title: Negative control  96 Negative scRNAseq

city: Caserta

first: Francesco

last: Cecere

state: Caserta

address: Via A. Vivaldi, n. 43

department: DiStABiF

country: Italy

institute: University of Campania "Luigi Vanvitelli"

data_processing:
A total of 96 libraries were adapted and quality trimmed (Phred score <20) using Trim Galore version 0.4.4 (Krueger, 2017). We also sequenced 4 negative controls to archive technical problems. The good quality reads were aligned to the Genome Reference Consortium mouse genome build 39 (GRCm39) with HiSat2 version 2.1.0 (Kim et al., 2015) in paired-end mode. The data were quantified in SeqMonk and analysed in Rstudio. We exported the raw count matrix by SeqMonk andwe calculate the differential expression following the DESeq2 pipeline (Love et al, 2014).
Assembly: mm39
Supplementary files format and content: raw count expression matrix

source_name: control

growth_protocol: For the experiment, males of 8-12 weeks of age and females of 4-8 weeks of age were used. The day before the start of the experiment, the males were separated. On day 1, at 2 pm, intraperitoneal injections of pregnant mare serum gonadotropin (PMSG) were given to the females. After approximately 52 hours, the same females received intraperitoneal injections of human chorionic gonadotropin (hCG). Male was sacrificed approximately 12 hours after the female hCG injection. The cauda epididymis and vasa deferentia were dissected and the spermatozoa were collected in the human tubal fluid medium (HTF) (EmbryoMax® HTF MR-070-D). Spermatozoa were counted and incubated at 37°C within a humidified atmosphere of 5% CO2 in air. Females were sacrificed approximately 13 hours after the hCG injection. Ampullae were placed in hyaluronidase 1mg/ml (H6254-500MG) drops to break down the oocyte-cumulus complex and collect MII oocyte. The oocytes were moved to the HTF medium and a 2x106 sperm/ml concentration of spermatozoa were added. After 4 - 6 hours of incubation at 37°C within a humidified atmosphere of 5% CO2 in air, the fertilised oocytes were washed, to remove the spermatozoa e debris, transferred in KSOM medium and incubated overnight at 37°C within a humidified atmosphere of 5% CO2 in air. The embryos' status was evaluated in the morning and the next 120 hours.

extract_protocol:
MII oocytes and 2-cell embryos were collected as described before. For 2-cell embryos, the zona pellucida was removed with Tyrode’s solution (SIGMA-ALDRICH), the blastomeres were separated and the polar body was discarded. Then single oocytes and blastomeres were picked and put into a lysis buffer (Buffer RLT Plus Qiagen). DNA and RNA from lysate were separated using the G&T protocol (Angermueller et al. 2016). The magnetic beads (MyOne C1, Life Technologies) were washed and then annealed to oligo dTs. These were used to capture polyadenylated mRNA from individual cell lysate. The supernatant containing the DNA was transferred to a new tube and the beads washed three times in 1xFSS buffer (Superscript II, Invitrogen), 10 mM DTT, 0.005% Tween-20 (Sigma) and 0.4 U/μl of RNAsin (Promega) to remove all DNA residue. Each washing solution was added to the DNA tube to maximise recovery.
mRNA on the beads was processed further for cDNA conversion. This involved the resuspension in 10 μl of reverse transcriptase mastermix (100 U SuperScript II (Invitrogen), 10 U RNAsin (Promega), 1 × Superscript II First-Strand Buffer, 5 mM DTT (Invitrogen), 1 M betaine (Sigma), 9 mM MgCl2 (Invitrogen), 1 μM Template-Switching Oligo (TSO, Eurogentec), 1 mM dNTP mix (Roche). The mRNA mixture was reverse transcribed by incubation for 60 min at 42 °C followed by 30 min at 50 °C and 10 min at 60 °C. The cDNA obtained was subjected to PCR amplification by adding 11 μl of 2x KAPA HiFi HotStart ReadyMix and 1 μl of ISPCR primer (2 μM). The amplification was carried out in a thermocycler at 98 °C for 3 min, followed by 15 cycles of 98 °C for 15 s, 67 °C for 20 s, 72 °C for 6 min and the final extension step at 72 °C for 5 min. The amplified product was purified using Ampure XP beads with a 1:1 ratio and eluted into 20 μl of water. Libraries were prepared from 100 to 400 pg of cDNA using the Nextera XT Kit (Illumina), per the manufacturer's instructions but with one-fifth volumes. All 96 single-cell RNA-seq libraries were pooled together and sequenced on the Illumina NextSeq platform to an average depth of 4.2 million reads, using paired-end 75 bp read-length settings.

value: control


title: 2cell embryo 80 Mutant scRNAseq

status: Public on Oct 18 2023

type: SRA

library_source: transcriptomic single cell

molecule: polyA RNA

organism: Mus musculus

source_name: embryo

tag: cell type

value: embryo

tag: genotype


title: 2cell embryo 92 Mutant scRNAseq


title: 2cell embryo 84 Mutant scRNAseq


title: 2cell embryo 82 Mutant scRNAseq


title: 2cell embryo 86 Mutant scRNAseq


title: 2cell embryo 94 Mutant scRNAseq


title: 2cell embryo 85 Mutant scRNAseq


title: 2cell embryo 87 Mutant scRNAseq


title: 2cell embryo 81 Mutant scRNAseq


title: 2cell embryo 83 Mutant scRNAseq


title: 2cell embryo 90 Mutant scRNAseq


title: 2cell embryo 91 Mutant scRNAseq


title: 2cell embryo 93 Mutant scRNAseq


title: 2cell embryo 88 Mutant scRNAseq


title: 2cell embryo 79 Mutant scRNAseq


title: 2cell embryo 89 Mutant scRNAseq


title: Negative control  95 Negative scRNAseq


title: 2cell embryo 75 Mutant scRNAseq


title: 2cell embryo 74 Mutant scRNAseq


title: 2cell embryo 77 Mutant scRNAseq


title: 2cell embryo 76 Mutant scRNAseq


title: 2cell embryo 73 Mutant scRNAseq


title: 2cell embryo 78 Mutant scRNAseq


title: Negative control  72 Negative scRNAseq


title: Negative control  71 Negative scRNAseq


title: 2cell embryo 70 wild-type scRNAseq


title: 2cell embryo 68 wild-type scRNAseq


title: 2cell embryo 69 wild-type scRNAseq


title: R002

status: Public on Oct 19 2023

city: Cleveland

first: Vladimir

last: Makarov

state: OH

address: 9500 Euclid Ave

country: USA

institute: CLEVELAND CLINIC LERNER COM-CWRU

description: Single-Arm Phase II Trial

library_source: transcriptomic

data_processing:
Raw reads in the FASTQ format were aligned to the mm10 reference genome using STAR aligner v2.7.6a. The featureCounts read summarization program was used to count mapped reads for each gene in the annotation file (Human GENECODE: Release 42 (GRCh38.p13)). Count files were then merged by an in-house R script and differential gene expression analysis was performed using DESeq2. DESeq2 normalizes the count data to account for differences in sequencing depth and composition. This is done using the median of ratios method, which involves dividing each gene's raw count by a size factor that accounts for library size and composition. DESeq2 models the variation in gene expression using a negative binomial distribution. The dispersion estimates are used to model the relationship between mean expression and variance, which is critical for accurate detection of differentially expressed genes.
Assembly: Human GENECODE: Release 42 (GRCh38.p13)
Supplementary files format and content: Raw (raw_count_matrix.csv) and DESeq normalized (DeseqNormalizedCount.csv) matrices are made available along with the FASTQ files used in current study.

organism: Homo sapiens

source_name: Metastatic Triple-Negative Breast Cancer PRE treatment

extract_protocol: RNA was isolated from frozen core biopsies of primary or metastatic TNBC tissue using the Qiagen AllPrep DNA/RNA kit.Libraries were prepared using the Takara SMART-Seq v4 Ultra Low Input RNA kit and sequenced on an Illumina NovaSeq for a target of 40 million reads per sample.

treatment_protocol: Pre-treatment samples were collected from patients with stage IV triple negative breast cancer prior to receiving chemo-immunotherapy with the following regimen which was administered intravenously on a 21 day cycle: carboplatin (C) day 1 (AUC 4.5), nab-paclitaxel (N) days 1,8,15 (75 mg/m2), and pembrolizumab (P) 200 mg on day 15. An optional post-therapy biopsy was obtained after the 3rd cycle of CNP chemo-immunotherapy

