title: unstimulated_CD4

first: Paul

last: Martin

state: Greater Manchester

address: Oxford Road

department: Centre for Genetics and Genomics Versus Arthritis

institute: Univeristy of Manchester

data_processing:
Raw sequence reads were aligned against the human reference (GENCODE Human Release 26 (GRCh38.p10)) using the Cell Ranger™ 2.1.0 pipeline (10X Genomics) and processed further using Seurat – R toolkit for single cell genomics 2.3.0.
Initial filtering removed cells expressing less than 200 genes and genes that were expressed in less than 3 cells. Poor quality cells and potential multiplets were classified as outside three median absolute deviations (MADs) for percentage mitochrondrial content, number of genes and number of UMIs and removed.
Following quality control, gene expression counts were normalised using the log normalisation method implemented in Seurat using default parameters. Highly variable genes were identified for downstream analysis using Seurat’s FindVariableGenes function using an average expression cut-offs of 0.0125 and 8 and a lower dispersion cut-off of 0.5. Data was scaled and centred, regressing out number of UMIs and percentage mitochondrial content. Principle component analysis was performed using the highly variable genes to identify the top 20 principle components (PCs). Graph based clustering of cells was performed using Seurat’s FindClusters method using a resolution of 1 and selected PCs. PCs were selected manually based on visual inspection of PC heat maps on the 500 most ‘extreme’ cells.
Genome_build: GRCh38
Supplementary_files_format_and_content: rds file containing clustered seurat object
Supplementary_files_format_and_content: The rds files contain the raw and processed counts for cells passing qc

growth_protocol: Cells were seeded at 1 million cells/ml in RPMI, 10% FBS, pen/strep and incubated overnight at 37˚C.

extract_protocol: 10X genomics V2 protocol as per manufacturer recommendations.

treatment_protocol: Either stimulated using Dynabeads Human T-Activator CD3/CD28 beads (ThermoFisher Scientific, Cat. No. 111.31D) for 4 hours at a ratio of 1:1 (beads:cells); or kept at the same conditions with no stimulation.

tag: stimulation

value: no


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A10_AD010

status: Public on Nov 13 2020

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 INTACT reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10 INTACT
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J P56 Mouse Brain

growth_protocol: All experimental procedures using live animals were approved by the Salk Institute Animal Care and Use Committee. The knock-in mouse line, R26R-CAG-loxp-stop-loxp-Sun1-sfGFP-Myc (INTACT) was used for most experiments4 and they were maintained on a C57BL/6J background. 42-49 day old adult male and female INTACT mice were used for the retrograde labeling experiment.

extract_protocol:
Approximately two weeks after the AAVretro injection, brains were extracted from the 56-63 day old INTACT mice, immediately submerged in ice-cold slicing buffer (2.5mM KCl, 0.5mM CaCl2, 7mM MgCl2, 1.25mM NaH2PO4, 110mM sucrose, 10mM glucose and 25mM NaHCO3) that was bubbled with carbogen, and sliced into 0.6 mm coronal sections starting from the frontal pole. From each AAVretro-injected brain, the slices were kept in the ice-cold dissection buffer from which selected brain regions (Supplementary Table 1) were manually dissected under a fluorescent dissecting microscope (Olympus SZX16), following the Allen Mouse Common Coordinate Framework (CCF), Reference Atlas, Version 3 (2015) (Extended Data Fig. 1). The dissected brain tissues were transferred to prelabeled microcentrifuge tubes, immediately frozen in dry ice, and subsequently stored at -80oC.   For each dissected brain region, samples from 2 males and 2 females were pooled separately as biological replicates for nuclei preparation. The 2-mL glass tissue dounce homogenizer and pestles (Sigma-Aldrich D8938-1SET) were pre-chilled on ice. Nuclei were prepared using a modified protocol as reported by Lacar et al., 201622. In summary, the frozen brain tissues were transferred to the dounce homogenizer with 1 mL ice-cold NIM buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT (Sigma 646563), 10μl of protease inhibitor (Sigma P8340)), with 0.1% Triton X-100 and 5μM Hoechst 33342 (Invitrogen H3570), and gently homogenized on ice with the pestle 10-15 times. The homogenate was transferred to pre-chilled microcentrifuge tubes and centrifuged at 1000 rcf for 8 min at 4oC to pellet the nuclei. The pellet was resuspended in 1 mL ice-cold NIM buffer, and again centrifuged at 1000 rcf for 8 min at 4oC. The pellet was then resuspended in 450 μL of ice-cold NSB buffer (0.25M sucrose, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT, 9ul of Protease inhibitor), and filtered through 40μM cell strainer. The filtered nuclei suspension was incubated on ice for at least 30 minutes with 50μl of nuclease-free BSA for at least 10 minutes, then incubated with GFP antibody, Alexa Fluor 488 (Invitrogen, A-21311) and anti-NeuN antibody (EMD Millipore MAB377) conjugated with Alexa Fluor 647 (Invitrogen A20173). GFP+/NeuN+ single nuclei were isolated using fluorescence-activated nuclei sorting (FANS) on a BD Influx sorter with 100μm nozzle, and sorted into 384-well plates preloaded with 2μl of digestion buffer for snmC-seq215 (20 mL digestion buffer consists of 10 mL M-digestion buffer (2×, Zymo D5021-9), 1 ml Proteinase K (20 mg, Zymo D3001-2-20), 9 mL water, and 10 µL unmethylated lambda DNA (100 pg/µL, Promega, D1521)). The collected plates were incubated at 50oC for 20 minutes then stored at -20 oC.
The bisulfite conversion and library preparation were performed following the detailed snmC-seq2 protocol as previously described (Luo, C. et al., Nat. Commun. 2018, 9(1):3824.). The snmC-Seq2 libraries were sequenced on Illumina Novaseq 6000 using the S4 flow cell 2 x 150 bp mode.

treatment_protocol: To label neurons projecting to regions of interest, injections of rAAV2-retro-Cre (produced by Salk Vector Core or Vigene, 2x10^12 to 1x10^13 viral genomes/ml, produced with capsid from Addgene plasmid #81070 packaging pAAV-EF1a-Cre from Addgene plasmid #55636) were made into both hemispheres of the INTACT mice. Animals were anesthetized with either ketamine/xylazine or isoflurane, placed in a stereotaxic frame, and 0.1 to 0.5 microliters of AAV was injected by pressure into stereotaxic coordinates corresponding to the desired projection target.

tag: strain

tag: age

tag: tissue

value: brain

tag: source

value: MOp

tag: target

value: STR

tag: gender

value: male


title: Mel-182-1_1 RNA-seq

city: Boston

first: Ben

middle: S.

last: Wittner

state: MA

address: 149 13th Street

department: Center for Cancer Research

institute: Massachusetts General Hospital

library_source: transcriptomic

data_processing:
RNA-seq reads were aligned to the GRCh38 build of the human genome reference using STAR 2.6.1d (PMID: 23104886).
Duplicated reads were identified and flagged using Picard Tools v2.18.24 MarkDuplicates.
Gene-level TPM values were calculated using RNA-SeQC v2.2.2 (PMID: 22539670).
The GENCODE v26 annotation was used for the STAR alignment and all other quantifications. All methods were run as part of the pipeline developed for the GTEx Consortium(PMID: 29022597).
Gene-level quantifications were obtained by collapsing the GENCODE annotation to a single transcript per gene, using the procedure described in GTEx Consortium(PMID: 29022597)
Genome_build: GRCh38
Supplementary_files_format_and_content: Transcripts Per Million (TPM). Rows correspond to genes, columns correspond to samples.

molecule: polyA RNA

organism: Homo sapiens

source_name: melanoma CTC line

growth_protocol: For ex vivo culture of melanoma CTCs, microfluidically processed samples were incubated in hypoxic, anchorage independent conditions as described in Yu et al (PMID: 25013076) with modifications. CTC cultures were grown in ultralow attachment plates (Corning) containing tumor sphere medium consisting of RPMI-1640 medium (with phenol red) supplemented with EGF (20ng/ml), basic FGF (20ng/ml), B27 (10ml), 1x Antibiotic-antimycotic (Life Technologies), 5μg/ml Heparin (Stemcell Technologies) and 100nM Rock inhibitor Y-27632 (EMD Millipore). Cells were cultured in a humid 37oC incubator with 5% CO2 and 4% O2. Medium was replenished 2-3 times per week, until CTCs initiated in vitro proliferation (4-8 weeks) with the following components included in CTC culture media: Mel-182 and Pem-22 blood samples were processed through the CTC-iChip using a recently developed blood stabilization method (PMID: 29170510) followed by 3-D fibrin matrigel culture initially and switched to anchorage independent condition after initial proliferation.

extract_protocol:
Cells of about 10^5-10^6 in total are disrupted in 350 microliter RLT buffer with the addition of  beta-mecaptoenthanol and then homogenized as described in the kit (RNeasy mini kit, Qiagen Cat # 74104). 70% Ethanol is added to the lysate with the volume ratio 1:1 which is then followed by column purification steps. The residual amount of DNA remaining is removed using on-column DNase treatment and RNA is eluted in 30 µl of nuclease-free water.
SmartSeqHT: According to the manufacturer’s protocol, amplified cDNA was generated by using the SMARTer HT RNA kit (Clontech/Takara) followed by Nextera® XT DNA Library Preparation kit (Illumina) for sample barcoding and fragmentation. Briefly, 10 ng of RNA was subjected to first‐strand synthesis of RNA molecules was performed using the poly‐dT‐based 3’‐SMART CDS primer II A (Clontech) followed by extension and template switching by the reverse transcriptase. The second strand synthesis and amplification polymerase chain reaction (PCR) was run for 18 cycles, and the amplified cDNA was purified with a 1× Agencourt AMPure XP bead cleanup (Beckman Coulter,). The Nextera XT DNA Library Preparation kit (Illumina) was used for sample barcoding and fragmentation according to the manufacturer's protocol. One nanogram of amplified cDNA was used for the enzymatic tagmentation, followed by 12 cycles of amplification and unique dual‐index barcoding of individual libraries. PCR product was purified with a 1.8× Agencourt AMPure XP bead cleanup (Beckman Coulter).

tag: donor

tag: cell line


title: Patient M M1

type: RNA

city: Manchester

first: Jorge

last: Barriuso

state: Please Select

address: Wilmslow Road

department: Division of Cancer Sciences

country: United Kingdom

institute: University of Manchester

hyb_protocol: Hybridation protocol as manufacturer using the Nanostring protocol for codeset plus / panel plus.

scan_protocol: Analysed in the Nanostring Digital Analyser at 555 field of view (FOV) count. Quality checks ran using Nanostring nSolverTM Software analysis was performed with no flags for any of the samples.

data_processing: Normalization was performed using the nCounter® Advanced Analysis Software 2.0. The setting was to allow the software to automatically select the best performing probes. The Advanced Nalysis uses the NormqPCR R packageto select co-expressed housekeeping genes prior to normalization and automatically find good normalization probes the threshold to omit low count data was set at 10.

label: Nanostring bar coding

molecule: total RNA

source_name: primary colon cancer

extract_protocol: Four 5μm FFPE sections mounted on unstained slides were marked up by a pathologist prior to macro-dissection and then deparaffinised using Qiagen deparaffination solution. Following RNA extraction using the RNeasy FFPE Kit from Qiagen RNA abundance was measured using a Qubit fluorometer.  The extracted RNA was then stored at minus 80°C. Total RNA average input into the hybridisation step was 103 ng.NA average input into the hybridisation step was 103 ng.

tag: subject id

value: Patient M

tag: status at the end of study

value: Alive

tag: histology

value: non mucinous

tag: Sex

value: Male

tag: Stage

value: IV

tag: overall survival in months

tag: tissue type

value: primary colon cancer


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A10_AD008

value: female


title: Mel-167_3 RNA-seq


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A10_AD007


title: stimulated_CD4

source_name: PBMC

value: yes


title: Patient K K1

label_protocol: Qiagen RNA abundance was measured using a Qubit fluorometer.  The extracted RNA was then stored at minus 80°C. Total RNA average input into the hybridisation step was 103 ng.NA average input into the hybridisation step was 103 ng.

value: Patient K

value: Dead

value: mucinous

value: Female


title: Mel-167_2 RNA-seq


title: Patient J J2

source_name: peritoneal metastases

value: Patient J

value: peritoneal metastases


title: Patient J J1


title: Mel-182-2_2 RNA-seq


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A10_AD006

value: brain

value: MOp

value: SC


title: ATACSeq_PSEN1_M146L_iPSCNeuron_rep1

first: Shankar

last: Subramaniam

address: 9500 Gilman Drive

department: Department of Bioengineering

institute: University of California, San Diego

data_processing:
ATAC-Seq data preprocessing was performed using the BBDuk package (v37.95) in the BBTools suite, removing sequencing adaptors and selecting for all paired-end reads above a quality score threshold (Phred Q>10).
Trimmed reads were aligned to the GRCh38 human genome (GCA_000001405.15 with no alternative analysis) using BBMap v37.95 in the BBtools suite with the options maxindel=20 ambig=random.
Sorting and indexing of bam files was performed using Samtools v1.3, and annotation of PCR duplicates using the Picard v2.3.0 markDuplicates function with the option VALIDATION_STRINGENCY=LENIENT. All duplicates and Mitochondrial, Chromosome X, Chromosome Y, and EBV reads were removed using Samtools v1.3 command view with the options -b -h -f 3 -F 4 -F 8 -F 256 -F 1024 -F 2048.
To determine regions of open chromatin, bam files were first converted to bedGraph format using bedtools v2.25.0 functions bamtobed and genomecov, and then finally converted to bigWig format using UCSC bedGraphToBigWig. HMMRATAC v1.0 was used to call peaks on the ATAC-Seq data and determine regions of open chromatin with the options –m 50,200,400,600 --score all.
These specifically called open regions of chromatin were then passed to the R package Diffbind v2.8.0 to determine regions of differential accessibility between the NDC and psen1M146L conditions using the edgeR method.
Differentially accessibly regions of DNA were annotated using the R packages ChIPpeakAnno v3.14.0 and TxDb.Hsapiens.UCSC.hg38.knownGene v3.4.0, defining the promoter region -1000 to 1000 bp from the TSS.
Genome_build: GCA_000001405.15
Supplementary_files_format_and_content: Bed files of HMMRATAC summits

source_name: hiPSC-derived neurons from human EOFAD patient, psen1 M146L mutation

growth_protocol: Non-Demented Control (NDC) and psen1M146L fibroblasts were derived from skin biopsies in accordance with UC San Diego IRB approval. The generation and characterization of the hiPSC lines were carried out as previously reported from fibroblasts by retroviral transduction using the reprogramming factors oct4, sox2, klf4, and c-myc. Neural stem cells (NSCs) were expanded in NSC growth medium (DMEM /F12, GlutamaxTM (Thermo Fisher Cat. 10565018), 1x B-27 (Thermo Fisher Cat. 17504044), 1x N-2 (Thermo Fisher Cat. 17502001), 1x Penicillin-Streptomycin (Thermo Fisher Cat. 15070063), and 20ng/mL human bFGF-2 (BioPioneer Cat. HRP-0011)). At 80% confluence, the medium was changed to neural differentiation medium (DMEM /F12, GlutamaxTM, 1x B-27, 1x N-2, and 1x Penicillin-Streptomycin) for 3 weeks of differentiation. After differentiation, the cultures were dissociated with Accutase (Sigma Cat. A6964). Cells were resuspended in 200μL of IMag buffer (1x neural differentiation medium, 0.5µM EDTA, 0.5% Bovine Serum Albumin) followed by incubation with PE Mouse Anti-Human CD184 and CD44 antibodies (BD Biosciences Cat. 561733 and 561858, respectively) for 15min on ice in the dark. The mixture was washed with IMag buffer and subsequently incubated with magnetic beads (BD Biosciences) for 30min at room temperature. Magnetic bead separation was carried out for 8min according to the manufacturer’s protocol (BD Biosciences). The supernatant containing purified CD184-/CD44- neurons was then removed and spun down for RNA-Seq.

