title: Fibrosis_Pseudoexfoliation Glaucoma(PXG)

description:
Test
SAMPLE 3

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: http://sabiosciences.com/pcrarraydataanalysis.php
For the normalization it uses the average of five housekeeping genes: B2M, HPRT1 , RPLP0, GAPDH, ACTB.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Fold Change file reports test/control ratios.

label: SYBR green

source_name: Human peripheral mononuclear cells

label_protocol: PCR array was performed using the RT2 profiler Fibrosis Pathway PCR array plates  (QIAGEN) following the Manufacturer’s instructions. Reverse transcription was performed from 2.1 µg total RNA using the RT2 First Strand Kit (QIAGEN). The thermal cycling conditions used were as follows: Stage 1(1 cycle): 95°C for 10min, Stage 2 (40cycles): 95°C for 15 sec, 60°C for 1 min followed by dissociation step.

extract_protocol: Total RNA extraction from isolated PBMC was done with QIAzol® Lysis reagent (QIAGEN).

value: Pseudoexfoliation Glaucoma(PXG)

value: Human blood


title: Fibrosis_Classical Pseudoexfoliation(Cl PXF)

status: Public on Oct 27 2020

type: RNA

city: Bhubaneswar

first: Munmun

last: Chakraborty

state: Odisha

address: MTC campus,Patia

department: Reasearch

country: India

institute: L.V Prasad Eye Institute

description:
Test
SAMPLE 2

molecule: total RNA

organism: Homo sapiens

tag: diagnosis

value: Classical Pseudoexfoliation(Cl PXF)

tag: tissue


title: Fibrosis_Ocular Hypertension(OHT)

description:
Test
SAMPLE 2

value: Ocular Hypertension(OHT)


title: Fibrosis_Pseudoexfoliation (PXF)

description:
Control
SAMPLE 1

value: Pseudoexfoliation (PXF)


title: miRNA_fibrosis_Cataract

description:
Control
miRNA
SAMPLE 1

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: https://www.qiagen.com/in/shop/genes-and-pathways/data-analysis-centre-overview-page/
For the normalization it uses the average of four housekeeping miRNA's: RNU6-6P, SNORD61, SNORD68 and SNORD95
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Fold Change file reports test/control.

label: SYBR Green

source_name: Human Peripheral mononuclear cells

label_protocol: The total RNA obtained after PBMC isolation was purified of erythrocytes by PBS wash and used for miRNA extraction using the miRNA extraction kit (Qiagen, Hilden, Germany) This was reverse transcribed using the miScript II RT Kit (Qiagen) with 400ng of cDNA and later loaded onto human fibrosis/human miFinder The thermal cycling conditions used were as follows: Stage 1(1 cycle): 95°C for 15min, Stage 2 (40cycles): 94°C for 15seconds, 55°C for 30seconds and 70°C for 30seconds.

extract_protocol: PBMC was extracted using ficol and miRNA was obtained from PBMC using Trizol reagent and following steps as mentioned in Qiagen miRNeasy mini kit protocol

value: Cataract

value: Blood


title: Fibrosis_Pigmentary Pseudoexfoliation(Pig PXF)

description:
Test
SAMPLE 3

value: Pigmentary Pseudoexfoliation(Pig PXF)


title: KP59_tail

type: SRA

city: Toronto

first: Cynthia

last: Hawkins

state: Ontario

address: 686 Bay Street

country: Canada

institute: Hospital for Sick Children

description:
normal tail
KP59.brain.vcf.gz

library_source: genomic

data_processing:
Sequencing quality was checked with FastQC
Reads were trimmed with Trimmomatic v0.32
Reads were aligned to GRCm38 v68 with bwa-mem v0.7.8, processed with GATK v.3.6.0, and duplicates marked with Picard v2.5.0.
Gene-level read counts were done with HTSeq
Somatic mutations were called with Varscan v2.3.8 and Mutect2 and annotated with SnpEFF v4.3k
Genome_build: GRCm38 v68
Supplementary_files_format_and_content: vcf files contain somatic variants per-sample

molecule: genomic DNA

organism: Mus musculus

source_name: normal tail

extract_protocol:
Genomic DNA was extracted with DNeasy kit and quality verified with Bioanalyzer
SureSelect Mouse All Exon Kit (Agilent)

tag: strain

tag: genotype

tag: developmental stage

value: adult

value: normal tail


title: KP59_brain_tumour

description:
brain tumour
KP59.brain.vcf.gz

source_name: brain tumour

value: brain tumour


title: miRNA_fibrosis_Classical PXF

description:
Test
miRNA
SAMPLE 2

value: Classical PXF


title: KP33_sarcoma

description:
sarcoma
KP33.abdomen.vcf.gz

source_name: sarcoma

value: sarcoma


title: miRNA_fibrosis_Pseudoexfoliation Glaucoma (PXG)

description:
Test
miRNA
SAMPLE 3

value: Pseudoexfoliation Glaucoma (PXG)


title: KP29_tail

description:
normal tail
KP29.brain.vcf.gz
KP29.lung_nodule.vcf.gz


title: Fibrosis_Cataract

description:
Control
SAMPLE 1


title: KP29_lung_carcinoma

description:
lung carcinoma
KP29.lung_nodule.vcf.gz

source_name: lung carcinoma

value: lung carcinoma


title: 14987_RN042

status: Public on Oct 28 2020

type: genomic

city: Pittsburgh

first: Anita

last: Bansal

state: PA

address: Biomedical Science Tower

department: Immunology

country: USA

institute: University of Pittsburgh

hyb_protocol: Standard Illumina Protocol

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

data_processing: Data was processed using ChAMP

label: Cy5 and Cy3

source_name: Genomic DNA from diabetic cells

label_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

growth_protocol: Both non-diabetic and diabetic proximal tubule epithelial cells in renal epithelial cell growth media from Lonza

extract_protocol: Standard Illumina Protocol

treatment_protocol: Cells were treated with TGFB1 for 24 hours, 72 hours and 96 hours

tag: cell type

value: Proximal Tubule Epithelial Cells

tag: disease state

value: Type 2 Diabetes

tag: treatment

value: untreated


title: KP29_brain_tumour

description:
brain tumour
KP29.brain.vcf.gz


title: KP177_muscle

description:
normal muscle
KP177.abdomen.vcf.gz
KP177.mediastinal.vcf.gz

source_name: normal muscle

value: normal muscle


title: KP177_lymphoma

description:
lymphoma
KP177.mediastinal.vcf.gz

source_name: lymphoma

value: lymphoma


title: KP161_med

description: rawCountMatrix.txt

library_source: transcriptomic

data_processing:
Sequencing quality was checked with FastQC
Reads were aligned to GRCm38 v68 with STAR 2.5.0 and duplicates marked with Picard v2.5.0
Gene-level read counts were done with HTSeq
Genome_build: GRCm38 v68
Supplementary_files_format_and_content: rawCountMatrix.txt contains raw gene-level counts

extract_protocol:
Total RNA was extracted using QIAGEN RNeasy kit and sample quality confirmed with Bioanalyzer.
TruSeq Stranded Total RNA Library Prep with Ribo-Zero Gold


title: KP123_med

description: rawCountMatrix.txt


title: K412_Med

description: rawCountMatrix.txt


title: KP177_sarcoma

description:
sarcoma
KP177.abdomen.vcf.gz


title: KP59_brain_tumor

description: rawCountMatrix.txt


title: 14982_RN037

source_name: Genomic DNA from Control cells

value: non-diabetic Control


title: KP33_liver

description:
normal liver
KP33.abdomen.vcf.gz

source_name: normal liver

value: normal liver


title: KP29_brain_tumor

description: rawCountMatrix.txt


title: C3

description: rawCountMatrix.txt

source_name: brain

value: brain


title: BPSM_Tris_Const  Rep1

city: Lille

first: Rudy

last: Antoine

address: 1, rue du Professeur Calmette

country: France

institute: CIIL

data_processing:
The RNAseq data of each sample were analyzed using Rockhopper v2.0.3 with the default parameters to calculate the RPKM value for each coding sequence with the Bordetella pertussis Tohama I NC_002929  or the Bordetella bronchiseptica NC_002927 genome annotations
Genome_build: Bordetella pertussis Tohama I NC_002929 and Bordetella bronchiseptica NC_002927
Supplementary_files_format_and_content: Excel files with RPKM values for each duplicated sample.

organism: Bordetella pertussis

source_name: Bordetella pertussis total RNAseq

growth_protocol: B. pertussis strains were grown on BG agar plates for 2 days at 37°C and then cultured in modified Stainer Scholte (SS) liquid medium at 37°C under agitation

extract_protocol:
Bacteria were pelleted, and total RNA was extracted using TriReagent (Invitrogen) following the manufacturer’s instructions. Genomic DNA was removed by DNase I treatment (Sigma Aldrich).
For each RNAseq sample, DNA-depleted total RNA was treated with the Ribo-Zero rRNA Removal Kit (Illumina) following the manufacturer’s recommendations. The rRNA-depleted RNA was then used to build the Illumina library using the TruSeq RNA Library Preparation Kit, followed by sequencing on an Illumina NextSeq 500 benchtop sequencer on SR150 high output run mode.

treatment_protocol: The bacterial cultures were stopped at mid exponential phase (OD600 =1.5) by adding 2 mL of a mixture of 5:95 phenol:ethanol (v:v) to 8 mL of bacterial suspensions.

tag: strains

value: BPSM

tag: protocol

value: RNAseq

tag: culture conditions

value: strain was cultivated in SS media for 16 h in the presence of 3.2 mM Tris pH5.5 to an OD600 nm = 1.5

value: Alex Rivera-Millot

value: March 2018


title: BPSM_Tris_Const  Rep2


title: BPSM_Cu_Const  Rep1

value: strain was cultivated in SS media for 16 h in the presence of 2 mM CuSO4 to an OD600 nm = 1.5


title: BPSM_Cu_Shock  Rep2

value: strain was cultivated in SS media to OD600 nm = 1.5 and 2 mM CuSO4 was added for 30 min

value: November 2018


title: BPSM_Tris_Shock  Rep2

value: strain was cultivated in SS media to OD600 nm = 1.5 and 3.2 mM Tris pH5.5 was added for 30 min


title: BPSM_Tris_Shock  Rep1


title: M_FGC_7W_NC_COOL_sc18

city: Guangzhou

first: Lin

last: Li

address: Shatai South Road

department: Pathophysiology

country: China

institute: Southern Medical University

description: bisulfite treated  genomic DNA

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Trim Galore (v0.3.3) was used to remove the first 9 bases of random primer, adaptor sequences and low quality bases;
Clean reads were first mapped to human reference genome hg19 with Bismark (v0.7.6) in paired-end and non-directional module, and then the unmapped reads were realigned to the same reference genome in single-end and non-directional module;
WCG and GCH methylation level of cytosines was estimated using comstomized scripts.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files which include the methylation level of cytosines in WCG and GCH context respectively

source_name: Fetal Germ Cell

extract_protocol:
Pick a single cell to the lysis buffer by mouth pipette. Add the GpC methyltransferase M.CviPI and S-adenosylmethionine (NEB, M0227L) to the lysate and incubate at 37°C for 45 minutes. After release the genomic DNA by Protease (QIAGEN), EZ-96 DNA Methylation-Direct™MagPrep (Zymo, D5044) was used to conduct bisulfite conversion and genome purification.
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 strands synthesis, the library was amplified by KAPA HiFi HotStart ReadyMix (Kapa Biosystems, KK2602) for 14 cycles.

