title: Ddx1 Chip-seq in Azin1-G overexpression rep1

first: Jiahuan

last: HE

address: Dong dan san tiao wu hao xie he ji chu suo

department: Department of Biochemistry and Molecular Biology

institute: Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College

data_processing:
DNA-seq reads were mapped with bwa, RNA-seq reads were mapped with bwa for RNA editing sites identification. RNA-Seq reads were mapped with tophat for RPKM calculation
ChIP-seq data were mapped with tophat and peaks were called through macs2
Differential gene expressions were calculated with Featurecounts and DESeq2 for RNA-seq.
Genome_build: GRCm38
Genome_build: annotation build: ensembl GRCm38.85
Supplementary_files_format_and_content: bigwig for ChIP-seq; expression matix for Ddx1 knock down/control data, bed format for 12 populations of hematopoietic cells

source_name: 32D cell line

extract_protocol:
32D cell lysates were clarified from sonicated nuclei and protein-DNA complex were isolated with indicated antibody.
ChIP-Seq libraries were prepared for sequencing according to Illumina's instruction.

treatment_protocol: The 32D cells were transduction with Azin1-TC or G overexpression lentivirus.

value: 32D cell line

value: DDX1 (11357-1-AP, Proteintech)

value: Azin1-G overexpression


title: Ddx1 input rep1 in Azin1-G overexpression rep1

status: Public on Sep 29 2020

type: SRA

city: Beijing

state: Beijing

country: China

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: cell type

tag: chip antibody

tag: treatment


title: Mutant strain, 3CN

city: Santiago

first: Melissa

last: Gómez

address: Las Palmeras 3425

department: Ciencias Ecológicas

country: Chile

institute: Universidad de Chile

description:
none
3AN_3BN_3CN.txt

library_source: transcriptomic

data_processing:
RNA-seq: The reads were mapped to protein coding genes obtained from the annotation of the genome assembly of the X. dendrorhous included in the BioPoject ID: PRJNA637109, using the RNA-seq analysis tools from the CLC Genomics Workbench 20 software to determine the count data values. Differentially Expressed Genes (DEGs) were estimated using the DESeq2 and edgeR packages of R/Bioconductor using the criteria |log2 fold change| ≥ 1, p-adjusted < 0.05 (DESeq2) or FDR < 0.05 (edgeR), and DEGs common to both analyses (DESeq2 and edgeR) were selected.
ChIP-exo: The reads obtained from Peconic LLC were mapped to the genome assembly of X. dendrorhous included in the BioPoject ID: PRJNA637109, using the aligner Bowtie2 version 2.3.5.1 with default settings for paired end reads. Reads were filtered to retain reads mapped in proper pairs using SAMtools. For the peak calling step, the MACS2 tool was used: the effective genome size was 20 Mb, the peak detection was based in a q-value of 0.05, and the control used for the treatment of BAM files was an IgG BAM file. The intersect function from the BEDtools tool was used to find overlap peaks among the MACS2 output files from each biological replicate. For comparative purposes, the Epigenetics Analysis tools from the CLC Genomics Workbench 20 software was also used for the peak calling step, using a maximum p-value of 0.01. To ensure the generation of a high confidence dataset, in addition to the standard computational analysis, a manual correction of the associated genes up- and downstream of some peaks was included. Additionally, common peaks between each FLAG-tagged strain and the untagged control strain were discarded.
Genome_build: PRJNA637109
Supplementary_files_format_and_content: RNA-seq: tab-delimited text files include the counts for each sample. ChIP-exo: Coverage tracks in bigwig format were generated with the bamCoverage tool and visualized with the IGV software. Peak text files include the common peaks of three biological replicas (3BR) of each strain: CBS.FLAG.SRE1N and CBS.cyp61-.FLAG.SRE1, using the peak caller MACS2 (the text file includes all the common peaks) and the peak caller from the CLC Genomics Workbench 20 software (the text file includes only common peaks associated to DEGs).

molecule: total RNA

organism: Phaffia rhodozyma

source_name: Cell pellet

extract_protocol:
For RNA-seq assays, total RNA was extracted and shipped to Macrogen (Macrogen Inc., Seoul, South Korea) for library preparation and sequencing. For the ChIP-exo assays, formaldehyde-cross linked cell pellets were prepared and shipped to Peconic LLC (State College, PA, USA) for the library preparation and sequencing.
Libraries were prepared using Illumina protocols.