extract_protocol:
ATAC-Seq transposition experiments were performed as previously reported on 50,000 NDC and psen1M146L (biological replicates, n = 2) hiPSC-derived neurons cells, using the Illumina Nextera DNA Sample Preperation kit (Illumina, Cat. 15028523) and Qiagen MinElute PCR Purification kit (Qiagen, Cat. 28004).
ATAC-Seq libraries were generated from transposed DNA using the Kapa Biosystems Real-Time Library Amplification kit (Kapa Biosystems, Cat. 07959028001) according to the manufacturer’s recommendations, monitoring amplification by qPCR and stopping the reaction when all samples reached a fluorescence amplification intensity between standards 1 and 3. ATAC-Seq libraries were further purified using the Qiagen MinElute PCR Purification kit and sequenced at the UC San Diego IGM sequencing core on an Illumina HiSeq4000 platform generating Paired-End, 50bp reads with an average of 25 million reads per sample.

tag: cell type

value: hiPSC-derived neuron


title: Patient I I2

value: Patient I


title: Mel-167_1 RNA-seq


title: ATACSeq_PSEN1_M146L_iPSCNeuron_rep2


title: Patient M M2

value: Patient M

value: Alive

value: non mucinous


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A10_AD004

value: male


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A11_AD004


title: ATACSeq_NDC_iPSCNeuron_rep2

source_name: hiPSC-derived neurons from human Non-Demented Control patient


title: Patient I I1

value: IV

value: primary colon cancer


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A10_AD002

value: female


title: Mut2_OR_80603-S6

city: LA

first: Yuanyuan

last: Ma

address: 2250 Alcazar Street

department: CCMB

institute: USC

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome and transcriptome using STAR 2.6.1d, and normalized
Lognormal with shrinkage mean value were calculated using Gene-specific analysis by Partek flow (Partek Inc., USA).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include lognormal with shrinkage mean value for each feature in individual sample.

source_name: molar

growth_protocol: Osr2-Cre;Ror2fl/+ male mice were crossed with Ror2fl/fl female mice to generate Osr2-Cre;Ror2fl/fl mice

extract_protocol: Dental pulp of the mandibular first molar was dissected out from Ror2fl/fl control mice and Osr2-Cre;Ror2fl/fl mice at PN3.5. RNA was then extracted using Rneasy® Micro kit (Qiagen).

value: Dental pulp

tag: developmental stage

tag: genotype


title: Mut1_OR_80602-S5

tag: strain


title: Mut3_OR_81401-S7

tag: tissue


title: Patient H H2

value: Patient H

value: Dead

value: mucinous

tag: age


title: 180118_CEMBA_mm_P56_P63_RS2_180117_P1_180117_P2_A10_AD001

tag: source

tag: target


title: Patient H H1

value: Female


title: Meninges_Colitis_6

city: Cambridge

first: John

middle: Robert

last: Ferdinand

address: Department of Medicine

institute: University of Cambridge

data_processing:
Files were demutiplexed using Casava
Reads were checked for quality with FastQC and trimmed using TrimGalore!
Trimed reads were alligned to the mm10 genome with Hisat2 and counted usign Feature Counts from Rseubread
Genome_build: mm10

source_name: Colon

extract_protocol:
Meninges were extracted into RNA later and stored at -80 until processing. RNA was extracted with RNEasy plus micro kit (Qiagen)
Libraries were produced with TruSeq stranded total RNA library prep kit (Illumina)

treatment_protocol: Mice recived 2%DSS for the first 5 days in drinking water after which it was replaced with normal water. The mice were culled after 6 days.

tag: treatment

value: DSS


title: Patient G G2

value: Patient G

value: peritoneal metastases


title: Meninges_Colitis_5


title: Meninges_Colitis_4


title: 92001_OW_S6-con


title: ATACSeq_PSEN1_A246E_iPSCNeuron_rep2

data_processing:
ATAC-Seq data preprocessing was performed using the TrimGalore! Package, removing sequencing adaptors and selecting for all paired-end reads above a quality score threshold (Phred Q>20).
Trimmed reads were aligned to the GRCh38 human genome (GCA_000001405.15 with no alternative analysis) using BBMap v37.95 in the BBtools suite with the options maxindel=20 ambig=random.
Sorting and indexing of bam files was performed using Samtools v1.3, and annotation of PCR duplicates using the Picard v2.3.0 markDuplicates function with the option VALIDATION_STRINGENCY=LENIENT. All duplicates and Mitochondrial, Chromosome X, Chromosome Y, and EBV reads were removed using Samtools v1.3 command view with the options -b -h -f 3 -F 4 -F 8 -F 256 -F 1024 -F 2048.
To determine regions of open chromatin, HMMRATAC v1.2.4 was used to call peaks on the ATAC-Seq data and determine regions of open chromatin with the options –m 50,200,400,600 --score all.
Genome_build: GCA_000001405.15
Supplementary_files_format_and_content: Bed files of HMMRATAC summits

source_name: hiPSC-derived neurons from human EOFAD patient, psen1 A246E mutation

growth_protocol: Non-Demented Control (NDC), PSEN1M146L, and PSEN1H163R, and PSEN1A431E fibroblasts were derived from skin biopsies in accordance with UC San Diego IRB approval, whereas PSEN1A246E fibroblasts were obtained commercially (Coriell Cat. AG06840). The generation and characterization of the hiPSC lines were carried out as previously reported from fibroblasts by retroviral transduction using the reprogramming factors OCT4, SOX2, KLF4, and c-MYC. PA6 cells were plated in a 10 cm dish and seeded with 100,000 cells iPSC next day. To enhance neural induction, cultures were treated with 500ng/ml Noggin (R&D Systems) and 10μM SB431542 (Tocris) for the first 6 days of differentiation. On day 12, neural stem cells (NSCs) were sorted using cell surface signature CD24+/CD184+/CD44-/CD271-. NSCs were expanded in NSC growth medium (DMEM:F12+GlutamaxTM (Thermo Fisher Cat. 10565018), 1x B-27 (Thermo Fisher Cat. 17504044), 1x N-2 (Thermo Fisher Cat. 17502001), 1x Penicillin-Streptomycin (Thermo Fisher Cat. 15070063), and 20ng/mL human bFGF-2 (BioPioneer Cat. HRP-0011)). At 80% confluence, the medium was changed to neuron differentiation medium (DMEM:F12+GlutamaxTM, 1x B-27, 1x N-2, 1x Penicillin-Streptomycin) for 3 weeks of differentiation. After differentiation, the cultures were dissociated with Accutase (Sigma Cat. A6964). Cells were resuspended in 200μL of iMag buffer (1x neural differentiation medium, 0.5µM EDTA, 0.5% Bovine Serum Albumin) followed by incubation with PE Mouse Anti-Human CD184 and CD44 antibodies (BD Biosciences Cat. 561733 and 561858, respectively) for 15min on ice in the dark. The mixture was washed with iMag buffer and subsequently incubated with anti-PE conjugated magnetic beads (BD Biosciences) for 30min at room temperature. Magnetic bead separation was carried out for 8min according to the manufacturer’s protocol (BD Biosciences). The supernatant containing purified CD184-/CD44- neurons was then removed and spun down for sequencing.

extract_protocol:
ATAC-Seq transposition experiments were performed as previously reported on 50,000 NDC (n = 5), PSEN1M146L (n = 2), PSEN1H163R (n = 3), PSEN1A246E (n = 2), and PSEN1A431E (n = 3) hiPSC-derived neurons using the Illumina Nextera DNA Sample Preperation kit (Illumina, Cat. 15028523) and Qiagen MinElute PCR Purification kit (Qiagen, Cat. 28004).
ATAC-Seq libraries were generated from transposed DNA using the Kapa Biosystems Real-Time Library Amplification kit (Kapa Biosystems, Cat. 07959028001) according to the manufacturer’s recommendations, monitoring amplification by qPCR and stopping the reaction when all samples reached a fluorescence amplification intensity between standards 1 and 3. ATAC-Seq libraries were further purified using the Qiagen MinElute PCR Purification kit and sequenced at the UC San Diego IGM sequencing core on an Illumina HiSeq4000 platform generating Paired-End, 50bp reads with an average of 25 million reads per sample.

value: hiPSC-derived neuron


title: 047-2_WT (BS-seq)

city: brookline

first: Harrison

middle: Wren

last: Gabel

state: Massachusetts

address: 220 longwood avenue

department: Neurbiology

institute: Harvard Medical School

data_processing:
Data were adapter-trimmed, mapped to mm9, then deduplicated and called for methylation using BS-seeker2. Methylation levels across regions was assessed using bedtools map -o sum, summing the number of reads mapping to Cs (supporting mC), and the amount of coverage in the region, then dividing those two numbers(Quinlan and Hall, 2010). Hydroxymethylation was calculated as the percent methylation found in the BS-seq minus the percent methylation found in the matching oxBS-seq. Due to count noise, this occasionally resulted in apparent negative hydroxymethylation. During bisulfite sequencing not all DNA can be efficiently bisulfite converted. Though our methods should maximize the amount of converted unmethylated C, there is still a small percentage of unmethylated cytosines that are called as methylated due to non-conversion (0.2-0.3%). Due to this non-conversion, very lowly methylated regions (e.g. mCA at CpG islands) may not show the same percent reduction in mCA as highly methylated regions. Data were visualized using the UCSC genome browser (http://genome.ucsc.edu) (Kent et al., 2002).
Genome_build: mm9
Supplementary_files_format_and_content: mdt_table_GEO2.tsv: Tab-separated table (with header) of genes, and acetyl peaks, of mCA and mCG values of these regions in DNMT3A heterozygous KO and WT cortex.

source_name: Cortex

growth_protocol: For cortical cultures, samples were chosen for whole genome bisulfite sequencing if mutant and WT samples expressed equal amounts of Dnmt3a mRNA as measured by qRT-PCR. For tissue samples, tissue was taken from mice maintained under standard housing conditions.

extract_protocol:
For tissue samples, tissue was dissected from littermate mice in ice-cold PBS, flash-frozen in liquid nitrogen, and stored at -80°C. DNA was isolated from tissue and cultured cells using the DNeasy Kit.
DNA was bisulfite converted and prepared for sequencing using the Tecan Ovation Ultralow Methyl-Seq Kit and the Epitect Bisulfite Kit was used for bisulfite conversion. We used alternate bisulfite conversion cycling conditions ([95°C, 5 min; 60°C, 20 min] x 4 cycles, 20°C hold) to ensure lowest possible bisulfite non-conversion rate.
Libraries were either sequenced at a depth of 0.01-0.03x genomic coverage using an Illumina MiSeq 2x150 through the Spike-In Cooperative at Washington University in St. Louis, sequenced at 6.4-7.8x coverage per biological rep with a Illumina HiSeq3000 at the Genome Technology Access Center at Washington University in St. Louis, or with a Illumina NextSeq500 at the Edison Family Center for Genome Sciences & Systems Biology.

value: wild type

value: Cortex

value: 8 weeks


title: Meninges_Colitis_3


title: Meninges_Colitis_2


title: RNASeq_PSEN1_M146L_iPSCNeuron_rep4

description: RNASeq_DESeq2_DEGs_PSEN1M146L_iPSCNeuron.csv

data_processing:
RNA-Seq data preprocessing was performed using the BBDuk package (v37.95) in the BBTools suite, removing sequencing adaptors and selecting for all paired-end reads above a quality score threshold (Phred Q>10).
Trimmed RNA-Seq reads were mapped to the GRCh38.p12 human transcriptome using Salmon v0.9.12 with the options --gcBias --seqBias --biasSpeedSamp 5.
Transcript level summation to the gene level using the R package tximport v1.8.0.
Differential expression analysis was performed for psen1M146L and psen1A246E iPSC-derived neurons relative to NDC using the R package DESeq2 v1.20.0, selecting for genes with a q-value (FDR-adjusted p-value) of <0.01 and a log2 fold-change of >0.5.
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: Differentially expressed genes relative to NDC

growth_protocol: Non-Demented Control (NDC) and psen1M146L fibroblasts were derived from skin biopsies in accordance with UC San Diego IRB approval, whereas psen1A246E fibroblasts were obtained commercially (Coriell Cat. AG06840). The generation and characterization of the hiPSC lines were carried out as previously reported from fibroblasts by retroviral transduction using the reprogramming factors oct4, sox2, klf4, and c-myc. Neural stem cells (NSCs) were expanded in NSC growth medium (DMEM /F12, GlutamaxTM (Thermo Fisher Cat. 10565018), 1x B-27 (Thermo Fisher Cat. 17504044), 1x N-2 (Thermo Fisher Cat. 17502001), 1x Penicillin-Streptomycin (Thermo Fisher Cat. 15070063), and 20ng/mL human bFGF-2 (BioPioneer Cat. HRP-0011)). At 80% confluence, the medium was changed to neural differentiation medium (DMEM /F12, GlutamaxTM, 1x B-27, 1x N-2, and 1x Penicillin-Streptomycin) for 3 weeks of differentiation. After differentiation, the cultures were dissociated with Accutase (Sigma Cat. A6964). Cells were resuspended in 200μL of IMag buffer (1x neural differentiation medium, 0.5µM EDTA, 0.5% Bovine Serum Albumin) followed by incubation with PE Mouse Anti-Human CD184 and CD44 antibodies (BD Biosciences Cat. 561733 and 561858, respectively) for 15min on ice in the dark. The mixture was washed with IMag buffer and subsequently incubated with magnetic beads (BD Biosciences) for 30min at room temperature. Magnetic bead separation was carried out for 8min according to the manufacturer’s protocol (BD Biosciences). The supernatant containing purified CD184-/CD44- neurons was then removed and spun down for RNA-Seq.