tag: gender

value: Male

value: 7 week gestation


title: M_FGC_7W_NC_COOL_sc19

description: bisulfite treated  genomic DNA


title: M_FGC_7W_NC_COOL_sc20

description: bisulfite treated  genomic DNA


title: M_FGC_7W_NC_COOL_sc23

description: bisulfite treated  genomic DNA


title: M_FGC_7W_NC_COOL_sc24

description: bisulfite treated  genomic DNA


title: M_FGC_7W_NC_COOL_sc25

description: bisulfite treated  genomic DNA


title: M_FGC_7W_NC_COOL_sc26

description: bisulfite treated  genomic DNA


title: M_FGC_7W_NC_COOL_sc22

description: bisulfite treated  genomic DNA


title: C1

description: rawCountMatrix.txt

value: adult


title: M_FGC_7W_NC_COOL_sc13

description: bisulfite treated  genomic DNA


title: M_FGC_7W_NC_COOL_sc15

description: bisulfite treated  genomic DNA


title: M_FGC_7W_NC_COOL_sc11

description: bisulfite treated  genomic DNA


title: M_FGC_7W_NC_COOL_sc14

description: bisulfite treated  genomic DNA


title: M_FGC_7W_NC_COOL_sc10

description: bisulfite treated  genomic DNA


title: M_FGC_7W_NC_COOL_sc9

description: bisulfite treated  genomic DNA


title: BPSM_Cu_Const  Rep2


title: M_FGC_7W_NC_COOL_sc7

description: bisulfite treated  genomic DNA


title: M_FGC_7W_NC_COOL_sc6

description: bisulfite treated  genomic DNA


title: M_FGC_7W_NC_COOL_sc5

description: bisulfite treated  genomic DNA


title: M_FGC_7W_NC_COOL_sc4

description: bisulfite treated  genomic DNA


title: M_FGC_7W_NC_COOL_sc3

description: bisulfite treated  genomic DNA


title: M_FGC_7W_NC_COOL_sc17

description: bisulfite treated  genomic DNA


title: M_FGC_7W_NC_COOL_sc16

description: bisulfite treated  genomic DNA


title: M_FGC_7W_NC_COOL_sc1

description: bisulfite treated  genomic DNA


title: M_FGC_7W_LDN_COOL_sc15

description: bisulfite treated  genomic DNA


title: M_FGC_7W_LDN_COOL_sc14

description: bisulfite treated  genomic DNA


title: M_FGC_7W_LDN_COOL_sc16

description: bisulfite treated  genomic DNA


title: M_FGC_7W_NC_COOL_sc2

description: bisulfite treated  genomic DNA


title: M_FGC_7W_LDN_COOL_sc13

description: bisulfite treated  genomic DNA


title: M_FGC_7W_LDN_COOL_sc17

description: bisulfite treated  genomic DNA


title: M_FGC_7W_LDN_COOL_sc18

description: bisulfite treated  genomic DNA


title: M_FGC_7W_NC_COOL_sc8

description: bisulfite treated  genomic DNA


title: M_FGC_7W_LDN_COOL_sc10

description: bisulfite treated  genomic DNA


title: M_FGC_7W_LDN_COOL_sc9

description: bisulfite treated  genomic DNA


title: M_FGC_7W_LDN_COOL_sc7

description: bisulfite treated  genomic DNA


title: M_FGC_7W_LDN_COOL_sc1

description: bisulfite treated  genomic DNA


title: M_FGC_7W_LDN_COOL_sc8

description: bisulfite treated  genomic DNA


title: Diagnosis and Relapse samples

city: Vienna

first: Iros

last: Barozzi

address: Borschkegasse 8a

country: Austria

institute: Medical University Vienna

description:
Diagnosis Hashing barcode: GTCAACTCTTTAGCG
Relapse Hashing barcode: TGATGGCCTATTGGG

data_processing:
CellRanger was run on the full set of fragments using GRCh38 annotation.
CITE-seq-count was used to demultiplex the two samples based on hashing barcodes and cell barcodes (the latter as determined by CellRanger).
List of cell barcodes for individual samples were collected and only those that were uniquely assigned to a specific sample were kept for the final list.
Genome_build: GRCh38
Supplementary_files_format_and_content: hdf5

molecule: polyA RNA

source_name: Peripheral blood

extract_protocol:
Heparinised blood was collected, and peripheral blood mononuclear cells (PBMCs) were isolated by Ficoll/Hypaque density-gradient centrifugation. At diagnosis, B cells were purified by negative selection against CD2, CD3, CD4, CD14, CD15, CD16, CD34, CD56, CD61, CD235a (Glycophorin A) and FceRIa was used. At relapse, no purification was performed. All cells were cryopreserved with 10% DMSO/FBS and stored liquid nitrogen until the time of analysis. The cryopreserved cells were thawed in a water bath at 37ᵒC and resuspended in warmed RPMI medium (Sigma). Cell concentration and viability was determined using a LUNA™ cell counter (Logos Biosytems) and their viability was quantified. Cell hashing was carried out prior to pooling and loading on the 10x Chromium instrument. One million cells from each sample were separately suspended in 100 µl cell staining buffer (BioLegend) and 5 µl of Human TruStain FcX™ Fc Blocking reagent (Biolegend) was added and the samples incubated at 4 ᵒC for 10'. Both samples were incubated with 1 µg of TotalSeq™-A0251 Hashtag 1 or  TotalSeq™-A0252 Hashtag 2 antibody for  diagnosis and relapse, respectively. Samples were then incubated at 4 ᵒC for 30'. Cells were then washed 3x with 1 mL cell staining buffer (Biolegend), resuspended in PBS at a concentration of 1'000 cells/µl and then filtered through 40 µm strainers to ensure single cell suspension. Cell concentration and viability were verified using the LUNA™ cell counter (Logos Biosytems) before the two samples were pooled at a 50:50 ratio. This pool was then loaded onto the Chromium instrument as detailed by the manufacture.
Libraries were generated using the 10x Genomics Chromium platform (version 3).
scRNA-seq

value: Primary Chronic Lymphoid Leukaemia and Advanced Chronic Lymphoid Leukaemia

value: Peripheral blood


title: M_FGC_7W_LDN_COOL_sc2

description: bisulfite treated  genomic DNA


title: M_FGC_7W_LDN_COOL_sc11

description: bisulfite treated  genomic DNA


title: M_FGC_7W_LDN_COOL_sc6

description: bisulfite treated  genomic DNA


title: M_FGC_7W_LDN_COOL_sc3

description: bisulfite treated  genomic DNA


title: M_FGC_7W_LDN_COOL_sc4

description: bisulfite treated  genomic DNA


title: F_Soma_17W_embryo1_COOL_sc14

description: bisulfite treated  genomic DNA

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Trim Galore (v0.3.3) was used to remove the first 9 bases of random primer, adaptor sequences and low quality bases;
Clean reads were first mapped to human reference genome hg19 with Bismark (v0.7.6) in paired-end and non-directional module, and then the unmapped reads were realigned to the same reference genome in single-end and non-directional module;
WCG and GCH methylation level of cytosines was estimated using cumstomized scripts.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files which include the methylation level of cytosines in WCG and GCH context respectively

source_name: Gonadal Somatic Cell

value: Female

value: 17 week gestation


title: M_FGC_7W_LDN_COOL_sc12

description: bisulfite treated  genomic DNA


title: F_Soma_17W_embryo1_COOL_sc12

description: bisulfite treated  genomic DNA


title: F_Soma_17W_embryo1_COOL_sc13

description: bisulfite treated  genomic DNA


title: F_Soma_17W_embryo1_COOL_sc15

description: bisulfite treated  genomic DNA


title: F_Soma_17W_embryo1_COOL_sc16

description: bisulfite treated  genomic DNA


title: F_Soma_17W_embryo1_COOL_sc11

description: bisulfite treated  genomic DNA


title: F_Soma_17W_embryo1_COOL_sc10

description: bisulfite treated  genomic DNA


title: F_Soma_17W_embryo1_COOL_sc9

description: bisulfite treated  genomic DNA


title: F_Soma_17W_embryo1_COOL_sc6

description: bisulfite treated  genomic DNA


title: miRNA-TC1

city: Beijing

first: Ying

last: Zhang

address: Haidian District, Yuanmingyuan West Road 2

institute: China Agricultural University

data_processing:
Illumina Hiseq used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-quality sequence, then aligned to the chicken reference genome (Gallus gallus 6.0) using HISAT2 (version 2.0.9) software
FPKM and TPM were calculated using the StringTie, Differential expression analysis comparing TC and CH was performed with the DESeq2 software.
Genome_build: Gallus-gallus-6.0 (ftp://ftp.ensembl.org/pub/release-96/fasta/gallus_gallus/dna)
Supplementary_files_format_and_content: bam profiles

organism: Gallus gallus

source_name: Chorioallantoic membrane (CAM) of embryos

extract_protocol:
Chorioallantoic membrane tissues were removed, frozen on liquid nitrogen, and total RNA was harvested using Trizol reagent. Illumina HiSeq RNA Sample Prep Kit (Cat.#RS-122-2002; Illumina, San Diego, CA, USA) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: embryo

value: Chorioallantoic membrane

tag: age

value: 11-day of embryo

value: Tibetan chicken


title: M_FGC_7W_NC_COOL_sc12

description: bisulfite treated  genomic DNA


title: M_FGC_7W_LDN_COOL_sc5

description: bisulfite treated  genomic DNA


title: Implanted tumor_PBS rep3

city: Daejeon

first: Myung Jin

last: Yang

country: South Korea

institute: Institute for Basic Science

data_processing:
quality assessment of raw sequence data was performed using FastQC
Sequenced reads were aligned to mouse reference genome (mm10) with STAR (version 2.7), and the aligned reads were used to quantify mRNA expression by using HTSeq-count
Fragments Per Kilobase of transcript per million mapped reads (FPKM) were calculated
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values all samples

source_name: breast tumor

extract_protocol:
Endothelial cells were sorted with FACS aria II (BD bioscience). RNA was extracted with Rneasy mini kit (Qiagen).  NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England BioLabs) was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tag

value: FVB

value: breast tumor

tag: time

value: post injection 3 hr

value: wild type


title: F_Soma_17W_embryo1_COOL_sc8

description: bisulfite treated  genomic DNA


title: F_Soma_17W_embryo1_COOL_sc7

description: bisulfite treated  genomic DNA


title: F_Soma_17W_embryo1_COOL_sc2

description: bisulfite treated  genomic DNA


title: F_Soma_17W_embryo1_COOL_sc5

description: bisulfite treated  genomic DNA


title: F_Soma_17W_embryo1_COOL_sc4

description: bisulfite treated  genomic DNA


title: F_Soma_10W_embryo1_COOL_sc2

description: bisulfite treated  genomic DNA

value: 10 week gestation


title: F_FGC_17W_embryo1_COOL_sc74

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_COOL_sc72

description: bisulfite treated  genomic DNA


title: F_Soma_10W_embryo1_COOL_sc5

description: bisulfite treated  genomic DNA


title: F_Soma_10W_embryo1_COOL_sc7

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_COOL_sc76

description: bisulfite treated  genomic DNA


title: F_Soma_10W_embryo1_COOL_sc3

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_COOL_sc73

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_COOL_sc75

description: bisulfite treated  genomic DNA


title: F_Soma_10W_embryo1_COOL_sc4

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_COOL_sc71

description: bisulfite treated  genomic DNA


title: F_Soma_10W_embryo1_COOL_sc6

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_COOL_sc70

description: bisulfite treated  genomic DNA


title: F_Soma_17W_embryo1_COOL_sc1

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_COOL_sc68

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_COOL_sc67

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_COOL_sc69

description: bisulfite treated  genomic DNA


title: F_Soma_10W_embryo1_COOL_sc1

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_COOL_sc66

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_COOL_sc64

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_COOL_sc65

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_COOL_sc63

description: bisulfite treated  genomic DNA


title: F_Soma_17W_embryo1_COOL_sc3

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_COOL_sc61

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_COOL_sc60

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_COOL_sc62

description: bisulfite treated  genomic DNA


title: C2

description: rawCountMatrix.txt

value: brain


title: F_FGC_17W_embryo1_COOL_sc55

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_COOL_sc56

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_COOL_sc57

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_COOL_sc53

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_COOL_sc59

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_COOL_sc54

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_COOL_sc58

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_COOL_sc52

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_COOL_sc48

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_COOL_sc47

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_COOL_sc50

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_COOL_sc46

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_COOL_sc44

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_COOL_sc45

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_COOL_sc51

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_COOL_sc42

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_COOL_sc40

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_COOL_sc41

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_COOL_sc39

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_COOL_sc38

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_COOL_sc37

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_COOL_sc36

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_COOL_sc33

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_COOL_sc49

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_COOL_sc35

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_COOL_sc30

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_COOL_sc34

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_COOL_sc29

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_COOL_sc43

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_COOL_sc28

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_COOL_sc25

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_COOL_sc24

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_COOL_sc23

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_COOL_sc27

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_COOL_sc21

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_COOL_sc13

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_COOL_sc16

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_COOL_sc15

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_COOL_sc20

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_COOL_sc12

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_COOL_sc17

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_COOL_sc18

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_COOL_sc19

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_COOL_sc14

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_COOL_sc11

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_COOL_sc10

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_COOL_sc8

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_COOL_sc26

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_COOL_sc9

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_COOL_sc7

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_COOL_sc5

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_COOL_sc6

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_COOL_sc2

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_COOL_sc3

description: bisulfite treated  genomic DNA


title: F_FGC_10W_embryo1_COOL_sc34

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_COOL_sc22

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_COOL_sc4

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_COOL_sc1

description: bisulfite treated  genomic DNA


title: F_FGC_10W_embryo1_COOL_sc35

description: bisulfite treated  genomic DNA


title: F_FGC_10W_embryo1_COOL_sc33

description: bisulfite treated  genomic DNA


title: BPSM_Cu_Shock  Rep1

value: BPSM

value: RNAseq

value: strain was cultivated in SS media to OD600 nm = 1.5 and 2 mM CuSO4 was added for 30 min

