S12). As support of this observation, AR distribution of autosomal genes clearly indicates AR=0.95 as the threshold separating biallelically expressed genes from monoallelic expressed genes (Figure S13). Therefore, we consider a gene as escapee in the relaxed set when the aggregate AR is ≤ 0.95 in at least 1 individual and as escapee in the robust set when the aggregate AR is ≤ 0.95 in at least 2 individuals. To reduce the effect of allele dropout, we only consider for the analysis SNV sites covered by at least 5 reads in at least three cells. To reduce sampling bias effects a gene is included in the analysis if detectable in more than 5 different cells and/or SNVs per sample.
Genome_build: GRCh37/hg19

molecule: total RNA

organism: Homo sapiens

source_name: Coriell

growth_protocol: Cells were cultured in DMEM GlutaMAX™ (Life Technologies) supplemented with 10% fetal bovine serum (Life Technologies) and 1% penicillin/streptomycin/fungizone mix (Amimed, BioConcept) at 37°C in a 5% CO2 atmosphere as described

extract_protocol:
Single-cell capture was performed using the C1 single-cell auto prep system (Fluidigm) following the manufacturer’s procedure. The integrated fluidic circuit used for the study is the C1™ Single-Cell mRNA Seq IFC, 17–25 μm with a capacity of 96 chambers. During the capture, all 96 chambers were inspected under an inverted phase contrast microscope; only chambers containing a non-damaged single cell were considered for downstream analysis. SMARTer Ultra Low RNA kit for Illumina sequencing (version 2, Clontech) was used for the cell lysis and cDNA synthesis.
Libraries were prepared with 0.3 ng of pre-amplified cDNA using Nextera XT DNA kit (Illumina)
Libraries were sequenced on an Illumina HiSeq2000 sequencer as 100 bp single ended reads. RNA sequences were mapped with GEM. Uniquely mapping reads were extracted by filtering for mapping quality (MQ>=150). An in-house algorithm was used to quantify RPKM expression using GENCODE v26. Cells with less than 1 million uniquely mapped reads were excluded from further analysis.

tag: cell culture

tag: cell type

value: primary skin fibroblast

tag: individual id

value: Individual 1


title: CAP41-C08


title: CAP41-C06


title: CAP41-C07


title: CAP41-C09


title: CAP41-C36


title: CAP41-C03


title: CAP41-C01


title: CAP41-C02


title: CAP41-C35


title: CAP39-C93


title: CAP39-C92


title: CAP39-C89


title: CAP39-C91


title: CAP39-C85


title: CAP39-C90


title: CAP39-C88


title: CAP39-C87


title: CAP39-C83


title: CAP39-C84


title: CAP39-C82


title: CAP39-C81


title: CAP39-C80


title: CAP39-C78


title: CAP39-C77


title: CAP41-C05


title: CAP39-C71


title: CAP39-C69


title: CAP39-C68


title: CAP39-C70


title: CAP39-C73


title: CAP39-C67


title: CAP39-C64


title: CAP39-C58


title: CAP39-C59


title: CAP39-C60


title: CAP39-C63


title: CAP39-C66


title: CAP39-C54


title: CAP39-C57


title: CAP39-C49


title: CAP39-C52


title: CAP39-C40


title: CAP39-C46


title: CAP39-C48


title: CAP39-C38


title: CAP39-C36


title: CAP39-C35


title: CAP39-C33


title: CAP39-C32


title: CAP39-C31


title: CAP39-C25


title: CAP39-C30


title: CAP39-C22


title: CAP39-C20


title: CAP39-C23


title: CAP39-C51


title: CAP39-C12


title: CAP39-C17


title: CAP39-C16


title: CAP39-C18


title: CAP39-C13


title: CAP39-C10


title: CAP39-C11


title: CAP39-C09


title: CAP39-C06


title: CAP39-C08


title: CAP39-C07


title: CAP39-C01


title: CAP39-C47


title: CAP39-C02


title: CAP29-C87


title: CAP39-C04


title: CAP29-C93


title: CAP39-C72


title: CAP29-C86


title: CAP29-C85


title: CAP29-C92


title: CAP29-C81


title: CAP29-C80


title: CAP29-C74


title: CAP29-C69


title: CAP29-C75


title: CAP29-C57


title: CAP29-C51


title: CAP29-C42


title: CAP29-C49


title: CAP29-C67


title: CAP29-C50


title: CAP29-C39


title: CAP29-C68


title: CAP29-C35


title: CAP29-C62


title: CAP29-C44


title: CAP29-C30


title: CAP29-C36


title: CAP29-C24


title: CAP29-C34


title: CAP29-C29


title: CAP29-C26


title: CAP29-C23


title: CAP29-C22


title: CAP29-C16


title: CAP29-C20


title: CAP29-C18


title: CAP29-C28


title: CAP29-C21


title: CAP29-C14


title: CAP29-C73


title: CAP29-C12


title: CAP29-C11


title: CAP29-C09


title: CAP29-C10


title: CAP29-C04


title: CAP29-C08


title: CAP29-C05


title: CAP29-C03


title: CAP29-C07


title: CAP29-C06


title: CAP29-C01


title: CAP29-C55


title: SUPT4H1_10_3: SUPT4H1 siRNAs, 10 nM, replicate 3

status: Public on Jan 01 2019

city: South San Francisco

first: Thomas

last: Sandmann

email: genomics@dnli.com, sandmann@dnli.com

state: California

address: 161 Oyster Point Blvd

country: USA

institute: Denali Therapeutics

data_processing:
Sequencing adapters were trimmed using skewer (Jiang et al., 2014; version 0.2.2) with default parameters. Quality control of the trimmed reads was performed using FastQC (version 0.11.5: www.bioinformatics.babraham.ac.uk/projects/fastqc).
Reads were aligned to a composite index of the human genome (version GRCh38_p10) and sequences of the 92 ERCC spike-in transcripts: A STAR index (Dobin et al., 2013; version 2.5.3a) was built with the --sjdbOverhang=50 argument. Splice junctions from Gencode gene models (release 27) were provided via the --sjdbGTFfile argument. STAR alignments were generated with the following parameters: --outFilterType BySJout --quantMode TranscriptomeSAM --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMstrandField intronMotif --outSAMattributes NH HI AS nM MD XS --outSAMunmapped Within. Post-alignment quality control reports were generated using MultiQC (Ewels et al., 2016; version 1.0).
The raw gene expression matrix was constructed from the 'forward' column of STAR's ReadsPerGene.out.tab output files using R (version 3.4.3). Gene symbols and Entrez gene identifiers were mapped using Ensembl (version 86) via the biomaRt R package (Durinck et al, 2009; version 2.34.0).
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited, gzip-compressed text file with matrix of raw quantitation results for each sample.

source_name: skin fibroblast

growth_protocol: Fibroblasts GM05757 (Coriell) cells were cultured in DMEM, 10% FBS, 100 units/ml penicillin and streptomycin, 37 deg.C, 5% carbon dioxide, 100% humidity

extract_protocol:
72 hours post transfection, total RNA was extracted with the RNEasy (Qiagen) kit from 25,000 cells per sample. Either ERCC mix1 or mix2 external standards (Invitrogen) were diluted 1:100 in water and 1 ul was added to each lysate.
Libraries were prepared from 100 ng of total RNA using the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen), following the ‘low-input’ procedure defined by the manufacturer.