extract_protocol:
Total RNA from magnetically purified human NDC, psen1M146L, and psen1A246E (biological replicates, n = 4) hiPSC-derived neurons was prepared using RNeasy Plus Micro Kit (Qiagen Cat. 74034) according to the manufacturer’s protocol. On-column DNAse digestion was subsequently performed on total RNA extracts according to the manufacturer’s recommendations to remove any genomic contamination (Qiagen Cat. 79254).
Libraries were prepared for RNA-Seq using the TruSeq Stranded Total RNA Library prep kit (Illumina, Cat. RS-122-2303) by the Ribo-Zero ribosomal RNA reduction method (Illumina, Cat. MRZG12324). Samples were sequenced at the UC San Diego Institute for Genomics Medicine (IGM) sequencing core on an Illumina HiSeq4000 generating Paired-End, 100bp reads with an average of 25 million reads per sample (Illumina, Cat. FC-410-1001).

value: psen1M146L fibroblasts


title: 047-1_hKO (BS-seq)

value: Heterozygous KO


title: RNASeq_PSEN1_M146L_iPSCNeuron_rep2


title: RNASeq_PSEN1_M146L_iPSCNeuron_rep3


title: Meninges_Colitis_1


title: ATACSeq_NDC_iPSCNeuron_rep1


title: Patient G G1

value: IV


title: 651-3_WT (BS-seq)


title: Patient F F1

value: Patient F

value: non mucinous

value: Male

value: primary colon cancer


title: Patient F F2

value: Dead


title: 92002_OW-S7-con

value: Dental pulp


title: RNASeq_PSEN1_M146L_iPSCNeuron_rep1


title: Meninges_Control_6

value: Control


title: Patient E E1

value: Patient E

value: Alive

value: Female


title: Patient E E2

value: peritoneal metastases


title: RNASeq_NDC_iPSCNeuron_rep4

value: hiPSC-derived neuron

value: Non-Demented Control (NDC)


title: 651-2_hKO (BS-seq)

value: Cortex

value: 8 weeks


title: Il33_2

city: Philadelphia

first: De'Broski

last: Herbert

state: PA

address: 3900 Spruce Street

department: Pathobiology

institute: University of Pennsylvania

data_processing:
Fastq files were trimmed with trimmomatic version 0.39, to remove Illumina Truseq universal and indexed adapter sequences, and low quality reads
trimmed fastq files were aligned to version 81 of mouse reference genome GRCm38 using the STAR aligner
Sorted BAM files resulting from the alignments were quantified to genes using htseq-count, using the union mode for read overlap resolution
Count data was filtered to remove genes with less than 5 counts,  and differential expression analysis was run with the DESeq2 package in R.
Genome_build: version 81 of mouse reference genome GRCm38
Supplementary_files_format_and_content: the tab-delimited text file includes un-normalized counts for each sample, and csv file contains normalized expression values for each sample, and Log2FoldChange and p-values resulting from DESeq2 analysis

growth_protocol: mice were injected with EL4-Flt3 tumor cells and grown for 10 days before sacrifice

extract_protocol:
Cell pellets were lysed and RNA was extracted using the Qiagen RNAeasy plus kit
Libraries were prepared using the Illumina Truseq mRNA prep kit

treatment_protocol: spleen and mesenteric lymph node cells were harvested and FACS sorted on CD45+, CD64-, CD11b+, MHCII+, CD103+

value: Injected with EL4-Flt3 tumor cells for 10 days

value: spleen + mesenteric lymph node


title: 91002-WW-S5-con


title: RNASeq_NDC_iPSCNeuron_rep3


title: Meninges_Control_5


title: Meninges_Control_4


title: Patient D D1

value: Patient D

value: mucinous

value: IV


title: Patient D D2

value: Male


title: Il33_1


title: Meninges_Control_3


title: Meninges_Control_2


title: Ctrl_1

source_name: Ctrl


title: RNASeq_NDC_iPSCNeuron_rep1


title: ChIPSeq_PSEN1_M146L_iPSCNeuron_H3K27Me3

data_processing:
ChIP-Seq data preprocessing was performed using the BBDuk package (v37.95) in the BBTools suite, removing sequencing adaptors and selecting for all -end reads above a quality score threshold (Phred Q>10).
Trimmed ChIP-Seq reads were aligned to the GRCh38 human genome (GCA_000001405.15 with no alternative analysis) using BBMap v37.95 in the BBtools suite with the options maxindel=20 ambig=random.
Sorting and indexing of bam files was performed using Samtools v1.3, and annotation of PCR duplicates using the Picard v2.3.0 markDuplicates function with the option VALIDATION_STRINGENCY=LENIENT.
ChIP-Seq peak calling and differential histone methylation was performed using Homer v4.10; briefly, tags were generated from preprocessed bam files using the function makeTagDirectory, peaks called at a FDR of 0.05 using the function findPeaks with the options -style histone -gsize 2.7e9 -fdr 0.05 -region -size 500 for H3K4Me3 and -style histone -gsize 2.7e9 -fdr 0.05 -region -size 2000 for H3K27Me3, and differential histone methylation calculated using the function getDifferentialPeaks with the options -F 2 and -size 600 for H3K4Me3 and -F 2 and -size 2500 for H3K27Me3. The Homer function annotatePeaks was used to annotate regions of differential histone methylation to the GRCh38 genome.
Genome_build: GCA_000001405.15
Supplementary_files_format_and_content: Homer peaks relative to 1% genomic DNA input

extract_protocol:
NDC and psen1M146L (biological replicates, n = 1) hiPSC-derived neurons were processed using the Active Motif ChIP-IT High Sensitivity kit according to the manufacturer’s recommendations (Active Motif, Cat. 53040). Briefly, cells were washed with cold 1x PBS and collected in a 1.5 mL tube in PBS, followed by formaldehyde fixation for 10 min at room temperature. After addition of stop solution, cells were incubated at room temperature for 5 min and subsequently washed with 1x PBS Wash Buffer and resuspended in Chromatin Prep Buffer. Following incubation on ice for 10 min, cells were lysed by performing 30 plunges in a chilled dounce homogenizer. Samples were then resuspended in Active Motif ChIP Buffer and chromatin sonication performed using a probe tip sonicator on ice for a total of 10 min per sample (30x 20 sec intervals). Optimal sonicated chromatin fragment lengths were confirmed by agarose gel and used for IP reactions. 500 ng of purified, sonicated chromatin was incubated with 5 µL of H3K4Me3 (Active Motif, Cat. 39159) or H3K27Me3 (Active Motif, Cat. 39155) Rabbit polyclonal antibody overnight at 4C. After de-crosslinking, ChIP DNA was purified using the Qiagen MinElute PCR Purification Kit (Qiagen, Cat. 28004).
Libraries for H3K4Me3, H3K27Me3, and 1% Input were generated for NDC and psen1M146L conditions at the UC San Diego IGM sequencing core using Illumina TruSeq LT adaptors (Illumina Cat. FC-121-2001). Sequencing performed on Illumina HiSeq4000 generating Single-Read, 75bp reads with an average of 20 million reads per sample.

tag: chip antibody

value: H3K27Me3 (Active Motif, Cat. 39155)


title: Meninges_Control_1


title: ChIPSeq_PSEN1_M146L_iPSCNeuron_H3K4Me3

value: H3K4Me3 (Active Motif, Cat. 39159)


title: Patient C C1

tag: subject id

value: Patient C

value: primary colon cancer


title: Patient B B1

value: Patient B

tag: status at the end of study

value: Alive

value: non mucinous


title: Patient C C2

tag: histology

value: Female

value: peritoneal metastases


title: Patient B B2

tag: Sex


title: Patient A A1

value: Patient A

value: Dead

tag: Stage


title: Patient A A2

tag: overall survival in months


title: pc6

city: Beijing

first: Jiacheng

last: Wang

address: Workers’ stadium south road No.8, Chao-Yang District, Beijing, China

country: China

institute: Beijing Chao-Yang Hospital

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
And reads were trimmed and cleaned by removing the sequences smaller than 15nt or longer than 35 nt.
At the same time, Q20, Q30, GC-content of the clean data were calculated.
All the downstream analyses were based on clean data with high  quality.
Genome_build:
Supplementary_files_format_and_content:

source_name: serum of parathyroid carcinoma

extract_protocol:
Exosomes were separated via ultracentrifugation
RNA degradation and contamination, especially DNA contamination, was monitored on 1.5% agarose gels. RNA concentration and purity were measured using the NanoDrop 2000 Spectrophotometer (Thermo Fisher Scientific, Wilmington, DE). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 System (Agilent Technologies, CA, USA).
A total amount of 2.5 ng RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNextR UltraTM small RNA Sample Library Prep Kit for IlluminaR(NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, first of all, ligated the 3′ SR Adaptor. Mixed 3′ SR Adaptor for Illumina, RNA and Nuclease-Free Water, mixture system after incubation for 2 minutes at 70 degrees in a preheated thermal cycler. Tube was transfer to ice. Then, add 3′ Ligation Reaction Buffer (2X) and 3′ Ligation Enzyme Mix ligate the 3′ SR Adaptor. Incubated for 1 hour at 25°C in a thermal cycler. To prevent adaptor-dimer formation, the SR RT Primer hybridizes to the excess of 3′ SR Adaptor (that remains free after the 3′ ligation reaction) and transforms the single stranded DNA adaptor into a double-stranded DNA molecule. dsDNAs are not substrates for ligation mediated. The second, ligated the 5′ SR Adaptor. Then, reverse transcription synthetic first chain. Last, PCR amplification and Size Selection. PAGE gel was used to electrophoresis fragment screening purposes, rubber cutting recycling as the pieces get small RNA libraries. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: All blood specimens were immediately centrifuged and the harvested serum specimens were stored at -80°C.

tag: subject status

value: parathyroid carcinoma (PC) patient

tag: tissue/sample type

value: exosome derived from serum

value: untreated

tag: time point

value: before surgery

tag: molecule subtype

value: microRNA


title: H4K20me3_SUV420H2_KO_mESC_rep2

city: Detroit

first: Benjamin

middle: L

last: Kidder

state: MI

address: 4100 John R St

department: Oncology

institute: Wayne State University

description: Hi-C

data_processing:
Juicer was utilized to convert the raw sequencing data to a hic file containing normalized Hi-C contact matrices.
Genome_build: mm9
Supplementary_files_format_and_content: Hic

source_name: ESC

growth_protocol: ES cells were cultured on gelatin-coated dishes in ES cell media containing 1.5 µM CHIR9901 (GSK3 inhibitor) for several passages to remove feeder cells. ES cells were passed by washing with PBS, and dissociating with trypsin.

extract_protocol:
In situ Hi-C was performed for WT and SUV420H2 KO ES cells using the Arima-HiC kit (Arima Genomics Inc) as described by the manufacturer.
In situ Hi-C was performed for WT and SUV420H2 KO ES cells using the Arima-HiC kit (Arima Genomics Inc) as described by the manufacturer.

tag: cell type

value: ESC

tag: genotype/variation


title: ChIPSeq_PSEN1_M146L_iPSCNeuron_INPUT

value: hiPSC-derived neuron

value: 1% Input


title: H4K20me3_WT_mESC_rep1_rep2_merge

description: Hi-C


title: IV LUHMES GFP - MPP+

city: Homburg

first: Lena

last: Krammes

address: Kirrbergerstraße

department: Institute for Human Genetics

country: Germany

institute: Saarland University

description: miRNA expression without MPP+ treatment of LUHMES cells

hyb_protocol: The expression profile of 2549 human miRNAs was determined using SurePrint G3 8x60k miRNA microarrays (Agilent) according to the manufacturers recommendations

scan_protocol: Arrays were scanned with the Agilent Scanner with default settings.

data_processing: Analysis of the received fluorescence signals was done by using Agilent AGW Feature Extraction software (version 10.7.1.1, Agilent Technologies, Santa Clara, CA, USA). Normalization of background corrected values was performed using GeneSpring by biological significance analysis (version 14.9, Agilent Technologies, Santa Clara, CA, USA).

label: Cyanine 3

source_name: LUHMES cell line

label_protocol: The expression profile of 2549 human miRNAs was determined using Agilent miRNA Complete Labeling and Hyb Kit (Agilent, Cat. No 5190-0456) according to the manufacturers recommendations

growth_protocol: LUHMES cells were cultured in flasks pre-coated with 50 µg/mL Poly-L-ornithin and 1 µg/mL Fibronectin. Cells were cultured in advanced DMEM/F12 (Life Technologies GmbH, Darmstadt, Germany) supplemented with 1% N2-Supplement, 2 mM L-glutamine and 40 ng/mL basic fibroblast growth factor.

extract_protocol: Total RNA including miRNAs was isolated using the Qiagen miRNeasy Kit according to manufacturers recommendations.