tag: tissue

value: metastatic tissue biopsy

tag: treatment

value: Carboplatin, Nab-Paclitaxel, and Pembrolizumab

tag: overall response

value: Progressive Disease

tag: os

tag: pfs

tag: os event

tag: pfs event

tag: age

tag: biomaterial provider

tag: collection date

tag: geo loc_name

value: Cleveland, OH, USA

tag: Sex

value: female

value: lympn node

tag: disease

value: TNBC

tag: disease stage

value: stage IV

tag: race

value: Black or African American


title: Negative control  47 Negative scRNAseq

tag: cell type


title: MII oocyte 46 Mutant scRNAseq

source_name: oocyte

value: oocyte

tag: genotype


title: 2cell embryo 67 wild-type scRNAseq


title: 2cell embryo 66 wild-type scRNAseq


title: 2cell embryo 62 wild-type scRNAseq


title: 2cell embryo 63 wild-type scRNAseq


title: 2cell embryo 57 wild-type scRNAseq


title: 2cell embryo 60 wild-type scRNAseq


title: 2cell embryo 53 wild-type scRNAseq


title: 2cell embryo 55 wild-type scRNAseq


title: 2cell embryo 64 wild-type scRNAseq


title: 2cell embryo 65 wild-type scRNAseq


title: 2cell embryo 49 wild-type scRNAseq


title: 2cell embryo 59 wild-type scRNAseq


title: 2cell embryo 61 wild-type scRNAseq


title: 2cell embryo 52 wild-type scRNAseq


title: 2cell embryo 54 wild-type scRNAseq


title: MII oocyte 45 Mutant scRNAseq


title: 2cell embryo 58 wild-type scRNAseq


title: 2cell embryo 51 wild-type scRNAseq


title: MII oocyte 44 Mutant scRNAseq


title: 2cell embryo 56 wild-type scRNAseq


title: Negative control  48 Negative scRNAseq


title: 2cell embryo 50 wild-type scRNAseq


title: MII oocyte 42 Mutant scRNAseq


title: MII oocyte 43 Mutant scRNAseq


title: MII oocyte 40 Mutant scRNAseq


title: MII oocyte 41 Mutant scRNAseq


title: MII oocyte 39 Mutant scRNAseq


title: MII oocyte 38 Mutant scRNAseq


title: MII oocyte 36 Mutant scRNAseq


title: MII oocyte 37 Mutant scRNAseq


title: MII oocyte 35 Mutant scRNAseq


title: MII oocyte 34 Mutant scRNAseq


title: Negative control  23 Negative scRNAseq


title: Negative control  24 Negative scRNAseq


title: MII oocyte 21 wild-type scRNAseq


title: MII oocyte 30 Mutant scRNAseq


title: MII oocyte 31 Mutant scRNAseq


title: MII oocyte 32 Mutant scRNAseq


title: MII oocyte 25 Mutant scRNAseq


title: MII oocyte 20 wild-type scRNAseq


title: MII oocyte 18 wild-type scRNAseq


title: MII oocyte 28 Mutant scRNAseq


title: MII oocyte 29 Mutant scRNAseq


title: MII oocyte 19 wild-type scRNAseq


title: MII oocyte 22 wild-type scRNAseq


title: MII oocyte 33 Mutant scRNAseq


title: MII oocyte 16 wild-type scRNAseq


title: MII oocyte 17 wild-type scRNAseq


title: MII oocyte 13 wild-type scRNAseq


title: MII oocyte 12 wild-type scRNAseq


title: MII oocyte 14 wild-type scRNAseq


title: MII oocyte 15 wild-type scRNAseq


title: MII oocyte 11 wild-type scRNAseq


title: MII oocyte 10 wild-type scRNAseq


title: MII oocyte 8 wild-type scRNAseq


title: MII oocyte 9 wild-type scRNAseq


title: MII oocyte 26 Mutant scRNAseq


title: MII oocyte 27 Mutant scRNAseq


title: MII oocyte 7 wild-type scRNAseq


title: MII oocyte 6 wild-type scRNAseq


title: MII oocyte 5 wild-type scRNAseq


title: MII oocyte 4 wild-type scRNAseq


title: MII oocyte 2 wild-type scRNAseq


title: MII oocyte 1 wild-type scRNAseq


title: Output screen with 1/4 X MTX Replicate 2

city: Basel

first: Alexandra

middle: Michaela

last: Bendel

address: Maulbeerstr. 66

department: Genome Regulation

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

library_source: genomic

data_processing:
For the DMS, barcode reads were matched to the expected barcode sequences, aggregated by amino acid substitutions and processed with mutscan
Supplementary files format and content: csv file. Contains counts
Supplementary files format and content: csv file. Contains average growth rates

molecule: genomic DNA

organism: Saccharomyces cerevisiae

extract_protocol:
DNA was extracted using a custom yeast Mini- or Midiprep protocol
Sequencing libraries were constructed by PCR with primers cotaining the illumina adapters

tag: cell line


title: Output screen with 1/4 X MTX Replicate 1


title: Output screen with MTX from Sigma Replicate 2


title: Output screen with 1/20 X MTX Replicate 1


title: Standard Input (harvested before pre-selection phase) Replicate 2


title: Input harvested after pre-selection phase Replicate 1


title: Output for input samples harvested after pre-selection phase Replicate 2


title: Sandard Output (screen with 1 X MTX) Replicate 2


title: Input harvested after pre-selection phase Replicate 2


title: Standard Input (harvested before pre-selection phase) Replicate 1


title: Output screen with 1/2 X MTX Replicate 2


title: Output screen with 2 X MTX Replicate 2


title: Output screen with 2 X MTX Replicate 1


title: Output sample DMSO Replicate 1


title: Output sample DMSO Replicate 2


title: Output 5 generations Replicate 2


title: Output 5 generations Replicate 1


title: Output 4.5 generations Replicate 2


title: Output 4 generations Replicate 2


title: Output 4.5 generations Replicate 1


title: Output screen with MTX from Sigma Replicate 1


title: Output 4 generations Replicate 1


title: Sandard Output (screen with 1 X MTX) Replicate 1


title: MII oocyte 3 wild-type scRNAseq


title: Output 3 generations Replicate 2


title: Output screen with 1/20 X MTX Replicate 2


title: Output screen with 1/2 X MTX Replicate 1


title: Output 2 generations Replicate 2


title: Output 3 generations Replicate 1


title: Output for input samples harvested after pre-selection phase Replicate 1


title: Output 2 generations Replicate 1


title: 3 ug Output Replicate 6


title: 333 ng Output Replicate 6


title: Input Replicate 1


title: 1 ug Outut Replicate 6


title: Input Replicate 2


title: 1 ug Outut Replicate 4


title: 100 ng Output Replicate 6


title: 3 ug Output Replicate 5


title: 3 ug Output Replicate 3


title: 1 ug Outut Replicate 3


title: 333 ng Output Replicate 4


title: 100 ng Output Replicate 4


title: 1 ug Outut Replicate 5


title: 20 ug Output Replicate 2


title: 20 ug Output Replicate 3


title: 333 ng Output Replicate 5


title: 20 ug Output Replicate 4


title: 20 ug Output Replicate 5


title: 333 ng Output Replicate 3


title: 3 ug Output Replicate 2


title: 333 ng Output Replicate 2


title: 100 ng Output Replicate 3


title: 1 ug Outut Replicate 2


title: 100 ng Output Replicate 2


title: 20 ug Output Replicate 1


title: 1 ug Outut Replicate 1


title: 3 ug Output Replicate 1


title: 20 ug Output Replicate 6


title: 3 ug Output Replicate 4


title: 333 ng Output Replicate 1


title: 100 ng Output Replicate 1


title: 20 ug Input Replicate 6


title: 3 ug Input Replicate 6


title: 1 ug Input Replicate 6


title: 333 ng Input Replicate 6


title: 333 ng Input Replicate 4


title: 1 ug Input Replicate 3


title: 333 ng Input Replicate 5


title: 20 ug Input Replicate 4


title: 100 ng Input Replicate 4


title: 100 ng Input Replicate 6


title: 20 ug Input Replicate 5


title: 1 ug Input Replicate 4


title: 20 ug Input Replicate 3


title: 1 ug Input Replicate 2


title: 20 ug Input Replicate 2


title: 3 ug Input Replicate 3


title: 333 ng Input Replicate 2


title: 3 ug Input Replicate 4


title: 3 ug Input Replicate 5


title: 100 ng Input Replicate 3


title: 1 ug Input Replicate 1


title: 1 ug Input Replicate 5


title: 20 ug Input Replicate 1


title: 100 ng Input Replicate 2


title: 333 ng Input Replicate 3


title: 100 ng Input Replicate 1


title: 333 ng Input Replicate 1


title: 3 ug Input Replicate 1


title: 3 ug Input Replicate 2


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_H8

city: Hangzhou

first: SHOU-WEN

last: WANG

state: Zhejiang Province

address: Shilongshan ST #18, Xihu District

country: China

institute: Westlake University

data_processing:
BS-seq libraries were aligned to the bisulfite-converted mm10 mouse genome using Bismark (v.0.23.0) in a paired-end, non-directional mode. Then the unmapped reads were aligned again in a single-end, non-directional mode. We used the coverage2cytosine script from Bismark with the –nom-seq option to generate CpG report files containing only A–C–G and T–C–G positions and GpC report files containing only G–C–A, G–C–C, and G–C–T positions. The DNA methylation rate (CpG rate) at a given CpG site was determined by the ratio between the number of methylated CpG reads over unmethylated CpG reads. The accessibility rate or GpC rate was computed similarly.
Assembly: mm10
Supplementary files format and content: Methylation calling tsv.gz files which include the methylation level of covered cytosines, including CpG and GpC contexts

source_name: HSC

extract_protocol:
Individual cells were directly sorted into 96-well plates containing methyltransferase reaction mixture and incubated for 30 minutes at 37°C. Dynabeads Myone Carboxylic Acid (Invitrogen, 65011) was used to capture nuclei, which were used to carry out scBisulfite-seq to profile DNA methylation and chromatin accessibility.
Bisulfite-converted DNA was amplified with biotinylated random primer and klenow exo– polymerase (NEB, M0212L) for 7 rounds and excess primer was removed by exonuclease I (NEB, M0293L). After second strand synthesis, the library was amplified by KAPA HiFi HotStart ReadyMix (Kapa Biosystems, KK2602) for 14 cycles.