treatment_protocol: Cells were transfected at 50% confluency in 6-well plates by combining either SUPT4H1 siRNA or scramble siRNA with 9 ul of RNAi max transfection reagent (Invitrogen) at a final concentration of 5, 10 or 20 nM in a total volumne of 1.3 ml.

tag: cell line

tag: tissue

value: skin fibroblast

tag: rin

tag: treatment concentration

value: 10 nM

tag: replicate

tag: treatment

value: SUPT4H1 siRNAs


title: SUPT4H1_5_2: SUPT4H1 siRNAs, 5 nM, replicate 2

value: 5 nM


title: SUPT4H1_10_2: SUPT4H1 siRNAs, 10 nM, replicate 2


title: SUPT4H1_10_1: SUPT4H1 siRNAs, 10 nM, replicate 1


title: SUPT4H1_5_1: SUPT4H1 siRNAs, 5 nM, replicate 1


title: sc20_3: Scrambled siRNAs, replicate 3

value: 20 nM

value: scrambled siRNAs


title: sc20_2: Scrambled siRNAs, replicate 2


title: sc20_1: Scrambled siRNAs, replicate 1


title: WS leaves infected with BcWT, biological rep3

type: RNA

city: VERSAILLES

first: Samantha

last: VERNHETTES

address: route de saint Cyr

country: France

institute: INRA

description: Gene expression data from WS leaves infected by wild-type Botrytis strain. This is the third of the four biological replicates used in this study.

hyb_protocol: Hybridization was performed on Gene Atlas array strips (Arabidopsis Gene 1,1 ST Array strip) at 48°C for 18 hours on the Affymetrix GeneAtlas Hybridization Station.

scan_protocol: Strips were scanned using the Gene Atlas imaging station.

data_processing: Data were normalized using the Expression Console software (Affymetrix) using default RMA-sketch normalization. Normalized .chp files were then analyzed using TAC 4.0 software (Affymetrix) using default settings.

label: biotin

organism: Arabidopsis thaliana

source_name: WS leaves infected with BcWT

label_protocol: Labeling was performed according to the GeneChip WTPLUS Reagent kit protocol

growth_protocol: 6 week-old WS Arabidopsis plants were grown in soil in a growth chamber at 22°C, 70% humidity, under irradiance of 100 mmol.m-2.s-1 with a photoperiod pf 8h light/16h dark.

extract_protocol: Leaves were frozen and ground at -80°C. Total RNA was extracted using the Nucleospin RNA XS purification kit including the removal of genomic DNA.

treatment_protocol: plants were infected with Botrytis cinerea strains during 24 hours.  20 microliters  of spore suspension were placed on Arabidopsis leaves with a final concentration of 3 105 conidia/ml. Control leaves were spotted with droplets of potato dextrose broth medium.

value: Arabidopsis leaves

value: WT Botritys cinerea


title: WS leaves infected with Bcpme1/2, biological rep1

description: Gene expression data from WS leaves infected by Botrytis strain mutated on PME1 and PME2 genes. This is the first of the three biological replicates used in this study.

source_name: WS leaves infected with Bcpme1/2

value: pme1/2 Botritys cinerea line


title: WS leaves infected with Bcpme1/2, biological rep3

description: Gene expression data from WS cells infected by Botrytis strain mutated on PME1 and PME2 genes. This is the third of the three biological replicates used in this study.


title: SUPT4H1_5_3: SUPT4H1 siRNAs, 5 nM, replicate 3


title: uninfected WS leaves, biological rep2

description: Gene expression data from  uninfected WS leaves. This is the second of the three biological replicates used in this study.

source_name: uninfected WS leaves

value: mock


title: uninfected WS leaves, biological rep3

description: Gene expression data from  uninfected WS leaves. This is the third of the three biological replicates used in this study.


title: WS leaves infected with Bcpme1/2, biological rep2

description: Gene expression data from WS cells infected by Botrytis strain mutated on PME1 and PME2 genes. This is the second of the three biological replicates used in this study.


title: WS leaves infected with BcWT, biological rep4

description: Gene expression data from WS leaves infected by wild-type Botrytis strain. This is the last biological replicate used in this study.


title: WS leaves infected with BcWT, biological rep1

description: Gene expression data from WS leaves infected by wild-type Botrytis strain. This is the first of the four biological replicates used in this study.


title: uninfected WS leaves, biological rep1

description: Gene expression data from uninfected WS leaves. This is the first of the three biological replicates used in this study.


title: AE104S_CH34_2

status: Public on Dec 31 2018

city: Mol

first: Rob

last: Van Houdt

address: Boeretang 200

department: Interdisciplinary Biosciences

country: Belgium

institute: SCK-CEN

description: Comparison of AE104S with CH34 normal conditions

hyb_protocol: Labeled cDNA was re-suspended in the universal hybridization buffer (Pronto kit), mixed and added to the spotted slide for overnight hybridization at 42 C in a Tecan HS4800 Pro hybridization station (Tecan Group Ltd, Switzerland). Afterwards, the slide was washed according to Pronto kit’s protocol.

scan_protocol: Slides were scanned (at 532 and 635 nm) using the GenePix Personal 4100A microarray scanner (Molecular Devices, USA).

data_processing: Micro-array spot-signals were analyzed using the GenePix Pro v.6.0.1 software and flagged according to build-in quality criteria. Raw median intensity data were imported into R version 2.7.0 for statistical analysis using the LIMMA package version 2.15.15 (Smyth 2005) as available from BioConductor. Raw data were background-corrected based on convolution of normal and exponential distributions with an offset of 50 (Ritchie et al. 2007). Data were normalized within each array using the printing-tip loess normalization algorithm (Smyth and Speed 2003). The in-slide replicate correlations were calculated using the Duplicate correlation function in the LIMMA package (Smyth 2005). The log expression values were fitted to al linear model and moderated t-statistics were calculated using empirical Bayes method (Smyth 2004). P-values were corrected for multiple testing using the Benjamin and Hochberg’s method to control the false discovery rate (Benjamini and Hochberg 1995).

organism: Cupriavidus metallidurans

label_protocol: Ten micrograms of RNA were reverse transcribed following the instructions provided with the Pronto kit (Promega, United States). Two color labeling, green for control samples and red for condition (metal challenge) samples, was performed using respectively CyTM3-dCTP and CyTM5-dCTP nucleotides (Amersham BioSciences, United Kingdom).

growth_protocol: The strains were cultivated by  inoculating 30 ml of MM284 in biological triplicates with 300 μL of a stationary phase culture at 30 °C. These subcultures were allowed to grow until an OD600 value of around 0.6 was reached. Next, cells were harvested by centrifugation for 2 min at 10000 rpm and the bacterial pellets were flash frozen by immersion into liquid nitrogen.

extract_protocol: The bacterial pellets were kept frozen at -80 °C until total RNA extraction was performed using the SV Total RNA Isolation system (Promega Corporation). The quantity of extracted RNA was measured using a NanoDropTM 1000 spectrophotometer (Thermo Scientific). The RNA quality was determined with a Bioanalyzer (Agilent 2100 Electrophoresis Bioanalyzer Agilent Technologies).

treatment_protocol: All strains were grown in normal conditions, as the aim of this study was to compare the general gene expression of two different strains.