value: Alex Rivera-Millot

value: November 2018


title: F_FGC_10W_embryo1_COOL_sc32

description: bisulfite treated  genomic DNA


title: F_FGC_10W_embryo1_COOL_sc27

description: bisulfite treated  genomic DNA


title: F_FGC_10W_embryo1_COOL_sc31

description: bisulfite treated  genomic DNA


title: F_FGC_10W_embryo1_COOL_sc26

description: bisulfite treated  genomic DNA


title: F_FGC_10W_embryo1_COOL_sc21

description: bisulfite treated  genomic DNA


title: F_FGC_10W_embryo1_COOL_sc29

description: bisulfite treated  genomic DNA


title: F_FGC_10W_embryo1_COOL_sc23

description: bisulfite treated  genomic DNA


title: F_FGC_10W_embryo1_COOL_sc24

description: bisulfite treated  genomic DNA


title: F_FGC_10W_embryo1_COOL_sc28

description: bisulfite treated  genomic DNA


title: F_FGC_10W_embryo1_COOL_sc19

description: bisulfite treated  genomic DNA


title: F_FGC_10W_embryo1_COOL_sc20

description: bisulfite treated  genomic DNA


title: F_FGC_10W_embryo1_COOL_sc13

description: bisulfite treated  genomic DNA


title: F_FGC_10W_embryo1_COOL_sc14

description: bisulfite treated  genomic DNA


title: F_FGC_10W_embryo1_COOL_sc15

description: bisulfite treated  genomic DNA


title: F_FGC_10W_embryo1_COOL_sc11

description: bisulfite treated  genomic DNA


title: F_FGC_10W_embryo1_COOL_sc17

description: bisulfite treated  genomic DNA


title: F_FGC_10W_embryo1_COOL_sc22

description: bisulfite treated  genomic DNA


title: F_FGC_10W_embryo1_COOL_sc30

description: bisulfite treated  genomic DNA


title: F_FGC_10W_embryo1_COOL_sc25

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_COOL_sc31

description: bisulfite treated  genomic DNA


title: F_FGC_10W_embryo1_COOL_sc10

description: bisulfite treated  genomic DNA


title: F_FGC_10W_embryo1_COOL_sc7

description: bisulfite treated  genomic DNA


title: F_FGC_10W_embryo1_COOL_sc6

description: bisulfite treated  genomic DNA


title: F_FGC_10W_embryo1_COOL_sc5

description: bisulfite treated  genomic DNA


title: F_FGC_10W_embryo1_COOL_sc4

description: bisulfite treated  genomic DNA


title: M_Soma_24W_embryo1_COOL_sc5

description: bisulfite treated  genomic DNA

value: Male

value: 24 week gestation


title: M_Soma_24W_embryo1_COOL_sc4

description: bisulfite treated  genomic DNA


title: M_Soma_24W_embryo1_COOL_sc6

description: bisulfite treated  genomic DNA


title: M_Soma_24W_embryo1_COOL_sc3

description: bisulfite treated  genomic DNA


title: F_FGC_10W_embryo1_COOL_sc2

description: bisulfite treated  genomic DNA

value: Female


title: F_FGC_10W_embryo1_COOL_sc3

description: bisulfite treated  genomic DNA


title: F_FGC_10W_embryo1_COOL_sc1

description: bisulfite treated  genomic DNA


title: F_FGC_10W_embryo1_COOL_sc18

description: bisulfite treated  genomic DNA


title: F_FGC_10W_embryo1_COOL_sc16

description: bisulfite treated  genomic DNA


title: M_Soma_24W_embryo1_COOL_sc2

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_COOL_sc32

description: bisulfite treated  genomic DNA

value: 17 week gestation


title: F_FGC_10W_embryo1_COOL_sc12

description: bisulfite treated  genomic DNA


title: F_FGC_10W_embryo1_COOL_sc9

description: bisulfite treated  genomic DNA


title: M_Soma_21W_T2_COOL_sc4

description: bisulfite treated  genomic DNA

value: 21 week gestation


title: M_Soma_21W_T2_COOL_sc5

description: bisulfite treated  genomic DNA


title: M_Soma_24W_embryo1_COOL_sc1

description: bisulfite treated  genomic DNA


title: M_Soma_21W_T1_COOL_sc5

description: bisulfite treated  genomic DNA


title: M_Soma_21W_T2_COOL_sc2

description: bisulfite treated  genomic DNA


title: M_Soma_21W_T2_COOL_sc1

description: bisulfite treated  genomic DNA


title: M_Soma_21W_T2_COOL_sc3

description: bisulfite treated  genomic DNA


title: F_FGC_10W_embryo1_COOL_sc8

description: bisulfite treated  genomic DNA


title: M_Soma_21W_T1_COOL_sc6

description: bisulfite treated  genomic DNA


title: M_Soma_21W_T1_COOL_sc4

description: bisulfite treated  genomic DNA


title: M_Soma_21W_T1_COOL_sc2

description: bisulfite treated  genomic DNA


title: M_Soma_21W_T1_COOL_sc3

description: bisulfite treated  genomic DNA


title: M_Soma_17W_embryo1_COOL_sc9

description: bisulfite treated  genomic DNA


title: M_Soma_21W_T1_COOL_sc1

description: bisulfite treated  genomic DNA


title: M_Soma_17W_embryo1_COOL_sc4

description: bisulfite treated  genomic DNA


title: M_Soma_17W_embryo1_COOL_sc5

description: bisulfite treated  genomic DNA


title: M_Soma_17W_embryo1_COOL_sc8

description: bisulfite treated  genomic DNA


title: M_Soma_17W_embryo1_COOL_sc6

description: bisulfite treated  genomic DNA


title: M_Soma_17W_embryo1_COOL_sc7

description: bisulfite treated  genomic DNA


title: M_Soma_17W_embryo1_COOL_sc2

description: bisulfite treated  genomic DNA


title: M_Soma_8W_embryo1_COOL_sc7

description: bisulfite treated  genomic DNA

value: 8 week gestation


title: M_Soma_8W_embryo1_COOL_sc8

description: bisulfite treated  genomic DNA


title: M_Soma_8W_embryo1_COOL_sc5

description: bisulfite treated  genomic DNA


title: M_Soma_8W_embryo1_COOL_sc3

description: bisulfite treated  genomic DNA


title: M_Soma_8W_embryo1_COOL_sc2

description: bisulfite treated  genomic DNA


title: M_Soma_8W_embryo1_COOL_sc4

description: bisulfite treated  genomic DNA


title: M_Soma_8W_embryo1_COOL_sc6

description: bisulfite treated  genomic DNA


title: M_Soma_7W_embryo3_COOL_sc4

description: bisulfite treated  genomic DNA

value: 7 week gestation


title: M_Soma_7W_embryo3_COOL_sc2

description: bisulfite treated  genomic DNA


title: M_Soma_7W_embryo3_COOL_sc5

description: bisulfite treated  genomic DNA


title: M_FGC_24W_embryo1_COOL_sc13

description: bisulfite treated  genomic DNA


title: M_Soma_7W_embryo3_COOL_sc3

description: bisulfite treated  genomic DNA


title: M_Soma_8W_embryo1_COOL_sc1

description: bisulfite treated  genomic DNA


title: M_FGC_24W_embryo1_COOL_sc11

description: bisulfite treated  genomic DNA


title: M_FGC_24W_embryo1_COOL_sc10

description: bisulfite treated  genomic DNA


title: M_FGC_24W_embryo1_COOL_sc12

description: bisulfite treated  genomic DNA


title: M_FGC_24W_embryo1_COOL_sc9

description: bisulfite treated  genomic DNA


title: M_FGC_24W_embryo1_COOL_sc6

description: bisulfite treated  genomic DNA


title: M_FGC_24W_embryo1_COOL_sc8

description: bisulfite treated  genomic DNA


title: M_Soma_17W_embryo1_COOL_sc1

description: bisulfite treated  genomic DNA


title: M_Soma_17W_embryo1_COOL_sc3

description: bisulfite treated  genomic DNA


title: M_FGC_24W_embryo1_COOL_sc7

description: bisulfite treated  genomic DNA


title: M_FGC_24W_embryo1_COOL_sc4

description: bisulfite treated  genomic DNA


title: M_FGC_24W_embryo1_COOL_sc5

description: bisulfite treated  genomic DNA


title: M_FGC_24W_embryo1_COOL_sc1

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T2_COOL_sc13

description: bisulfite treated  genomic DNA


title: M_Soma_7W_embryo3_COOL_sc1

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T2_COOL_sc7

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T2_COOL_sc8

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T2_COOL_sc11

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T2_COOL_sc10

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T2_COOL_sc9

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T2_COOL_sc5

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T2_COOL_sc3

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T2_COOL_sc4

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T2_COOL_sc6

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T2_COOL_sc12

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T2_COOL_sc2

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T2_COOL_sc1

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T1_COOL_sc35

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T1_COOL_sc37

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T1_COOL_sc34

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T1_COOL_sc36

description: bisulfite treated  genomic DNA


title: M_FGC_24W_embryo1_COOL_sc3

description: bisulfite treated  genomic DNA


title: M_FGC_24W_embryo1_COOL_sc2

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T1_COOL_sc32

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T1_COOL_sc31

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T1_COOL_sc30

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T1_COOL_sc26

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T1_COOL_sc27

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T1_COOL_sc25

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T1_COOL_sc28

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T1_COOL_sc29

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T1_COOL_sc23

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T1_COOL_sc24

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T1_COOL_sc22

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T1_COOL_sc20

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T1_COOL_sc21