tag: parental strain

tag: genotype

value: Interruption CYP61 locus


title: Ddx1 knockdown RNA_seq rep2

source_name: c-Kit+ cell

extract_protocol:
The cells were sorted and RNA was harvested using an RNeasy Mini Kit (QIAGEN).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: The c-Kit+ HSPCs were transduction with Ddx1 knockdown lentivirus.

value: c-Kit+ cell

value: Ddx1 knock down


title: Ddx1 input rep1 in Azin1-TC overexpression rep1

value: Azin1-TC overexpression


title: Azin1-G RNA_seq rep2

treatment_protocol: The c-Kit+ HSPCs were transduction with Azin1-TC or G overexpression lentivirus.


title: Ddx1 normal control RNA-seq rep1


title: Ddx1 Chip-seq in Azin1-TC overexpression rep1


title: LSK+ HSPC DNA-seq rep2

data_processing:
Library strategy: DNA-seq
DNA-seq reads were mapped with bwa, RNA-seq reads were mapped with bwa for RNA editing sites identification. RNA-Seq reads were mapped with tophat for RPKM calculation
ChIP-seq data were mapped with tophat and peaks were called through macs2
Differential gene expressions were calculated with Featurecounts and DESeq2 for RNA-seq.
Genome_build: GRCm38
Genome_build: annotation build: ensembl GRCm38.85
Supplementary_files_format_and_content: bigwig for ChIP-seq; expression matix for Ddx1 knock down/control data, bed format for 12 populations of hematopoietic cells

source_name: LSK+ HSPC

extract_protocol:
LSK+ HSPCs were sorted and DNA was extracted using a TIANamp Genomic DNA Kit (TIANGEN).
DNA libraries were prepared for sequencing using standard Illumina protocols.

value: LSK+ HSPC


title: Ddx1 normal control RNA-seq rep2


title: Mutant strain, 3BN

description:
none
3AN_3BN_3CN.txt


title: Ddx1 knockdown RNA_seq rep1


title: Azin1-TC RNA_seq rep2


title: Azin1-G RNA_seq rep1


title: Azin1-TC RNA_seq rep1


title: LSK+ HSPC DNA-seq rep1


title: ZSZ1_leaf

city: Changsha

first: Touming

last: Liu

address: NO.348, western road of xianjia lake

department: Institute of Bast Fiber Crops

institute: Chinese Academy of Agricultural Sciences

data_processing:
the raw reads for each sample were filtered, generating clean reads used in next analysis.
To estimate the expression level of ramie genes in various tissues, the clean reads from transcriptome sequencing of ZSZ1 and QYZM tissues were aligned to ramie genome (NCBI  accession PRJNA663427) using the Bowtie2 software, and read number of each transcript was calculated using the RSEM software. The fragments per kilobase of transcript sequence, per millions base pairs sequenced (FPKM) were estimated to measure the expression of each transcript.
Supplementary_files_format_and_content: ramie_fpkm.txt contains the gene name, sample name, and FPKM value

organism: Boehmeria nivea

source_name: Cultivar ZSZ1

extract_protocol:
The total RNA of roots, stems, and leaves were extracted from QYZM and ZSZ1. Total RNA of this sample was extracted using an E.Z.N.A. Plant RNA Kit (OMEGA Bio-Tek, Norcross, GA, USA) according to the manufacturer’s protocol.
Total RNAs for all 6 samples were separately extracted and used to construct the cDNA library with fragment lengths of ~350 bp.