tag: strain

value: CH34 grown in normal conditions

tag: genotype

value: wildtype

value: AE104S grown in normal conditions

value: CH34-derived evolved strain


title: AE104S_CH34_3


title: NA4S_CH34_2

description: Comparison of NA4S with CH34 normal conditions

value: NA4S grown in normal conditions

value: NA4-derived evolved strain


title: NA4S_CH34_3


title: CH34S2_CH34_3

description: Comparison of CH34S2 with CH34 normal conditions

value: CH34S2 grown in normal conditions


title: 181102_snm3C_H6_AD002_indexed

status: Public on Dec 26 2018

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Raw reads were trimmed first 25bp and last 3bp of both read1 and read2 to remove random primer sequence and adaptase low complexity tails. For the alignment, Bismark is used24. C to T converted and G to A converted reference genomes are prepared for mm10 and hg38 using bismark_genome_preparation. Each read end is mapped separately using Bismark with Bowtie1 with read1 as complementary (always G to A converted) and read2 (always C to T converted) as original strand. After first alignment, unmapped reads are retained and splitted into 3 pieces by 40bp, 32bp, and 40bp after removing 5bp of both ends results in having 6 reads (read1 and read2). Six reads derived from unmapped reads are mapped separately using Bismark Bowtie1. All aligned reads are merged into BAM using picard that is query name sorted. The fragments with all the mapped reads aligned to the same positions are considered as duplicates and removed and DNA methylation tracks are generated. For each fragment, the outermost aligned reads are chosen for the chromatin conformation map generation.
Supplementary_files_format_and_content: tab delimited text files of methylcytosine calls; columns in allc files are: column 1 - chromosome; column 2 - position; column 3 - strand; column 4 - class; column 5 - mC reads; column 6 - total reads; column 7 - methylated (Boolean value indicating the result of statistical test for methylated cytosines)

molecule: genomic DNA

source_name: Human GM12878 Cell Line

growth_protocol: Mouse ES cells (E14TG2a) were purchased from American Type Culture Collection (ATCC CRL-1821). ES cells were grown in DMEM media (Corning 10-013-CV) supplemented with 10% HyClone FBS (Fisher SH3007003E), 1X MEM Non-essential amino acids (ThermoFisher 11140050), 1X Glutamax supplement (ThermoFisher 35050061), 1X ß-mercaptoethanol (Millipore ES-007-E), 100U/mL Penicillin-Streptomycin (ThermoFisher 15140122), and 1000U/mL Leukemia Inhibitory Factor (Millipore ESG1107). ES cells were cultured in feeder free conditions on 0.5% gelatin coated plates. GM12878 cells were obtained from Coriell Institute for Medical Research. GM12878 cells were grown in RPMI-1640 medium (ThermoFisher 11875093) supplemented with 15% Fetal Bovine Serum (Corning 35-010-CV) and 100U/mL Penicillin-Streptomycin (ThermoFisher 15140122). NMuMg cells (RBRC-RCB2868) were obtained from the RIKEN BioResource Center. NMuMg cells were grown in DMEM (Corning 10-013-CV) with 10% Fetal Bovine Serum (Corning 35-010-CV), 10ug/mL Insulin (ThermoFisher 12585014), and 100U/mL Penicillin-Streptomycin (ThermoFisher 15140122). All cell lines were routinely tested for mycoplasma contamination and tested negative.

extract_protocol: in situ Hi-C was performed as previously described using the MboI restriction enzyme. in situ 3C experiments were performed based on the previously described in situ Hi-C protocol with minor modifications. Briefly, prior to fixation, adherent cells were trypsinized, counted, and collected by centrifugation, and suspension cells were counted and collected by centrifugation. Cells were resuspended in culture media at a concentration of 1x106 cells per mL of media and fixed in 1% formaldehyde for 10 minutes at room temperature with shaking. For standard species mixture experiments, equal numbers of mouse and human cells were combined into a single tube prior to fixation. For the 1:10 dilution species mixture experiment, cells were resuspended at a concentration of 1x105 cells per mL of media prior to fixation. For the species mixture experiments where samples were mixed after fixation, each cell type was fixed independently as described above and combined at later stages in the protocol. in situ Hi-C samples were digested with the MboI restriction enzyme and processed as described previously. For in situ 3C experiments, samples were digested with DpnII enzyme overnight at 37ºC with gentle mixing. The following day, the sample was incubated at 62ºC for 10 minutes to inactivate the restriction enzyme. The typical biotin fill in step in the Hi-C protocol is omitted. The sample is then ligated for 4 hours at room temperature with T4 DNA ligase in the same manner as in in situ Hi-C experiments. The sample is then stained with Hoechst (0.1ug/uL) for the final 30 minutes of the ligation step. The sample is then passed through a 40 uM nylon cell strainer (Corning 431750) into a FACS tube prior to sorting. As a quality control step, 10% of the sample is taken for conventional library preparation and sequenced using shallow sequencing on a MiSeq. Libraries for bulk and single-cell methylomes were generated using snmC-seq2. A detailed step-by-step bench protocol for snmC-seq2 is provided as Supplement Methods in Luo et al. (2018) 23. Bulk methylome libraries were prepared manually using individual tubes. Single-cell methylome libraries were prepared using a Tecan Evo 100 robotic platform as described in Luo et al. (2018) 23. Sequencing libraries were sequenced using Illumina MiSeq and HiSeq 4000 instruments in PE150 mode.

tag: Sex

value: Female

tag: genome build

tag: library strategy


title: AE104S_CH34_1


title: 181102_snm3C_H5_AD006_indexed


title: CH34S2_CH34_1


title: CH34S2_CH34_2


title: 181102_snm3C_H4_AD002_indexed


title: 181102_snm3C_H4_AD001_indexed


title: 181102_snm3C_H5_AD004_indexed


title: CH34S1_CH34_2

description: Comparison of CH34S1 with CH34 normal conditions

value: CH34S1 grown in normal conditions


title: CH34S1_CH34_3


title: NA4S_CH34_1


title: CH34S1_CH34_1


title: 181102_snm3C_G6_AD006_indexed


title: 181102_snm3C_G6_AD001_indexed


title: 181102_snm3C_F6_AD006_indexed


title: 181102_snm3C_G4_AD002_indexed


title: 181102_snm3C_E5_AD002_indexed


title: 181102_snm3C_E6_AD004_indexed


title: 181102_snm3C_E5_AD004_indexed


title: 181102_snm3C_F4_AD001_indexed


title: 181102_snm3C_E6_AD001_indexed


title: 181102_snm3C_G5_AD004_indexed


title: 181102_snm3C_F5_AD006_indexed


title: 181102_snm3C_F5_AD001_indexed


title: 181102_snm3C_E5_AD006_indexed


title: FTM2 (flank, old)

status: Public on Dec 28 2018

city: Yufu-shi

first: Takashi

last: Sakai

state: Oita

address: 1-1 Idaigaoka, Hasama-machi,

department: Faculty of Medicine

country: Japan

institute: Oita University

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Human Gene Expression Microarray 8x60K v2; 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. In addition, the raw signal intensities of all samples were normalized by the quantile algorithm with the Bioconductor.

organism: Mus musculus

source_name: non-lesional skin of flank, old FTM

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

extract_protocol: Total RNA was isolated from tissues using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega)

value: STOCK a/a Tmem79ma Flgft/J

value: whole skin

tag: gender

value: female

tag: age


title: FTM1 (flank, old)


title: FTM3 (flank, old)


title: 181102_snm3C_F5_AD002_indexed


title: 181102_snm3C_E4_AD006_indexed


title: 181102_snm3C_D6_AD002_indexed


title: FTM1 (neck, old)

source_name: lesional skin of neck, old FTM


title: 181102_snm3C_D5_AD004_indexed


title: 181102_snm3C_D5_AD002_indexed


title: FTM3 (neck, old)


title: WS leaves infected with BcWT, biological rep2

description: Gene expression data from WS leaves infected by wild-type Botrytis strain. This is the second of the four biological replicates used in this study.