value: HSC


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_H6


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_H5


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_H7


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_H3


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_H9


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_G9


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_H4


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_H1


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_H11


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_G8


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_G6


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_G12


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_G4


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_G7


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_G2


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_G11


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_H10


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_G5


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_G10


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_G3


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_H2


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_G1


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_F9


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_F8


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_F5


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_F7


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_F6


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_F4


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_H12


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_F2


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_F3


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_F11


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_F12


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_F1


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_F10


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_E7


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_E8


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_E6


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_E4


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_E1


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_E2


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_E5


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_E11


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_E10


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_E3


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_E12


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_D7


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_D6


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_D8


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_D5


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_D12


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_D3


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_D10


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_D2


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_D9


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_D1


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_D11


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_E9


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_C8


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_C9


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_C4


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_C2


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_C3


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_C11


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_C12


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_C1


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_B8


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_B9


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_B5


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_B7


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_B2


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_B6


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_B12


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_D4


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_B10


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_B11


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_B1


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_A8


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_B4


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_A6


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_A5


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_C7


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_C6


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_C5


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_A7


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_A4


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_C10


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_A12


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_B3


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_A3


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_A10


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_A1


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_A9


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_H9


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_H2


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_H12


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_H3


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_H8


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_H5


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_H1


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_H11


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_G8


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_G7


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_G6


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_G5


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_G4


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_G3


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_A2


title: Camellia_BoneMarrow-HSC_LL901_P3_DNA_A11


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_G2


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_G11


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_G10


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_G12


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_H7


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_H6


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_G1


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_H4


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_H10


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_F5


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_F8


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_F6


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_F7


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_G9


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_F3


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_F9


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_F4


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_F11


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_F2


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_E9


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_F10


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_F1


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_E8


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_E4


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_E5


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_E6


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_E2


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_E7


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_E3


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_E11


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_D9


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_E12


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_D7


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_D8


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_E10


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_F12


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_D3


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_D11


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_D4


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_D6


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_C9


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_D2


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_D1


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_D12


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_D5


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_D10


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_C6


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_C7


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_C8


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_C5


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_C4


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_C2


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_C12


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_C11


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_C10


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_E1


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_C3


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_C1


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_B9


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_B6


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_B5


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_B4


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_B7


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_B3


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_B8


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_B2


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_B12


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_B11


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_A9


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_B10


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_A8


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_B1


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_A5


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_A6


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_A2


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_A4


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_A3


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_A12


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_A11


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_A10


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_A1


title: Camellia_BoneMarrow-HSC_LL901_P3_RNA

data_processing:
We first extract cell barcode (8bp) and UMI (8bp) with UMI_tools
Then, we use customized script to trim TSO and polyA, and discard low-quality reads
Next, we use featureCounts to add gene annotation, use samtools to sort and index bam files, and finally run umi_tools to generate the count matrix
Assembly: mm10
Supplementary files format and content: tsv files, cell-by-gene matrix from UMI_counts software

extract_protocol:
Individual cells were directly sorted into 96-well plates containing methyltransferase reaction mixture and incubated for 30 minutes at 37°C. Dynabeads Myone Carboxylic Acid (Invitrogen, 65011) was used to remove nuclei. Assisted with magnetic stand, the binding buffer containing cytoplasmic mRNA was transferred to a separate 96-well plate.
The cytoplasmic mRNA was processed with scSTRT-seq with minor modifications to profile the whole transcriptome


title: 10X_transcriptome_LL837-lung

data_processing:
Each 10X run generates 4 files (R1, R2, I1, I2) associated with a biological sample. We used Cell Ranger v.7.0.0 pipeline to generate the count matrix
Assembly: mm10
Supplementary files format and content: H5 - CellRanger single-cell count matrix

molecule: total RNA

extract_protocol:
Cells were sorted by FACS and encapsulated by 10x
Libraries were prepared according to 10x Chromium single-cell RNA protocols. Library was sequenced on an Illumina NextSeq sequencer