tag: tissue

value: leaves

tag: developmental stage

tag: cultivar


title: C41_cell

city: Chicago

first: Xiaowei

last: Wang

state: IL

address: 909 S Wolcott Ave, Rm 5137

country: USA

institute: University of Illinois at Chicago

description: RNA-seq read counts combined from two sequencing runs

data_processing:
Raw sequence reads were mapped to the NCBI RefSeq transcriptome with Bowtie then normalized using the RPKM method (reads per kilobase of transcript per million mapped reads). For miRNA analysis, The reads were aligned to miRBase human miRNAs with Blat. The aligned reads were then normalized to RPM counts (reads per million mapped miRNA reads), with a floor value of 5 established for lowly expressed miRNAs.
Genome_build: NCBI RefSeq, miRBase
Supplementary_files_format_and_content: Tab-delimited text files containing normalized read count values for individual samples

organism: Homo sapiens

source_name: C4I cells

growth_protocol: All the cells were cultured in medium containing 10% EV-free FBS and 0.1 mM MEM nonessential Amino acids at 37°C.

extract_protocol:
Total RNA was extracted from the extracellular vesicles (EVs) by miRNeasy micro kit with the addition of glycogen.
RNA libraries were prepared for sequencing using NEBNext small RNA-seq library preparation kit.

treatment_protocol: EVs derived from cell culture medium were isolated by differential ultracentrifugation according to the standard protocols.

value: Cervical cancer cell line


title: SW756_cell

source_name: SW756 cells


title: SCC-47_MV

source_name: SCC-47 cells

value: Head and neck cancer cell line


title: SCC154_cell

source_name: SCC-154 cells


title: SCC4_cell

source_name: SCC-4 cells


title: UPCI-017_cell

source_name: UPCI-017 cells


title: HeLa_cell

source_name: HeLa cells


title: UPCI-068_cell

source_name: UPCI-068 cells


title: HT-3_cell

source_name: HT-3 cells


title: UPCI-068_EXO


title: UPCI-017_EXO


title: UPCI-068_MV


title: SW756_MV


title: HeLa_MV


title: HeLa_EXO


title: SCC154_EXO


title: C33A_MV

source_name: C33A cells


title: SCC4_MV


title: C33A_EXO


title: HT-3_MV


title: SCC154_MV


title: SW756_EXO


title: HT-3_EXO


title: UPCI-017_MV


title: SCC4_EXO


title: C41_EXO


title: SCC-090_MV

source_name: SCC-090 cells


title: C41_MV


title: SiHa_MV

source_name: SiHa cells


title: SCC-1_MV

source_name: SCC-1 cells


title: SCC-1_cell


title: SCC-1_EXO


title: SCC-090_cell


title: SiHa_EXO


title: Caski_cell

source_name: Caski cells


title: D17_LEC_4G4_2h

city: Turku

first: Sirpa

last: Jalkanen

address: Tykistökatu 6a

department: Medical Microbiology and Immunology

country: Finland

institute: Univeristy of Turku

data_processing:
Basecalls performed using Illumina's standard bcl2fastq2 software with automatic adapter trimming.
RNA-seq reads were pre-processed using Trimmomatics v0.32 with the following configurations ILLUMINACLIP:TruSeqAdapters-2.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Pre-processed RNA-seq reads were aligned to the GRCh38 genome assembly (EnsEMBL v82) using the STAR per-sample 2-pass mapping strategy. STAR v2.3.0e aligner was used with the following configurations --outSAMattributes All --outSAMunmapped Within. The STAR indexes were build from primary assembly sequences and by taking into account transcript annotations.
PCR duplicates were marked with the MarkDuplicates tool of PICARD v1.63 with following configurations CREATE_INDEX=true VALIDATION_STRINGENCY=SILENT
Counts, Counts per Megabase of library size (CPM), and Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using Rsubread (v 1.30.9) and edgeR (v 3.22.5) as implemented in the statistical environment R (v.3.5.1)
Normalization factors for scaling the raw library sizes were computed with edgeR (v 3.22.5) using function "calcNormFactors" with method "TMM" as implemented in the statistical environment R (v 3.5.1)
Genome_build: GRCh38
Supplementary_files_format_and_content: xlsx files for the metadata of the genes (GeneID, Chr, Start, End, Strand, Length), the metadata of the samples (SamplesID, Donor, Cell, Type, Antibody, Time, LibrarySize, NormalizationFactor) and the raw counts (GeneID and Sample description. As an example Donor10_BEC_118_2h indicates donor 10, blood endothelial cells, treated with the 118 antibody for 2 hours).