title: FTM2 (neck, old)


title: 181102_snm3C_C6_AD006_indexed


title: 181102_snm3C_E4_AD002_indexed


title: 181102_snm3C_C5_AD006_indexed


title: 181102_snm3C_C5_AD002_indexed


title: 181102_snm3C_C4_AD006_indexed


title: 181102_snm3C_C4_AD002_indexed


title: 181102_snm3C_D4_AD001_indexed


title: 181102_snm3C_B6_AD004_indexed


title: 181102_snm3C_B6_AD006_indexed


title: 181102_snm3C_A6_AD002_indexed


title: 181102_snm3C_B4_AD006_indexed


title: 181102_snm3C_A5_AD006_indexed


title: 181102_snm3C_B5_AD002_indexed


title: 181102_snm3C_A4_AD004_indexed


title: 181102_snm3C_A5_AD004_indexed


title: 181102_snm3C_H12_AD002_indexed


title: 181102_snm3C_H12_AD004_indexed


title: 181102_snm3C_A5_AD002_indexed


title: 181102_snm3C_H12_AD001_indexed


title: 181102_snm3C_H11_AD002_indexed


title: 181102_snm3C_H11_AD001_indexed


title: 181102_snm3C_H10_AD004_indexed


title: 181102_snm3C_F12_AD006_indexed


title: 181102_snm3C_G10_AD002_indexed


title: 181102_snm3C_F12_AD004_indexed


title: 181102_snm3C_E12_AD001_indexed


title: 181102_snm3C_E11_AD002_indexed


title: 181102_snm3C_A6_AD001_indexed


title: 181102_snm3C_A5_AD001_indexed


title: 181102_snm3C_E10_AD002_indexed


title: 181102_snm3C_E10_AD006_indexed


title: 181102_snm3C_E11_AD001_indexed


title: 181102_snm3C_D12_AD004_indexed


title: 181102_snm3C_D12_AD001_indexed


title: 181102_snm3C_A4_AD002_indexed


title: 181102_snm3C_H11_AD004_indexed


title: 181102_snm3C_D10_AD004_indexed


title: 181102_snm3C_D11_AD006_indexed


title: 181102_snm3C_C12_AD001_indexed


title: 181102_snm3C_G11_AD002_indexed


title: 181102_snm3C_C11_AD002_indexed


title: 181102_snm3C_C12_AD004_indexed


title: 181102_snm3C_B12_AD006_indexed


title: 181102_snm3C_C11_AD001_indexed


title: 181102_snm3C_B11_AD006_indexed


title: 181102_snm3C_B12_AD001_indexed


title: 181102_snm3C_H8_AD001_indexed


title: 181102_snm3C_A11_AD006_indexed


title: 181102_snm3C_A12_AD002_indexed


title: 181102_snm3C_A11_AD004_indexed


title: 181102_snm3C_A12_AD004_indexed


title: 181102_snm3C_G9_AD002_indexed


title: 181102_snm3C_H9_AD006_indexed


title: 181102_snm3C_G8_AD004_indexed


title: 181102_snm3C_F9_AD006_indexed


title: 181102_snm3C_G8_AD002_indexed


title: 181102_snm3C_F9_AD001_indexed


title: 181102_snm3C_F7_AD001_indexed


title: 181102_snm3C_E9_AD002_indexed


title: 181102_snm3C_G7_AD004_indexed


title: 181102_snm3C_E8_AD004_indexed


title: 181102_snm3C_E7_AD001_indexed


title: 181102_snm3C_D9_AD002_indexed


title: 181102_snm3C_D7_AD002_indexed


title: 181102_snm3C_D7_AD001_indexed


title: 181102_snm3C_C7_AD002_indexed


title: 181102_snm3C_C7_AD001_indexed


title: 181102_snm3C_B9_AD004_indexed


title: 181102_snm3C_B8_AD006_indexed


title: 181102_snm3C_B8_AD004_indexed


title: 181102_snm3C_G8_AD006_indexed


title: 181102_snm3C_B9_AD001_indexed


title: 181102_snm3C_B11_AD001_indexed


title: 181102_snm3C_B8_AD001_indexed


title: 181102_snm3C_A8_AD006_indexed


title: 181102_snm3C_A8_AD004_indexed


title: 181102_snm3C_A7_AD006_indexed


title: 181102_snm3C_A8_AD001_indexed


title: 181102_snm3C_H3_AD004_indexed


title: 181102_snm3C_H3_AD001_indexed


title: 181102_snm3C_H3_AD006_indexed


title: 181102_snm3C_F7_AD004_indexed


title: 181102_snm3C_F8_AD006_indexed


title: 181102_snm3C_H2_AD004_indexed


title: 181102_snm3C_H1_AD006_indexed


title: 181102_snm3C_H1_AD002_indexed


title: 181102_snm3C_H1_AD001_indexed


title: 181102_snm3C_G2_AD004_indexed


title: 181102_snm3C_G3_AD002_indexed


title: 181102_snm3C_G3_AD001_indexed


title: 181102_snm3C_G3_AD006_indexed


title: 181102_snm3C_G1_AD006_indexed


title: 181102_snm3C_G1_AD001_indexed


title: 181102_snm3C_G2_AD002_indexed


title: 181102_snm3C_F3_AD004_indexed


title: 181102_snm3C_F1_AD002_indexed


title: 181102_snm3C_F1_AD006_indexed


title: 181102_snm3C_E3_AD001_indexed


title: 181102_snm3C_E2_AD006_indexed


title: 181102_snm3C_D3_AD006_indexed


title: 181102_snm3C_H1_AD004_indexed


title: 181102_snm3C_C3_AD001_indexed


title: 181102_snm3C_C3_AD002_indexed


title: 181102_snm3C_C1_AD006_indexed


title: 181102_snm3C_D1_AD001_indexed


title: 181102_snm3C_G1_AD004_indexed


title: 181102_snm3C_D1_AD004_indexed


title: 181102_snm3C_C2_AD006_indexed


title: 181102_snm3C_D1_AD006_indexed


title: 181102_snm3C_A3_AD006_indexed


title: 181102_snm3C_B1_AD002_indexed


title: 181102_snm3C_A2_AD002_indexed


title: 181102_snm3C_A3_AD004_indexed


title: 181102_snm3C_A1_AD002_indexed


title: 181102_snm3C_E2_AD002_indexed


title: 181102_snm3C_A1_AD006_indexed


title: 181102_snm3C_F3_AD001_indexed


title: T-ALL leukemia [Tumor69]

status: Public on Dec 21 2018

city: New York

first: Robert

last: Albero

state: New York

address: 1130 St Nicholas Ave

department: Institute of Cancer Genetics

institute: Columbia Unviersity

data_processing:
Fastq files of ATAC-Seq were aligned to genome build hg19 using Bowtie 2 v2.3.4.1 and SAMTOOLS v.1.7 , and mitochondrial reads were filtered.
Duplicates were removed PICARD tools v2.18.11 .
Big wig files were generated with bedtools v2.26.0 (https://bedtools.readthedocs.io/en/latest/) and UCSC pre-compiled utilities. Bigwigs were normalized to number of mapped reads.
Genome_build: hg19
Supplementary_files_format_and_content: BigWig

source_name: T-ALL tumor

extract_protocol: Library amplificiation with NEBNext High-Fidelity 2 698 PCR Master Mix (NEB M0541) and custom primer indexes.