treatment_protocol: For differentiation of LUHMES cells towards dopaminergic neurons, cells were cultured in advanced DMEM/F12 (Life Technologies GmbH, Darmstadt, Germany) supplemented with 1% N2-Supplement, 2 mM L‑glutamine, 1 mM dibutyryl cAMP, 2 ng/mL GDNF and 1 μg/mL tetracycline. After 48 hours, cells were trypsinized and seeded with 7.5 x 104 cell/cm² in pre-coated flasks. Every 48 hours after re-seeding, fresh differentiation medium was added to the cells for six days. To induce a PD-like phenotype, LUHMES cells were treated with 10 µM 1-methyl-4-phenylpyridinium (MPP+; Sigma Aldrich, Munich, Germany) 6 days after initiation of differentiation for 48 hours. Control cells were supplemented with H2O.

tag: pd phenotype

value: n


title: IV LUHMES GFP + MPP+

description: miRNA expression after MPP+ treatment of LUHMES cells

value: y


title: ChIPSeq_NDC_iPSCNeuron_H3K4Me3

value: H3K4Me3 (Active Motif, Cat. 39159)


title: ChIPSeq_NDC_iPSCNeuron_H3K27Me3

value: H3K27Me3 (Active Motif, Cat. 39155)


title: Ctrl_2

value: Injected with EL4-Flt3 tumor cells for 10 days

tag: genotype

tag: tissue

value: spleen + mesenteric lymph node


title: pc5

tag: treatment


title: RNASeq_NDC_iPSCNeuron_rep2

value: Non-Demented Control (NDC)


title: H4K20me3_SUV420H2_KO_mESC_rep1_rep2_merge

description: Hi-C


title: ChIPSeq_NDC_iPSCNeuron_INPUT

tag: chip antibody


title: II LUHMES GFP + MPP+


title: III LUHMES GFP - MPP+


title: pc4


title: III LUHMES GFP + MPP+


title: H4K20me3_WT_mESC_rep1

description: Hi-C

value: wild type


title: pc1


title: sample1

city: jinan

first: Yuanxue

last: Yang

state: Shandong

address: No.202 Gongyebei Road

institute: Shandong Academy of Agricultural Sciences

data_processing:
Cutadapt and perl scripts in house were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases
The sequence quality was verified using FastQC
Trinity 2.4.0 was performed to de novo assembly of the transcripts
he longest transcript in the cluster was chosen as the representative gene sequence. All assembled transcripts were aligned against the non-redundant (Nr) protein database (http://www.ncbi.nlm.nih.gov/), Gene Ontology (GO) (http://www.geneontology.org), SwissProt (http://www.expasy.ch/sprot/), Kyoto Encyclopedia of Genes and Genomes (KEGG) (http://www.genome.jp/kegg/), and eggnog (http://eggnogdb.embl.de/) databases using DIAMOND with a threshold of E-value < 10-5

organism: Aphis craccivora

source_name: total insect

growth_protocol: The SUS strain of A. craccivora  reared without any contact with insecticides in the laboratory.

extract_protocol:
The total RNA was extracted using Trizol reagent (Life Technologies, USA) following the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: sample type

value: total insect

tag: strain

value: susceptible strain

tag: age

value: adult


title: pa5

source_name: serum of parathyroid adenoma

value: parathyroid adenoma (PA) patient

value: exosome derived from serum

value: untreated


title: pa6

value: before surgery

value: microRNA


title: SUV420H1_H2_DKO_mESC_diff_d12

description: RNA-Seq

data_processing:
Sequence reads were obtained and mapped to the mouse (mm9) genomes with Bowtie2.
The RPKM measure (read per kilo bases of exon model per million reads) was used to quantify the mRNA expression level of a gene from RNA-Seq data sets. The RBPM measure (read per base per million reads) was used to generate graph files.
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph

source_name: mouse ES cells

extract_protocol:
RNA was harvest using RNeasy and miRNeasy Qiagen kits.
RNA-Seq libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina and sequenced on an Illumina platform.

value: SUV420H1_H2 DKO differentiated day 12

value: ES cell


title: H4K20me3_SUV420H2_KO_mESC_rep1

description: Hi-C

value: ESC


title: SUV420H1_H2_DKO_mESC_diff_d8

description: RNA-Seq

value: SUV420H1_H2 DKO differentiated day 8


title: SH2

city: Fort Collins

first: Ahmed

last: Gad

state: Colorado

address: 3107 Rampart Rd

department: Biomedical Sciences

institute: Colorado State University

description: Isolated from extracellular vesicles

data_processing:
FASTQ files for each sample were generated using the bcl2fastq software (Illumina Inc.)
Information of adapter and UMI in raw reads was extracted using Cutadapt1.11
The output from cutadapt is used to remove adapter sequences and reads ≥18 nucleotides were analyzed for the presence of Unique Molecular Indices (UMIs). All reads containing identical insert sequence and UMI sequence (insert-UMI pair) were collapsed into a single read.
Sequence reads were mapped to Bos taurus reference genome (UMD3.1) using Bowtie2 (2.2.2)
Mapped reads were used for annotation against both mature and precursor miRNAs of bovine and all other organism listed in the mirBase database (release 21)
Raw expression data were normalized using the trimmed mean of M-values normalization method (TMM normalization)
The differential expression analysis was done using TMM in the EdgeR statistical software package
Genome_build: UMD3.1
Supplementary_files_format_and_content: Tab separated values file include TPM values for each sample

organism: Bos taurus

source_name: Blood Plasma

extract_protocol:
Total EV-RNA, including miRNA, was isolated from blood plasma samples using exoRNeasy Serum/Plasma Kit (Qiagen) according to the manufacturer’s instructions.
A total of 50 ng RNA was converted into miRNA NGS libraries using the QIAseq miRNA Library Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.

treatment_protocol: Immediately after collection, blood samples were centrifuged at 1,900 x g and 4 °C, for 10 min. The supernatant was further centrifuged at 16,000 x g and 4 °C, for 10 min, before freezing and storing at -20 °C in plastic pour off tubes until analysis.

value: Blood Plasma

value: Superstimulated

tag: ovarian response

value: High


title: SUV420H2_KO_mESC_diff_d12

description: RNA-Seq

value: SUV420H2 KO differentiated day 12


title: HL60_ATRA_myb 4C

city: Shanghai

first: Mengjia

last: Li

address: 999 Hucheng Ring Road

department: College of Fisheries and Life Science

institute: Shanghai Ocean University

data_processing:
Illumina Casava1.8 software used for basecalling.
4C-Seq reads were trimmed for adaptor sequence and are  mapped to a reduced genome consisting of unique sequence fragments adjacent to the primary restriction enzyme sites in the genome  using bowtie2 with parameters -p 4 -N 0 -5 34 -3 80
Removing the self-ligated and undigested fragments
Analyzing 4C interactions using 4C-ker
Genome_build: hg19
Supplementary_files_format_and_content: BedGraph files include normalized counts for long-range interactions by 4C-ker

source_name: acute promyelocytic leukemia cells

extract_protocol:
10×106 cells were cross-linked by 2% formaldehyde for 10 min and 0.125 M glycine was added to prevent further cross-linking. Cells were collected and washed with 14 ml PBS twice, then cells were centrifuged and suspended in lysis buffer to disrupt membranes and isolate chromatin. A primary 6-base cutter, 400 U HindⅢ was used for the first digestion at 37°C with shaking overnight followed by diluted ligations. After precipitation, chromatin was further subjected to a second round of digestions with a 4-base cutter Dpn Ⅱ and ligation. Primers for the c-myb viewpoint (forward, AGTATTAATTTGCC-TTGTCC; reverse, GCTAATGTTGGATATATTGC) were designed. Inverse polymerase chain reaction (PCR) was carried out to amplify sample libraries.
Libraries were pooled and sequenced using the Illumina HiSeq machine as 150-bp paire-end sequencing reads.

value: peripheral blood

tag: tumor

value: acute promyelocytic leukemia

value: HL60 ATRA


title: II LUHMES GFP - MPP+

value: n


title: HL60_control_myb 4C

value: HL60 control


title: pa4

value: parathyroid adenoma (PA) patient

value: exosome derived from serum


title: pa1

value: untreated

value: before surgery


title: SL3

description: Isolated from extracellular vesicles

value: Low


title: H4K20me3_WT_mESC_rep2

description: Hi-C

value: wild type


title: SUV420H2_KO_mESC_diff_d8

description: RNA-Seq

value: SUV420H2 KO differentiated day 8

value: ES cell


title: SH3

description: Isolated from extracellular vesicles

value: Blood Plasma


title: 7donor_PBMC_SCMK

city: San Francisco

first: Christopher

middle: S

last: McGinnis

address: 600 16th Street

department: Pharmaceutical Chemistry

institute: University of California, San Francisco

description: SCMK Antibody-DNA barcode

data_processing:
FASTQ files were generated directly from Illumina BCL files using Illumina bcl2fastq version 2.19
Gene-barcode matrices were determined using 10X Genomics Cellranger version 2.2 with default parameters (cellranger count).
Read-depth normalization was performed (when appropriate) using 10X Genomics CellRanger version 3.1 with default parameters (cellranger aggr).
Low-quality cell barcodes were excluded as described in the paper.
MULTI-seq and SCMK barcode alignment and sample classification results were performed using the deMULTIplex R package (https://github.com/chris-mcginnis-ucsf/MULTI-seq)
Genome_build: hg19
Supplementary_files_format_and_content: Expression Libraries: gene-cell matrices are provided in the format produced by CellRanger. The matrix itself is in matrix market exchange format, with the column (cell barcodes) and row (gene identities) labels given in TSV format as described in the cellranger documentation. MULTI-seq Libraries: MULTI-seq barcode-cell matrices are provided in CSV format. SCMK Libraries: SMCK barcode-cell matrices are provided in CSV format.

source_name: PBMC

extract_protocol:
Single cells were lysed in droplets using the 10X Chromium instrument. Reverse transcription was performed in droplet and library construction was performed according to the 10X Chromium Single Cell 3' Reagent Kit User Guide Rev C.
Library preparation was performed according to the 10X Chromium Single Cell 3' Reagent Kit User Guide Rev C and using custom MULTI-seq and/or SCMK library preparation protocols.

tag: multiplexing reagent

value: SCMK


title: WT_mESC_diff_d12

description: RNA-Seq

value: WT differentiated day 12


title: U937_control_myb 4C

source_name: histiocytic lymphoma cells

value: pleural effusion

value: histiocytic lymphoma

value: U937 control


title: SL2

description: Isolated from extracellular vesicles

value: Superstimulated


title: I LUHMES GFP - MPP+

value: n


title: SL1

description: Isolated from extracellular vesicles


title: 8donor_PBMC_AD_SCMK

description: SCMK Antibody-DNA barcode


title: UH3

description: Isolated from extracellular vesicles

value: Unstimulated

value: High


title: 8donor_PBMC_AH_SCMK

description: SCMK Antibody-DNA barcode


title: WT_mESC_diff_d8

description: RNA-Seq

value: WT differentiated day 8


title: SH1

description: Isolated from extracellular vesicles


title: SUV420H1_H2_DKO_mESC_rep2

description: RNA-Seq

value: SUV420H1_H2 DKO


title: UH2

description: Isolated from extracellular vesicles


title: I LUHMES GFP + MPP+

value: y


title: K562_control_myb 4C

source_name: chronic myelogenous leukemia cells

value: bone marrow

value: chronic myelogenous leukemia

value: K562 control


title: U937_TPA_myb 4C

value: U937 TPA


title: 7donor_PBMC_RNA


title: HL60_myb 4C

value: peripheral blood

value: acute promyelocytic leukemia

value: normal culture


title: SUV420H2_KO_mESC_rep2

description: RNA-Seq

value: SUV420H2 KO

value: ES cell


title: 8donor_PBMC_AH_RNA


title: HeLa_myb 4C

source_name: adenocarcinoma cells

value: cervix

value: adenocarcinoma


title: SUV420H1_H2_DKO_mESC_rep1

description: RNA-Seq


title: SUV420H2_KO_mESC_rep1

description: RNA-Seq


title: UH1

description: Isolated from extracellular vesicles

value: Blood Plasma


title: UL3

description: Isolated from extracellular vesicles

value: Unstimulated

value: Low


title: K562_myb_4C


title: WT_mESC_rep2

description: RNA-Seq

value: WT


title: U937_myb 4C

value: pleural effusion

value: histiocytic lymphoma


title: UL1

description: Isolated from extracellular vesicles


title: K562_hemin_myb 4C

value: bone marrow

value: K562 hemin


title: UL2

description: Isolated from extracellular vesicles


title: WT_mESC_rep1

description: RNA-Seq


title: 8donor_PBMC_AD_RNA


title: 8donor_PBMC_A1_RNA


title: P16_scRNA-seq

status: Public on Nov 12 2020

first: Bao-Fa

last: Sun

address: Da-Tun Road

institute: Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)

data_processing:
FASTQs generated from Illumina HiSeq X Ten platform output were aligned to the human reference genome (hg19) using the Cell Ranger software (v2.1.0).
Next, the digital gene expression matrices were  imported into the Seurat (v3.1.2.9010) R toolkit for quality control and downstream analysis of our single cell RNA-seq data (Satija et al., 2015)
Genome_build: hg19
Supplementary_files_format_and_content: Each processed data comes from Cell Ranger output and contain 3 file (matrix.mtx, barcodes.tsv, genes.tsv)

source_name: human vaginal wall

extract_protocol:
The concentration of single cell suspension was counted using Countess (Thermo) and adjusted to 1000 cells/μl.
Cells were loaded according to standard protocol of the Chromium single cell 3’ kit in order to capture between 5000 cells/chip position. The library was constructed with Chromium Single Cell 3' V2 Reagent Kits
The Chromium™ Single Cell 3’ v2 Protocol (CG00052) produces Single Cell 3’ v2 libraries ready for Illumina® sequencing.