tag: protocol

value: 10x-v3 Chromium single-cell protocols


title: Camellia_BoneMarrow-HSC_LL901_P2_RNA


title: 10X_transcriptome_LL837-LeftLeg


title: 10X_transcriptome_LL837-liver


title: 10X_transcriptome_LL837-spleen


title: Camellia_BoneMarrow-HSC_LL901_P2_DNA_A7


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_H6

source_name: Fetal Liver

tag: tissue

value: Fetal Liver


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_H5


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_H3


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_G9


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_H7


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_H2


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_H9


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_H4


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_H8


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_H12


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_H11


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_G8


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_H1


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_G7


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_G5


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_G4


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_H10


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_G2


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_G1


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_F9


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_G11


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_G10


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_F6


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_F8


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_F7


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_G12


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_F5


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_F4


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_G6


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_F12


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_F11


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_F1


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_G3


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_F2


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_E9


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_E7


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_F10


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_F3


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_E2


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_E4


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_E5


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_E11


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_D9


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_E1


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_D6


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_D4


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_D8


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_D2


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_D12


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_D3


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_D5


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_D11


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_E3


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_E8


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_E6


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_C8


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_E12


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_D10


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_C5


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_D1


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_C2


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_C6


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_C7


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_C11


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_E10


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_C10


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_C4


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_C3


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_D7


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_C9


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_C12


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_B9


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_B7


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_C1


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_B6


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_B5


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_B4


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_B3


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_B2


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_B11


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_B10


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_B1


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_A8


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_A5


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_A4


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_A6


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_A7


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_A11


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_A9


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_H9


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_A12


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_H8


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_H6


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_A3


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_A2


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_A10


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_H7


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_A1


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_H12


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_H3


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_H4


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_B8


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_H2


title: Camellia_FetalLiver-HSC_LL653E6P2_DNA_B12


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_H11


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_H5


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_G8


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_H1


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_G7


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_G6


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_G9


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_G5


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_G4


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_G3


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_G11


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_G2


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_F9


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_F8


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_G1


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_G12


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_F7


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_G10


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_F4


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_F3


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_F6


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_F12


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_F5


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_F11


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_F10


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_E9


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_F2


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_F1


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_E7


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_H10


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_E8


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_E6


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_E3


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_E5


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_E4


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_E2


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_E12


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_E11


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_E10


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_D9


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_D8


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_D6


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_D12


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_D10


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_D11


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_D7


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_D3


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_E1


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_D2


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_C8


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_C6


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_D4


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_C3


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_D1


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_C7


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_C4


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_C2


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_C12


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_C11


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_C10


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_C5


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_B6


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_C1


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_C9


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_B5


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_B9


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_B4


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_B3


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_D5


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_B12


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_B2


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_A9


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_B10


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_A8


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_A7


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_B11


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_B1


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_A3


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_B7


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_A4


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_A11


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_H9


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_A1


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_A10


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_H4


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_H2


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_H11


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_H8


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_H3


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_H7


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_H10


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_H5


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_H12


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_G7


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_H1


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_G5


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_G4


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_G2


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_G10


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_A5


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_G3


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_G12


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_H6


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_G1


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_F8


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_F9


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_G11


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_A12


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_G9


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_A2


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_G8


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_G6


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_F4


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_F7


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_F5


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_F12


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_F2


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_E8


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_E9


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_E3


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_E6


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_F1


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_E10


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_F11


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_D8


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_E4


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_E12


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_E2


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_D6


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_D7


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_E1


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_D9


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_F6


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_F3


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_F10


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_D5


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_D4


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_D12


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_E7


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_D3


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_E11


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_A6


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_C8


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_D11


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_D1


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_C4


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_C6


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_C9


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_C5


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_C11


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_B8


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_C3


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_C2


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_D2


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_C10


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_B4


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_C1


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_B12


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_B3


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_B9


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_B7


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_C12


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_B1


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_D10


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_A8


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_B6


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_C7


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_B5


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_B2


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_A6


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_A7


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_B11


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_B10


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_A5


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_H9


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_A9


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_A4


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_H8


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_A12


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_A3


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_A11


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_H5


title: Camellia_FetalLiver-HSC_LL653E6P1_DNA_B8


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_A2


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_A10


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_H3


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_H11


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_A1


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_H12


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_H1


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_G9


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_H2


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_H4


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_H10


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_H6


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_G8


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_H7


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_G7


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_G5


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_G3


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_G2


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_G4


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_G12


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_G11


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_F8


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_F9


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_F5


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_F7


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_G10


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_F4


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_F6


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_G1


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_F3


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_G6


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_F11


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_F10


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_F12


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_E9


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_F2


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_F1


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_E6


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_E8


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_E7


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_E3


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_E4


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_E5


title: Camellia_FetalLiver-HSC_LL653E1P3_DNA_E5


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_E11


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_E12


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_E10


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_D9


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_E1


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_D7


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_D5


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_D3


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_D11


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_D12


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_D6


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_D2


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_D1


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_D10


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_C9


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_D4


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_C8


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_E2


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_C6


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_C7


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_C5


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_C4


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_C12


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_C3


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_C2


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_C1


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_C11


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_D8


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_B8


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_B9


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_B5


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_C10


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_B3


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_A9


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_B11


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_A7


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_B10


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_A8


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_A5


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_A6


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_B2


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_B7


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_B6


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_A3


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_B4


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_A2


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_A12


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_H8


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_A1


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_A4


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_A11


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_H6


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_H9


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_A10


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_H7


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_H2


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_H3


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_H5


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_H4


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_B1


title: Camellia_FetalLiver-HSC_LL653E1P2_DNA_B12


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_H12


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_H11


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_H1


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_H10


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_G4


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_G5


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_G8


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_G6


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_G9


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_G7


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_G3


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_G2


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_G12


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_G11


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_G1


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_G10


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_F7


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_F9


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_F6


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_F11


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_F2


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_E9


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_F3


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_F5


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_F1


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_F12


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_F4


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_F10


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_E7


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_E8


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_E4


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_E5


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_E3


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_E2


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_E12


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_E1


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_E11


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_F8


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_E10


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_D9


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_D8


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_E6


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_D4


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_D7


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_D2


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_D3


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_D6


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_D5


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_D12


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_C8


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_D1


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_D11


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_C7


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_C4


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_D10


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_C3


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_C9


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_C5


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_C2


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_C6


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_C12


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_C11


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_B7


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_B5


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_B6


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_C10


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_B8


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_C1


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_B9


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_B3


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_B2


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_B4


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_B12


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_B11


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_A9


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_B10


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_A6


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_A4


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_A8


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_A5


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_A3


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_B1


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_A7


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_A11


title: Camellia_BoneMarrow-HSC_LL731_P3_DNA_F9

source_name: Bone Marrow

value: Bone Marrow


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_A10


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_A12


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_A2


title: Camellia_BoneMarrow-HSC_LL731_P3_DNA_F8


title: Camellia_BoneMarrow-HSC_LL731_P3_DNA_F6


title: Camellia_BoneMarrow-HSC_LL731_P3_DNA_F4


title: Camellia_BoneMarrow-HSC_LL731_P3_DNA_F3


title: Camellia_BoneMarrow-HSC_LL731_P3_DNA_F5


title: Camellia_BoneMarrow-HSC_LL731_P3_DNA_F10


title: Camellia_BoneMarrow-HSC_LL731_P3_DNA_F12


title: Camellia_BoneMarrow-HSC_LL731_P3_DNA_F11


title: Camellia_BoneMarrow-HSC_LL731_P3_DNA_E9


title: Camellia_BoneMarrow-HSC_LL731_P3_DNA_F1


title: Camellia_BoneMarrow-HSC_LL731_P3_DNA_E7


title: Camellia_FetalLiver-HSC_LL653E1P1_DNA_A1


title: Camellia_BoneMarrow-HSC_LL731_P3_DNA_E8


title: Camellia_BoneMarrow-HSC_LL731_P3_DNA_E5


title: Camellia_BoneMarrow-HSC_LL731_P3_DNA_F7


title: Camellia_BoneMarrow-HSC_LL731_P3_DNA_E4


title: Camellia_BoneMarrow-HSC_LL731_P3_DNA_E6


title: Camellia_BoneMarrow-HSC_LL731_P3_DNA_E10


title: Camellia_BoneMarrow-HSC_LL731_P3_DNA_E11


title: Camellia_BoneMarrow-HSC_LL731_P3_DNA_D9


title: Camellia_BoneMarrow-HSC_LL731_P3_DNA_E3


title: Camellia_BoneMarrow-HSC_LL731_P3_DNA_D6


title: Camellia_BoneMarrow-HSC_LL731_P3_DNA_E1


title: Camellia_BoneMarrow-HSC_LL731_P3_DNA_D7


title: Camellia_BoneMarrow-HSC_LL731_P3_DNA_D5


title: Camellia_BoneMarrow-HSC_LL731_P3_DNA_E12


title: Camellia_BoneMarrow-HSC_LL731_P3_DNA_D8


title: Camellia_BoneMarrow-HSC_LL731_P3_DNA_D4


title: Camellia_BoneMarrow-HSC_LL731_P3_DNA_F2


title: Camellia_BoneMarrow-HSC_LL731_P3_DNA_D11


title: Camellia_BoneMarrow-HSC_LL731_P3_DNA_E2


title: Camellia_BoneMarrow-HSC_LL731_P3_DNA_C8


title: Camellia_BoneMarrow-HSC_LL731_P3_DNA_C9


title: Camellia_BoneMarrow-HSC_LL731_P3_DNA_C7


title: Camellia_BoneMarrow-HSC_LL731_P3_DNA_C6


title: Camellia_BoneMarrow-HSC_LL731_P3_DNA_C5


title: Camellia_BoneMarrow-HSC_LL731_P3_DNA_C2


title: Camellia_BoneMarrow-HSC_LL731_P3_DNA_D3


title: Camellia_BoneMarrow-HSC_LL731_P3_DNA_C3


title: Camellia_BoneMarrow-HSC_LL731_P3_DNA_C10


title: Camellia_BoneMarrow-HSC_LL731_P3_DNA_C12


title: Camellia_BoneMarrow-HSC_LL731_P3_DNA_D2


title: Camellia_BoneMarrow-HSC_LL731_P3_DNA_C11


title: Camellia_BoneMarrow-HSC_LL731_P3_DNA_B9


title: Camellia_BoneMarrow-HSC_LL731_P3_DNA_B8


title: Camellia_BoneMarrow-HSC_LL731_P3_DNA_B3


title: Camellia_BoneMarrow-HSC_LL731_P3_DNA_B4


title: Camellia_BoneMarrow-HSC_LL731_P3_DNA_B5


title: Camellia_BoneMarrow-HSC_LL731_P3_DNA_B12


title: Camellia_BoneMarrow-HSC_LL731_P3_DNA_B2


title: Camellia_BoneMarrow-HSC_LL731_P3_DNA_C4


title: Camellia_BoneMarrow-HSC_LL731_P3_DNA_B6


title: Camellia_BoneMarrow-HSC_LL731_P3_DNA_D1


title: Camellia_BoneMarrow-HSC_LL731_P3_DNA_D10


title: Camellia_BoneMarrow-HSC_LL731_P3_DNA_D12


title: Camellia_BoneMarrow-HSC_LL731_P3_DNA_C1


title: Camellia_BoneMarrow-HSC_LL731_P3_DNA_A9


title: Camellia_BoneMarrow-HSC_LL731_P3_DNA_B1


title: Camellia_BoneMarrow-HSC_LL731_P3_DNA_A8


title: Camellia_BoneMarrow-HSC_LL731_P3_DNA_A7


title: Camellia_BoneMarrow-HSC_LL731_P3_DNA_B10


title: Camellia_BoneMarrow-HSC_LL731_P3_DNA_B11


title: Camellia_BoneMarrow-HSC_LL731_P3_DNA_A4


title: Camellia_BoneMarrow-HSC_LL731_P3_DNA_A5


title: Camellia_BoneMarrow-HSC_LL731_P3_DNA_B7


title: Camellia_BoneMarrow-HSC_LL731_P3_DNA_A6


title: Camellia_BoneMarrow-HSC_LL731_P3_DNA_A3


title: Camellia_BoneMarrow-HSC_LL731_P3_DNA_A2


title: Camellia_BoneMarrow-HSC_LL731_P3_DNA_A12


title: Camellia_BoneMarrow-HSC_LL731_P3_DNA_A11


title: Camellia_BoneMarrow-HSC_LL731_P3_DNA_A10


title: Camellia_BoneMarrow-HSC_LL731_P3_DNA_A1


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_H9


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_H8


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_H5


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_H2


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_H12


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_H10


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_H1


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_G9


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_G6


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_G7


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_G4


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_G2


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_G3


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_G10


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_G11


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_F8


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_G1


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_F9


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_F7


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_F6


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_F5


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_F4


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_H3


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_H7


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_H4


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_H6


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_H11


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_F12


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_F1


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_F10


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_G5


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_G8


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_F2


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_E9


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_G12


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_E7


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_E5


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_E6


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_E8


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_E4


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_E3


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_E2


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_E12


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_E10


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_D9


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_E11


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_E1


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_F3


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_D8


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_F11


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_D7


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_D6


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_D3


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_D5


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_D4


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_D12


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_D2


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_D11


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_D1


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_C7


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_D10


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_C8


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_C6


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_C5


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_C9


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_C4


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_C11


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_C2


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_C1


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_B8


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_C12


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_B4


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_C10


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_B9


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_B5


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_B7


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_B3


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_B6


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_B2


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_B11


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_A8


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_B10


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_B1


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_A7


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_B12


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_A9


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_A11


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_C3


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_A12


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_A5


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_A3


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_H9


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_H8


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_A6


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_A4


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_A2


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_A1


title: Camellia_BoneMarrow-HSC_LL731_P2_DNA_A10


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_H7


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_H5


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_H2


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_H12


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_H3


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_H4


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_H6


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_H11


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_H1


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_G9


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_G7


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_G4


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_G5


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_G6


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_G2


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_G3


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_G8


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_G10


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_G12


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_G1


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_F9


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_G11


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_F4


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_F3


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_F6


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_F7


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_F2


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_F5


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_F12


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_F11


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_H10


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_E9


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_E8


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_E7


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_E4


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_E5


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_F8


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_E11


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_E10


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_E2


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_E12


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_E3


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_E1


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_D4


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_D6


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_D5


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_F10


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_F1


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_D2


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_D11


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_D7


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_D3


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_D10


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_D8


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_E6


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_C8


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_C9


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_C7


title: ID100_NEC_cctrl

type: genomic

city: La Laguna

first: Javier

last: Perez-Garcia

address: Avenida Astrofisico Francisco Sanchez s/n

department: Biochemistry, Microbiology, Cell Biology, and Genetics

country: Spain

institute: Universidad de La Laguna

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium MethylationEPIC BeadChip v1 using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
GenomeStudio v2011.1
BDR_200samp_AvgBeta-pval.txt represents Average Beta and Detection.Pval

label: Cy5 and Cy3

source_name: Nasal Epithelial Cells after chronic stimulation with mock solution

label_protocol: Standard Illumina Protocol

extract_protocol: Samples were lysed using Zymo DNA/RNA Lysis Buffer (Zymo Research, Irvine, USA) supplemented with 40 mM DTT, and triplicates were pooled for DNA isolation as per manufacturer instructions.

treatment_protocol: paired epithelial cell samples with chronic stimulation with albuterol or mock solution