value: Hematologic malignancy

value: T-ALL leukemia


title: Human DP3 minus

source_name: Human DP3 minus sorted B cell

value: Normal T cell

value: Human DP3 minus sorted B cell


title: 181102_snm3C_D2_AD001_indexed


title: 181102_snm3C_D3_AD004_indexed


title: Tumor1

data_processing:
Fastq files of ATAC-Seq were aligned to genome build GRCm38 (mm10) using Bowtie 2 v2.3.4.1 and SAMTOOLS v.1.7 , and mitochondrial reads were filtered.
Duplicates were removed PICARD tools v2.18.11 .
Big wig files were generated with bedtools v2.26.0 (https://bedtools.readthedocs.io/en/latest/) and UCSC pre-compiled utilities. Bigwig were normalized to number of maped reads.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig


title: d6PGCLC_2

status: Public on Dec 18 2018

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

institute: Kyoto University, Graduate school of medicine

description: Transcriptome of amplified cDNA of d6 PGCLC induced from 585B1-868 iPSC via iPSC, sorted BTAG population, rep2

data_processing:
All reads were processed with cutadapt v1.9.1 program to remove low quality bases and adaptor sequences.
Reads with 30 bases or longer were mapped onto human genome (GRCh38.p2/hg38) genome and ERCC spike-in RNA sequences with Tophat v2.0.11/Bowtie v1.1.2 program with options of “--bowtie1”, “--library-type fr-secondstrand” and  “--no-coverage-search”.
Mapped reads were subsequently processed with cufflinks v2.2.0 program with options of “--compatible-hits-norm”, “--no-length-correction”, “--library-type fr-secondstrand”, and “--max-mle-iterations 50000” for abundance estimation of genes expressions.
Genome_build: GRCh38.p2
Supplementary_files_format_and_content: tab-delimited text files include RPM values for each Sample.

source_name: day6 PGCLC, from 585B1-868 iPSC

growth_protocol: 585B1 hiPSCs (XY) and 1390G3 hiPSCs (XX) were cultured with AK03N medium on iMatrix coated plate as reported previously (Sasaki and Yokobayashi et al., 2015).

extract_protocol:
The cells were pelleted down and snap frozen until use.  RNA samples were extracted with RNeasy kit following manufacturer's protocol.
For 3'-seq analysis, cDNA synthesis / amplification from RNA samples and library construction from the cDNAs were performed as described previously (Nakamura et al. 2015, NAR, 43, e60).

treatment_protocol:
The iMeLC induction was induced from iPSC cultured in above condition, passaged to fibronectin coated plate with Activin A (50 ng/ml), CHIR99021 (3µM) and Y27632 (10µM) in GMEM containing 15% KSR, and cultured for 44 to 48 hours.
Above iMeLCs were then dissociated and replated to low-adherent V-bottom plates to form aggregates with BMP4 (200 ng/ml), SCF (100 ng/ml), EGF (50 ng/ml), LIF(1000U/ml), and Y27632 (10µM) in GMEM containing 15% KSR for 6 days.
d6 PGCLC were dissociated and reaggregate with fetal ovarian somatic cells from E12.5 mouse. After for 2days of floating culture with Y27632 (10µM) in GMEM containing 15% KSR, the reconstituted ovary were transferred on  Transwell-COL culture inserts soaked in a alpha-MEM containing 10%FBS, 2-melcaptoethanol (55µM), L-ascorbic acid (150µM), until the harvest day.

tag: markers

value: BLIMP1-tdTomato, TFAP2C-EGFP

value: wild type


title: 2DPI IBV infected cells

status: Public on Dec 05 2018

city: Durham

first: Nicholas

last: Heaton

state: NC

address: 213 Research Drive, 426 CARL Building

department: Molecular Genetics and Microbiology

institute: Duke University School of Medicine

data_processing:
Libraries were then sequenced over 2 lanes of Illumina HiSeq 4000 with 150 bp paired end reads.
The reads were then processed according to 10X Genomics Cell Ranger pipeline.
Samples were demultiplexed and converted to FASTQ files, then mapped against the mouse transcriptome (mm10) and the B/Mal/04 viral genome.
Finally, samples were aggregated to normalize samples to the same sequencing depth.
Data was then analyzed using R and the R package Seurat.
Supplementary_files_format_and_content: normalized and scaled data

molecule: polyA RNA

source_name: Whole lung

extract_protocol:
Cells were sorted by a FACS DIVA using EpCam and CD45 using expression of tdTomato as the marker for infection in the 2 DPI timepoint sample.
Cells were washed and libraries were prepped from 5000 cells using Chromium Single Cell 3′ Reagent Kit (10× Genomics) by the Duke University Molecular Genomics Core.

treatment_protocol: Mice were infected at the indicated timepoints and collected

value: C57BL/6 transgenic line; 'tdTomato transgenic mice' (Jax catalog # 007914)

tag: infected with

value: influenza virus

tag: timepoint

value: 2 dpi

value: lung epithelial cells


title: 181102_snm3C_B3_AD002_indexed


title: Mock infected cells

value: none (mock)

tag: cell type


title: 181102_snm3C_B1_AD001_indexed


title: ChIP-seq from GM23338 (ENCLB162FOM)

status: Public on Dec 03 2018

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR987GXT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR987GXT
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR773IYZ
encode release date: 2017-10-19
lab: Bradley Bernstein, Broad
library encode accession: ENCLB162FOM
size range: 200-600

data_processing: See GSM*_README.txt supplementary file linked below

source_name: Homo sapiens induced pluripotent stem cell line male adult (53 years) derived from fibroblast of arm

tag: antibody

value: CTCF

tag: line

value: cell line

tag: description

value: These are induced pluripotent stem cells (iPSC) created from the PGP1 donor from the Personal Genome Project (PGP).

tag: biosample encode accession

value: 53 year

tag: dev stage

value: adult

value: male

tag: lab

value: Thomas Gingeras, CSHL

tag: link

value: ENCBS368AAA at ENCODE; https://www.encodeproject.org/ENCBS368AAA/

value: Derived from ENCODE donor ENCDO336AAA; https://www.encodeproject.org/ENCDO336AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_F182; http://web.expasy.org/cellosaurus/CVCL_F182

value: Coriell sample source; http://www.ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM23338&PgId=166


title: ChIP-seq from GM23338 (ENCLB378YEF)

description:
https://www.encodeproject.org/experiments/ENCSR987GXT/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR987GXT
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR773IYZ
encode release date: 2017-10-19
lab: Bradley Bernstein, Broad
library encode accession: ENCLB378YEF
size range: 200-600

value: ENCBS373AAA at ENCODE; https://www.encodeproject.org/ENCBS373AAA/


title: T-ALL leukemia [Tumor73]

tag: tissue

value: Hematologic malignancy

value: T-ALL leukemia


title: T-ALL leukemia [Tumor67]


title: Lgr5Pos_EduNeg_S98

status: Public on Nov 05 2018

city: Boston

first: Adam

last: Haber

state: Massachusetts

address: 665 Huntington Ave, HSPH Building 1, Room 305

institute: Harvard T. H. Chan School of Public Health

data_processing:
Full-length RNAseq (SMART-Seq2)
Tophat
Bowtie
RSEM
PCA (prcomp in R)
kNN-based graph clustering (R code)
Genome_build: mm10
Supplementary_files_format_and_content: Transcripts per million (TPM) expression values (derived from RSEM for each gene (rows) in each cell (columns).