value: vaginal wall


title: P13_scRNA-seq


title: P14_scRNA-seq


title: P12_scRNA-seq


title: P15_scRNA-seq


title: P10_scRNA-seq


title: P8_scRNA-seq


title: P7_scRNA-seq


title: 8donor_PBMC_A2_RNA


title: P6_scRNA-seq


title: P4_scRNA-seq


title: P9_scRNA-seq


title: P11_scRNA-seq


title: N4_scRNA-seq


title: N5_scRNA-seq


title: N1_scRNA-seq


title: P3_scRNA-seq


title: N2_scRNA-seq


title: SampleTag_01-04_GBM and adjacent tissue

city: Hefei

first: Bingshan

last: Wu

state: Anhui

address: 218 Jixi Road

department: Department of Neurosurgery

institute: First Affiliated Hospital of Anhui Medical University

description:
SC106
R19021729-JZsc106-JZ201902221220_combined
R19021730-JZsc107-JZ201902221220_combined

data_processing:
Raw reads were processed through the BD Rhapsody Whole Transcriptome Assay Analysis Pipeline
The quality-filtered R1 reads were analyzed to identify the cell label sequence (CL), Molecular Identifier sequence (UMI), and poly-dT tail sequence
Putative cells information were combined together with RSEC/DBEC-adjusted molecules to generate a single-cell expression matrix
Raw gene expression matrices from two cartridges were read into R (version 3.6.0) separately and converted to Seurat objects using the Seurat R package (version 3.0.1)
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every single cell

source_name: GBM and adjacent brain tissue

extract_protocol:
Tissues were were cut into about 1-mm2 pieces and digested in SoloTM Tumor Dissociation Kit (JZ-SC-58201) at 37 °C for 90min.
Based on BD Rhapsody system Whole transcriptome analysis alpha protocol for single cell whole transcriptome analysis, Microbeads-captured single cell transcriptome were generated into cDNA library containing Cell label and UMI information. Briefly, double strand cDNA were firstly generated from Microbeads-captured single cell transcriptome following several steps including reverse transcription, second strand synthesis, end preparation, adapter ligation and whole transcriptome amplification. Then final cDNA library were generated from double strand full length cDNA by random priming amplification with BD Rhapsody cDNA Kit (BD Biosciences, 633773) and BD Rhapsody Targeted mRNA & AbSeq Amplification Kit (BD Biosciences, 633774). Library was sequenced in a PE150 mode (Pair-End for 150bp read) on the X Ten instrument (Illumina).

value: GBM and adjacent brain tissue

value: mixed sample (non-demultiplexed)


title: P12_RNA-seq

data_processing:
FASTQs generated from Illumina HiSeq X Ten platform output were aligned to the human reference genome (hg19) using the HISAT2 software (v2.0.5).
FeatureCounts (version 1.6.0) (Liao et al., 2014) was employed to calculate the read counts of per gene
Genome_build: hg19

extract_protocol:
Total RNA was extracted with TRIzol reagent (Invitrogen, 15596-018) , mRNA was purified from total RNAs using Dynabeads mRNA purification kit (Ambion, 61006). RNA-seq libraries were directly generated using the KAPA Stranded Mrna-Seq Kit (KAPA, KK8401) following the manufacturer’s instructions, and then sequenced using the Illumina HiSeq X Ten platform.
Libraries were directly constructed using the KAPA Stranded mRNA-Seq Kit (KAPA) and were sequenced using HiSeqX Ten (Illumina) in paired-read mode, creating reads with a length of 150 bp.


title: SampleTag_05-08_GBM and adjacent tissue

description:
SC106
R19021731-JZsc108-JZ201902221220_combined
R19021732-JZsc109-JZ201902221220_combined


title: P13_RNA-seq


title: P11_RNA-seq


title: P9_RNA-seq


title: P10_RNA-seq


title: P14_RNA-seq


title: P8_RNA-seq


title: P6_RNA-seq


title: P7_RNA-seq


title: P5_scRNA-seq


title: P4_RNA-seq


title: P2_RNA-seq


title: P3_RNA-seq


title: P1_scRNA-seq


title: N1_RNA-seq


title: qMcSC_3

city: New York City

first: Katherine

last: Stewart

state: NY

address: 1230 York Avenue

department: Laboratory of Mammalian Cell Biology and Development

institute: The Rockefeller University

description: Biological replicate #3 (cels from 4 males pooled)

data_processing:
Raw sequence reads were aligned to the mm10 genome using Rsubread (version 1.30.6) in paired end mode.
Bigwigs were created from properly paired reads (fragments between 0 -5000 bp) using rtracklayer package (version 1.40.6) and normalised to total mapped and properly paired reads.
Peak calls were made using Macs2 (2.2.6) in BAMPE mode
Signals in peaks were counted using featureCounts in Rsubread package (version 1.30.6)  and differential ATAC-seq signal analysis was performed with DESeq2 (version 1.20.0)
Genome_build: Mm10-UCSC (Genome sequence from Bioconductor package BSgenome.Mmusculus.UCSC.mm10 v1.4.0, Transcript models from  Bioconductor package TxDb.Mmusculus.UCSC.mm10.knownGene Version = 3.4.0)
Supplementary_files_format_and_content: bigWig files contain ATAC-seq signal normalised to total mapped and properly paired reads

source_name: mouse back skin

extract_protocol:
ATAC
Illumina Nextera, Buenrostro et al., 2015

tag: cell stage

value: Quiescent melanocyte stem cells

tag: Sex

value: Male

tag: hair cycle stage

value: 2nd telogen

tag: mouse strain

value: Dct-eGFP+ (CD1/C57Bl6J mix)

tag: sorting strategy

value: Dct-eGFP+, integrin α6medium-low, dump (CD31, CD45, CD140a)-, Sca1-, and CD34-


title: qMcSC_2

description: Biological replicate #2 (cells from 4 males pooled)


title: qMcSC_1

description: Biological replicate #1 (cells from 3 males poole)


title: Mc_1

description: Biological replicate #1 (cells from 1 male)

value: Melanocytes (Differentiating McSC progeny)

value: Full anagen

value: Dct-eGFP high, CD117+, dump (CD31, CD45, CD140a)-, Sca1-, and CD34-


title: Mc_3

description: Biological replicate #3 (cells from 2 males pooled)


title: Mc_2

description: Biological replicate #2 (cells from 2 males pooled)


title: smallRNAseq_MEFs_nontarget control-1

city: Dallas

first: Joshua

last: Mendell

state: TX

address: 6000 Harry Hines Blvd., NA6.200A

department: Molecular Biology

institute: UT Southwestern Medical Center

data_processing:
The raw reads were trimmed using Cutadapt
Reads with base quality less than 30 at any position were dropped
The miRNA sequences were downloaded from miRBase v22
Each read was assigned to an miRNA according to the first 18nt.
TMM normalization and differential expression analysis is performed using edgeR
Genome_build: hg19
Supplementary_files_format_and_content: a table of miRNA reads per million from edgeR analysis of these RNA-seq data

source_name: MEFs

growth_protocol: K562 cells were grown in RPMI supplemented with 10% FBS and Antibiotic-Antimycotic solution, HEK293T and MEFs cells were grown in DMEM supplemented with 10% FBS and Antibiotic-Antimycotic solution

extract_protocol:
RNA was isolated using the miRNeasy Mini kit (Qiagen) for small RNA seq.
Total RNA was isolated from biological triplicates of each cell line using the miRNeasy Mini RNA isolation kit (Qiagen) including a DNase I digestion step to remove genomic DNA. Library preparation was performed following a previously published protocol (H. Kim et al., Bias-minimized quantification of microRNA reveals widespread alternative processing and 3' end modification. Nucleic Acids Res 47, 2630-2640 (2019)).

value: sgNT

tag: sgrna received

value: ATTGTTCGACCGTCTACGGG

tag: cell line

value: MEFs


title: smallRNAseq_MEFs_sgZswim8-1

tag: genotype

value: AGTGCGGATGAGTTTCAGCG


title: smallRNAseq_MEFs_sgZswim8-3


title: KLp_1_mRNA

city: Oslo

first: Magnus

middle: D.

last: Vigeland

address: Kirkeveien 166

department: Medical Genetics

country: Norway

institute: University of Oslo

description: processed data file: counts_gencode.M16_LEFT.txt

data_processing:
Trimming of fastq files with Trim Galore! (v0.4.3; default parameters).
RRBS alignment to mm10, by Bismark v0.20, powered by bowtie2.
RRBS analysis of methylated/unmethylated read counts, by R package edgeR.
RNA-Seq alignment and feature counts, by R package Rsubread.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Bismark coverage file: Tab-delimited file with one row for each covered cytosine position in the experiment, and the following columns: <chromosome> <start position> <end position> <methylation percentage> <count methylated> <count non-methylated>
Supplementary_files_format_and_content: counts_gencode.M16_LEFT.txt: Feature counts: Tab-delimited file with one row per gene. The first column has Gene ID (Ensembl), followed by one column per sample, with unnormalised counts.

source_name: Hippocampus

extract_protocol:
24 hours after status epilepticus right hippocampi were extracted and flash frozen. Tissue was thawed in homogenization buffer and homogenized on a GentleMACS dissociator (Miltenyi). Debris was removed by density gradient centrifugation, using Debris Removal Solution (Miltenyi cat.no. 130-109-398). Nuclei were resuspended in buffer and stained with anti-NeuN-Alexa Fluor488 (Millipore cat.no. MAB377X), followed by sorting on BD FACSAria (BD Biosciences). RNA was extracted from NeuN positive nuclei, following procedures E and F.I in the mirVana miRNA Isolation Kit protocol (Ambion cat. no. AM 1560). RNA was up-concentrated using the RNA Clean & Concentrator-5 kit (Zymo Research cat.no. R1015).
SMART-Seqv4 Ultra Low InputRNA Kit for Sequencing (Takara Bio cat.no. 634891) was used to amplify 1 ng mRNA from total RNA, with 10 cycles of PCR performed. The resulting cDNA was used as input in library preparation with ThruPlex DNAseq Kit (Rubicon Genomics cat.no. R400407).

tag: tissue

value: Hippocampus

value: Kainate

tag: neun

value: positive

tag: biol. repl.


title: smallRNAseq_MEFs_nontarget control-3


title: smallRNAseq_MEFs_nontarget control-2


title: KLn_1_mRNA

extract_protocol:
24 hours after status epilepticus right hippocampi were extracted and flash frozen. Tissue was thawed in homogenization buffer and homogenized on a GentleMACS dissociator (Miltenyi). Debris was removed by density gradient centrifugation, using Debris Removal Solution (Miltenyi cat.no. 130-109-398). Nuclei were resuspended in buffer and stained with anti-NeuN-Alexa Fluor488 (Millipore cat.no. MAB377X), followed by sorting on BD FACSAria (BD Biosciences). RNA was extracted from NeuN negative nuclei, following procedures E and F.I in the mirVana miRNA Isolation Kit protocol (Ambion cat. no. AM 1560). RNA was up-concentrated using the RNA Clean & Concentrator-5 kit (Zymo Research cat.no. R1015).
SMART-Seqv4 Ultra Low InputRNA Kit for Sequencing (Takara Bio cat.no. 634891) was used to amplify 1 ng mRNA from total RNA, with 10 cycles of PCR performed. The resulting cDNA was used as input in library preparation with ThruPlex DNAseq Kit (Rubicon Genomics cat.no. R400407).

tag: treatment

value: negative


title: SLp_1_mRNA

value: Sham


title: P5_RNA-seq

value: vaginal wall


title: SLn_1_mRNA

extract_protocol:
24 hours after status epilepticus right hippocampi were extracted and flash frozen. Tissue was thawed in homogenization buffer and homogenized on a GentleMACS dissociator (Miltenyi). Debris was removed by density gradient centrifugation, using Debris Removal Solution (Miltenyi cat.no. 130-109-398). Nuclei were resuspended in buffer and stained with anti-NeuN-Alexa Fluor488 (Millipore cat.no. MAB377X), followed by sorting on BD FACSAria (BD Biosciences). RNA was extracted from NeuN negative nuclei, following procedures E and F.I in the mirVana miRNA Isolation Kit protocol (Ambion cat. no. AM 1560). RNA was up-concentrated using the RNA Clean & Concentrator-5 kit (Zymo Research cat.no. R1015).
SMART-Seqv4 Ultra Low InputRNA Kit for Sequencing (Takara Bio cat.no. 634891) was used to amplify approximately 0.05 ng mRNA from total RNA, with 15 cycles of PCR performed. The resulting cDNA was used as input in library preparation with ThruPlex DNAseq Kit (Rubicon Genomics cat.no. R400407).


title: M12_cKO_P2_H5_S156_quant

description:
stage-matched cKO mouse replicate #2
Infarinato_etal_2020_ALL_DATA_counts.csv
Infarinato_etal_2020_ALL_DATA_TPM.csv

data_processing:
Sequence reads were obtained. Adaptors were trimmed from reads using Skewer (version 0.2.2), and the resulting reads were mapped to the mouse genome (GENCODE release M23 (GRCm38.p6)) using STAR (version 2.5.2a). ERCC spike-ins were added to the mouse genome as artificial chromosomes.
Expression values of each gene were quantified as transcript per million (TPM), as well as by raw counts, using Salmon (version 0.14.1) and Tximport (version 1.12.3).
Genome_build: GENCODE release M23 (GRCm38.p6)
Supplementary_files_format_and_content: comma separated value text files contain either TPMs or raw counts for all samples

source_name: Mouse back skin

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

value: commited melanocyte progenitor

value: male

value: wax-induced anagen (1 week post wax)

tag: strain

value: Bmpr1a fl/fl, TyrCreER+, R26YFP fl/+ (C57Bl6 mix)