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T1_COOL_sc13

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T1_COOL_sc16

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T1_COOL_sc14

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T1_COOL_sc8

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T1_COOL_sc18

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T1_COOL_sc19

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T1_COOL_sc11

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T1_COOL_sc12

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T1_COOL_sc33

description: bisulfite treated  genomic DNA


title: M_FGC_7W_NC_COOL_sc21

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T1_COOL_sc10

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T1_COOL_sc15

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T1_COOL_sc6

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T1_COOL_sc9

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T1_COOL_sc7

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T1_COOL_sc3

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T1_COOL_sc2

description: bisulfite treated  genomic DNA


title: M_FGC_17W_embryo1_COOL_sc34

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T1_COOL_sc5

description: bisulfite treated  genomic DNA


title: M_FGC_17W_embryo1_COOL_sc33

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T1_COOL_sc1

description: bisulfite treated  genomic DNA


title: M_FGC_17W_embryo1_COOL_sc35

description: bisulfite treated  genomic DNA


title: M_FGC_17W_embryo1_COOL_sc32

description: bisulfite treated  genomic DNA


title: M_FGC_17W_embryo1_COOL_sc31

description: bisulfite treated  genomic DNA


title: M_FGC_17W_embryo1_COOL_sc30

description: bisulfite treated  genomic DNA


title: M_FGC_17W_embryo1_COOL_sc29

description: bisulfite treated  genomic DNA


title: M_FGC_17W_embryo1_COOL_sc27

description: bisulfite treated  genomic DNA


title: M_FGC_17W_embryo1_COOL_sc28

description: bisulfite treated  genomic DNA


title: M_FGC_17W_embryo1_COOL_sc26

description: bisulfite treated  genomic DNA


title: M_FGC_17W_embryo1_COOL_sc24

description: bisulfite treated  genomic DNA


title: M_FGC_17W_embryo1_COOL_sc23

description: bisulfite treated  genomic DNA


title: M_FGC_17W_embryo1_COOL_sc21

description: bisulfite treated  genomic DNA


title: M_FGC_17W_embryo1_COOL_sc22

description: bisulfite treated  genomic DNA


title: M_FGC_17W_embryo1_COOL_sc20

description: bisulfite treated  genomic DNA


title: M_FGC_17W_embryo1_COOL_sc16

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T1_COOL_sc4

description: bisulfite treated  genomic DNA


title: M_FGC_17W_embryo1_COOL_sc18

description: bisulfite treated  genomic DNA


title: M_FGC_17W_embryo1_COOL_sc25

description: bisulfite treated  genomic DNA


title: M_FGC_17W_embryo1_COOL_sc15

description: bisulfite treated  genomic DNA


title: M_FGC_17W_embryo1_COOL_sc14

description: bisulfite treated  genomic DNA


title: M_FGC_17W_embryo1_COOL_sc12

description: bisulfite treated  genomic DNA


title: M_FGC_17W_embryo1_COOL_sc10

description: bisulfite treated  genomic DNA


title: M_FGC_17W_embryo1_COOL_sc11

description: bisulfite treated  genomic DNA


title: M_FGC_17W_embryo1_COOL_sc9

description: bisulfite treated  genomic DNA


title: M_FGC_17W_embryo1_COOL_sc8

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T1_COOL_sc17

description: bisulfite treated  genomic DNA


title: M_FGC_17W_embryo1_COOL_sc4

description: bisulfite treated  genomic DNA


title: M_FGC_17W_embryo1_COOL_sc3

description: bisulfite treated  genomic DNA


title: M_FGC_17W_embryo1_COOL_sc1

description: bisulfite treated  genomic DNA


title: M_FGC_8W_embryo1_COOL_sc23

description: bisulfite treated  genomic DNA


title: M_FGC_17W_embryo1_COOL_sc19

description: bisulfite treated  genomic DNA


title: M_FGC_8W_embryo1_COOL_sc22

description: bisulfite treated  genomic DNA


title: M_FGC_17W_embryo1_COOL_sc17

description: bisulfite treated  genomic DNA


title: M_FGC_8W_embryo1_COOL_sc20

description: bisulfite treated  genomic DNA


title: M_FGC_17W_embryo1_COOL_sc13

description: bisulfite treated  genomic DNA


title: M_FGC_8W_embryo1_COOL_sc21

description: bisulfite treated  genomic DNA


title: M_FGC_8W_embryo1_COOL_sc18

description: bisulfite treated  genomic DNA


title: M_FGC_8W_embryo1_COOL_sc19

description: bisulfite treated  genomic DNA


title: M_FGC_17W_embryo1_COOL_sc7

description: bisulfite treated  genomic DNA


title: M_FGC_8W_embryo1_COOL_sc16

description: bisulfite treated  genomic DNA


title: M_FGC_8W_embryo1_COOL_sc15

description: bisulfite treated  genomic DNA


title: M_FGC_8W_embryo1_COOL_sc11

description: bisulfite treated  genomic DNA


title: M_FGC_8W_embryo1_COOL_sc10

description: bisulfite treated  genomic DNA


title: M_FGC_8W_embryo1_COOL_sc9

description: bisulfite treated  genomic DNA


title: M_FGC_8W_embryo1_COOL_sc17

description: bisulfite treated  genomic DNA


title: M_FGC_8W_embryo1_COOL_sc8

description: bisulfite treated  genomic DNA


title: M_FGC_17W_embryo1_COOL_sc6

description: bisulfite treated  genomic DNA


title: M_FGC_8W_embryo1_COOL_sc12

description: bisulfite treated  genomic DNA


title: M_FGC_8W_embryo1_COOL_sc13

description: bisulfite treated  genomic DNA


title: M_FGC_17W_embryo1_COOL_sc5

description: bisulfite treated  genomic DNA


title: M_FGC_8W_embryo1_COOL_sc14

description: bisulfite treated  genomic DNA


title: M_FGC_8W_embryo1_COOL_sc7

description: bisulfite treated  genomic DNA


title: M_FGC_8W_embryo1_COOL_sc5

description: bisulfite treated  genomic DNA


title: M_FGC_8W_embryo1_COOL_sc3

description: bisulfite treated  genomic DNA


title: M_FGC_8W_embryo1_COOL_sc4

description: bisulfite treated  genomic DNA


title: M_FGC_8W_embryo1_COOL_sc2

description: bisulfite treated  genomic DNA


title: M_FGC_8W_embryo1_COOL_sc1

description: bisulfite treated  genomic DNA


title: M_FGC_7W_embryo3_COOL_sc24

description: bisulfite treated  genomic DNA


title: M_FGC_7W_embryo3_COOL_sc22

description: bisulfite treated  genomic DNA


title: M_FGC_7W_embryo3_COOL_sc21

description: bisulfite treated  genomic DNA


title: M_FGC_7W_embryo3_COOL_sc23

description: bisulfite treated  genomic DNA


title: M_FGC_7W_embryo3_COOL_sc20

description: bisulfite treated  genomic DNA


title: M_FGC_7W_embryo3_COOL_sc19

description: bisulfite treated  genomic DNA


title: M_FGC_7W_embryo3_COOL_sc17

description: bisulfite treated  genomic DNA


title: M_FGC_7W_embryo3_COOL_sc18

description: bisulfite treated  genomic DNA


title: M_FGC_8W_embryo1_COOL_sc6

description: bisulfite treated  genomic DNA


title: M_FGC_7W_embryo3_COOL_sc15

description: bisulfite treated  genomic DNA


title: M_FGC_7W_embryo3_COOL_sc14

description: bisulfite treated  genomic DNA


title: M_FGC_7W_embryo3_COOL_sc7

description: bisulfite treated  genomic DNA


title: M_FGC_7W_embryo3_COOL_sc11

description: bisulfite treated  genomic DNA


title: M_FGC_7W_embryo3_COOL_sc12

description: bisulfite treated  genomic DNA


title: M_FGC_7W_embryo3_COOL_sc13

description: bisulfite treated  genomic DNA


title: M_FGC_7W_embryo3_COOL_sc9

description: bisulfite treated  genomic DNA


title: M_FGC_7W_embryo3_COOL_sc16

description: bisulfite treated  genomic DNA


title: M_FGC_7W_embryo3_COOL_sc6

description: bisulfite treated  genomic DNA


title: M_FGC_7W_embryo3_COOL_sc8

description: bisulfite treated  genomic DNA


title: M_FGC_7W_embryo3_COOL_sc3

description: bisulfite treated  genomic DNA


title: M_FGC_7W_embryo3_COOL_sc5

description: bisulfite treated  genomic DNA


title: M_FGC_7W_embryo3_COOL_sc4

description: bisulfite treated  genomic DNA


title: M_FGC_7W_embryo3_COOL_sc2

description: bisulfite treated  genomic DNA


title: M_FGC_7W_embryo3_COOL_sc1

description: bisulfite treated  genomic DNA


title: F_Soma_21W_embryo1_sc15

description: bisulfite treated  genomic DNA

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Trim Galore (v0.3.3) was used to remove the first 9 bases of random primer, adaptor sequences and low quality bases;
Clean reads were first mapped to human reference genome hg19 with Bismark (v0.7.6) in paired-end and non-directional module, and then the unmapped reads were realigned to the same reference genome in single-end and non-directional module;
Methylation level of covered cytosines, including CpG, CHH and CHG were estimated using comstomized perl scripts.
Genome_build: hg19
Supplementary_files_format_and_content: Methylation calling bed files which include the methylation level of covered cytosines, including CpG, CHH and CHG context

extract_protocol:
Pick a single cell to the lysis buffer by mouth pipette and lyse the cell at 50°C for 3 hrs. Genome DNA was bisulfite converted and purified with EZ-96 DNA Methylation-Direct™MagPrep (Zymo. D5044).
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 strands synthesis, the library was amplified by KAPA HiFi HotStart ReadyMix (Kapa Biosystems, KK2602) for 13 cycles.