tag: pair

tag: phase

value: Discovery

value: NEC

tag: treatment

value: cctrl

tag: quality control

value: OK


title: ID99_NEC_csalb

source_name: Nasal Epithelial Cells after chronic stimulation with albuterol

value: csalb


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_C6


title: ID100_NEC_csalb


title: ID98_NEC_csalb


title: ID99_NEC_cctrl


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_C5


title: ID98_NEC_cctrl


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_C4


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_C3


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_D12


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_C2


title: ID97_NEC_csalb


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_C12


title: ID97_NEC_cctrl


title: ID96_NEC_csalb


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_C10


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_D1


title: ID95_NEC_cctrl


title: ID95_NEC_csalb


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_C1


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_B9


title: ID94_NEC_csalb


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_C11


title: ID94_NEC_cctrl


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_B8


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_B6


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_B7


title: ID93_NEC_csalb


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_B5


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_D9


title: ID92_NEC_csalb


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_B4


title: ID91_NEC_csalb


title: ID92_NEC_cctrl


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_B2


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_B3


title: ID91_NEC_cctrl


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_B12


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_B11


title: ID96_NEC_cctrl


title: ID90_NEC_cctrl


title: ID90_NEC_csalb


title: ID89_NEC_csalb


title: ID89_NEC_cctrl


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_B1


title: ID88_NEC_csalb


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_B10


title: ID88_NEC_cctrl


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_A9


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_A8


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_A6


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_A7


title: ID87_NEC_csalb


title: ID86_NEC_csalb


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_A5


title: ID87_NEC_cctrl


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_A3


title: ID93_NEC_cctrl


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_A4


title: ID86_NEC_cctrl


title: ID85_NEC_csalb


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_A2


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_A12


title: ID84_NEC_csalb


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_A11


title: ID85_NEC_cctrl


title: ID84_NEC_cctrl


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_A10


title: Camellia_BoneMarrow-HSC_LL731_P1_DNA_A1


title: ID83_NEC_csalb


title: ID82_NEC_csalb


title: ID82_NEC_cctrl


title: Camellia_AGM-HSC_LL744EP2_DNA_D8

source_name: AGM

value: AGM


title: Camellia_AGM-HSC_LL744EP2_DNA_D9


title: ID83_NEC_cctrl


title: ID81_NEC_csalb


title: Camellia_AGM-HSC_LL744EP2_DNA_D6


title: ID80_NEC_csalb


title: Camellia_AGM-HSC_LL744EP2_DNA_D7


title: Camellia_AGM-HSC_LL744EP2_DNA_D4


title: ID80_NEC_cctrl


title: Camellia_AGM-HSC_LL744EP2_DNA_D5


title: ID81_NEC_cctrl


title: Camellia_AGM-HSC_LL744EP2_DNA_D2


title: ID79_NEC_csalb


title: ID79_NEC_cctrl


title: Camellia_AGM-HSC_LL744EP2_DNA_D11


title: ID77_NEC_csalb


title: ID78_NEC_csalb


title: Camellia_AGM-HSC_LL744EP2_DNA_C9


title: Camellia_AGM-HSC_LL744EP2_DNA_D3


title: Camellia_AGM-HSC_LL744EP2_DNA_D1


title: Camellia_AGM-HSC_LL744EP2_DNA_D12


title: Camellia_AGM-HSC_LL744EP2_DNA_D10


title: ID78_NEC_cctrl


title: ID76_NEC_csalb


title: ID77_NEC_cctrl


title: Camellia_AGM-HSC_LL744EP2_DNA_C7


title: ID76_NEC_cctrl


title: Camellia_AGM-HSC_LL744EP2_DNA_C6


title: Camellia_AGM-HSC_LL744EP2_DNA_C5


title: ID74_NEC_csalb


title: Camellia_AGM-HSC_LL744EP2_DNA_C3


title: ID74_NEC_cctrl


title: ID73_NEC_csalb


title: ID73_NEC_cctrl


title: ID72_NEC_cctrl


title: ID72_NEC_csalb


title: Camellia_AGM-HSC_LL744EP2_DNA_C11


title: Camellia_AGM-HSC_LL744EP2_DNA_C2


title: Camellia_AGM-HSC_LL744EP2_DNA_B9


title: Camellia_AGM-HSC_LL744EP2_DNA_C1


title: ID69_NEC_csalb


title: ID70_NEC_csalb


title: ID71_NEC_csalb


title: ID69_NEC_cctrl


title: Camellia_AGM-HSC_LL744EP2_DNA_B6


title: Camellia_AGM-HSC_LL744EP2_DNA_C12


title: ID70_NEC_cctrl


title: Camellia_AGM-HSC_LL744EP2_DNA_B7


title: Camellia_AGM-HSC_LL744EP2_DNA_B8


title: ID71_NEC_cctrl


title: Camellia_AGM-HSC_LL744EP2_DNA_C4


title: ID68_NEC_csalb


title: ID75_NEC_csalb


title: ID75_NEC_cctrl


title: Camellia_AGM-HSC_LL744EP2_DNA_B3


title: Camellia_AGM-HSC_LL744EP2_DNA_B4


title: ID68_NEC_cctrl


title: ID67_NEC_csalb


title: Camellia_AGM-HSC_LL744EP2_DNA_B2


title: Camellia_AGM-HSC_LL744EP2_DNA_C10


title: ID67_NEC_cctrl


title: Camellia_AGM-HSC_LL744EP2_DNA_B11


title: Camellia_AGM-HSC_LL744EP2_DNA_B5


title: Camellia_AGM-HSC_LL744EP2_DNA_C8


title: Camellia_AGM-HSC_LL744EP2_DNA_B10


title: ID66_NEC_cctrl


title: ID65_NEC_cctrl


title: ID64_NEC_csalb


title: Camellia_AGM-HSC_LL744EP2_DNA_A8


title: Camellia_AGM-HSC_LL744EP2_DNA_B1


title: ID64_NEC_cctrl


title: Camellia_AGM-HSC_LL744EP2_DNA_A6


title: Camellia_AGM-HSC_LL744EP2_DNA_A9


title: Camellia_AGM-HSC_LL744EP2_DNA_A7


title: Camellia_AGM-HSC_LL744EP2_DNA_A4


title: Camellia_AGM-HSC_LL744EP2_DNA_A2


title: Camellia_AGM-HSC_LL744EP2_DNA_A3


title: Camellia_AGM-HSC_LL744EP2_DNA_B12


title: Camellia_AGM-HSC_LL744EP2_DNA_A12


title: ID66_NEC_csalb


title: Camellia_AGM-HSC_LL744EP2_DNA_A11


title: Camellia_AGM-HSC_LL744EP2_DNA_A10


title: ID65_NEC_csalb


title: Camellia_AGM-HSC_LL744EP2_DNA_A1


title: Camellia_AGM-HSC_LL744EP1_DNA_H9


title: ID60_NEC_csalb


title: ID61_NEC_csalb


title: ID60_NEC_cctrl


title: ID59_NEC_csalb


title: ID62_NEC_cctrl


title: ID63_NEC_cctrl


title: ID59_NEC_cctrl


title: ID63_NEC_csalb


title: Camellia_AGM-HSC_LL744EP2_DNA_A5


title: ID61_NEC_cctrl


title: ID62_NEC_csalb


title: ID57_NEC_csalb


title: ID56_NEC_csalb


title: ID56_NEC_cctrl


title: Camellia_AGM-HSC_LL744EP1_DNA_H7


title: Camellia_AGM-HSC_LL744EP1_DNA_H5


title: Camellia_AGM-HSC_LL744EP1_DNA_H4


title: Camellia_AGM-HSC_LL744EP1_DNA_H6


title: Camellia_AGM-HSC_LL744EP1_DNA_H12


title: Camellia_AGM-HSC_LL744EP1_DNA_H11


title: Camellia_AGM-HSC_LL744EP1_DNA_H3


title: Camellia_AGM-HSC_LL744EP1_DNA_H2


title: ID55_NEC_csalb


title: ID53_NEC_csalb


title: ID55_NEC_cctrl

value: Bad-quality


title: ID53_NEC_cctrl


title: ID54_NEC_csalb


title: ID54_NEC_cctrl


title: ID58_NEC_csalb


title: ID52_NEC_csalb


title: Camellia_AGM-HSC_LL744EP1_DNA_H8


title: ID52_NEC_cctrl


title: ID57_NEC_cctrl


title: Camellia_AGM-HSC_LL744EP1_DNA_G9


title: Camellia_AGM-HSC_LL744EP1_DNA_H1


title: ID58_NEC_cctrl


title: ID51_NEC_cctrl


title: ID50_NEC_csalb


title: Camellia_AGM-HSC_LL744EP1_DNA_G7


title: Camellia_AGM-HSC_LL744EP1_DNA_G5


title: Camellia_AGM-HSC_LL744EP1_DNA_G4


title: Camellia_AGM-HSC_LL744EP1_DNA_H10


title: ID50_NEC_cctrl


title: Camellia_AGM-HSC_LL744EP1_DNA_G3