value: YFP+ dump (CD31, CD45, CD140a)-, Sca-1- and CD34-


title: M12_cKO_P2_H3_S155_quant

tag: age


title: M12_cKO_P2_H10_S157_quant


title: M12_cKO_P2_H1_S153_quant


title: M12_cKO_P2_H12_S158_quant


title: M12_cKO_P2_G8_S148_quant


title: N3_RNA-seq


title: M12_cKO_P2_H2_S154_quant


title: M12_cKO_P2_G9_S149_quant


title: M12_cKO_P2_G5_S146_quant


title: M12_cKO_P2_G7_S147_quant


title: M12_cKO_P2_G4_S145_quant


title: M12_cKO_P2_G2_S143_quant


title: M12_cKO_P2_G3_S144_quant


title: M12_cKO_P2_G12_S152_quant


title: smallRNAseq_MEFs_sgZswim8-2


title: M12_cKO_P2_F9_S138_quant


title: M12_cKO_P2_F8_S137_quant


title: M12_cKO_P2_F4_S133_quant


title: M12_cKO_P2_F5_S134_quant


title: M12_cKO_P2_F3_S132_quant


title: M12_cKO_P2_F7_S136_quant


title: M12_cKO_P2_G1_S142_quant


title: M12_cKO_P2_F12_S141_quant


title: M12_cKO_P2_F2_S131_quant


title: M12_cKO_P2_F10_S139_quant


title: P2_scRNA-seq


title: M12_cKO_P2_F11_S140_quant


title: M12_cKO_P2_F6_S135_quant


title: M12_cKO_P2_E9_S126_quant


title: M12_cKO_P2_E7_S124_quant


title: M12_cKO_P2_E8_S125_quant


title: M12_cKO_P2_E6_S123_quant


title: M12_cKO_P2_E5_S122_quant


title: M12_cKO_P2_E4_S121_quant


title: M12_cKO_P2_E3_S120_quant


title: M12_cKO_P2_G10_S150_quant


title: M12_cKO_P2_F1_S130_quant


title: M12_cKO_P2_E2_S119_quant


title: M12_cKO_P2_E1_S118_quant


title: M12_cKO_P2_E12_S129_quant


title: M12_cKO_P2_E11_S128_quant


title: M12_cKO_P2_G11_S151_quant


title: M12_cKO_P2_D9_S114_quant


title: M12_cKO_P2_D7_S112_quant


title: M12_cKO_P2_D6_S111_quant


title: M12_cKO_P2_D8_S113_quant


title: M12_cKO_P2_D3_S108_quant


title: M12_cKO_P2_D5_S110_quant


title: M12_cKO_P2_D4_S109_quant


title: M12_cKO_P2_D12_S117_quant


title: M12_cKO_P2_C8_S102_quant


title: M12_cKO_P2_C9_S103_quant


title: M12_cKO_P2_C7_S101_quant


title: M12_cKO_P2_D11_S116_quant


title: M12_cKO_P2_D10_S115_quant


title: M12_cKO_P2_D1_S107_quant


title: M12_cKO_P2_C5_S99_quant


title: M12_cKO_P2_C4_S98_quant


title: M12_cKO_P2_C6_S100_quant


title: M12_cKO_P2_C12_S106_quant


title: M12_cKO_P2_E10_S127_quant


title: M12_cKO_P2_C11_S105_quant


title: M12_cKO_P2_C1_S95_quant


title: M12_cKO_P2_B8_S90_quant


title: M12_cKO_P2_C10_S104_quant


title: M12_cKO_P2_C3_S97_quant


title: M12_cKO_P2_B9_S91_quant


title: M12_cKO_P2_B5_S88_quant


title: M12_cKO_P2_B7_S89_quant


title: M12_cKO_P2_B12_S94_quant


title: M12_cKO_P2_B2_S87_quant


title: M12_cKO_P2_B10_S92_quant


title: M12_cKO_P2_B1_S86_quant


title: M12_cKO_P2_B11_S93_quant


title: M12_cKO_P2_A11_S85_quant


title: M12_cKO_P2_C2_S96_quant


title: M12_cKO_P2_A2_S82_quant


title: M12_Bmpr1a_cKO_Plate1_H3_S80_quant


title: M12_Bmpr1a_cKO_Plate1_H12_S83_quant


title: M12_cKO_P2_A1_S81_quant


title: M12_Bmpr1a_cKO_Plate1_G8_S74_quant


title: M12_Bmpr1a_cKO_Plate1_G9_S75_quant


title: M12_Bmpr1a_cKO_Plate1_H2_S79_quant


title: M12_Bmpr1a_cKO_Plate1_H10_S82_quant


title: M12_Bmpr1a_cKO_Plate1_G5_S71_quant


title: M12_Bmpr1a_cKO_Plate1_G6_S72_quant


title: M12_Bmpr1a_cKO_Plate1_G3_S69_quant


title: M12_Bmpr1a_cKO_Plate1_G2_S68_quant


title: M12_Bmpr1a_cKO_Plate1_G12_S78_quant


title: M12_Bmpr1a_cKO_Plate1_G1_S67_quant


title: M12_Bmpr1a_cKO_Plate1_F9_S63_quant


title: M12_Bmpr1a_cKO_Plate1_G10_S76_quant


title: M12_Bmpr1a_cKO_Plate1_G4_S70_quant


title: M12_Bmpr1a_cKO_Plate1_G11_S77_quant


title: M12_Bmpr1a_cKO_Plate1_F8_S62_quant


title: M12_Bmpr1a_cKO_Plate1_F7_S61_quant


title: M12_cKO_P2_A4_S83_quant


title: M12_cKO_P2_A5_S84_quant


title: M12_Bmpr1a_cKO_Plate1_H4_S81_quant


title: M12_Bmpr1a_cKO_Plate1_F6_S60_quant


title: M12_Bmpr1a_cKO_Plate1_F4_S58_quant


title: M12_Bmpr1a_cKO_Plate1_F5_S59_quant


title: M12_Bmpr1a_cKO_Plate1_F12_S66_quant


title: M12_Bmpr1a_cKO_Plate1_F3_S57_quant


title: M12_Bmpr1a_cKO_Plate1_F2_S56_quant


title: M12_Bmpr1a_cKO_Plate1_F1_S55_quant


title: M12_Bmpr1a_cKO_Plate1_F10_S64_quant


title: M12_Bmpr1a_cKO_Plate1_E9_S51_quant


title: M12_Bmpr1a_cKO_Plate1_F11_S65_quant


title: M12_Bmpr1a_cKO_Plate1_E8_S50_quant


title: M12_Bmpr1a_cKO_Plate1_E7_S49_quant


title: M12_Bmpr1a_cKO_Plate1_E5_S48_quant


title: M12_Bmpr1a_cKO_Plate1_E12_S54_quant


title: M12_Bmpr1a_cKO_Plate1_G7_S73_quant


title: M12_Bmpr1a_cKO_Plate1_E2_S45_quant


title: M12_Bmpr1a_cKO_Plate1_E11_S53_quant


title: M12_Bmpr1a_cKO_Plate1_E10_S52_quant


title: M12_Bmpr1a_cKO_Plate1_E3_S46_quant


title: M12_Bmpr1a_cKO_Plate1_E4_S47_quant


title: M12_Bmpr1a_cKO_Plate1_D7_S39_quant


title: M12_Bmpr1a_cKO_Plate1_D6_S38_quant


title: M12_Bmpr1a_cKO_Plate1_D9_S41_quant


title: M12_Bmpr1a_cKO_Plate1_E1_S44_quant


title: M12_Bmpr1a_cKO_Plate1_D5_S37_quant


title: M12_Bmpr1a_cKO_Plate1_D4_S36_quant


title: M12_Bmpr1a_cKO_Plate1_D3_S35_quant


title: N3_scRNA-seq


title: M12_Bmpr1a_cKO_Plate1_D2_S34_quant


title: M12_Bmpr1a_cKO_Plate1_D12_S43_quant


title: M12_Bmpr1a_cKO_Plate1_D1_S33_quant


title: M12_Bmpr1a_cKO_Plate1_D10_S42_quant


title: M12_Bmpr1a_cKO_Plate1_C8_S28_quant


title: M12_Bmpr1a_cKO_Plate1_C7_S27_quant


title: M12_Bmpr1a_cKO_Plate1_C9_S29_quant


title: M12_Bmpr1a_cKO_Plate1_C6_S26_quant


title: M12_Bmpr1a_cKO_Plate1_C4_S25_quant


title: M12_Bmpr1a_cKO_Plate1_C3_S24_quant


title: M12_Bmpr1a_cKO_Plate1_D8_S40_quant


title: M12_Bmpr1a_cKO_Plate1_B9_S18_quant


title: M12_Bmpr1a_cKO_Plate1_B2_S11_quant


title: M12_Bmpr1a_cKO_Plate1_B5_S14_quant


title: M12_Bmpr1a_cKO_Plate1_B7_S16_quant


title: M12_Bmpr1a_cKO_Plate1_B4_S13_quant


title: M12_Bmpr1a_cKO_Plate1_B8_S17_quant


title: M12_Bmpr1a_cKO_Plate1_B3_S12_quant


title: M12_Bmpr1a_cKO_Plate1_B12_S21_quant


title: M12_Bmpr1a_cKO_Plate1_B10_S19_quant


title: M12_Bmpr1a_cKO_Plate1_B11_S20_quant


title: M12_Bmpr1a_cKO_Plate1_A9_S7_quant


title: M12_Bmpr1a_cKO_Plate1_B1_S10_quant


title: M12_Bmpr1a_cKO_Plate1_A5_S5_quant


title: M12_Bmpr1a_cKO_Plate1_A7_S6_quant


title: M12_Bmpr1a_cKO_Plate1_A4_S4_quant


title: M12_Bmpr1a_cKO_Plate1_A2_S2_quant


title: M12_Bmpr1a_cKO_Plate1_C12_S32_quant


title: M12_Bmpr1a_cKO_Plate1_A3_S3_quant


title: M12_Bmpr1a_cKO_Plate1_A12_S9_quant


title: M12_Bmpr1a_cKO_Plate1_A1_S1_quant


title: M12_Bmpr1a_cKO_Plate1_C2_S23_quant


title: M12_Bmpr1a_cKO_Plate1_C11_S31_quant


title: M12_Bmpr1a_cKO_Plate1_A11_S8_quant


title: M12_Bmpr1a_cKO_Plate1_C1_S22_quant


title: M12_Bmpr1a_cKO_Plate1_C10_S30_quant


title: M12_Bmpr1a_cKO_Plate1_B6_S15_quant


title: M116_cKO_P4_H8_S340_quant

description:
stage-matched cKO mouse replicate #1
Infarinato_etal_2020_ALL_DATA_counts.csv
Infarinato_etal_2020_ALL_DATA_TPM.csv