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduNeg_S98]

extract_protocol:
Full length RNAseq (SMART-Seq2)
This sample represents a single cell processed with SMART-Seq2 protocol.

value: Lgr5-GFP mouse intestinal epithelial cells

tag: strain

tag: treatment

tag: time point

tag: genotype


title: Lgr5Pos_EduNeg_S99

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduNeg_S99]


title: Lgr5Pos_EduNeg_S97

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduNeg_S97]


title: d6PGCLC_3

description: Transcriptome of amplified cDNA of d6 PGCLC induced from 585B1-868 iPSC via iPSC, sorted BTAG population, rep3

tag: cell line

value: BLIMP1-tdTomato, TFAP2C-EGFP

value: wild type


title: Lgr5Pos_EduPos_S91

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S91]


title: Lgr5Pos_EduPos_S95

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S95]


title: Lgr5Pos_EduPos_S92

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S92]


title: Lgr5Pos_EduPos_S90

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S90]


title: Lgr5Pos_EduPos_S96

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S96]


title: Lgr5Pos_EduPos_S89

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S89]


title: Lgr5Pos_EduPos_S93

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S93]


title: Lgr5Pos_EduPos_S8

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S8]


title: ChIP-seq from GM23338 (ENCLB114JCW)

description:
https://www.encodeproject.org/experiments/ENCSR045YHA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR045YHA
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR773IYZ
encode release date: 2017-11-10
lab: Bradley Bernstein, Broad
library encode accession: ENCLB114JCW
size range: 200-600

tag: age

tag: Sex


title: Lgr5Pos_EduPos_S85

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S85]


title: d6PGCLC_1

description: Transcriptome of amplified cDNA of d6 PGCLC induced from 585B1-868 iPSC via iPSC, sorted BTAG population, rep1

tag: markers


title: Lgr5Pos_EduPos_S94

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S94]

tag: cell type


title: Lgr5Pos_EduPos_S87

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S87]


title: Lgr5Pos_EduPos_S83

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S83]


title: Lgr5Pos_EduPos_S84

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S84]


title: Lgr5Pos_EduPos_S88

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S88]


title: Lgr5Pos_EduPos_S86

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S86]


title: Lgr5Pos_EduPos_S7

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S7]


title: Lgr5Pos_EduPos_S81

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S81]


title: Lgr5Pos_EduPos_S82

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S82]


title: Lgr5Pos_EduPos_S79

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S79]


title: Lgr5Pos_EduPos_S78

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S78]


title: Lgr5Pos_EduPos_S77

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S77]


title: Lgr5Pos_EduPos_S9

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S9]


title: Lgr5Pos_EduPos_S80

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S80]


title: Lgr5Pos_EduPos_S76

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S76]


title: Lgr5Pos_EduPos_S72

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S72]


title: Lgr5Pos_EduPos_S74

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S74]


title: Lgr5Pos_EduPos_S75

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S75]


title: Lgr5Pos_EduPos_S71

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S71]


title: Lgr5Pos_EduPos_S70

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S70]


title: Lgr5Pos_EduPos_S6

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S6]


title: Lgr5Pos_EduPos_S73

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S73]


title: Lgr5Pos_EduPos_S64

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S64]


title: Lgr5Pos_EduPos_S67

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S67]


title: Lgr5Pos_EduPos_S66

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S66]


title: Lgr5Pos_EduPos_S65

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S65]


title: Lgr5Pos_EduPos_S69

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S69]


title: Lgr5Pos_EduPos_S61

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S61]


title: Lgr5Pos_EduPos_S62

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S62]


title: Lgr5Pos_EduPos_S59

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S59]


title: Lgr5Pos_EduPos_S60

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S60]


title: Lgr5Pos_EduPos_S68

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S68]


title: Lgr5Pos_EduPos_S5

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S5]


title: Lgr5Pos_EduPos_S57

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S57]


title: Lgr5Pos_EduPos_S58

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S58]


title: Lgr5Pos_EduPos_S55

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S55]


title: Lgr5Pos_EduPos_S63

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S63]


title: Lgr5Pos_EduPos_S54

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S54]


title: Lgr5Pos_EduPos_S52

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S52]


title: Lgr5Pos_EduPos_S56

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S56]


title: Lgr5Pos_EduPos_S51

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S51]


title: Lgr5Pos_EduPos_S48

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S48]


title: Lgr5Pos_EduPos_S50

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S50]


title: Lgr5Pos_EduPos_S53

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S53]


title: Lgr5Pos_EduPos_S49

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S49]


title: Lgr5Pos_EduPos_S47

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S47]


title: Lgr5Pos_EduPos_S4

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S4]


title: Lgr5Pos_EduPos_S46

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S46]


title: Lgr5Pos_EduPos_S43

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S43]


title: Lgr5Pos_EduPos_S3

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S3]


title: Lgr5Pos_EduPos_S45

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S45]


title: Lgr5Pos_EduPos_S39

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S39]


title: Lgr5Pos_EduPos_S38

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S38]


title: Lgr5Pos_EduPos_S37

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S37]


title: Lgr5Pos_EduPos_S42

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S42]


title: Lgr5Pos_EduPos_S36

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S36]


title: Lgr5Pos_EduPos_S40

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S40]


title: Lgr5Pos_EduPos_S41

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S41]


title: Lgr5Pos_EduPos_S2

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S2]


title: Lgr5Pos_EduPos_S30

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S30]


title: Lgr5Pos_EduPos_S35

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S35]


title: Lgr5Pos_EduPos_S34

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S34]


title: Lgr5Pos_EduPos_S33

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S33]


title: Lgr5Pos_EduPos_S32

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S32]


title: Lgr5Pos_EduPos_S29

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S29]


title: Lgr5Pos_EduPos_S31

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S31]


title: Lgr5Pos_EduPos_S44

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S44]


title: Lgr5Pos_EduPos_S27

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S27]


title: Lgr5Pos_EduPos_S26

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S26]


title: Lgr5Pos_EduPos_S25

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S25]


title: Lgr5Pos_EduPos_S22

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S22]


title: Lgr5Pos_EduPos_S21

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S21]


title: Lgr5Pos_EduPos_S24

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S24]


title: Lgr5Pos_EduPos_S23

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S23]


title: Lgr5Pos_EduPos_S1

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S1]


title: Lgr5Pos_EduPos_S20

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S20]


title: Lgr5Pos_EduPos_S190

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S190]


title: Lgr5Pos_EduPos_S188

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S188]


title: Lgr5Pos_EduPos_S191

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S191]


title: Lgr5Pos_EduPos_S28

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S28]


title: Lgr5Pos_EduPos_S189

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S189]


title: Lgr5Pos_EduPos_S192

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S192]


title: Lgr5Pos_EduPos_S18

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S18]


title: Lgr5Pos_EduPos_S185

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S185]


title: Lgr5Pos_EduPos_S186

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S186]


title: Lgr5Pos_EduPos_S19

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S19]


title: Lgr5Pos_EduPos_S184

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S184]


title: Lgr5Pos_EduPos_S187

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S187]


title: Lgr5Pos_EduPos_S17

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S17]


title: Lgr5Pos_EduPos_S182

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S182]


title: Lgr5Pos_EduPos_S180

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S180]


title: Lgr5Pos_EduPos_S181

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S181]


title: Lgr5Pos_EduPos_S183

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S183]


title: Lgr5Pos_EduPos_S177

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S177]