title: F_Soma_21W_embryo1_sc16

description: bisulfite treated  genomic DNA


title: F_Soma_21W_embryo1_sc14

description: bisulfite treated  genomic DNA


title: F_Soma_21W_embryo1_sc13

description: bisulfite treated  genomic DNA


title: F_Soma_21W_embryo1_sc17

description: bisulfite treated  genomic DNA


title: M_FGC_7W_embryo3_COOL_sc10

description: bisulfite treated  genomic DNA


title: F_Soma_21W_embryo1_sc8

description: bisulfite treated  genomic DNA


title: F_Soma_21W_embryo1_sc6

description: bisulfite treated  genomic DNA


title: F_Soma_21W_embryo1_sc11

description: bisulfite treated  genomic DNA


title: F_Soma_21W_embryo1_sc5

description: bisulfite treated  genomic DNA


title: F_Soma_21W_embryo1_sc10

description: bisulfite treated  genomic DNA


title: F_Soma_21W_embryo1_sc9

description: bisulfite treated  genomic DNA


title: F_Soma_21W_embryo1_sc7

description: bisulfite treated  genomic DNA


title: F_Soma_21W_embryo1_sc4

description: bisulfite treated  genomic DNA


title: F_Soma_21W_embryo1_sc3

description: bisulfite treated  genomic DNA


title: F_Soma_17W_embryo1_sc5

description: bisulfite treated  genomic DNA


title: F_Soma_17W_embryo1_sc3

description: bisulfite treated  genomic DNA


title: F_Soma_21W_embryo1_sc2

description: bisulfite treated  genomic DNA


title: F_Soma_17W_embryo1_sc6

description: bisulfite treated  genomic DNA


title: F_Soma_21W_embryo1_sc1

description: bisulfite treated  genomic DNA


title: F_Soma_17W_embryo1_sc4

description: bisulfite treated  genomic DNA


title: M_FGC_17W_embryo1_COOL_sc2

description: bisulfite treated  genomic DNA


title: F_Soma_9W_embryo1_sc15

description: bisulfite treated  genomic DNA

value: 9 week gestation


title: F_Soma_17W_embryo1_sc2

description: bisulfite treated  genomic DNA


title: F_Soma_17W_embryo1_sc1

description: bisulfite treated  genomic DNA


title: F_Soma_9W_embryo1_sc11

description: bisulfite treated  genomic DNA


title: F_Soma_9W_embryo1_sc12

description: bisulfite treated  genomic DNA


title: F_Soma_9W_embryo1_sc13

description: bisulfite treated  genomic DNA


title: F_Soma_21W_embryo1_sc12

description: bisulfite treated  genomic DNA


title: F_Soma_9W_embryo1_sc9

description: bisulfite treated  genomic DNA


title: F_Soma_9W_embryo1_sc10

description: bisulfite treated  genomic DNA


title: F_Soma_9W_embryo1_sc8

description: bisulfite treated  genomic DNA


title: F_Soma_9W_embryo1_sc7

description: bisulfite treated  genomic DNA


title: F_Soma_9W_embryo1_sc6

description: bisulfite treated  genomic DNA


title: F_Soma_9W_embryo1_sc4

description: bisulfite treated  genomic DNA


title: F_Soma_8W_embryo1_sc13

description: bisulfite treated  genomic DNA


title: F_Soma_9W_embryo1_sc3

description: bisulfite treated  genomic DNA


title: F_Soma_9W_embryo1_sc5

description: bisulfite treated  genomic DNA


title: F_Soma_9W_embryo1_sc1

description: bisulfite treated  genomic DNA


title: F_Soma_8W_embryo1_sc14

description: bisulfite treated  genomic DNA


title: F_Soma_9W_embryo1_sc2

description: bisulfite treated  genomic DNA


title: F_Soma_8W_embryo1_sc11

description: bisulfite treated  genomic DNA


title: F_Soma_8W_embryo1_sc5

description: bisulfite treated  genomic DNA


title: F_FGC_21W_embryo1_sc54

description: bisulfite treated  genomic DNA


title: F_FGC_21W_embryo1_sc53

description: bisulfite treated  genomic DNA


title: F_Soma_8W_embryo1_sc6

description: bisulfite treated  genomic DNA


title: F_Soma_8W_embryo1_sc7

description: bisulfite treated  genomic DNA


title: F_Soma_8W_embryo1_sc4

description: bisulfite treated  genomic DNA


title: F_Soma_8W_embryo1_sc8

description: bisulfite treated  genomic DNA


title: F_Soma_8W_embryo1_sc2

description: bisulfite treated  genomic DNA


title: F_FGC_21W_embryo1_sc50

description: bisulfite treated  genomic DNA


title: F_FGC_21W_embryo1_sc51

description: bisulfite treated  genomic DNA


title: F_FGC_21W_embryo1_sc52

description: bisulfite treated  genomic DNA


title: F_Soma_8W_embryo1_sc3

description: bisulfite treated  genomic DNA


title: F_Soma_8W_embryo1_sc10

description: bisulfite treated  genomic DNA


title: F_FGC_21W_embryo1_sc48

description: bisulfite treated  genomic DNA


title: F_FGC_21W_embryo1_sc49

description: bisulfite treated  genomic DNA


title: F_FGC_21W_embryo1_sc47

description: bisulfite treated  genomic DNA


title: F_FGC_21W_embryo1_sc45

description: bisulfite treated  genomic DNA


title: F_FGC_21W_embryo1_sc46

description: bisulfite treated  genomic DNA


title: F_FGC_21W_embryo1_sc44

description: bisulfite treated  genomic DNA


title: F_Soma_9W_embryo1_sc14

description: bisulfite treated  genomic DNA


title: F_FGC_21W_embryo1_sc42

description: bisulfite treated  genomic DNA


title: F_FGC_21W_embryo1_sc43

description: bisulfite treated  genomic DNA


title: F_Soma_8W_embryo1_sc12

description: bisulfite treated  genomic DNA


title: F_FGC_21W_embryo1_sc41

description: bisulfite treated  genomic DNA


title: F_Soma_8W_embryo1_sc9

description: bisulfite treated  genomic DNA


title: F_FGC_21W_embryo1_sc40

description: bisulfite treated  genomic DNA


title: F_FGC_21W_embryo1_sc39

description: bisulfite treated  genomic DNA


title: F_FGC_21W_embryo1_sc38

description: bisulfite treated  genomic DNA


title: F_FGC_21W_embryo1_sc37

description: bisulfite treated  genomic DNA


title: F_Soma_8W_embryo1_sc1

description: bisulfite treated  genomic DNA


title: F_FGC_21W_embryo1_sc36

description: bisulfite treated  genomic DNA


title: F_FGC_21W_embryo1_sc34

description: bisulfite treated  genomic DNA


title: F_FGC_21W_embryo1_sc31

description: bisulfite treated  genomic DNA


title: F_FGC_21W_embryo1_sc35

description: bisulfite treated  genomic DNA


title: F_FGC_21W_embryo1_sc28

description: bisulfite treated  genomic DNA


title: F_FGC_21W_embryo1_sc29

description: bisulfite treated  genomic DNA


title: F_FGC_21W_embryo1_sc30

description: bisulfite treated  genomic DNA


title: F_FGC_21W_embryo1_sc27

description: bisulfite treated  genomic DNA


title: F_FGC_21W_embryo1_sc26

description: bisulfite treated  genomic DNA


title: F_FGC_21W_embryo1_sc25

description: bisulfite treated  genomic DNA


title: F_FGC_21W_embryo1_sc24

description: bisulfite treated  genomic DNA


title: F_FGC_21W_embryo1_sc32

description: bisulfite treated  genomic DNA


title: F_FGC_21W_embryo1_sc23

description: bisulfite treated  genomic DNA


title: F_FGC_21W_embryo1_sc20

description: bisulfite treated  genomic DNA


title: F_FGC_21W_embryo1_sc19

description: bisulfite treated  genomic DNA


title: F_FGC_21W_embryo1_sc16

description: bisulfite treated  genomic DNA


title: F_FGC_21W_embryo1_sc18

description: bisulfite treated  genomic DNA


title: F_FGC_21W_embryo1_sc21

description: bisulfite treated  genomic DNA


title: F_FGC_21W_embryo1_sc17

description: bisulfite treated  genomic DNA


title: F_FGC_21W_embryo1_sc15

description: bisulfite treated  genomic DNA


title: F_FGC_21W_embryo1_sc12

description: bisulfite treated  genomic DNA


title: F_FGC_21W_embryo1_sc13

description: bisulfite treated  genomic DNA


title: F_FGC_21W_embryo1_sc33

description: bisulfite treated  genomic DNA


title: F_FGC_21W_embryo1_sc8

description: bisulfite treated  genomic DNA


title: F_FGC_21W_embryo1_sc7

description: bisulfite treated  genomic DNA


title: F_FGC_21W_embryo1_sc11

description: bisulfite treated  genomic DNA


title: F_FGC_21W_embryo1_sc5

description: bisulfite treated  genomic DNA


title: F_FGC_21W_embryo1_sc9

description: bisulfite treated  genomic DNA


title: F_FGC_21W_embryo1_sc22

description: bisulfite treated  genomic DNA


title: F_FGC_21W_embryo1_sc10

description: bisulfite treated  genomic DNA


title: F_FGC_21W_embryo1_sc6

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_sc21

description: bisulfite treated  genomic DNA


title: F_FGC_21W_embryo1_sc1

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_sc19

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_sc17

description: bisulfite treated  genomic DNA


title: F_FGC_21W_embryo1_sc2

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_sc22

description: bisulfite treated  genomic DNA


title: F_FGC_21W_embryo1_sc4

description: bisulfite treated  genomic DNA


title: F_FGC_21W_embryo1_sc14

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_sc15

description: bisulfite treated  genomic DNA


title: F_FGC_21W_embryo1_sc3

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_sc16

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_sc12

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_sc10

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_sc3

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_sc5

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_sc4

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_sc7

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_sc6

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_sc2

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_sc1

description: bisulfite treated  genomic DNA


title: F_FGC_10W_embryo1_sc21

description: bisulfite treated  genomic DNA


title: F_FGC_10W_embryo1_sc20

description: bisulfite treated  genomic DNA


title: F_FGC_10W_embryo1_sc19

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_sc20

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_sc18

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_sc14

description: bisulfite treated  genomic DNA


title: F_FGC_10W_embryo1_sc18

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_sc11

description: bisulfite treated  genomic DNA


title: F_FGC_10W_embryo1_sc14

description: bisulfite treated  genomic DNA


title: F_FGC_10W_embryo1_sc11

description: bisulfite treated  genomic DNA


title: F_FGC_10W_embryo1_sc10

description: bisulfite treated  genomic DNA


title: F_FGC_10W_embryo1_sc15

description: bisulfite treated  genomic DNA


title: F_FGC_10W_embryo1_sc8

description: bisulfite treated  genomic DNA


title: F_FGC_10W_embryo1_sc16

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_sc13

description: bisulfite treated  genomic DNA


title: F_FGC_10W_embryo1_sc17

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_sc8

description: bisulfite treated  genomic DNA


title: F_FGC_10W_embryo1_sc7

description: bisulfite treated  genomic DNA


title: F_FGC_10W_embryo1_sc9

description: bisulfite treated  genomic DNA


title: F_FGC_17W_embryo1_sc9

description: bisulfite treated  genomic DNA


title: F_FGC_10W_embryo1_sc6

description: bisulfite treated  genomic DNA


title: F_FGC_10W_embryo1_sc5

description: bisulfite treated  genomic DNA


title: F_FGC_10W_embryo1_sc4

description: bisulfite treated  genomic DNA


title: F_FGC_10W_embryo1_sc3

description: bisulfite treated  genomic DNA


title: F_FGC_10W_embryo1_sc13

description: bisulfite treated  genomic DNA


title: F_FGC_10W_embryo1_sc12

description: bisulfite treated  genomic DNA


title: F_FGC_9W_embryo1_sc16

description: bisulfite treated  genomic DNA


title: F_FGC_9W_embryo1_sc20

description: bisulfite treated  genomic DNA


title: F_FGC_9W_embryo1_sc18

description: bisulfite treated  genomic DNA


title: F_FGC_9W_embryo1_sc27

description: bisulfite treated  genomic DNA


title: F_FGC_9W_embryo1_sc22

description: bisulfite treated  genomic DNA


title: F_FGC_10W_embryo1_sc1

description: bisulfite treated  genomic DNA


title: F_FGC_9W_embryo1_sc28

description: bisulfite treated  genomic DNA


title: F_FGC_9W_embryo1_sc29

description: bisulfite treated  genomic DNA


title: F_FGC_9W_embryo1_sc31

description: bisulfite treated  genomic DNA


title: F_FGC_9W_embryo1_sc26

description: bisulfite treated  genomic DNA


title: F_FGC_10W_embryo1_sc2

description: bisulfite treated  genomic DNA


title: F_FGC_9W_embryo1_sc24

description: bisulfite treated  genomic DNA


title: F_FGC_9W_embryo1_sc21

description: bisulfite treated  genomic DNA


title: F_FGC_9W_embryo1_sc30

description: bisulfite treated  genomic DNA


title: F_FGC_9W_embryo1_sc25

description: bisulfite treated  genomic DNA


title: F_FGC_9W_embryo1_sc23

description: bisulfite treated  genomic DNA


title: F_FGC_9W_embryo1_sc7

description: bisulfite treated  genomic DNA


title: F_FGC_9W_embryo1_sc10

description: bisulfite treated  genomic DNA


title: F_FGC_9W_embryo1_sc8

description: bisulfite treated  genomic DNA


title: F_FGC_9W_embryo1_sc9

description: bisulfite treated  genomic DNA


title: F_FGC_9W_embryo1_sc15

description: bisulfite treated  genomic DNA


title: F_FGC_9W_embryo1_sc6

description: bisulfite treated  genomic DNA


title: F_FGC_9W_embryo1_sc12

description: bisulfite treated  genomic DNA


title: F_FGC_9W_embryo1_sc13

description: bisulfite treated  genomic DNA


title: F_FGC_9W_embryo1_sc14

description: bisulfite treated  genomic DNA


title: F_FGC_9W_embryo1_sc4

description: bisulfite treated  genomic DNA


title: F_FGC_9W_embryo1_sc5

description: bisulfite treated  genomic DNA


title: F_FGC_9W_embryo1_sc19

description: bisulfite treated  genomic DNA


title: F_FGC_9W_embryo1_sc17

description: bisulfite treated  genomic DNA


title: F_FGC_9W_embryo1_sc11

description: bisulfite treated  genomic DNA


title: F_FGC_9W_embryo1_sc3

description: bisulfite treated  genomic DNA


title: F_FGC_8W_embryo1_sc20

description: bisulfite treated  genomic DNA


title: F_FGC_8W_embryo1_sc21

description: bisulfite treated  genomic DNA


title: F_FGC_9W_embryo1_sc2

description: bisulfite treated  genomic DNA


title: F_FGC_9W_embryo1_sc1

description: bisulfite treated  genomic DNA


title: F_FGC_8W_embryo1_sc9