source_name: Lymphatic endothelial cells

growth_protocol: Primary human dermal microvascular endothelial cells (HDMEC) were grown in commercial MV/MV2 medium (Promocell). After sorting into lymphatic endothelial cells (LECs) and blood endothelial cells (BECs) these have been cultured in MV2 and MV media, respectively.

extract_protocol:
Original cell extraction had been done by the commercial vendor (Promocell). Treated cells were stored in RNAprotect (Qiagen) before RNA was extracted with the NucleoSpin RNA kit (Macherey Nagel).
Library preparation was done according to Illumina TruSeq Stranded mRNA Sample Preparation Guide. For data extraction, the base calling was performed using Illumina's standard bcl2fastq2 software (automatic adapter trimming).
Stranded mRNA Sequencing. 1 x 50 bp read length was used, followed by 8 + 8 bp dual index run. The raw read per sample was 13-15M.

treatment_protocol: HDMECs were stained with Podoplanin antibody and sorted into positive and negative populations. The obtained cells were cultured and treated with siRNA or antibodies, respectively.

value: Juvenile foreskin

tag: cells

value: Lymphatic endothelial cells

tag: donor

tag: cell

value: LEC

tag: type

tag: antibody

tag: time


title: SiHa_cell


title: D17_LEC_IgG2b_2h


title: SCC-47_cell


title: D17_LEC_D118_2h


title: D17_LEC_AD2_2h


title: C33A_cell


title: D12_LEC_AD2_2h


title: D12_LEC_IgG2b_2h


title: Caski_MV


title: D17_LEC_siCtrl_2h

value: siRNA

value: siCtrl


title: D12_LEC_4G4_2h


title: D17_LEC_siCD73_2h


title: D12_LEC_IgG1_2h


title: SCC-47_EXO


title: D12_LEC_D118_2h


title: SCC-090_EXO


title: D11_LEC_4G4_2h


title: D11_LEC_D118_2h


title: Caski_EXO


title: D11_LEC_IgG2b_2h


title: D17_LEC_IgG1_2h


title: D12_LEC_siCtrl_2h


title: D12_LEC_siCD73_2h


title: D11_LEC_IgG1_2h


title: D11_LEC_AD2_2h


title: D11_LEC_siCD73_2h


title: D10_LEC_IgG2b_2h


title: D17_BEC_IgG2b_2h

source_name: Blood endothelial cells

value: Blood endothelial cells

value: BEC


title: D10_LEC_D118_2h


title: D11_LEC_siCtrl_2h


title: D10_LEC_AD2_2h


title: D17_BEC_4G4_2h


title: D10_LEC_4G4_2h


title: D10_LEC_siCD73_2h


title: D17_BEC_IgG1_2h


title: D10_LEC_siCtrl_2h


title: D11_BEC_4G4_2h


title: D17_BEC_D118_2h


title: D11_BEC_AD2_2h


title: D17_BEC_AD2_2h


title: D12_BEC_4G4_2h


title: D12_BEC_D118_2h


title: D12_BEC_AD2_2h


title: D12_BEC_IgG1_2h


title: D12_BEC_IgG2b_2h


title: D10_BEC_4G4_2h


title: D11_BEC_D118_2h