title: Lgr5Pos_EduPos_S178

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S178]


title: Lgr5Pos_EduPos_S179

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S179]


title: Lgr5Pos_EduPos_S176

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S176]


title: Lgr5Pos_EduPos_S174

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S174]


title: Lgr5Pos_EduPos_S172

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S172]


title: Lgr5Pos_EduPos_S173

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S173]


title: Lgr5Pos_EduPos_S171

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S171]


title: Lgr5Pos_EduPos_S170

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S170]


title: Lgr5Pos_EduPos_S169

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S169]


title: Lgr5Pos_EduPos_S16

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S16]


title: Lgr5Pos_EduPos_S168

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S168]


title: Lgr5Pos_EduPos_S167

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S167]


title: Lgr5Pos_EduPos_S165

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S165]


title: Lgr5Pos_EduPos_S166

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S166]


title: Lgr5Pos_EduPos_S164

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S164]


title: Lgr5Pos_EduPos_S161

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S161]


title: Lgr5Pos_EduPos_S15

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S15]


title: Lgr5Pos_EduPos_S162

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S162]


title: Lgr5Pos_EduPos_S160

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S160]


title: Lgr5Pos_EduPos_S163

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S163]


title: Lgr5Pos_EduPos_S159

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S159]


title: Lgr5Pos_EduPos_S158

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S158]


title: Lgr5Pos_EduPos_S155

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S155]


title: Lgr5Pos_EduPos_S152

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S152]


title: Lgr5Pos_EduPos_S157

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S157]


title: Lgr5Pos_EduPos_S156

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S156]


title: Lgr5Pos_EduPos_S153

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S153]


title: Lgr5Pos_EduPos_S14

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S14]


title: Lgr5Pos_EduPos_S151

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S151]


title: Lgr5Pos_EduPos_S175

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S175]


title: Lgr5Pos_EduPos_S150

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S150]


title: Lgr5Pos_EduPos_S148

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S148]


title: Lgr5Pos_EduPos_S149

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S149]


title: Lgr5Pos_EduPos_S147

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S147]


title: Lgr5Pos_EduPos_S12

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S12]


title: Lgr5Pos_EduPos_S145

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S145]


title: Lgr5Pos_EduPos_S13

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S13]


title: Lgr5Pos_EduPos_S146

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S146]


title: Lgr5Pos_EduNeg_S123

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduNeg_S123]


title: Lgr5Pos_EduPos_S11

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S11]


title: Lgr5Pos_EduNeg_S118

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduNeg_S118]


title: Lgr5Pos_EduNeg_S121

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduNeg_S121]


title: Lgr5Pos_EduNeg_S119

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduNeg_S119]


title: Lgr5Pos_EduNeg_S122

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduNeg_S122]


title: Lgr5Pos_EduNeg_S120

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduNeg_S120]


title: Lgr5Pos_EduPos_S154

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S154]


title: Lgr5Pos_EduNeg_S112

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduNeg_S112]


title: Lgr5Pos_EduNeg_S111

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduNeg_S111]


title: Lgr5Pos_EduNeg_S114

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduNeg_S114]


title: Lgr5Pos_EduNeg_S110

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduNeg_S110]


title: Lgr5Pos_EduNeg_S116

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduNeg_S116]


title: Lgr5Pos_EduPos_S10

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduPos_S10]


title: Lgr5Pos_EduNeg_S115

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduNeg_S115]


title: Lgr5Pos_EduNeg_S117

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduNeg_S117]


title: Lgr5Pos_EduNeg_S113

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduNeg_S113]


title: Lgr5Pos_EduNeg_S106

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduNeg_S106]


title: Lgr5Pos_EduNeg_S105

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduNeg_S105]


title: Lgr5Pos_EduNeg_S107

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduNeg_S107]


title: Lgr5Pos_EduNeg_S109

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduNeg_S109]


title: Lgr5Pos_EduNeg_S103

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduNeg_S103]


title: Lgr5Pos_EduNeg_S102

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduNeg_S102]


title: MHCII.Low_S98

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S98]


title: MHCII.Low_S97

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S97]


title: MHCII.Low_S382

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S382]


title: MHCII.Low_S99

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S99]


title: Lgr5Pos_EduNeg_S104

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduNeg_S104]


title: Lgr5Pos_EduNeg_S100

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduNeg_S100]


title: MHCII.Low_S381

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S381]


title: MHCII.Low_S378

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S378]


title: MHCII.Low_S375

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S375]


title: MHCII.Low_S376

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S376]


title: MHCII.Low_S377

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S377]


title: Lgr5Pos_EduNeg_S108

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduNeg_S108]


title: MHCII.Low_S380

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S380]


title: MHCII.Low_S374

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S374]


title: MHCII.Low_S371

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S371]


title: MHCII.Low_S370

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S370]


title: MHCII.Low_S369

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S369]


title: MHCII.Low_S373

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S373]


title: MHCII.Low_S372

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S372]


title: MHCII.Low_S364

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S364]


title: MHCII.Low_S365

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S365]


title: MHCII.Low_S367

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S367]


title: MHCII.Low_S368

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S368]


title: Lgr5Pos_EduNeg_S101

source_name: Div-Seq' data, single-nucleus RNA-seq after staining for EdU from Lgr5-GFP mice [Fig.S1E] [Lgr5Pos_EduNeg_S101]


title: MHCII.Low_S360

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S360]


title: MHCII.Low_S363

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S363]


title: MHCII.Low_S359

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S359]


title: MHCII.Low_S358

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S358]


title: MHCII.Low_S356

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S356]


title: MHCII.Low_S357

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S357]


title: MHCII.Low_S379

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S379]


title: MHCII.Low_S355

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S355]


title: MHCII.Low_S361

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S361]


title: MHCII.Low_S354

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S354]


title: MHCII.Low_S366

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S366]


title: MHCII.Low_S352

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S352]


title: MHCII.Low_S351

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S351]


title: MHCII.Low_S349

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S349]


title: MHCII.Low_S348

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S348]


title: MHCII.Low_S346

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S346]


title: MHCII.Low_S345

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S345]


title: MHCII.Low_S343

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S343]


title: MHCII.Low_S341

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S341]


title: MHCII.Low_S362

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S362]


title: MHCII.Low_S338

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S338]


title: MHCII.Low_S340

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S340]


title: MHCII.Low_S339

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S339]


title: MHCII.Low_S337

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S337]


title: MHCII.Low_S336

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S336]


title: MHCII.Low_S335

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S335]


title: MHCII.Low_S333

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S333]


title: MHCII.Low_S334

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S334]


title: MHCII.Low_S332

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S332]


title: MHCII.Low_S327

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S327]


title: MHCII.Low_S329

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S329]


title: MHCII.Low_S330

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S330]


title: MHCII.Low_S331

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S331]


title: MHCII.Low_S328

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S328]


title: MHCII.Low_S353

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S353]


title: MHCII.Low_S344

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S344]


title: MHCII.Low_S350

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S350]


title: MHCII.Low_S347

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S347]


title: MHCII.Low_S324

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S324]


title: MHCII.Low_S326

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S326]


title: MHCII.Low_S325

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S325]


title: MHCII.Low_S323

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S323]


title: MHCII.Low_S318

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S318]


title: MHCII.Low_S319

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S319]


title: MHCII.Low_S342

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S342]


title: MHCII.Low_S322

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S322]


title: MHCII.Low_S321

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S321]


title: MHCII.Low_S320

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S320]