description: bisulfite treated  genomic DNA


title: F_FGC_8W_embryo1_sc14

description: bisulfite treated  genomic DNA


title: F_FGC_8W_embryo1_sc7

description: bisulfite treated  genomic DNA


title: F_FGC_8W_embryo1_sc13

description: bisulfite treated  genomic DNA


title: F_FGC_8W_embryo1_sc12

description: bisulfite treated  genomic DNA


title: F_FGC_8W_embryo1_sc10

description: bisulfite treated  genomic DNA


title: F_FGC_8W_embryo1_sc15

description: bisulfite treated  genomic DNA


title: F_FGC_8W_embryo1_sc16

description: bisulfite treated  genomic DNA


title: F_FGC_8W_embryo1_sc19

description: bisulfite treated  genomic DNA


title: F_FGC_8W_embryo1_sc5

description: bisulfite treated  genomic DNA


title: F_FGC_8W_embryo1_sc4

description: bisulfite treated  genomic DNA


title: F_FGC_8W_embryo1_sc2

description: bisulfite treated  genomic DNA


title: F_FGC_8W_embryo1_sc3

description: bisulfite treated  genomic DNA


title: F_FGC_8W_embryo1_sc8

description: bisulfite treated  genomic DNA


title: F_FGC_8W_embryo1_sc18

description: bisulfite treated  genomic DNA


title: F_FGC_8W_embryo1_sc1

description: bisulfite treated  genomic DNA


title: F_FGC_8W_embryo1_sc11

description: bisulfite treated  genomic DNA


title: M_Soma_21W_embryo3_sc8

description: bisulfite treated  genomic DNA


title: M_Soma_21W_embryo3_sc9

description: bisulfite treated  genomic DNA


title: M_Soma_21W_embryo3_sc10

description: bisulfite treated  genomic DNA


title: F_FGC_8W_embryo1_sc6

description: bisulfite treated  genomic DNA


title: M_Soma_21W_embryo3_sc7

description: bisulfite treated  genomic DNA


title: M_Soma_21W_embryo3_sc6

description: bisulfite treated  genomic DNA


title: F_FGC_8W_embryo1_sc17

description: bisulfite treated  genomic DNA


title: F_FGC_8W_embryo1_sc22

description: bisulfite treated  genomic DNA


title: M_Soma_21W_embryo3_sc5

description: bisulfite treated  genomic DNA


title: M_Soma_21W_embryo3_sc4

description: bisulfite treated  genomic DNA


title: M_Soma_21W_embryo3_sc3

description: bisulfite treated  genomic DNA


title: M_Soma_21W_embryo3_sc2

description: bisulfite treated  genomic DNA


title: M_Soma_21W_T2_sc4

description: bisulfite treated  genomic DNA


title: M_Soma_21W_T2_sc3

description: bisulfite treated  genomic DNA


title: M_Soma_21W_T1_sc7

description: bisulfite treated  genomic DNA


title: M_Soma_21W_T1_sc9

description: bisulfite treated  genomic DNA


title: M_Soma_21W_T1_sc8

description: bisulfite treated  genomic DNA


title: M_Soma_21W_T2_sc1

description: bisulfite treated  genomic DNA


title: M_Soma_21W_T1_sc6

description: bisulfite treated  genomic DNA


title: M_Soma_21W_T2_sc5

description: bisulfite treated  genomic DNA


title: M_Soma_21W_T2_sc6

description: bisulfite treated  genomic DNA


title: M_Soma_21W_T1_sc2

description: bisulfite treated  genomic DNA


title: M_Soma_17W_embryo1_sc4

description: bisulfite treated  genomic DNA


title: M_Soma_17W_embryo1_sc5

description: bisulfite treated  genomic DNA


title: M_Soma_21W_T1_sc5

description: bisulfite treated  genomic DNA


title: M_Soma_21W_T2_sc2

description: bisulfite treated  genomic DNA


title: M_Soma_21W_T1_sc1

description: bisulfite treated  genomic DNA


title: M_Soma_17W_embryo1_sc3

description: bisulfite treated  genomic DNA


title: M_Soma_17W_embryo1_sc2

description: bisulfite treated  genomic DNA


title: M_Soma_17W_embryo1_sc1

description: bisulfite treated  genomic DNA


title: M_Soma_21W_T1_sc4

description: bisulfite treated  genomic DNA


title: M_Soma_21W_embryo3_sc1

description: bisulfite treated  genomic DNA


title: M_Soma_17W_embryo1_sc7

description: bisulfite treated  genomic DNA


title: M_Soma_7W_embryo1_sc9

description: bisulfite treated  genomic DNA


title: M_Soma_17W_embryo1_sc6

description: bisulfite treated  genomic DNA


title: M_Soma_7W_embryo1_sc10

description: bisulfite treated  genomic DNA


title: M_Soma_7W_embryo1_sc11

description: bisulfite treated  genomic DNA


title: M_Soma_7W_embryo1_sc8

description: bisulfite treated  genomic DNA


title: M_Soma_21W_T1_sc3

description: bisulfite treated  genomic DNA


title: M_Soma_7W_embryo1_sc7

description: bisulfite treated  genomic DNA


title: M_Soma_7W_embryo1_sc6

description: bisulfite treated  genomic DNA


title: M_Soma_7W_embryo1_sc2

description: bisulfite treated  genomic DNA


title: M_Soma_7W_embryo1_sc1

description: bisulfite treated  genomic DNA


title: M_Soma_6W_embryo2_sc1

description: bisulfite treated  genomic DNA

value: 6 week gestation


title: M_Soma_6W_embryo1_sc15

description: bisulfite treated  genomic DNA


title: M_Soma_7W_embryo1_sc3

description: bisulfite treated  genomic DNA


title: M_Soma_6W_embryo1_sc8

description: bisulfite treated  genomic DNA


title: M_Soma_6W_embryo1_sc9

description: bisulfite treated  genomic DNA


title: M_Soma_6W_embryo1_sc5

description: bisulfite treated  genomic DNA


title: M_Soma_6W_embryo1_sc14

description: bisulfite treated  genomic DNA


title: M_Soma_7W_embryo1_sc5

description: bisulfite treated  genomic DNA


title: M_Soma_6W_embryo1_sc7

description: bisulfite treated  genomic DNA


title: M_Soma_7W_embryo1_sc4

description: bisulfite treated  genomic DNA


title: M_Soma_6W_embryo1_sc11

description: bisulfite treated  genomic DNA


title: M_Soma_6W_embryo1_sc10

description: bisulfite treated  genomic DNA


title: M_Soma_6W_embryo1_sc13

description: bisulfite treated  genomic DNA


title: M_Soma_6W_embryo1_sc6

description: bisulfite treated  genomic DNA


title: M_Soma_6W_embryo1_sc2

description: bisulfite treated  genomic DNA


title: M_Soma_6W_embryo1_sc1

description: bisulfite treated  genomic DNA


title: M_FGC_24W_embryo1_sc12

description: bisulfite treated  genomic DNA


title: M_FGC_24W_embryo1_sc14

description: bisulfite treated  genomic DNA


title: M_Soma_6W_embryo1_sc3

description: bisulfite treated  genomic DNA


title: M_FGC_24W_embryo1_sc13

description: bisulfite treated  genomic DNA


title: M_FGC_24W_embryo1_sc11

description: bisulfite treated  genomic DNA


title: M_FGC_24W_embryo1_sc15

description: bisulfite treated  genomic DNA


title: M_FGC_24W_embryo1_sc9

description: bisulfite treated  genomic DNA


title: M_FGC_24W_embryo1_sc8

description: bisulfite treated  genomic DNA


title: M_Soma_6W_embryo1_sc12

description: bisulfite treated  genomic DNA


title: M_Soma_6W_embryo1_sc4

description: bisulfite treated  genomic DNA


title: M_FGC_24W_embryo1_sc6

description: bisulfite treated  genomic DNA


title: M_FGC_24W_embryo1_sc5

description: bisulfite treated  genomic DNA


title: M_FGC_24W_embryo1_sc3

description: bisulfite treated  genomic DNA


title: M_FGC_24W_embryo1_sc1

description: bisulfite treated  genomic DNA


title: M_FGC_21W_embryo3_sc36

description: bisulfite treated  genomic DNA


title: M_FGC_21W_embryo3_sc32

description: bisulfite treated  genomic DNA


title: M_FGC_24W_embryo1_sc2

description: bisulfite treated  genomic DNA


title: M_FGC_21W_embryo3_sc35

description: bisulfite treated  genomic DNA


title: M_FGC_21W_embryo3_sc37

description: bisulfite treated  genomic DNA


title: M_FGC_21W_embryo3_sc31

description: bisulfite treated  genomic DNA


title: M_FGC_24W_embryo1_sc16

description: bisulfite treated  genomic DNA


title: M_FGC_21W_embryo3_sc29

description: bisulfite treated  genomic DNA


title: M_FGC_21W_embryo3_sc30

description: bisulfite treated  genomic DNA


title: M_FGC_21W_embryo3_sc28

description: bisulfite treated  genomic DNA


title: M_FGC_21W_embryo3_sc26

description: bisulfite treated  genomic DNA


title: M_FGC_21W_embryo3_sc25

description: bisulfite treated  genomic DNA


title: M_FGC_21W_embryo3_sc24

description: bisulfite treated  genomic DNA


title: M_FGC_21W_embryo3_sc23

description: bisulfite treated  genomic DNA


title: M_FGC_21W_embryo3_sc22

description: bisulfite treated  genomic DNA


title: M_FGC_21W_embryo3_sc21

description: bisulfite treated  genomic DNA


title: M_FGC_21W_embryo3_sc20

description: bisulfite treated  genomic DNA


title: M_FGC_21W_embryo3_sc19

description: bisulfite treated  genomic DNA


title: M_FGC_24W_embryo1_sc10

description: bisulfite treated  genomic DNA


title: M_FGC_24W_embryo1_sc7

description: bisulfite treated  genomic DNA


title: M_FGC_21W_embryo3_sc18

description: bisulfite treated  genomic DNA


title: M_FGC_24W_embryo1_sc4

description: bisulfite treated  genomic DNA


title: M_FGC_21W_embryo3_sc33

description: bisulfite treated  genomic DNA


title: M_FGC_21W_embryo3_sc16

description: bisulfite treated  genomic DNA


title: M_FGC_21W_embryo3_sc17

description: bisulfite treated  genomic DNA


title: M_FGC_21W_embryo3_sc15

description: bisulfite treated  genomic DNA


title: M_FGC_21W_embryo3_sc34

description: bisulfite treated  genomic DNA


title: M_FGC_21W_embryo3_sc13

description: bisulfite treated  genomic DNA


title: M_FGC_21W_embryo3_sc14

description: bisulfite treated  genomic DNA


title: M_FGC_21W_embryo3_sc11

description: bisulfite treated  genomic DNA


title: M_FGC_21W_embryo3_sc12

description: bisulfite treated  genomic DNA


title: M_FGC_21W_embryo3_sc9

description: bisulfite treated  genomic DNA


title: M_FGC_21W_embryo3_sc10

description: bisulfite treated  genomic DNA


title: M_FGC_21W_embryo3_sc8

description: bisulfite treated  genomic DNA


title: M_FGC_21W_embryo3_sc27

description: bisulfite treated  genomic DNA


title: M_FGC_21W_embryo3_sc6

description: bisulfite treated  genomic DNA


title: M_FGC_21W_embryo3_sc7

description: bisulfite treated  genomic DNA


title: M_FGC_21W_embryo3_sc5

description: bisulfite treated  genomic DNA


title: M_FGC_21W_embryo3_sc2

description: bisulfite treated  genomic DNA


title: M_FGC_21W_embryo3_sc3

description: bisulfite treated  genomic DNA


title: M_FGC_21W_embryo3_sc4

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T2_sc33

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T2_sc30

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T2_sc31

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T2_sc34

description: bisulfite treated  genomic DNA


title: M_FGC_21W_embryo3_sc1

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T2_sc29

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T2_sc28

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T2_sc27

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T2_sc26

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T2_sc25

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T2_sc24

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T2_sc20

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T2_sc21

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T2_sc22

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T2_sc19

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T2_sc15

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T2_sc17

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T2_sc14

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T2_sc13

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T2_sc16

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T2_sc11

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T2_sc10

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T2_sc9

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T2_sc12

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T2_sc32

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T2_sc8

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T2_sc5

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T2_sc1

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T2_sc2

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T2_sc3

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T2_sc7

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T2_sc4

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T2_sc6

description: bisulfite treated  genomic DNA


title: Nannochloropsis T48h-P-c

last: Shi

address: Chengfu Road, Haidian District

department: College Of Engineering

institute: Peking University

data_processing:
Hisat2 tools soft were used to map with reference genome.
Gene function was annotated based on the following databases:Nr (NCBI non-redundant protein sequences)；Nt (NCBI non-redundant nucleotide sequences)；Pfam (Protein family)；KOG/COG (Clusters of Orthologous Groups of proteins)；Swiss-Prot (A manually annotated and reviewed protein sequence database)；KO (KEGG Ortholog database)；GO (Gene Ontology).
Quantification of gene expression levelsGene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped.
Gene Ontology (GO) enrichment analysis of the differentially expressed genes (DEGs) was implemented by the GOseq R packages based Wallenius non-central hyper-geometric distribution
Used KOBAS  software to test the statistical enrichment of differential expression genes in KEGG pathways.
Genome_build: ASM187094v1
Supplementary_files_format_and_content: tab-delimited text files include gene ID, FPKM values, COG class annotation, GO annotation, KEGG annotation, KEGG pathway annotation, KOG class, KOG class annotation, Pfam annotation, Swiss Prot annotation, eggNOG class, eggNOG class annotation, and NR annotation for each Sample. The gene IDs can be searched at http://nandesyn.single-cell.cn/find/genes

organism: Nannochloropsis oceanica

source_name: Nannochloropsis cell

growth_protocol: Nannochloropsis. oceanica. IMET1 was cultured in modified f/2 medium containing 20 g L-1 sea salt, cultures started under continuous illumination of 50 μmol photons m-2 s-1 at 23±1 °C with the same initial algal dry weight of 0.5 g/l.