title: M116_cKO_P4_H4_S339_quant


title: M116_cKO_P4_H3_S338_quant


title: M116_cKO_P4_H2_S337_quant


title: M116_cKO_P4_H1_S336_quant


title: M116_cKO_P4_G9_S332_quant


title: M116_cKO_P4_H10_S342_quant


title: M116_cKO_P4_H12_S344_quant


title: M116_cKO_P4_H11_S343_quant


title: M116_cKO_P4_G6_S329_quant


title: M116_cKO_P4_G7_S330_quant


title: M116_cKO_P4_G3_S326_quant


title: M116_cKO_P4_G5_S328_quant


title: M116_cKO_P4_G4_S327_quant


title: M116_cKO_P4_G2_S325_quant


title: M116_cKO_P4_G10_S333_quant


title: M116_cKO_P4_H9_S341_quant


title: M116_cKO_P4_G12_S335_quant


title: M116_cKO_P4_G1_S324_quant


title: M116_cKO_P4_G8_S331_quant


title: M116_cKO_P4_F8_S319_quant


title: M116_cKO_P4_F3_S314_quant


title: M116_cKO_P4_F6_S317_quant


title: M116_cKO_P4_F5_S316_quant


title: M116_cKO_P4_F7_S318_quant


title: M116_cKO_P4_F4_S315_quant


title: M116_cKO_P4_F12_S323_quant


title: M116_cKO_P4_F2_S313_quant


title: M116_cKO_P4_F11_S322_quant


title: M116_cKO_P4_F10_S321_quant


title: M116_cKO_P4_F1_S312_quant


title: M116_cKO_P4_E9_S309_quant


title: M116_cKO_P4_E8_S308_quant


title: M116_cKO_P4_E6_S306_quant


title: M116_cKO_P4_E5_S305_quant


title: M116_cKO_P4_E4_S304_quant


title: M116_cKO_P4_G11_S334_quant


title: M116_cKO_P4_E7_S307_quant


title: M116_cKO_P4_E3_S303_quant


title: M116_cKO_P4_E2_S302_quant


title: M116_cKO_P4_E12_S311_quant


title: M116_cKO_P4_F9_S320_quant


title: M116_cKO_P4_E1_S301_quant


title: M116_cKO_P4_D9_S297_quant


title: M116_cKO_P4_D7_S295_quant


title: M116_cKO_P4_D6_S294_quant


title: M116_cKO_P4_D5_S293_quant


title: M116_cKO_P4_D3_S291_quant


title: M116_cKO_P4_D4_S292_quant


title: M116_cKO_P4_D2_S290_quant


title: M116_cKO_P4_D12_S300_quant


title: M116_cKO_P4_D10_S298_quant


title: M116_cKO_P4_D11_S299_quant


title: M116_cKO_P4_C9_S286_quant


title: M116_cKO_P4_C8_S285_quant


title: M116_cKO_P4_C7_S284_quant


title: M116_cKO_P4_C6_S283_quant


title: M116_cKO_P4_C4_S281_quant


title: M116_cKO_P4_C2_S279_quant


title: M116_cKO_P4_C3_S280_quant


title: M116_cKO_P4_C12_S289_quant


title: M116_cKO_P4_B9_S274_quant


title: M116_cKO_P4_E11_S310_quant


title: M116_cKO_P4_B8_S273_quant


title: M116_cKO_P4_C1_S278_quant


title: M116_cKO_P4_C11_S288_quant


title: M116_cKO_P4_B5_S271_quant


title: M116_cKO_P4_D8_S296_quant


title: M116_cKO_P4_B12_S277_quant


title: M116_cKO_P4_B11_S276_quant


title: M116_cKO_P4_B10_S275_quant


title: M116_cKO_P4_B4_S270_quant


title: M116_cKO_P4_B6_S272_quant


title: M116_cKO_P4_A3_S263_quant


title: M116_cKO_P4_A2_S262_quant


title: M116_cKO_P4_A8_S265_quant


title: M116_cKO_P4_A1_S261_quant


title: M116_cKO_P4_A11_S267_quant


title: M116_cKO_P3_H9_S257_quant


title: M116_cKO_P4_A7_S264_quant


title: M116_cKO_P4_C5_S282_quant


title: M116_cKO_P3_H5_S255_quant


title: M116_cKO_P3_H4_S254_quant


title: M116_cKO_P3_H8_S256_quant


title: M116_cKO_P4_C10_S287_quant


title: M116_cKO_P3_H3_S253_quant


title: M116_cKO_P3_H11_S259_quant


title: M116_cKO_P3_H1_S251_quant


title: M116_cKO_P3_H2_S252_quant


title: M116_cKO_P3_H10_S258_quant


title: M116_cKO_P3_G8_S247_quant


title: M116_cKO_P3_G6_S245_quant


title: M116_cKO_P4_B1_S269_quant


title: M116_cKO_P3_G9_S248_quant


title: M116_cKO_P4_A9_S266_quant


title: M116_cKO_P4_A12_S268_quant


title: M116_cKO_P3_G5_S244_quant


title: M116_cKO_P3_G3_S242_quant


title: M116_cKO_P3_G4_S243_quant


title: M116_cKO_P3_G2_S241_quant


title: M116_cKO_P3_H12_S260_quant


title: M116_cKO_P3_G7_S246_quant


title: M116_cKO_P3_G12_S250_quant


title: M116_cKO_P3_F6_S233_quant


title: M116_cKO_P3_F4_S231_quant


title: M116_cKO_P3_G11_S249_quant


title: M116_cKO_P3_G1_S240_quant


title: M116_cKO_P3_F8_S235_quant


title: M116_cKO_P3_F2_S229_quant


title: M116_cKO_P3_F11_S238_quant


title: M116_cKO_P3_F7_S234_quant


title: M116_cKO_P3_F12_S239_quant


title: M116_cKO_P3_F5_S232_quant


title: M116_cKO_P3_F3_S230_quant


title: M116_cKO_P3_F10_S237_quant


title: M116_cKO_P3_E7_S223_quant


title: M116_cKO_P3_E9_S224_quant


title: M116_cKO_P3_E6_S222_quant


title: M116_cKO_P3_E3_S219_quant


title: M116_cKO_P3_E4_S220_quant


title: M116_cKO_P3_F9_S236_quant


title: M116_cKO_P3_E12_S227_quant


title: M116_cKO_P3_E10_S225_quant


title: M116_cKO_P3_D8_S214_quant


title: M116_cKO_P3_E2_S218_quant


title: M116_cKO_P3_D6_S212_quant


title: M116_cKO_P3_D7_S213_quant


title: M116_cKO_P3_E11_S226_quant


title: M116_cKO_P3_E1_S217_quant


title: M116_cKO_P3_D2_S208_quant


title: M116_cKO_P3_D12_S216_quant


title: M116_cKO_P3_D10_S215_quant


title: M116_cKO_P3_D5_S211_quant


title: M116_cKO_P3_D3_S209_quant


title: M116_cKO_P3_C8_S202_quant


title: M116_cKO_P3_C9_S203_quant


title: M116_cKO_P3_D1_S207_quant


title: M116_cKO_P3_C7_S201_quant


title: M116_cKO_P3_C6_S200_quant


title: M116_cKO_P3_F1_S228_quant


title: M116_cKO_P3_C5_S199_quant


title: M116_cKO_P3_C3_S197_quant


title: M116_cKO_P3_C11_S205_quant


title: M116_cKO_P3_C12_S206_quant


title: M116_cKO_P3_C10_S204_quant


title: M116_cKO_P3_B9_S193_quant


title: M116_cKO_P3_B8_S192_quant


title: M116_cKO_P3_B5_S190_quant


title: M116_cKO_P3_B7_S191_quant


title: M116_cKO_P3_D4_S210_quant


title: M116_cKO_P3_B3_S189_quant


title: M116_cKO_P3_B2_S188_quant


title: M116_cKO_P3_B12_S196_quant


title: M116_cKO_P3_A9_S185_quant


title: M116_cKO_P3_B11_S195_quant


title: M116_cKO_P3_A7_S183_quant


title: M116_cKO_P3_B10_S194_quant


title: M116_cKO_P3_A8_S184_quant


title: M116_cKO_P3_A3_S180_quant


title: M116_cKO_P3_A4_S181_quant


title: M116_cKO_P3_A2_S179_quant


title: M116_cKO_P3_A5_S182_quant


title: M116_cKO_P3_A12_S187_quant


title: M116_cKO_P2_H7_S225_quant


title: M116_cKO_P2_H9_S226_quant


title: M116_cKO_P3_A10_S186_quant


title: M116_cKO_P2_H5_S223_quant


title: M116_cKO_P3_C4_S198_quant


title: M116_cKO_P2_H6_S224_quant


title: M116_cKO_P2_H3_S221_quant


title: M116_cKO_P2_H12_S229_quant


title: M116_cKO_P3_E5_S221_quant


title: M116_cKO_P2_H11_S228_quant


title: M116_cKO_P2_H1_S219_quant


title: M116_cKO_P2_G8_S215_quant


title: M116_cKO_P2_G5_S212_quant


title: M116_cKO_P2_G9_S216_quant


title: M116_cKO_P2_H10_S227_quant


title: M116_cKO_P2_G6_S213_quant


title: M116_cKO_P2_G7_S214_quant


title: M116_cKO_P2_G4_S211_quant


title: M116_cKO_P2_G12_S218_quant


title: M116_cKO_P2_G3_S210_quant


title: M116_cKO_P2_F8_S203_quant


title: M116_cKO_P2_G10_S217_quant


title: M116_cKO_P2_F9_S204_quant


title: M116_cKO_P2_F7_S202_quant


title: M116_cKO_P2_G1_S208_quant


title: M116_cKO_P2_F6_S201_quant


title: M116_cKO_P2_F3_S198_quant


title: M116_cKO_P2_F5_S200_quant


title: M116_cKO_P2_F4_S199_quant


title: M116_cKO_P2_F11_S206_quant


title: M116_cKO_P2_F2_S197_quant


title: M116_cKO_P2_H4_S222_quant


title: M116_cKO_P2_H2_S220_quant


title: M116_cKO_P2_F12_S207_quant


title: M116_cKO_P2_E9_S193_quant


title: M116_cKO_P2_F10_S205_quant


title: M116_cKO_P2_G2_S209_quant


title: M116_cKO_P2_E7_S191_quant


title: M116_cKO_P2_E6_S190_quant


title: M116_cKO_P2_E4_S188_quant


title: M116_cKO_P2_E5_S189_quant


title: M116_cKO_P2_E2_S186_quant


title: M116_cKO_P2_E10_S194_quant


title: M116_cKO_P2_E1_S185_quant


title: M116_cKO_P2_E12_S195_quant


title: M116_cKO_P2_E3_S187_quant


title: M116_cKO_P2_D8_S181_quant


title: M116_cKO_P2_D6_S179_quant


title: M116_cKO_P2_D7_S180_quant


title: M116_cKO_P2_D5_S178_quant


title: M116_cKO_P2_D4_S177_quant


title: M116_cKO_P2_D2_S175_quant


title: M116_cKO_P2_D12_S184_quant


title: M116_cKO_P2_D10_S182_quant


title: M116_cKO_P2_C8_S169_quant


title: M116_cKO_P2_C9_S170_quant


title: M116_cKO_P2_D3_S176_quant


title: M116_cKO_P2_F1_S196_quant


title: M116_cKO_P2_C5_S166_quant


title: M116_cKO_P2_C6_S167_quant


title: M116_cKO_P2_C7_S168_quant


title: M116_cKO_P2_D1_S174_quant


title: M116_cKO_P2_E8_S192_quant


title: M116_cKO_P2_C3_S164_quant


title: M116_cKO_P2_C2_S163_quant


title: M116_cKO_P2_C12_S173_quant


title: M116_cKO_P2_C11_S172_quant


title: M116_cKO_P2_C4_S165_quant


title: M116_cKO_P2_C1_S162_quant


title: M116_cKO_P2_B9_S160_quant


title: M116_cKO_P2_B4_S155_quant


title: M116_cKO_P2_B8_S159_quant


title: M116_cKO_P2_B7_S158_quant


title: M116_cKO_P2_B3_S154_quant


title: M116_cKO_P2_B2_S153_quant


title: M116_cKO_P2_D11_S183_quant


title: M116_cKO_P2_B5_S156_quant


title: M116_cKO_P2_B10_S161_quant


title: M116_cKO_P2_A8_S150_quant


title: M116_cKO_P2_A4_S148_quant


title: M116_cKO_P2_A2_S146_quant


title: M116_cKO_P2_A10_S151_quant


title: M116_cKO_P1_H9_S93_quant


title: M116_cKO_P1_H8_S92_quant


title: M116_cKO_P2_A5_S149_quant


title: M116_cKO_P2_A1_S145_quant


title: M116_cKO_P2_A3_S147_quant


title: M116_cKO_P1_H5_S89_quant


title: M116_cKO_P1_H7_S91_quant


title: M116_cKO_P2_C10_S171_quant


title: M116_cKO_P1_H3_S87_quant


title: M116_cKO_P1_H12_S96_quant


title: M116_cKO_P1_H2_S86_quant


title: M116_cKO_P2_B6_S157_quant


title: M116_cKO_P1_H6_S90_quant


title: M116_cKO_P1_H1_S85_quant


title: M116_cKO_P1_H11_S95_quant


title: M116_cKO_P1_G8_S80_quant


title: M116_cKO_P1_G9_S81_quant


title: M116_cKO_P2_B1_S152_quant


title: M116_cKO_P1_G3_S75_quant


title: M116_cKO_P1_G2_S74_quant


title: M116_cKO_P1_G7_S79_quant


title: M116_cKO_P1_G4_S76_quant


title: M116_cKO_P1_G5_S77_quant


title: M116_cKO_P1_G6_S78_quant


title: M116_cKO_P1_G11_S83_quant


title: M116_cKO_P1_G10_S82_quant


title: M116_cKO_P1_F9_S69_quant


title: M116_cKO_P1_G1_S73_quant


title: M116_cKO_P1_F7_S67_quant


title: M116_cKO_P1_F8_S68_quant


title: M116_cKO_P1_F6_S66_quant


title: M116_cKO_P1_F5_S65_quant


title: M116_cKO_P1_F4_S64_quant


title: M116_cKO_P1_F2_S62_quant


title: M116_cKO_P1_F12_S72_quant


title: M116_cKO_P1_H10_S94_quant


title: M116_cKO_P1_F10_S70_quant


title: M116_cKO_P1_E8_S56_quant


title: M116_cKO_P1_E9_S57_quant


title: M116_cKO_P1_E7_S55_quant


title: M116_cKO_P1_F1_S61_quant


title: M116_cKO_P1_E6_S54_quant


title: M116_cKO_P1_F11_S71_quant


title: M116_cKO_P1_E5_S53_quant


title: M116_cKO_P1_E3_S51_quant


title: M116_cKO_P1_E11_S59_quant


title: M116_cKO_P1_E2_S50_quant


title: M116_cKO_P1_D3_S39_quant


title: M116_cKO_P1_E1_S49_quant


title: M116_cKO_P1_D2_S38_quant


title: M116_cKO_P1_D7_S43_quant


title: M116_cKO_P1_D6_S42_quant


title: M116_cKO_P1_D5_S41_quant


title: M116_cKO_P1_D1_S37_quant


title: M116_cKO_P1_F3_S63_quant


title: M116_cKO_P1_C7_S31_quant


title: M116_cKO_P1_C5_S29_quant


title: M116_cKO_P1_C12_S36_quant


title: M116_cKO_P1_D11_S47_quant


title: M116_cKO_P1_C1_S25_quant


title: M116_cKO_P1_D10_S46_quant


title: M116_cKO_P1_C11_S35_quant


title: M116_cKO_P1_C10_S34_quant


title: M116_cKO_P1_B3_S15_quant


title: M116_cKO_P1_B10_S22_quant


title: M116_cKO_P1_B4_S16_quant


title: M116_cKO_P1_B11_S23_quant


title: M116_cKO_P1_D4_S40_quant


title: M116_cKO_P1_B1_S13_quant


title: M116_cKO_P1_A9_S9_quant


title: M116_cKO_P1_B7_S19_quant


title: M116_cKO_P1_C6_S30_quant


title: M116_cKO_P1_C3_S27_quant


title: M116_cKO_P1_A8_S8_quant


title: M116_cKO_P1_A11_S11_quant


title: M116_cKO_P1_A7_S7_quant


title: M4_Bmpr1a_Het_Plate1_H12_S251_quant

description:
stage-matched control mouse replicate #3
Infarinato_etal_2020_ALL_DATA_counts.csv
Infarinato_etal_2020_ALL_DATA_TPM.csv

value: Bmpr1a fl/+, TyrCreER+, R26YFP fl/+ (C57Bl6 mix)