title: ID49_NEC_csalb


title: ID51_NEC_csalb


title: Camellia_AGM-HSC_LL744EP1_DNA_G8


title: Camellia_AGM-HSC_LL744EP1_DNA_G6


title: Camellia_AGM-HSC_LL744EP1_DNA_G11


title: Camellia_AGM-HSC_LL744EP1_DNA_G12


title: Camellia_AGM-HSC_LL744EP1_DNA_G10


title: Camellia_AGM-HSC_LL744EP1_DNA_F9


title: Camellia_AGM-HSC_LL744EP1_DNA_G1


title: ID49_NEC_cctrl


title: ID48_NEC_csalb


title: ID48_NEC_cctrl

value: Potential cross-sample contaminated


title: Camellia_AGM-HSC_LL744EP1_DNA_G2


title: ID41_NEC_csalb


title: ID46_NEC_csalb


title: ID44_NEC_csalb


title: ID44_NEC_cctrl


title: ID45_NEC_cctrl


title: ID47_NEC_cctrl


title: ID42_NEC_csalb


title: ID41_NEC_cctrl


title: ID42_NEC_cctrl


title: ID43_NEC_csalb


title: ID46_NEC_cctrl


title: ID47_NEC_csalb


title: ID45_NEC_csalb


title: Camellia_AGM-HSC_LL744EP1_DNA_F12


title: Camellia_AGM-HSC_LL744EP1_DNA_F3


title: Camellia_AGM-HSC_LL744EP1_DNA_F6


title: Camellia_AGM-HSC_LL744EP1_DNA_F8


title: Camellia_AGM-HSC_LL744EP1_DNA_F7


title: Camellia_AGM-HSC_LL744EP1_DNA_F2


title: Camellia_AGM-HSC_LL744EP1_DNA_F4


title: ID40_NEC_csalb


title: Camellia_AGM-HSC_LL744EP1_DNA_F5


title: ID43_NEC_cctrl


title: ID40_NEC_cctrl


title: Camellia_AGM-HSC_LL744EP1_DNA_F1


title: Camellia_AGM-HSC_LL744EP1_DNA_F11


title: Camellia_AGM-HSC_LL744EP1_DNA_F10


title: ID39_NEC_cctrl


title: ID37_NEC_csalb


title: ID35_NEC_cctrl


title: ID37_NEC_cctrl


title: ID34_NEC_csalb


title: ID34_NEC_cctrl


title: ID38_NEC_cctrl


title: ID36_NEC_cctrl


title: ID35_NEC_csalb


title: ID36_NEC_csalb


title: ID39_NEC_csalb


title: ID38_NEC_csalb


title: ID33_NEC_csalb


title: Camellia_AGM-HSC_LL744EP1_DNA_E6


title: Camellia_AGM-HSC_LL744EP1_DNA_D5


title: Camellia_AGM-HSC_LL744EP1_DNA_E8


title: Camellia_AGM-HSC_LL744EP1_DNA_D8


title: Camellia_AGM-HSC_LL744EP1_DNA_E2


title: Camellia_AGM-HSC_LL744EP1_DNA_E5


title: Camellia_AGM-HSC_LL744EP1_DNA_E10


title: Camellia_AGM-HSC_LL744EP1_DNA_E3


title: Camellia_AGM-HSC_LL744EP1_DNA_E12


title: Camellia_AGM-HSC_LL744EP1_DNA_D6


title: Camellia_AGM-HSC_LL744EP1_DNA_D9


title: Camellia_AGM-HSC_LL744EP1_DNA_E7


title: Camellia_AGM-HSC_LL744EP1_DNA_E11


title: Camellia_AGM-HSC_LL744EP1_DNA_E9


title: Camellia_AGM-HSC_LL744EP1_DNA_E4


title: Camellia_AGM-HSC_LL744EP1_DNA_D7


title: Camellia_AGM-HSC_LL744EP1_DNA_E1


title: ID32_NEC_cctrl


title: ID33_NEC_cctrl


title: Camellia_AGM-HSC_LL744EP1_DNA_D4


title: Camellia_AGM-HSC_LL744EP1_DNA_D2


title: Camellia_AGM-HSC_LL744EP1_DNA_D12


title: Camellia_AGM-HSC_LL744EP1_DNA_D10


title: Camellia_AGM-HSC_LL744EP1_DNA_D3


title: Camellia_AGM-HSC_LL744EP1_DNA_D11


title: Camellia_AGM-HSC_LL744EP1_DNA_D1


title: Camellia_AGM-HSC_LL744EP1_DNA_C9


title: ID29_NEC_cctrl


title: ID31_NEC_csalb


title: ID29_NEC_csalb


title: ID31_NEC_cctrl


title: ID30_NEC_cctrl


title: ID30_NEC_csalb


title: ID28_NEC_csalb


title: ID28_NEC_cctrl


title: ID26_NEC_csalb


title: ID27_NEC_csalb


title: ID26_NEC_cctrl


title: Camellia_AGM-HSC_LL744EP1_DNA_C5


title: ID32_NEC_csalb


title: ID27_NEC_cctrl


title: Camellia_AGM-HSC_LL744EP1_DNA_C6


title: ID25_NEC_cctrl


title: ID24_NEC_csalb


title: Camellia_AGM-HSC_LL744EP1_DNA_C12


title: ID25_NEC_csalb


title: Camellia_AGM-HSC_LL744EP1_DNA_C2


title: Camellia_AGM-HSC_LL744EP1_DNA_C4


title: ID24_NEC_cctrl


title: Camellia_AGM-HSC_LL744EP1_DNA_C11


title: Camellia_AGM-HSC_LL744EP1_DNA_C10


title: Camellia_AGM-HSC_LL744EP1_DNA_C8


title: Camellia_AGM-HSC_LL744EP1_DNA_C7


title: Camellia_AGM-HSC_LL744EP1_DNA_C3


title: ID23_NEC_csalb


title: ID23_NEC_cctrl


title: ID22_NEC_cctrl


title: Camellia_AGM-HSC_LL744EP1_DNA_B7


title: ID22_NEC_csalb


title: Camellia_AGM-HSC_LL744EP1_DNA_B5


title: Camellia_AGM-HSC_LL744EP1_DNA_B4


title: Camellia_AGM-HSC_LL744EP1_DNA_B8


title: ID20_NEC_csalb


title: ID21_NEC_csalb


title: Camellia_AGM-HSC_LL744EP1_DNA_B6


title: Camellia_AGM-HSC_LL744EP1_DNA_B3


title: Camellia_AGM-HSC_LL744EP1_DNA_B9


title: ID20_NEC_cctrl


title: ID21_NEC_cctrl


title: Camellia_AGM-HSC_LL744EP1_DNA_B2


title: Camellia_AGM-HSC_LL744EP1_DNA_C1


title: ID19_NEC_csalb


title: ID19_NEC_cctrl


title: Camellia_AGM-HSC_LL744EP1_DNA_B12


title: ID18_NEC_csalb


title: ID18_NEC_cctrl


title: Camellia_AGM-HSC_LL744EP1_DNA_B11


title: Camellia_AGM-HSC_LL744EP1_DNA_B1


title: ID17_NEC_csalb


title: Camellia_AGM-HSC_LL744EP1_DNA_A9


title: ID17_NEC_cctrl


title: ID16_NEC_csalb


title: Camellia_AGM-HSC_LL744EP1_DNA_A8


title: ID16_NEC_cctrl


title: Camellia_AGM-HSC_LL744EP1_DNA_A5


title: ID15_NEC_csalb


title: ID14_NEC_csalb


title: Camellia_AGM-HSC_LL744EP1_DNA_A6


title: Camellia_AGM-HSC_LL744EP1_DNA_A4


title: Camellia_AGM-HSC_LL744EP1_DNA_A3


title: ID15_NEC_cctrl


title: Camellia_AGM-HSC_LL744EP1_DNA_A12


title: ID13_NEC_csalb


title: Camellia_AGM-HSC_LL744EP1_DNA_A2


title: ID13_NEC_cctrl


title: ID12_NEC_cctrl


title: Camellia_AGM-HSC_LL744EP1_DNA_A1


title: ID11_NEC_csalb


title: ID11_NEC_cctrl


title: Camellia_AGM-HSC_LL744EP1_DNA_A10


title: Camellia_FetalLiver-HSC_LL653E6P2_RNA


title: Camellia_AGM-HSC_LL744EP1_DNA_B10


title: Camellia_FetalLiver-HSC_LL653E6P1_RNA


title: ID10_NEC_csalb


title: Camellia_FetalLiver-HSC_LL653E1P3_RNA


title: Camellia_FetalLiver-HSC_LL653E1P2_RNA


title: ID10_NEC_cctrl


title: ID9_NEC_csalb


title: ID14_NEC_cctrl


title: Camellia_AGM-HSC_LL744EP1_DNA_A7


title: ID9_NEC_cctrl


title: Camellia_BoneMarrow-HSC_LL731_P3_RNA


title: Camellia_BoneMarrow-HSC_LL731_P2_RNA


title: Camellia_FetalLiver-HSC_LL653E1P1_RNA


title: ID8_NEC_cctrl


title: ID8_NEC_csalb


title: Camellia_AGM-HSC_LL744EP2_RNA


title: ID6_NEC_csalb


title: Camellia_AGM-HSC_LL744EP1_RNA


title: ID12_NEC_csalb


title: ID7_NEC_cctrl


title: Camellia_AGM-HSC_LL744EP1_DNA_A11


title: Camellia_BoneMarrow-HSC_LL731_P1_RNA


title: ID6_NEC_cctrl


title: 10X_transcriptome_LL837-skull-RNA

data_processing:
We used Cell Ranger v.7.0.0 pipeline to generate the count matrix
Assembly: mm10
Supplementary files format and content: skull_RNA_filtered_feature_bc_matrix.h5

extract_protocol: We labeled DARLIN-v2 mouse at E17.0 and generated a single-cell lineage tracing dataset of blood cells across left leg bone, liver, lung, skull, spleen. The single-cell transcriptome library is generated according to the 10X Chromium single-cell protocols, and analyzed with next generation sequencing.


title: ID5_NEC_csalb


title: ID5_NEC_cctrl


title: ID4_NEC_csalb


title: ID4_NEC_cctrl


title: ID3_NEC_csalb


title: M1-Neuron-Input

city: Blacksburg

first: Chang

last: Lu

state: VA

address: 235 Goodwin Hall, 635 Prices Fork Road, Virginia Tech

department: Chemical Engineering

institute: Virginia Tech

description: MOWChIP-seq data. Name format: Mouse number-Left/right hemisphere-Slice number-Neuron/glia-Marker-Replicate number

data_processing:
Raw reads were trimmed with TrimGalore 0.4.1
Trimmed reads were aligned using bowtie 1.1.2. Uniquely mapped reads were filtered for known blacklisted genome regions using Samtools and bedtools to remove ChIP-seq artifacts.
Reads were extended by 100 bp on either ends
Sample was normalized and input subtracted. The reference genome was then divided into 100-bp bins and ChIP-seq signal for each bin was counted for both ChIP and input samples.
Sample was converted to BigWig format
Assembly: mm10
Supplementary files format and content: Normalized ChIP-seq and RNA-seq signal in BigWig format.