title: D11_BEC_IgG1_2h


title: D10_LEC_IgG1_2h


title: D10_BEC_IgG2b_2h


title: D10_BEC_D118_2h


title: D17_LEC_Untouched_3d

value: Untouched


title: D12_LEC_Untouched_3d


title: D11_BEC_IgG2b_2h


title: D11_LEC_Untouched_3d


title: D10_LEC_Untouched_3d


title: D17_LEC_IgG1_3d


title: D17_LEC_IgG2b_3d


title: D17_LEC_AD2_3d


title: D17_LEC_siCD73_3d


title: D17_LEC_siCtrl_3d


title: D17_LEC_4G4_3d


title: D12_LEC_D118_3d


title: D12_LEC_4G4_3d


title: D11_LEC_4G4_3d


title: D12_LEC_siCtrl_3d


title: D12_LEC_AD2_3d


title: D12_LEC_IgG1_3d


title: D12_LEC_IgG2b_3d


title: D11_LEC_IgG2b_3d


title: D11_LEC_D118_3d


title: D10_BEC_AD2_2h


title: D11_LEC_IgG1_3d


title: D11_LEC_siCD73_3d


title: D11_LEC_AD2_3d


title: D11_LEC_siCtrl_3d


title: D10_BEC_IgG1_2h


title: D10_LEC_D118_3d


title: D10_LEC_IgG2b_3d


title: D10_LEC_4G4_3d


title: D10_LEC_IgG1_3d


title: D10_LEC_siCtrl_3d


title: D10_LEC_AD2_3d


title: D12_LEC_siCD73_3d


title: D17_LEC_D118_3d


title: D12_BEC_Untouched_3d


title: D10_LEC_siCD73_3d


title: D17_BEC_Untouched_3d


title: D11_BEC_Untouched_3d


title: D17_BEC_IgG2b_3d


title: D17_BEC_IgG1_3d


title: D17_BEC_D118_3d


title: D17_BEC_AD2_3d


title: D12_BEC_4G4_3d


title: D12_BEC_D118_3d


title: D11_BEC_4G4_3d


title: D11_BEC_IgG1_3d


title: D12_BEC_IgG1_3d


title: D10_BEC_IgG2b_3d


title: D11_BEC_AD2_3d


title: D11_BEC_IgG2b_3d


title: D11_BEC_118_3d


title: D12_BEC_IgG2b_3d


title: D10_BEC_4G4_3d


title: D10_BEC_IgG1_3d


title: D17_BEC_4G4_3d


title: D10_BEC_AD2_3d


title: D10_BEC_118_3d


title: CSF_BT_60

type: RNA

city: Goyang

first: Ho-Shin

last: Gwak

state: Non US

address: 323 Ilsan-ro, Ilsandong-gu

department: Dept. of Cancer Control

country: South Korea

institute: National Cancer Center Graduate School of Cancer Science and Policy

description: microRNA expression

hyb_protocol: Labeled RNA was hybridized to Affymetrix GeneChip microRNA 4.0 arrays and run using a Fluidics Station 450 protocol.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with RMA-DMBG as normalization method using Affymetrix Expression Console default analysis settings.

label: Biotin

source_name: CSF from Glioblastoma

label_protocol: RNA was labeled with an Affymetrix Flash Tag Biotin HSR RNA Labeling Kit according to standard procedure.

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

treatment_protocol: All LMC samples are pretreatment, but BM & BT are mixed in terms of treatment status.