title: M116_cKO_P1_A6_S6_quant


title: M116_cKO_P1_A5_S5_quant


title: M4_Bmpr1a_Het_Plate1_H3_S248_quant


title: M116_cKO_P1_A3_S3_quant


title: M4_Bmpr1a_Het_Plate1_H5_S249_quant


title: M116_cKO_P1_A2_S2_quant


title: M4_Bmpr1a_Het_Plate1_G7_S240_quant


title: M116_cKO_P1_A1_S1_quant


title: M4_Bmpr1a_Het_Plate1_G8_S241_quant


title: M4_Bmpr1a_Het_Plate1_G5_S238_quant


title: M116_cKO_P1_B9_S21_quant


title: M4_Bmpr1a_Het_Plate1_H2_S247_quant


title: M4_Bmpr1a_Het_Plate1_G2_S235_quant


title: M4_Bmpr1a_Het_Plate1_H1_S246_quant


title: M4_Bmpr1a_Het_Plate1_F6_S229_quant


title: M4_Bmpr1a_Het_Plate1_F7_S230_quant


title: M116_cKO_P1_B5_S17_quant


title: M4_Bmpr1a_Het_Plate1_G9_S242_quant


title: M116_cKO_P1_B8_S20_quant


title: M4_Bmpr1a_Het_Plate1_F2_S225_quant


title: M4_Bmpr1a_Het_Plate1_F3_S226_quant


title: M4_Bmpr1a_Het_Plate1_G6_S239_quant


title: M4_Bmpr1a_Het_Plate1_G4_S237_quant


title: M4_Bmpr1a_Het_Plate1_G3_S236_quant


title: M4_Bmpr1a_Het_Plate1_G12_S245_quant


title: M4_Bmpr1a_Het_Plate1_G11_S244_quant


title: M4_Bmpr1a_Het_Plate1_G10_S243_quant


title: M4_Bmpr1a_Het_Plate1_G1_S234_quant


title: M4_Bmpr1a_Het_Plate1_E8_S219_quant


title: M4_Bmpr1a_Het_Plate1_H11_S250_quant


title: M4_Bmpr1a_Het_Plate1_F5_S228_quant


title: M4_Bmpr1a_Het_Plate1_F11_S232_quant


title: M4_Bmpr1a_Het_Plate1_E2_S213_quant


title: M4_Bmpr1a_Het_Plate1_E4_S215_quant


title: M4_Bmpr1a_Het_Plate1_F10_S231_quant


title: M4_Bmpr1a_Het_Plate1_F1_S224_quant


title: M4_Bmpr1a_Het_Plate1_E9_S220_quant


title: M4_Bmpr1a_Het_Plate1_E7_S218_quant


title: M4_Bmpr1a_Het_Plate1_F4_S227_quant


title: M4_Bmpr1a_Het_Plate1_F12_S233_quant


title: M4_Bmpr1a_Het_Plate1_E10_S221_quant


title: M4_Bmpr1a_Het_Plate1_D8_S208_quant


title: M4_Bmpr1a_Het_Plate1_E6_S217_quant


title: M4_Bmpr1a_Het_Plate1_E12_S223_quant


title: M4_Bmpr1a_Het_Plate1_D5_S205_quant


title: M4_Bmpr1a_Het_Plate1_E11_S222_quant


title: M4_Bmpr1a_Het_Plate1_D2_S202_quant


title: M4_Bmpr1a_Het_Plate1_D7_S207_quant


title: M4_Bmpr1a_Het_Plate1_E3_S214_quant


title: M4_Bmpr1a_Het_Plate1_E1_S212_quant


title: M4_Bmpr1a_Het_Plate1_D6_S206_quant


title: M4_Bmpr1a_Het_Plate1_D4_S204_quant


title: M4_Bmpr1a_Het_Plate1_D1_S201_quant


title: M4_Bmpr1a_Het_Plate1_C6_S194_quant


title: M4_Bmpr1a_Het_Plate1_D11_S210_quant


title: M4_Bmpr1a_Het_Plate1_E5_S216_quant


title: M4_Bmpr1a_Het_Plate1_D10_S209_quant


title: M4_Bmpr1a_Het_Plate1_C5_S193_quant


title: M4_Bmpr1a_Het_Plate1_C2_S190_quant


title: M4_Bmpr1a_Het_Plate1_C4_S192_quant


title: M4_Bmpr1a_Het_Plate1_C7_S195_quant


title: M4_Bmpr1a_Het_Plate1_C8_S196_quant


title: M4_Bmpr1a_Het_Plate1_C9_S197_quant


title: M4_Bmpr1a_Het_Plate1_C3_S191_quant


title: M4_Bmpr1a_Het_Plate1_C10_S198_quant


title: M4_Bmpr1a_Het_Plate1_C12_S200_quant


title: M4_Bmpr1a_Het_Plate1_C1_S189_quant


title: M4_Bmpr1a_Het_Plate1_D3_S203_quant


title: M4_Bmpr1a_Het_Plate1_B4_S182_quant


title: M4_Bmpr1a_Het_Plate1_B9_S185_quant


title: M4_Bmpr1a_Het_Plate1_B7_S184_quant


title: M4_Bmpr1a_Het_Plate1_B10_S186_quant


title: M4_Bmpr1a_Het_Plate1_D12_S211_quant


title: M4_Bmpr1a_Het_Plate1_A5_S175_quant


title: M4_Bmpr1a_Het_Plate1_B1_S180_quant


title: M4_Bmpr1a_Het_Plate1_B6_S183_quant


title: M4_Bmpr1a_Het_Plate1_B2_S181_quant


title: M4_Bmpr1a_Het_Plate1_A9_S176_quant


title: M4_Bmpr1a_Het_Plate1_A3_S174_quant


title: M4_Bmpr1a_Het_Plate1_A12_S179_quant


title: M4_Bmpr1a_Het_Plate1_A10_S177_quant


title: M4_Bmpr1a_Het_Plate1_B11_S187_quant


title: M4_Bmpr1a_Het_Plate1_A2_S173_quant


title: M120_HetCtrl_P3_H6_S174_quant

description:
stage-matched control mouse replicate #2
Infarinato_etal_2020_ALL_DATA_counts.csv
Infarinato_etal_2020_ALL_DATA_TPM.csv


title: M4_Bmpr1a_Het_Plate1_A1_S172_quant


title: M120_HetCtrl_P3_H7_S175_quant


title: M120_HetCtrl_P3_H4_S173_quant


title: M4_Bmpr1a_Het_Plate1_A11_S178_quant


title: M120_HetCtrl_P3_H1_S171_quant


title: M120_HetCtrl_P3_G9_S167_quant


title: M4_Bmpr1a_Het_Plate1_B12_S188_quant


title: M120_HetCtrl_P3_G7_S165_quant


title: M120_HetCtrl_P3_H11_S177_quant


title: M120_HetCtrl_P3_H12_S178_quant


title: M120_HetCtrl_P3_G5_S163_quant


title: M120_HetCtrl_P3_G8_S166_quant


title: M120_HetCtrl_P3_G6_S164_quant


title: M120_HetCtrl_P3_G2_S161_quant


title: M120_HetCtrl_P3_G12_S170_quant


title: M120_HetCtrl_P3_G4_S162_quant


title: M120_HetCtrl_P3_G11_S169_quant


title: M120_HetCtrl_P3_G10_S168_quant


title: M120_HetCtrl_P3_G1_S160_quant


title: M120_HetCtrl_P3_F8_S155_quant


title: M120_HetCtrl_P3_F9_S156_quant


title: M120_HetCtrl_P3_F4_S152_quant


title: M120_HetCtrl_P3_F2_S150_quant


title: M120_HetCtrl_P3_F3_S151_quant


title: M120_HetCtrl_P3_H3_S172_quant


title: M120_HetCtrl_P3_F12_S159_quant


title: M120_HetCtrl_P3_F11_S158_quant


title: M120_HetCtrl_P3_H10_S176_quant


title: M120_HetCtrl_P3_F10_S157_quant


title: M120_HetCtrl_P3_F1_S149_quant


title: M120_HetCtrl_P3_E8_S144_quant


title: M120_HetCtrl_P3_E7_S143_quant


title: M120_HetCtrl_P3_E9_S145_quant


title: M120_HetCtrl_P3_E6_S142_quant


title: M120_HetCtrl_P3_E5_S141_quant


title: M120_HetCtrl_P3_E3_S139_quant


title: M120_HetCtrl_P3_E4_S140_quant


title: M120_HetCtrl_P3_E10_S146_quant


title: M120_HetCtrl_P3_E12_S148_quant


title: M120_HetCtrl_P3_D8_S136_quant


title: M120_HetCtrl_P3_E1_S138_quant


title: M120_HetCtrl_P3_D6_S134_quant


title: M120_HetCtrl_P3_E11_S147_quant


title: M120_HetCtrl_P3_D7_S135_quant


title: M120_HetCtrl_P3_D5_S133_quant


title: M120_HetCtrl_P3_F7_S154_quant


title: M120_HetCtrl_P3_F6_S153_quant


title: M120_HetCtrl_P3_D4_S132_quant


title: M120_HetCtrl_P3_D3_S131_quant


title: M120_HetCtrl_P3_D2_S130_quant


title: M120_HetCtrl_P3_D12_S137_quant


title: M120_HetCtrl_P3_C9_S125_quant


title: M120_HetCtrl_P3_D1_S129_quant


title: M120_HetCtrl_P3_C5_S122_quant


title: M120_HetCtrl_P3_C7_S123_quant


title: M120_HetCtrl_P3_C4_S121_quant


title: M120_HetCtrl_P3_C8_S124_quant


title: M120_HetCtrl_P3_C3_S120_quant


title: M120_HetCtrl_P3_C2_S119_quant


title: M120_HetCtrl_P3_C10_S126_quant


title: M120_HetCtrl_P3_C12_S128_quant


title: M120_HetCtrl_P3_C1_S118_quant


title: M120_HetCtrl_P3_B8_S115_quant


title: M120_HetCtrl_P3_B7_S114_quant


title: M120_HetCtrl_P3_B6_S113_quant


title: M120_HetCtrl_P3_B5_S112_quant


title: M120_HetCtrl_P3_B4_S111_quant


title: M120_HetCtrl_P3_B11_S116_quant


title: M120_HetCtrl_P3_B3_S110_quant


title: M120_HetCtrl_P3_B2_S109_quant


title: M120_HetCtrl_P3_B12_S117_quant


title: M120_HetCtrl_P3_A8_S104_quant


title: M120_HetCtrl_P3_A7_S103_quant


title: M120_HetCtrl_P3_A6_S102_quant


title: M120_HetCtrl_P3_A3_S99_quant


title: M120_HetCtrl_P3_A5_S101_quant


title: M120_HetCtrl_P3_A11_S106_quant


title: M120_HetCtrl_P3_A2_S98_quant


title: M120_HetCtrl_P3_A12_S107_quant


title: M120_HetCtrl_P3_A1_S97_quant


title: M120_HetCtrl_P3_A10_S105_quant


title: M120_HetCtrl_P2_H7_S140_quant


title: M120_HetCtrl_P3_A4_S100_quant


title: M120_HetCtrl_P2_H9_S141_quant


title: M120_HetCtrl_P2_H6_S139_quant


title: M120_HetCtrl_P3_C11_S127_quant


title: M120_HetCtrl_P2_H2_S136_quant


title: M120_HetCtrl_P2_H5_S138_quant


title: M120_HetCtrl_P2_H4_S137_quant


title: M120_HetCtrl_P2_H11_S143_quant


title: M120_HetCtrl_P2_H10_S142_quant


title: M120_HetCtrl_P2_H12_S144_quant


title: M120_HetCtrl_P2_G9_S131_quant


title: M120_HetCtrl_P2_G8_S130_quant


title: M120_HetCtrl_P3_B1_S108_quant


title: M120_HetCtrl_P2_G7_S129_quant


title: M120_HetCtrl_P2_G6_S128_quant


title: M120_HetCtrl_P2_G4_S126_quant


title: M120_HetCtrl_P2_G2_S124_quant


title: M120_HetCtrl_P2_G5_S127_quant


title: M120_HetCtrl_P2_G1_S123_quant


title: M120_HetCtrl_P2_F8_S118_quant


title: M120_HetCtrl_P2_G10_S132_quant


title: M120_HetCtrl_P2_F7_S117_quant


title: M120_HetCtrl_P2_F9_S119_quant


title: M120_HetCtrl_P2_G12_S134_quant


title: M120_HetCtrl_P2_F5_S115_quant


title: M120_HetCtrl_P2_F4_S114_quant


title: M120_HetCtrl_P2_F3_S113_quant


title: M120_HetCtrl_P2_F10_S120_quant


title: M120_HetCtrl_P2_H1_S135_quant


title: M120_HetCtrl_P2_F2_S112_quant


title: M120_HetCtrl_P2_F11_S121_quant


title: M120_HetCtrl_P2_F12_S122_quant


title: M120_HetCtrl_P2_F1_S111_quant


title: M120_HetCtrl_P2_E7_S106_quant


title: M120_HetCtrl_P2_E9_S60_quant


title: M120_HetCtrl_P2_E5_S104_quant


title: M120_HetCtrl_P2_G3_S125_quant


title: M120_HetCtrl_P2_E6_S105_quant


title: M120_HetCtrl_P2_E3_S102_quant


title: M120_HetCtrl_P2_E12_S110_quant


title: M120_HetCtrl_P2_E2_S101_quant


title: M120_HetCtrl_P2_E4_S103_quant


title: M120_HetCtrl_P2_F6_S116_quant


title: M120_HetCtrl_P2_G11_S133_quant


title: M120_HetCtrl_P2_E10_S84_quant


title: M120_HetCtrl_P2_D9_S98_quant


title: M120_HetCtrl_P2_D8_S97_quant


title: M120_HetCtrl_P2_D7_S96_quant


title: M120_HetCtrl_P2_D11_S100_quant


title: M120_HetCtrl_P2_D3_S52_quant


title: M120_HetCtrl_P2_D4_S58_quant


title: M120_HetCtrl_P2_D10_S99_quant


title: M120_HetCtrl_P2_D2_S48_quant


title: M120_HetCtrl_P2_D1_S91_quant


title: M120_HetCtrl_P2_C8_S86_quant


title: M120_HetCtrl_P2_C2_S81_quant


title: M120_HetCtrl_P2_C12_S90_quant


title: M120_HetCtrl_P2_C4_S83_quant


title: M120_HetCtrl_P2_C5_S84_quant


title: M120_HetCtrl_P2_C3_S82_quant


title: M120_HetCtrl_P2_C9_S87_quant


title: M120_HetCtrl_P2_C7_S85_quant


title: M120_HetCtrl_P2_B9_S79_quant


title: M120_HetCtrl_P2_B6_S76_quant


title: M120_HetCtrl_P2_B8_S78_quant


title: M120_HetCtrl_P2_E11_S88_quant


title: M120_HetCtrl_P2_B5_S75_quant


title: M120_HetCtrl_P2_C11_S89_quant


title: M120_HetCtrl_P2_C10_S88_quant


title: M120_HetCtrl_P2_B7_S77_quant


title: M120_HetCtrl_P2_B2_S44_quant


title: M120_HetCtrl_P2_B3_S45_quant


title: M120_HetCtrl_P2_D6_S95_quant


title: M120_HetCtrl_P2_B1_S33_quant


title: M120_HetCtrl_P2_B10_S80_quant


title: M120_HetCtrl_P2_A3_S67_quant


title: M120_HetCtrl_P2_A12_S71_quant


title: M120_HetCtrl_P2_A7_S69_quant


title: M120_HetCtrl_P2_A10_S70_quant


title: M120_HetCtrl_P2_A1_S66_quant


title: M120_HetCtrl_P1_H9_S311_quant


title: M120_HetCtrl_P1_H6_S310_quant


title: M120_HetCtrl_P1_H12_S314_quant


title: M120_HetCtrl_P1_H10_S312_quant


title: M120_HetCtrl_P1_H4_S308_quant


title: M120_HetCtrl_P1_H3_S307_quant


title: M120_HetCtrl_P1_H1_S305_quant


title: M120_HetCtrl_P1_G6_S32_quant