source_name: C57BL/6J brain

extract_protocol:
Nuclei extraction from dissected brain tissue was performed using previously described protocol with minor modifications. All steps were conducted on ice and centrifugation was conducted at 4 ℃. A neocortex slice was thawed on ice and transferred to a glass tissue homogenizer (Sigma, d9036-1SET). 3 ml of ice-cold nuclei extraction buffer was added [0.32 M sucrose, 5mM CaCl2, 2 mM Mg(Ac)2 , 0.1 mM EDTA, 10 mM tris-HCl, 0.1% (v/v) Triton X-100, freshly added 1% protease inhibitor cocktail (PIC, Sigma-Aldrich), 0.1 mM PMSF, 1 mM DTT, and 0.06 U/µl ribonuclease (RNase) inhibitor (2313A,Takara Bio, needed when mRNA extraction was performed)]. The tissue was homogenized with 10 times of slow douncing using a loose pestle and 15 times of douncing using a tight pestle (D9063, Sigma-Aldrich). The homogenate was filtered through a 40-µm cell strainer (22363547, Thermo Fisher Scientific) into a 15-ml centrifuge tube and centrifuged at 1000 rcf for 10 min at 4 ℃. Supernatant was discarded and the pellet was resuspended in 0.5 ml of ice-cold nuclei extraction buffer. 0.75 ml of 50% (w/v) iodixanol (made by mixing 4 ml of OptiPrepTM gradient (Sigma-Aldrich) and 0.8 ml of diluent [150 mM KCl, 30 mM MgCl2, and 120 mM tris-HCl]) was added. The suspension was gently mixed by inverting the tube up and down 5 times and then centrifuged at 10,000 rcf for 20 min. Supernatant was carefully removed and the pellet incubated with 100 µl of 2% (w/v) normal goat serum (50062Z, Life Technologies) in Dulbecco’s PBS (DPBS, Life technologies) on ice. The pellet was then resuspended and transferred into a new Eppendorf tube with an addition of 200 µl of 2% normal goat serum. To differentiate neurons from glia, 10 µl of 2 ng/µl Anti-NeuN antibody conjugated with Alexa 488 (MAB377X, EMD Millipore) was mixed with the suspension. The mixture was incubated at 4 ℃ for 1 h on a rotator. The nuclei solution was sorted using FACS (BS FACSAria, BD Bioscience) to separate neuronal (NeuN+) and glial (NeuN-) fractions.   Chromatin fragmentation:  M1-2: 4,000 nuclei per replicate was used so that both neuronal and glial fractions of every neocortex slice sample yielded enough material for two ChIP-seq replicates. The nuclei suspension (containing 8,000 nuclei) was topped up to 1 ml using Dulbecco’s PBS (DPBS; 14190144, Life Technologies). 200 µl of 1.8M sucrose, 10 µl of 1M CaCl2, and 3 µl of 1M Mg(Ac)2 were then added sequentially. The sample was mixed gently by inverting the tube up and down and then incubated for 15 min on ice. The suspension was centrifuged at 3,000 rpm for 15 min at 4 ℃. Supernatant was carefully removed, and the pellet was resuspended in 10 µl DPBS. 0.1 µl of PIC, 0.1 µl of 100 mM PMSF and 10 µl of lysis buffer [4% Triton X-100, 100 mM tris (pH 7.5), 100 mM NaCl, and 30 mM MgCl2] were added, mixed by vortexing and then incubated at room temperature for 10 min. 1 µl of 0.1 M CaCl2 and 0.4 µl of 100 U/µl MNase (88216, Thermo Fisher Scientific) were then added, mixed by vortexing and incubated at room temperature for 10 min. 2.22 µl of 0.5 M EDTA (pH 8) was added to quench the rection. The sample was vortexed and incubated on ice for 10 min before it was centrifuged at 16,100 g for 5min. The supernatant (~20 µl, containing chromatin) was transferred to a new tube and 60 µl of IP buffer [20 mM Tris-HCl, 140 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% (w/v) sodium deoxycholate, 0.1% SDS, 1% (v/v) Triton X-100] was added to obtain a total volume of ~80 µl. The solution was finally split for two ChIP-seq replicates. The chromatin was stored on ice before loaded into the MOWChIP device.  M4-5: 200 µl of sorted neuronal nuclei suspension from one neocortex slice sample was used to prepare chromatin (containing ~30,000 nuclei). 2 µl of PIC, 2 µl of 100 mM PMSF and 200 µl of lysis buffer were added, mixed by vortexing and incubated at room temperature for 10 min. 4 µl of 1 M CaCl2 and 5 µl of 100 U MNase (88216, Thermo Fisher Scientific) were added, mixed by vortexing and incubated at room temperature for 10 min. 44 µl of 0.5 M EDTA was then added, mixed by vortexing and incubated on ice for 10 min. The mixture was finally centrifuged at 16,100g for 5 min at 4 °C. Supernatant containing fragmented chromatin (~ 440 µl) was collected into a new 1.5 ml tube and placed on ice before use. 70 µl of chromatin (containing chromatin from ~4,000 nuclei) was used for each MOWChIP-seq assay for consistency with data on M1-2.  Antibody coating on IP beads:  5 µl of Dynabeads Protein A (10002D, Thermo Fisher Scientific) were used in each MOWChIP assay. Beads were washed twice with 150 µl of IP buffer [20 mM Tris-HCl, pH 8.0, 140 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% (w/v) sodium deoxycholate, 0.1% SDS, 1% (v/v) Triton X-100] and then resuspended in 150 µl of IP buffer. An antibody that targets a specific modified histone was added to coat the beads: anti-H3K27ac (ab4729, Abcam) at 0.125 µg/assay or anti-H3K27me3 (39155, Active Motif) at 0.5 µg/assay. The bead/antibody suspension was incubated on a rotator at 4 °C overnight. Beads were then washed with IP buffer twice and resuspended in 5 µl of IP buffer for use in MOWChIP.  MOWChIP:  The MOWChIP process, including device fabrication and operation, was performed following our published protocol (Zhu, B., Hsieh, YP., Murphy, T.W. et al. MOWChIP-seq for low-input and multiplexed profiling of genome-wide histone modifications. Nat Protoc 14, 3366–3394 (2019).).
ChIP-seq libraries:  ~4,000 neuronal or glial nuclei were used to produce each ChIP-seq library and two technical replicates were generated on each neocortex slice sample. The input libraries were created using the same starting quantity of nuclei (~ 4,000 per library) with the MOWChIP step skipped. Libraries were constructed using 2S Plus DNA Library kit (10009877, IDT) and 2S CDI Adapter S1 indexing kit (10009895, IDT) following the manufacturer’s instructions. 5% (v/v) EvaGreen (31000, Biotium) was added to the amplification mixture to monitor the progress of library amplification. Amplification was stopped once an increase of 2,000 RFU was reached. Library was eluted to 10 µl of low EDTA TE buffer.  mRNA-seq:  mRNA libraries were prepared following Smart-seq2 protocol55 with minor modifications. ~7,500 neuronal nuclei (from M3) were used to generate each RNA-seq library, and each slice sample has two technical replicates. 50 μl of neuronal suspension containing about 7,500 nuclei was used for RNA extraction using RNeasy Mini kit (QIAGEN) and RNase-Free DNase Set (79254, QIAGEN). Extracted RNA was concentrated using ethanol precipitation and resuspended in 5 μl of RNase-free water. 4.6 μl of RNA solution, 2 μl of 10 μM oligo-dT primer and 2 μl of 10 mM dNTP mix were mixed, incubated at 72°C for 3 mins and then stored on ice. 11.4 μl of reverse-transcription mix (made from 1 μl of SuperScript II reverse transcriptase (200 U/μl), 0.5 μL of RNase inhibitor (40 U/μl), 4 μL of Superscript II first-strand buffer, 1 μl of DTT (100mM), 4 μl of 5 M Betaine, 0.12 μl of 1 M MgCl2, 0.2 μl of TSO (10 μM), 0.58 μl of nuclease-free water) was added to the RNA solution and incubated at 42°C for 90 min, followed by 10 cycles of (50°C for 2 min, 42°C for 2 min), and at 70°C for 15 min. 25 μl KAPA HiFi HotStart ReadyMix, 0.5 μl of 10 μM IS PCR primers, 2.5 μl of 20x Evagreen, and 4 μl of RNase-free water were then added. cDNA was amplified by incubation at 98°C for 1 min, followed by 9-11 cycles (to achieve an increase of 50-100 RFU) of (98°C for 15 s, 67°C for 30 s, 72°C for 6 min). After amplification, cDNA was purified using 0.8× SPRIselect beads. Tn5 transposase (14-17 mg/ml) was produced following a published protocol56.  Tn5 transposase and T5/T7 transposons were assembled to form Tn5 transposome using a published protocol57. Briefly, 1.5 μl of 100 μM T5 transposon (IDT) was mixed with 1.5 μl of 100 μM pMENTS (a 5'-phosphorylated 19-bp mosaic end complementary oligonucleotide, IDT), while 1.5 μl of 100 μM T7 transposon (IDT) was mixed with 1.5 μl of 100 μM pMENTS. 3 μl of T5-pMENTS solution and 3 μl of T7-pMENTS solution were separately incubated at 95℃ for 5 min followed by a slow ramp to 25℃ at -0.1℃/sec. 2.5 μl of T5-pMENTS solution was then mixed with 2.5 μl of Tn5 transposase (14-17 mg/ml), while 2.5 μl of T7-pMENTS solution was mixed with 2.5 μl of Tn5 transposase. T5-Tn5 solution and T7-Tn5 solution were separately incubated at 37℃ for 1 h to form T5-Tn5 transposome and T7-Tn5 transposome, respectively. 4 μl of T5-Tn5 transposome and 4 μl of T7-Tn5 transposome were mixed to form 8 μl of assembled Tn5 transposome before it was mixed with 1 μl cDNA (containing ~500 pg cDNA) and 1 μl reaction buffer (TNP92110, Lucigen). The reaction mixture was incubated at 37 ℃ for 1 h. 1 μl of 10× stop solution (TNP92110, Lucigen) was added to the reaction mixture to stop tagmentation. Two rounds of 1× SPRIselect beads cleanup were performed to purify tagmented cDNA. The tagmented cDNA was then eluted in 10 μl low EDTA TE buffer. 25 μl KAPA HiFi HotStart ReadyMix was activated at 98 ℃ for 30 sec and then mixed with 9.5 μl tagmented cDNA and 10 μl Nuclease-free water, followed by incubation at 72 ℃ for 5 min. 1.5 μl of 25 M P5 primer, 1.5 μl of 25 M P7 primer and 2.5 μl 20x Evagreen were then added. The following amplification program was used to achieve a 300-400 RFU increase: 98 ℃ for 30 s; 11-12 cycles of (98 ℃ for 10 s, 63 ℃ for 30 s, 72 ℃ for 30 s) and 72 ℃ for 1 min. Amplified library was purified with 0.8× SPRIselect beads and eluted in 8 μl low EDTA TE buffer.  Library quality control and sequencing:  Library size and concentration were measured by Tapestation (Agilent) and KAPA Library Quantification Kit (07960140001, Roche), respectively. Libraries were pooled for sequencing by Illumina HiSeq 4000 with single-end 50 nt reads or NovaSeq 6000 in S4 200 mode with paired-end 100 nt reads. Averagely, 19 million reads were generated for each ChIP-seq library, 12 million reads for each ChIP-seq input library, and 16 million reads for each RNA-seq library.
ChIP-seq, RNA-seq

treatment_protocol: All procedures were conducted in accordance with NIH guidelines and were approved by the Institutional Animal Care and Use Committee (IACUC) at Virginia Tech. Adult (P56) C57BL/6J male mice were purchased from the Jackson Laboratory and housed on a 12 h light/dark cycle at 23 °C with food and water ad libitum for 2 weeks before experiments.  M1-M3 were euthanized using compressed CO2 followed by cervical dislocation. Mouse brain was then isolated and cut into coronal slices with a thickness of 0.5 mm using an adult mouse brain slicer (BSMAS005-1, Zivic Instruments) on ice. Left and right neocortex sections were dissected from each slice and immediately frozen in dry ice. The dissected neocortex slice samples (a total of 18-21 slices for either left or right hemisphere of a neocortex) were stored at -80 ℃ until use.M4 and M5 were treated for the study of chemically induced seizure. 2 mg/ml kainic acid (K0133, LKT Laboratories) in sterile saline was prepared freshly. M4 was injected intraperitoneally with repeated 5 mg/kg doses of kainic acid at 30 min intervals until behavioral seizures were observed (after 2 doses). M5 (control) was injected with the same amount of sterile saline at 30 min intervals for 2 doses. M4 and M5 were euthanized by cervical dislocation and death was confirmed by bilateral thoracotomy. Mouse brain was processed to extract 0.5 mm-thick left and right coronal neocortex slices and the slice samples were stored at -80 °C until use.