extract_protocol:
The total RNA of N.oceanica (10e8 cells) was extracted by the TaKaRa Mini BEST Plant RNA Extraction Kit (TAKARA, Beijing, China). The concentration of the total RNA was determined at 260 nm using NannoDrop 2000c (Thermo Scientific, Beijing, China) and the quality was checked by electrophoresis.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The algal cells were collected at the linear growth phase (biomass = 2 g/l) by centrifugation and washed three times with axenic seawater and respectively inoculated into phosphate deprivation (PD) f/2 medium (200 mL, n = 3) and f/2 medium (200 mL, n = 3) in triplicates.

value: phosphate deprivation


title: Nannochloropsis T48h-P-b


title: M_FGC_21W_T1_sc34

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T2_sc23

description: bisulfite treated  genomic DNA


title: Nannochloropsis T48h-P-a


title: M_FGC_21W_T2_sc18

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T1_sc32

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T1_sc33

description: bisulfite treated  genomic DNA


title: Nannochloropsis T24h-P-c


title: M_FGC_21W_T1_sc31

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T1_sc29

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T1_sc30

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T1_sc27

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T1_sc28

description: bisulfite treated  genomic DNA


title: Nannochloropsis T24h-P-a


title: Nannochloropsis T12h-P-b


title: Nannochloropsis T12h-P-a


title: Nannochloropsis T24h-P-b


title: M_FGC_21W_T1_sc26

description: bisulfite treated  genomic DNA


title: Nannochloropsis T6h-P-c

value: 6 h


title: M_FGC_21W_T1_sc25

description: bisulfite treated  genomic DNA


title: Nannochloropsis T6h-P-b


title: M_FGC_21W_T1_sc24

description: bisulfite treated  genomic DNA


title: Nannochloropsis T6h-P-a


title: M_FGC_21W_T1_sc23

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T1_sc22

description: bisulfite treated  genomic DNA


title: Nannochloropsis T0h-b

value: 0 h


title: Nannochloropsis T0h-c


title: Nannochloropsis T0h-a


title: M_FGC_21W_T1_sc20

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T1_sc21

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T1_sc19

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T1_sc18

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T1_sc17

description: bisulfite treated  genomic DNA


title: Nannochloropsis T12h-P-c


title: M_FGC_21W_T1_sc16

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T1_sc15

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T1_sc14

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T1_sc12

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T1_sc13

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T1_sc11

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T1_sc10

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T1_sc8

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T1_sc7

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T1_sc6

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T1_sc5

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T1_sc9

description: bisulfite treated  genomic DNA


title: M_FGC_21W_T1_sc3

description: bisulfite treated  genomic DNA


title: PS19_rescue rep3

city: atlanta

first: David

middle: J

last: Katz

state: ga

address: 615 Michael st

department: Cell Biology

institute: Emory University

data_processing:
FASTQ files were quality assessed using FASTQC (v.0.11.7), trimmed using Trimmomatic (v.0.36.5) and minimum QC score of 20 and minimum read length of 36bp.
Paired-end reads were subsequently mapped to the GRCm38 genome using HISAT2 (v.2.1.0). Unmapped, unpaired and multiply mapped reads were removed using Filter SAM or BAM (v.1.1.2).
Assignment of transcripts to GRCm38 genomic features was performed using Featurecounts (v.1.6.0.6) and the Ensembl GRCm38.93 gtf file
Differentially expressed transcripts were determined using DESEQ2 (v.2.11.40.2) ((46)). For all datasets, a cutoff of adjusted p-value < 0.1 and abs (log2 fold change) > 0.58 was applied
Genome_build: GRCm38.93
Supplementary_files_format_and_content: tab-delimited text files include raw count data for each sample

source_name: Hippocampus

extract_protocol:
hippocampi were dissected and snap frozen with liquid nitrogen in 1mL Trizol, and stored at -80°C. For RNA isolation, samples were thawed at 37°C then kept on ice prior to homogenization with Polytron homogenizer with a 5 second pulse. After a 5 minute incubation at room temperature, one tenth the sample volume of 1-bromo-3chloropropane was added, mixed by inversion and incubated for 3 minutes at room temperature. Samples were then centrifuged at 13,000 X g for 15 minutes at 4°C to separate the aqueous and organic layers. As much of the aqueous layer was recovered as possible, then RNA was precipitated with isoproponal. Pellets were then washed with 75% ethanol and resuspended in 50μL of dionized water.
RNA library preparation and sequencing were performed by HudsonAlpha Genomic Services Lab. RNA was Poly(A) selected and 300bp size selected

value: hippocampus

value: PS19 tg ; LSD1 +/+

value: PS19 LSD1 viral rescue


title: PS19_rescue rep2


title: Paracancerous3

city: Changsha

first: Zhaojian

last: Gong

state: Hunan Province

address: 139 Renmin Road

department: Oral and Maxillofacial Surgery

institute: The Second Xiangya Hospital of Central South University

description:
Gene expression profiling of Tongue paracancerous tissue
GC_006

hyb_protocol: The task consists of the following steps:1.Add 500 μL of nuclease-free water to the vial containing lyophilized 10X Blocking Agent. Mix by gently vortexing. 2.Equilibrate water bath to 60°C. 3.For each microarray, add each of the components as indicated in the tables as below to a 1.5 mL nuclease-free microfuge tube. 4.Mix well but gently on a vortex mixer. 5.Incubate at 60°C for exactly 30 minutes to fragment RNA. 6.Add 2x GEx Hybridization Buffer HI-RPM to the array to stop the fragmentation reaction. 7.Mix well by careful pipetting. Take care to avoid introducing bubbles. Do not mix on a vortex mixer; mixing on a vortex mixer introduces bubbles. 8.Spin for 1 minute at room temperature at 13,000 rpm in a microcentrifuge to drive the sample off the walls and lid and to aid in bubble reduction. 9.Place sample on ice and load onto the array as soon as possible. 10.Load a clean gasket slide into the Agilent SureHyb chamber base with the label facing up and aligned with the rectangular section of the chamber base. Ensure that the gasket slide is flush with the chamber base and is not ajar. 11.Slowly dispense the volume of hybridization sample onto the gasket well in a “drag and dispense” manner. 12.Slowly place an array “active side” down onto the SureHyb gasket slide, so that the “Agilent”-labeled barcode is facing down and the numeric barcode is facing up. Verify that the sandwich-pair is properly aligned. 13.Place the SureHyb chamber cover onto the sandwiched slides and slide the clamp assembly onto both pieces. 14.Hand-tighten the clamp onto the chamber. 15.Vertically rotate the assembled chamber to wet the gasket and assess the mobility of the bubbles. 16.Place assembled slide chamber in rotisserie in a hybridization oven set to 65°C. Set your hybridization rotator to rotate at 10 rpm. 17.Hybridize at 65°C for 17 hours.

scan_protocol: After washing, the arrays were scanned by the Agilent Scanner G2505C(Agilent Technologies).The task consists of the following steps:1.Assemble the slides into an slide holder. 2.Place assembled slide holders into scanner carousel. 3.Verify scan settings for one-color scans. 4.Click Scan Slot m-n on the Scan Control main window where the letter m represents the Start slot where the first slide is located and the letter n represents the End slot where the last slide is located.

data_processing: Feature Extraction software (version10.7.1.1, Agilent Technologies) was used to analyze array images to get raw data. Genespring(version 13.1, Agilent Technologies) were employed to finish the basic analysis with the raw data. To begin with, the raw data was normalized with the quantile algorithm. The probes that at least 1 conditions out of 2 conditions have flags in “P” were chosen for further data analysis.

source_name: Tongue paracancerous tissue

label_protocol: total RNA were transcribed to double strand cDNA, then synthesized into cRNA and labeled with Cyanine-3-CTP. The task consists of the following steps: 1.Add 200ng of total RNA (2.5μL) to a 1.5-mL microcentrifuge tube.  2.Add 0.8 μL of Random Primer.  3.Add 2 μL of Spike Mix. 4.Denature the primer and the template by incubating the reaction at 65°C in a circulating water bath for 10 minutes. 5.Place the reactions on ice and incubate for 5 minutes. 6.Immediately prior to use, gently mix the components listed in the following table for the cDNA Master Mix by adding in the order indicated, and put on ice. 7.Briefly spin each sample tube in a microcentrifuge to drive down the contents from the tube walls and the lid. Return the tubes to ice. 8.Add 4.7 μL of cDNA Master Mix to each sample tube and mix by pipetting up and down. 9.Incubate samples at 40°C in a circulating water bath for 2 hours. 10.Move samples to a 70°C circulating water bath and incubate for 15 minutes. 11.Move samples to ice. Incubate for 5 minutes. 12.Spin samples briefly in a microcentrifuge to drive down tube contents from the tube walls and lid. 13.Immediately prior to use, gently mix the components listed in the following table in the order indicated for the Transcription Master Mix by pipetting at room temperature. 14.Add 6μL of Transcription Master Mix to each sample tube. Gently mix by pipetting. 15.Incubate samples in a circulating water bath at 40°C for 2 hours.

extract_protocol: Tissue RNA is extracted using Trizol reagent, and all reagents and materials used are processed by DEPC. First,  50-100 mg human tissue sample was ground and crushed in liquid nitrogen. After volatilization of liquid nitrogen, 1 mL Trizol was added rapidly. After that, RNA was extracted according to the standard operating procedure provided by the manufacturer

treatment_protocol: Tongue cancer and paracancerous tissues were collected from patients with tongue cancer. The weight of the tissues ranged from 0.5 mg to 250 mg. Tissues should be immersed in liquid nitrogen within 15 minutes of removal from the living body.