value: Cerebrospinal fluids

tag: age


title: CSF_BT_59

description: microRNA expression

source_name: CSF from Acoustic neurinoma


title: D10_BEC_Untouched_3d


title: CSF_BT_61

description: microRNA expression

source_name: CSF from Melanoma


title: CSF_BT_63

description: microRNA expression

source_name: CSF from Chondroma


title: CSF_BT_57

description: microRNA expression

source_name: CSF from Pituitray Adenoma


title: CSF_BT_62

description: microRNA expression


title: CSF_BT_58

description: microRNA expression


title: D12_BEC_AD2_3d


title: CSF_BT_56

description: microRNA expression

source_name: CSF from Brainstem Glioma


title: CSF_BM_53

description: microRNA expression

source_name: CSF from NSCLC


title: CSF_BM_54

description: microRNA expression


title: CSF_LMC_44

description: microRNA expression

source_name: CSF from Ovarian Cancer


title: CSF_BM_52

description: microRNA expression


title: CSF_BT_64

description: microRNA expression

source_name: CSF from Cerebellar Hemangioblastoma


title: CSF_BM_49

description: microRNA expression


title: CSF_LMC_45

description: microRNA expression


title: CSF_LMC_39

description: microRNA expression

source_name: CSF from Adenocarcinoma of Lung


title: CSF_BM_48

description: microRNA expression

source_name: CSF from Breast Cancer


title: CSF_LMC_40

description: microRNA expression


title: CSF_BT_65

description: microRNA expression

source_name: CSF from Meningioma


title: CSF_BM_47

description: microRNA expression


title: CSF_BM(Brain_Metastasis)_46

description: microRNA expression

source_name: CSF from Hepatocellular Carcinoma


title: CSF_LMC_42

description: microRNA expression

source_name: CSF from Lung Cancer


title: CSF_LMC_41

description: microRNA expression


title: CSF_BT(Brain_Tumor)_55

description: microRNA expression

source_name: CSF from Schwannoma


title: CSF_BM_51

description: microRNA expression


title: CSF_LMC_43

description: microRNA expression


title: CSF_LMC_38

description: microRNA expression


title: CSF_LMC_36

description: microRNA expression


title: CSF_LMC_28

description: microRNA expression


title: CSF_LMC_35

description: microRNA expression


title: CSF_LMC_29

description: microRNA expression


title: CSF_LMC_34

description: microRNA expression


title: CSF_LMC_32

description: microRNA expression

source_name: CSF from Lung Cancer, Rectal Cancer


title: CSF_LMC_30

description: microRNA expression


title: CSF_LMC_31

description: microRNA expression


title: CSF_LMC_33

description: microRNA expression

source_name: CSF from Breast cancer


title: CSF_LMC_24

description: microRNA expression


title: CSF_HealthyControl_22

description: microRNA expression

source_name: CSF from Unruptured aneurysm


title: CSF_LMC_26

description: microRNA expression


title: CSF_BM_50

description: microRNA expression

source_name: CSF from SCLC


title: CSF_HealthyControl_23

description: microRNA expression

source_name: CSF from Intracerebral hemorrhage


title: CSF_HealthyControl_21

description: microRNA expression

source_name: CSF from Unruptured ophthalmic aneurysm, Lt


title: CSF_LMC_37

description: microRNA expression


title: CSF_HealthyControl_15

description: microRNA expression

source_name: CSF from Unruptured an, MCABA


title: CSF_HealthyControl_20

description: microRNA expression

source_name: CSF from Unruptured aneurysm, middle cerebral artery


title: CSF_HealthyControl_14

description: microRNA expression

source_name: CSF from Unruptured an, AcoA


title: CSF_HealthyControl_18

description: microRNA expression

source_name: CSF from Unruptued an., ACoA


title: CSF_HealthyControl_17

description: microRNA expression

source_name: CSF from Unruptured an, ACoA


title: CSF_HealthyControl_13

description: microRNA expression

source_name: CSF from essential hypertension


title: CSF_CancerControl_12

description: microRNA expression

source_name: CSF from Germ Cell Tumor


title: CSF_HealthyControl_16

description: microRNA expression


title: CSF_LMC_27

description: microRNA expression

source_name: CSF from NSCLC


title: CSF_CancerControl_11

description: microRNA expression

source_name: CSF from Chordoma, Bone and articular cartilage


title: CSF_CancerControl_9

description: microRNA expression

source_name: CSF from Mature B-cell leukemia Burkitt-type


title: CSF_CancerControl_10

description: microRNA expression


title: CSF_LMC_25

description: microRNA expression


title: CSF_HealthyControl_19

description: microRNA expression


title: CSF_CancerControl_8

description: microRNA expression


title: CSF_CancerControl_2

description: microRNA expression

source_name: CSF from Cholangioca


title: CSF_CancerControl_5

description: microRNA expression

source_name: CSF from Pre-B All


title: Neonatal dermal cells

city: Berkeley

first: Junren

last: Sia

state: California

address: 156 Stanley Hall

department: Bioengineering

institute: University of California, Berkeley

data_processing:
Demultiplexing and alignment was performed with Cell ranger v3.1.0
Alignment files were then processed with velocyto v0.17.17 to generate loom files containing the count matrices
Genome_build: mm10
Supplementary_files_format_and_content: Count matrix in loom format

source_name: Neonatal skin

extract_protocol:
Cultured cells were detachd with 0.05% Trypsin for 5 minutes, spun down, resuspended in PBS and sent to core facility for 10X Genomics Chromium Controller workflow.
10X Chromium Single Cell 3ʹ v3

tag: strain


title: 15900X2

city: Salt Lake City

first: Dean

last: Tantin

state: UT

address: 15 North Medical Drive East

department: Department of Pathology

institute: University of Utah

data_processing:
Fastq files were demultiplexed with cellranger mkfastq version 3.1.0 to create the I1 sample index, R1 cell barcode and UMI, R2 RNA sequence
Reads were aligned to the refdata-cellranger-mm10-3.0.0 reference from 10x Genomics
Barcodes and UMIs were counted using cellranger count with expected-cells=6000
Genome_build: mm10
Supplementary_files_format_and_content:  Filtered feature-barcode matrices in TSV and MTX format from cellranger count.