value: brain

tag: strain


title: ID3_NEC_cctrl


title: ID2_NEC_csalb


title: ID2_NEC_cctrl


title: ID1_NEC_cctrl


title: M3-Right-22-Neuron-RNA-R2

data_processing:
Raw reads were trimmed with TrimGalore 0.4.1
Trimmed reads were aligned using bowtie 1.1.2. Uniquely mapped reads were filtered for known blacklisted genome regions using Samtools and bedtools to remove ChIP-seq artifacts.
Reads were extended by 100 bp on either ends
Sample was normalized and input subtracted. The reference genome was then divided into 100-bp bins and ChIP-seq signal for each bin was counted for both ChIP and input samples.
Sample was converted to BigWig format
Assembly: mm10
Supplementary files format and content: Normalized ChIP-seq and RNA-seq signal in BigWig format


title: M3-Right-19-Neuron-RNA-R2


title: M3-Right-21-Neuron-RNA-R2


title: M3-Right-22-Neuron-RNA-R1


title: M3-Right-21-Neuron-RNA-R1


title: M3-Right-20-Neuron-RNA-R1


title: Case 70: Aneurysmal bone cyst

city: Heidelberg

first: Daniel

last: Schrimpf

address: Im Neuenheimer Feld 224

department: Neuropathology

country: Germany

institute: University Hospital Heidelberg, Intitute of Pathology

description: Aneurysmal bone cyst

hyb_protocol: Illumina protocol

scan_protocol: Illumina iScan System according to the manufacturer's protocol

data_processing:
Bioconductor (Version 3.3) package minifi (Version 1.18) using function 'preprocessIllumina'  Average beta
Average Beta

label: Cy3 and Cy5

source_name: Aneurysmal bone cyst

label_protocol: Illumina protocol

extract_protocol: Illumina protocol

treatment_protocol: An automated extraction was done with a Maxwell system (Promega, Fitchburg, WI, USA) and the Maxwell 16 FFPE Plus LEV DNA Purification Kit according to the manufacturer’s instructions.

tag: material

value: FFPE


title: M3-Right-19-Neuron-RNA-R1


title: M3-Right-18-Neuron-RNA-R2


title: M3-Right-18-Neuron-RNA-R1


title: Case 68: Aneurysmal bone cyst

description: Aneurysmal bone cyst


title: Case 69: Aneurysmal bone cyst

description: Aneurysmal bone cyst


title: M1-Glia-Input


title: M3-Right-20-Neuron-RNA-R2


title: M3-Right-16-Neuron-RNA-R2


title: Case 66: Aneurysmal bone cyst

description: Aneurysmal bone cyst


title: M3-Right-16-Neuron-RNA-R1


title: M3-Right-17-Neuron-RNA-R1


title: Case 65: Aneurysmal bone cyst

description: Aneurysmal bone cyst


title: H226-I2

city: Thiruvananthapuram

first: Makeshkumar

last: T

state: Kerala

address: Sreekaryam

department: Division of Crop Protection

country: India

institute: ICAR CTCRI

data_processing:
Sequence reads were trimmed for adapter sequences and aligned against the host and pathogen genome
Supplementary_files_format_and_content: tab limited text files include length and read number of the sRNA sequences

organism: Manihot esculenta

source_name: Virus-infected leaf replicate2

growth_protocol: Three-week old plants that are positive for SLCMV infection was used as the treatment. In-vitro grown disease free plants were used as the control.

extract_protocol:
Total RNA was isolated from the control and infected plants using Trizol Reagent.
Illumina TruSeq miRNA sample preperation protocol
HiSeq2500 with 1x50bp reads

treatment_protocol: Treatment plants were the three-weeks old field-grown plants positive for SLCMV infection. Two replictaes of the treatments were used.

tag: tissues

value: SLCMV infected leaf

tag: genotype/variety


title: M3-Right-17-Neuron-RNA-R2


title: Case 63: Aneurysmal bone cyst

description: Aneurysmal bone cyst


title: Case 64: Aneurysmal bone cyst

description: Aneurysmal bone cyst


title: M3-Right-15-Neuron-RNA-R2


title: H226-C

source_name: Control, uninfected leaf

value: Uninfected leaf


title: Case 62: Aneurysmal bone cyst

description: Aneurysmal bone cyst


title: Case 60: Aneurysmal bone cyst

description: Aneurysmal bone cyst


title: Case 61: Aneurysmal bone cyst

description: Aneurysmal bone cyst


title: H226-I1

source_name: Virus-infected leaf replicate1


title: Case 59: Aneurysmal bone cyst

description: Aneurysmal bone cyst


title: Case 67: Aneurysmal bone cyst

description: Aneurysmal bone cyst


title: Case 58: Aneurysmal bone cyst

description: Aneurysmal bone cyst


title: ID1_NEC_csalb


title: Run 2 Peripheral Immune cells

city: Frankfurt

first: Julius

middle: C

last: Enssle

address: Theodor-Stern-Kai 7

department: Hematology/Oncology

institute: University Hospital Frankfurt

description: read1 file contains cell barcode and UMI; read2 file contains transcript, Antibody Derived Tag or Sample Tag

library_source: other

data_processing:
After Illumina sequencing, the SevenBridges platform (Seven Bridges Genomics, https://www.sevenbridges.com) was used to upload the FASTQ files and reference sequences for mRNAs and AbSeqs. The data was then processed using the BD Rhapsody analysis pipeline (BD Biosciences) with default settings. In summary, low quality read pairs were ejected before the leftover R1 reads were mapped for the identification of cell label and unique molecular identifier (UMI) sequences. Second, the R2 reads were annotated to the reference sequences allowing reads with identical cell label, UMI sequence and reference gene to be collapsed into a single molecule. With the help of a recursive substitution error correction (RSEC) algorithm, the molecule counts were corrected for sequencing errors. Then, Sample Tags were mapped to cells and cell counts were determined to create RSEC-adjusted molecule count matrices.
Assembly: hg18 reference genome and antibody dependent tags (T_NK_NKT_49AbSeqPanel_ref_file.fasta).
Supplementary files format and content: BD Rhapsody pipeline output files: *_Sample_Tag_Calls_Donors.csv, *_RSEC_MolsPerCell.csv
Library strategy: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)

molecule: other

source_name: peripheral blood

extract_protocol:
Thawed cells were washed and 1 million cells were stained per donor. As recommended, equal amounts (in µg) of fluorescent-labelled (FACS) and oligonucleotide-labelled (AbSeq) anti-CD3 and anti-CD56 antibodies were added to allow appropriate antibody staining for both read-outs. Both antibodies were from the same clone (SK7 for CD3 and NCAM16.2 for CD56). After 10 minutes of incubation on ice, the remaining fluorescent-labeled antibodies (anti-CD19, anti-CD14, anti-CD45) and sample tags were added and incubated for another 30minutes. Samples were washed and labelled with 7AAD for live/dead discrimination. Cells were sorted with the BD FACS Aria Fusion device (BD Biosciences) with a 70µm nozzle under sterile conditions. Per donor, equal amounts of T-cells (defined as 7AAD-, CD45+, CD19- CD14-, CD56-, CD3+; 3x10E4 cells), B cells (7AAD-, CD45+, CD19+, CD14-; 1x10E4 cells), NK-cells (defined as, 7AAD-, CD45+, CD19-, CD14-, CD56+ CD3-; 1x10E4 cells) and NKT-cells (defined as 7AAD-, CD45+, CD19-, CD14-, CD56+ CD3+; 5x10E3 cells) were aimed and sorted in the same tube to gain constant cell distributions between donors. Afterwards, single cell sequencing was performed using a BD Rhapsody™ Single-cell analysis system (BD Biosciences).
Following the instructions of the BD Rhapsody whole transcriptome analysis (WTA), AbSeq and Sample Tag amplification kit (BD Biosciences, cat# 633801), DNA libraries were generated. The final libraries including indexes for Illumina sequencing were assessed regarding their concentration and size with a Qubit 4 Fluorometer using a High Sensitivity dsDNA kit (ThermoFisher Scientific, cat# Q32851) and an Agilent 4150 TapeStation using a High Sensitivity D1000 ScreenTape (Agilent, cat# 5067-5584, 5067-5585). At last, library pools with a final concentration of 1 nM were mixed and loaded in multiple runs (75 bp paired-end) on a NextSeq2000 sequencer (Illumina) together with 20 % PhiX DNA.

value: peripheral blood

value: T-, NK-, NKT-, B-cells

tag: library type

value: mRNA  + ADT + sample barcode

tag: antibodies/tags

value: Sample tags:1-Donor7_TP5, 2-Donor7_BTI, 3-Donor8_TP5, 4-Donor8_BTI, 5-Donor4_TP5, 6-Donor4_BTI, 7-Donor9_TP5, 8-Donor9_BTI, 9-Donor10_TP5, 10-Donor10_BTI, 11-Donor11_TP5, 12-Donor11_BTI


title: M3-Right-14-Neuron-RNA-R2


title: ID7_NEC_csalb


title: Case 56: Aneurysmal bone cyst

description: Aneurysmal bone cyst