title: MHCII.Low_S315

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S315]


title: MHCII.Low_S314

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S314]


title: MHCII.Low_S316

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S316]


title: MHCII.Low_S313

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S313]


title: MHCII.Low_S311

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S311]


title: MHCII.Low_S310

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S310]


title: MHCII.Low_S307

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S307]


title: MHCII.Low_S309

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S309]


title: MHCII.Low_S312

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S312]


title: MHCII.Low_S305

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S305]


title: MHCII.Low_S304

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S304]


title: MHCII.Low_S303

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S303]


title: MHCII.Low_S302

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S302]


title: MHCII.Low_S301

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S301]


title: MHCII.Low_S306

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S306]


title: MHCII.Low_S300

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S300]


title: MHCII.Low_S298

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S298]


title: MHCII.Low_S296

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S296]


title: MHCII.Low_S297

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S297]


title: MHCII.Low_S292

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S292]


title: MHCII.Low_S295

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S295]


title: MHCII.Low_S299

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S299]


title: MHCII.Low_S290

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S290]


title: MHCII.Low_S289

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S289]


title: MHCII.Low_S189

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S189]


title: MHCII.Low_S187

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S187]


title: MHCII.Low_S186

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S186]


title: MHCII.Low_S185

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S185]


title: MHCII.Low_S294

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S294]


title: MHCII.Low_S291

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S291]


title: MHCII.Low_S308

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S308]


title: MHCII.Low_S184

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S184]


title: MHCII.Low_S183

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S183]


title: MHCII.Low_S188

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S188]


title: MHCII.Low_S182

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S182]


title: MHCII.Low_S177

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S177]


title: MHCII.Low_S180

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S180]


title: MHCII.Low_S179

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S179]


title: MHCII.Low_S181

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S181]


title: MHCII.Low_S176

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S176]


title: MHCII.Low_S178

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S178]


title: MHCII.Low_S174

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S174]


title: MHCII.Low_S175

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S175]


title: MHCII.Low_S293

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S293]


title: MHCII.Low_S173

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S173]


title: MHCII.Low_S190

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S190]


title: MHCII.Low_S171

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S171]


title: MHCII.Low_S169

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S169]


title: MHCII.Low_S166

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S166]


title: MHCII.Low_S164

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S164]


title: MHCII.Low_S168

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S168]


title: MHCII.Low_S165

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S165]


title: MHCII.Low_S161

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S161]


title: MHCII.Low_S162

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S162]


title: MHCII.Low_S160

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S160]


title: MHCII.Low_S159

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S159]


title: MHCII.Low_S317

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S317]


title: MHCII.Low_S158

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S158]


title: MHCII.Low_S156

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S156]


title: MHCII.Low_S153

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S153]


title: MHCII.Low_S150

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S150]


title: MHCII.Low_S148

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S148]


title: MHCII.Low_S172

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S172]


title: MHCII.Low_S152

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S152]


title: MHCII.Low_S146

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S146]


title: MHCII.Low_S170

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S170]


title: MHCII.Low_S167

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S167]


title: MHCII.Low_S163

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S163]


title: MHCII.Low_S142

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S142]


title: MHCII.Low_S145

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S145]


title: MHCII.Low_S143

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S143]


title: MHCII.Low_S144

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S144]


title: MHCII.Low_S139

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S139]


title: MHCII.Low_S140

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S140]


title: MHCII.Low_S136

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S136]


title: MHCII.Low_S135

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S135]


title: MHCII.Low_S141

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S141]


title: MHCII.Low_S134

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S134]


title: MHCII.Low_S157

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S157]


title: MHCII.Low_S137

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S137]


title: MHCII.Low_S132

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S132]


title: MHCII.Low_S133

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S133]


title: MHCII.Low_S131

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S131]


title: MHCII.Low_S154

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S154]


title: MHCII.Low_S151

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S151]


title: MHCII.Low_S149

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S149]


title: MHCII.Low_S147

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S147]


title: MHCII.Low_S155

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S155]


title: MHCII.Low_S130

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S130]


title: MHCII.Low_S128

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S128]


title: MHCII.Low_S125

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S125]


title: MHCII.Low_S129

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S129]


title: MHCII.Low_S127

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S127]


title: MHCII.Low_S124

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S124]


title: MHCII.Low_S123

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S123]


title: MHCII.Low_S120

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S120]


title: MHCII.Low_S122

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S122]


title: MHCII.Low_S118

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S118]


title: MHCII.Low_S138

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S138]


title: MHCII.Low_S121

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S121]


title: MHCII.Low_S117

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S117]


title: MHCII.Low_S115

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S115]


title: MHCII.Low_S114

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S114]


title: MHCII.Low_S113

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S113]


title: MHCII.Low_S119

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S119]


title: MHCII.Low_S111

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S111]


title: MHCII.Low_S116

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S116]


title: MHCII.Low_S109

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S109]


title: MHCII.Low_S112

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S112]


title: MHCII.Low_S110

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S110]


title: MHCII.Low_S107

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S107]


title: MHCII.Low_S106

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S106]


title: MHCII.Low_S105

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S105]


title: MHCII.Low_S104

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S104]


title: MHCII.Low_S103

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S103]


title: MHCII.Low_S102

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S102]


title: MHCII.Low_S100

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S100]


title: MHCII.Hi_S99

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S99]


title: MHCII.Hi_S97

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S97]


title: MHCII.Hi_S98

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S98]


title: MHCII.Low_S101

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S101]


title: MHCII.Hi_S94

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S94]


title: MHCII.Hi_S93

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S93]


title: MHCII.Hi_S91

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S91]


title: MHCII.Hi_S90

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S90]


title: MHCII.Hi_S9

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S9]


title: MHCII.Hi_S92

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S92]


title: MHCII.Hi_S89

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S89]


title: MHCII.Hi_S87

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S87]


title: MHCII.Hi_S86

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S86]


title: MHCII.Hi_S88

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S88]


title: MHCII.Hi_S84

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S84]


title: MHCII.Hi_S82

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S82]


title: MHCII.Low_S108

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S108]


title: MHCII.Hi_S83

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S83]


title: MHCII.Hi_S80

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S80]


title: MHCII.Hi_S78

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S78]


title: MHCII.Hi_S8

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S8]


title: MHCII.Hi_S79

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S79]


title: MHCII.Hi_S77

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S77]


title: MHCII.Hi_S76

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S76]


title: MHCII.Hi_S74

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S74]


title: MHCII.Hi_S75

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S75]


title: MHCII.Hi_S85

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S85]


title: MHCII.Hi_S73

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S73]


title: MHCII.Hi_S7

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S7]


title: MHCII.Hi_S72

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S72]


title: MHCII.Hi_S70

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S70]


title: MHCII.Hi_S71

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S71]


title: MHCII.Hi_S69

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S69]


title: MHCII.Hi_S68

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S68]


title: MHCII.Hi_S67

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S67]


title: MHCII.Hi_S66

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S66]


title: MHCII.Hi_S65

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S65]


title: MHCII.Hi_S81

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S81]


title: MHCII.Hi_S63

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S63]


title: MHCII.Hi_S60

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S60]


title: MHCII.Hi_S61

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S61]


title: MHCII.Hi_S62

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S62]


title: MHCII.Hi_S58

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S58]


title: MHCII.Hi_S57

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S57]


title: MHCII.Hi_S64

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S64]


title: MHCII.Hi_S59

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S59]


title: MHCII.Hi_S53

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S53]


title: MHCII.Hi_S54

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S54]