source_name: T cells in Pancreatic lymph node

extract_protocol:
Pancreatic leukocytes were isolated from pre-diabetic 12 week-old females of Ocabfl/fl (control) and Ocabfl/fl.CD4Cre (4 mice each group). CD45+ cells were sorted by flow cytometry.   T cells of Pancreatic lymph nodes were isolated from pre-diabetic 8 week-old females of Ocabfl/fl (control) and Ocabfl/fl.CD4Cre (5 mice each group). CD3 T cells were sorted by magnetic separation.
10X Genomics Single Cell 5' Gene Expression library prep

value: T cells in Pancreatic lymph node


title: Neonatal dermal cells with FR treatment


title: CSF_CancerControl_1

description: microRNA expression

source_name: CSF from melanoma


title: 17349X1

source_name: Pancreatic leukocytes

value: Ocabfl/fl

value: Pancreatic leukocytes


title: 17349X2


title: Hindlimb skeletal muscle stromal cells

source_name: Adult hindlimb muscle


title: CEMBA190122_6C_3_CEMBA190122_6C_4_H9_ad007

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

value: SSs

tag: Sex

value: male


title: CEMBA190122_6C_3_CEMBA190122_6C_4_H9_ad004


title: CEMBA190122_6C_3_CEMBA190122_6C_4_H9_ad008


title: CEMBA190122_6C_3_CEMBA190122_6C_4_H9_ad001


title: CSF_CancerControl_4

description: microRNA expression

source_name: CSF from Pre-T All


title: CSF_CancerControl_6

description: microRNA expression

source_name: CSF from Lymphoma NOS


title: CEMBA190122_6C_3_CEMBA190122_6C_4_H9_ad010


title: CEMBA190122_6C_3_CEMBA190122_6C_4_H9_ad006


title: CEMBA190122_6C_3_CEMBA190122_6C_4_H9_ad012


title: CEMBA190122_6C_3_CEMBA190122_6C_4_H8_ad001


title: CSF_CancerControl_7

description: microRNA expression


title: CEMBA190122_6C_3_CEMBA190122_6C_4_H8_ad007


title: CSF_CancerControl_3

description: microRNA expression


title: 15900X1

tag: cell type


title: CEMBA190122_6C_3_CEMBA190122_6C_4_H8_ad010


title: Adult dermal cells with FR treatment

source_name: Adult skin


title: CEMBA190122_6C_3_CEMBA190122_6C_4_H8_ad006


title: CEMBA190122_6C_3_CEMBA190122_6C_4_H8_ad012


title: CEMBA190122_6C_3_CEMBA190122_6C_4_H8_ad002


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title: CEMBA190122_6C_3_CEMBA190122_6C_4_H9_ad002


title: CEMBA190122_6C_3_CEMBA190122_6C_4_H7_ad004


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title: CEMBA190122_6C_3_CEMBA190122_6C_4_H6_ad004


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title: CEMBA190122_6C_3_CEMBA190122_6C_4_H5_ad001


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title: CEMBA190122_6C_3_CEMBA190122_6C_4_H6_ad006


title: CEMBA190122_6C_3_CEMBA190122_6C_4_H4_ad012


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title: CEMBA190122_6C_3_CEMBA190122_6C_4_H5_ad002


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title: CEMBA190122_6C_3_CEMBA190122_6C_4_F3_ad001


title: CEMBA190122_6C_3_CEMBA190122_6C_4_F4_ad008


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title: CEMBA190122_6C_3_CEMBA190122_6C_4_F5_ad010


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title: CEMBA190122_6C_3_CEMBA190122_6C_4_F12_ad010


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title: CEMBA190122_6C_3_CEMBA190122_6C_4_F12_ad002


title: CEMBA190122_6C_3_CEMBA190122_6C_4_F12_ad004


title: CEMBA190122_6C_3_CEMBA190122_6C_4_F4_ad012


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