tag: individual

value: patient 3

value: Tongue tissue

tag: tissue type

value: Tongue paracancerous tissue

value: male

tag: histological grade

value: Well

tag: tnm stage


title: Paracancerous1

description:
Gene expression profiling of Tongue paracancerous tissue
GC_002

value: patient 1

tag: tissue

value: Well/Moderate


title: PS19_HA rep3

tag: strain

tag: genotype

value: PS19 control


title: WT_HA rep2

value: wildtype

value: HA control


title: PS19_HA rep2


title: WT_HA rep3


title: Paracancerous4

description:
Gene expression profiling of Tongue paracancerous tissue
GC_008

value: patient 4


title: PS19_HA rep1


title: TSCC4

description:
Gene expression profiling of TSCC
GC_007

source_name: Tongue Squamous Cell Carcinoma

value: Tongue cancer


title: TSCC3

description:
Gene expression profiling of TSCC
GC_005


title: TSCC2

description:
Gene expression profiling of TSCC
GC_003

value: patient 2

value: Moderate


title: M_FGC_21W_T1_sc4

description: bisulfite treated  genomic DNA

value: Male

tag: developmental stage

value: 21 week gestation


title: WT_HA rep1

value: hippocampus

tag: treatment


title: TSCC1

description:
Gene expression profiling of TSCC
GC_001


title: TSCC5

description:
Gene expression profiling of TSCC
GC_009

value: patient 5


title: M_FGC_21W_T1_sc1

description: bisulfite treated  genomic DNA


title: M_FGC_17W_embryo1_sc31

description: bisulfite treated  genomic DNA

value: 17 week gestation


title: PS19;Lsd1Δ/+ rep4

value: PS19 tg; LSD1 +/-

value: PS19 transgene, Lsd1 heterozygote


title: PS19_rescue rep1

value: PS19 tg ; LSD1 +/+

value: PS19 LSD1 viral rescue


title: M_FGC_21W_T1_sc2

description: bisulfite treated  genomic DNA


title: Paracancerous2

description:
Gene expression profiling of Tongue paracancerous tissue
GC_004

value: Tongue tissue

value: Tongue paracancerous tissue

value: male


title: M_FGC_17W_embryo1_sc30

description: bisulfite treated  genomic DNA


title: PS19;Lsd1Δ/+ rep3


title: Paracancerous5

description:
Gene expression profiling of Tongue paracancerous tissue
GC_010

value: Well/Moderate


title: PS19 rep4

value: PS19 transgene


title: M_FGC_17W_embryo1_sc29

description: bisulfite treated  genomic DNA


title: M_FGC_17W_embryo1_sc28

description: bisulfite treated  genomic DNA


title: M_FGC_17W_embryo1_sc27

description: bisulfite treated  genomic DNA


title: WT rep4

value: wild type

value: control


title: WT rep3


title: M_FGC_17W_embryo1_sc24

description: bisulfite treated  genomic DNA


title: M_FGC_17W_embryo1_sc22

description: bisulfite treated  genomic DNA


title: M_FGC_17W_embryo1_sc21

description: bisulfite treated  genomic DNA


title: M_FGC_17W_embryo1_sc23

description: bisulfite treated  genomic DNA


title: M_FGC_17W_embryo1_sc19

description: bisulfite treated  genomic DNA


title: M_FGC_17W_embryo1_sc25

description: bisulfite treated  genomic DNA


title: M_FGC_17W_embryo1_sc20

description: bisulfite treated  genomic DNA


title: Adult2

city: Vancouver

first: Maryam

last: Ghaedi

state: BC

address: 675 West 10th Avenue

department: Terry Fox Laboratory

institute: BC Cancer Agency

data_processing:
The obtained libraries were sequenced on NextSeq 500 (Illumina). Cell Ranger software (v2.0.1; 10X Genomics) was used to perform demultiplexing, alignment, counting as well as initial clustering, and differential gene expression analysis. The reads were aligned to the mm10 genome, with the genome re-annotated to include YFP, TCR and immunoglobulin genes. ScRNA-seq analysis was performed using Seurat package (Butler et al., 2018) (version 2.1.0) in R (version 3.4.2) (R core team, 2017).
Genome_build: The reads were aligned to the mm10 genome, with the genome re-annotated to include YFP, TCR and immunoglobulin genes.

source_name: Lung CD45low/+Linlow cells

extract_protocol:
To acquire lung tissue single cell suspensions, tissue was minced and fragments were digested in 5 ml DMEM containing collagenase IV (142.5 U/ml; Thermo Fisher, 17104019) and DNase I (118,050 U/ml, Sigma-Aldrich, 9003-98-9) for 25 minutes at 37°C on a shaker (150 rpm). The single cell suspension was filtered through a 70μm cell strainer and washed once with 5 ml DMEM containing 10% FBS and Penicillin-Streptomycin (10,000 U/mL). The acquired cells were enriched for leukocytes by a 36% Percoll (Sigma-Aldrich, P4937) gradient media and red blood cell lysis.   Adult or neonatal (12-day-old) RORα-YFP mouse lungs were process as described. Pooled adult or neonatal single cell suspensions were incubated with anti-mouse CD16/32 antibody (clone 2.4G2). The cells were then stained with Viability Dye (Thermo Fisher, 65-0865-18), anti-CD45 and Lin-cocktail antibodies including anti-CD3, TCRαβ, TCRγδ, NKp46, CD19, CD11b, CD11c, Ly-6C/G (Gr-1) and Ter119. Viable CD45low/+LinlowYFP− and YFP+ cells were purified at 2 to 1 ratio for adult mice samples. Neonatal sample cells were purified as CD45low/+LinlowCD8−YFP− and YFP+ cells at 2 to 1 ratio.
Purified ells were loaded on the Chromium Single Cell Controller (10X Genomics) and libraries were prepped using the Chromium Single Cell 3′ Reagents Kits (v2 chemistry; 10X Genomics), according to the manufacturer’s protocol.

tag: mouse model and strain

value: RORα-YFP (B6.RoraIRES-Cre (Chou et al., 2013) × B6.R26R-EYFP)

value: Pooled lungs from 3 mice (41-day-old), 2 mice (45-day-old), 3 mice (54-day-old), 2 mice (58-day-old), 1 mice (63-day-old), 3 mice (60-day-old)

tag: Sex

value: Female


title: P30 Stria Vascularis nuclei capture MethFix

city: Bethesda

first: Michael

last: Hoa

state: MD

address: 35 Convent Dr, Rm 1F-226

institute: National Institutes on Deafness and Other Communication Disorders, NIH

description: Single nuclei RNA-seq

data_processing:
Basecalls performed using Illumina’s RTA  2.0.12
Sample demultiplexing, alignment and gene counts were performed using the CellRanger v3.0.1 pipeline using default settings.
Dataset pre-processing, clustering, and data visualization were performed using Scanpy (v1.4.5) package.
Computational removal of doublets was performed using Scrublet (v0.2.1)
Differential expression analysis was performed using DEsingle (v1.6.0).
Regulatory network inference was performed using pySCENIC (v0.10.0).
Genome_build: GRCm38 with custom transcript annotation with introns (pre-mRNA)
Supplementary_files_format_and_content: CellRanger v3.0.1 gene counts matrices.

source_name: P30 Stria Vascularis

extract_protocol:
(single nucleus RNA-Seq with methanol fixation)  Single nucleus suspension from stria vascularis: Published single nucleus suspension protocol from 10x genomics was used to isolate the nuclei. Briefly, stria vascularis from ~5-6 P30 animals were isolated and collected in 3ml DMEM F-12 media. Following collection, the media was replaced with 3ml chilled lysis buffer (10mM Tris-HCl, 10mM Nacl, 3mM MgCl2,0.005% Nonidet P40 in Nuclease free water) and the tissue were lysed at 4°C for 25 minutes. The lysis buffer was then replaced with 1.5ml DMEM F-12 media. The tissues were triturated and filtered through a 20um filter. The filtrate was centrifuged at 500rcf for 5 minutes at 4°C. The supernatant was removed, and the cell pellet was resuspended in 1ml nuclei wash and resuspension buffer (1xPBS with 1% BSA and 0.2U/ul RNase Inhibitor). The nuclei were filtered through a 10um filter and centrifuged at 500rcf for 5 minutes at 4°C. The supernatant was removed, and pellet resuspended in 50ul of nuclei wash and resuspension buffer.  After nucleus isolation, nuclei were fixed with 4 volumes of methanol (200 ul) added dropwise to avoid clumping of nuceli and allowed to undergo fixation at -20°C for 30 minutes.  The nuclei were centrifuged at 500rcf for 5 minutes at 4°C. The supernatant was removed, and pellet resuspended in 50ul of nuclei wash and resuspension buffer. Nuclei were counted in a Luna cell counter and a nuclear density of 1x10^6 cells/ml was used to load onto the 10X genomics chip.
(single nucleus RNA-Seq)  Microdissected tissues were treated with RNAlater overnight at 4°C prior to single nucleus isolation. Single nucleus suspension from stria vascularis: Published single nucleus suspension protocol from 10x genomics was used to isolate the nuclei. Briefly, stria vascularis from ~10 P30 animals were isolated and collected in 3ml DMEM F-12 media. Following collection, the media was replaced with 3ml chilled lysis buffer (10mM Tris-HCl, 10mM Nacl, 3mM MgCl2, 0.005% Nonidet P40 in Nuclease free water) and the tissue were lysed at 4°C for 25 minutes. The lysis buffer was then replaced with 1.5ml DMEM F-12 media. The tissues were triturated and filtered through a 20um filter. The filtrate was centrifuged at 500rcf for 5 minutes at 4°C. The supernatant was removed, and the cell pellet was resuspended in 1ml nuclei wash and resuspension buffer (1xPBS with 1% BSA and 0.2U/ul RNase Inhibitor). The cells were filtered through a 10um filter and centrifuged at 500rcf for 5 minutes at 4°C. The supernatant was removed, and pellet resuspended in 50ul of nuclei wash and resuspension buffer. Nuclei were counted in a Luna cell counter and a nuclear density of 1x10^6 cells/ml was used to load onto the 10X genomics chip.
Library preparation was performed according to the manufacturer’s instructions for the 10x Genomics Chromium platform (10x Genomics). The libraries were sequenced on four lanes on a NextSeq500 sequencer (Illumina).

value: Stria Vascularis

value: CBA/J mice (strain 000656)

tag: sample preservation method

value: methanol fixation


title: M_FGC_17W_embryo1_sc18

description: bisulfite treated  genomic DNA

tag: gender

value: Male

value: 17 week gestation


title: M_FGC_17W_embryo1_sc17

description: bisulfite treated  genomic DNA


title: M_FGC_17W_embryo1_sc15

description: bisulfite treated  genomic DNA


title: P8 NSC diff D2 Con

first: Lining

last: Liang

address: 190,Kaiyuan Ave.

institute: Guangzhou Institute of Biomedicine and Health,Chinese Academy of Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie
Transcripts Per Million were  calculated using a protocol from RSEM
Genome_build: mm10
Supplementary_files_format_and_content: TPM

source_name: NSC

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: neural stem cells

tag: passages


title: P8 NSC diff D2 Dam


title: M_FGC_17W_embryo1_sc13

description: bisulfite treated  genomic DNA


title: P8 NSC diff D2 Nal


title: P8 NSC Con


title: M_FGC_17W_embryo1_sc12

description: bisulfite treated  genomic DNA


title: M_FGC_17W_embryo1_sc11

description: bisulfite treated  genomic DNA


title: M_FGC_17W_embryo1_sc10

description: bisulfite treated  genomic DNA


title: M_FGC_17W_embryo1_sc26

description: bisulfite treated  genomic DNA


title: eCLIP_rep2_INPUT

city: Wuhan

first: Jinglei

last: Xu

state: Hubei

address: Bayi road

department: The Institute of Advanced Studies

institute: Wuhan University

description: Flag-tag

data_processing:
Sequenced reads were trimmed for adaptor sequence, and segregated for repetitive elements, then mapped to hg38 whole genome using STAR (v 2.4.0i)
cluster identification was performed on usable reads using CLIPper with options -s GRCh38 -o --binomial 0.05 --save-pickle
Peak normalization vs paired SMInput datasets is run as eCLIP Standard Operating Procedure
The overlap between 2 replicates were calculated by bedtools intersect with options -wa -wb -s
Genome_build: hg38
Supplementary_files_format_and_content: peak text files

source_name: Hela cells

growth_protocol: stable SERBP1-Flag Hela cells were grown at 37 °C and 5% CO2 in Dulbecco’s modified Eagle medium (DMEM), supplemented with 10% fetal bovine serum (vol/vol) and 1% penicillin/streptomycin.

extract_protocol:
cells were resuspended in iCLIP buffer and sonicated in Bioruptor, lysates were digested by RNase I and RNA-RBP complexes were isolated with antibody
library construction were prepared according to eCLIP Standard Operating Procedure v1.P 20151108

treatment_protocol: UV crosslinking (254 nm, 400 mJ/cm2) in cold PBS

value: UV-crosslinking

tag: clip antibody

value: ANTI-FLAG®(sigma #F7430)


title: eCLIP_rep2_NX

description: Flag-tag

value: untreated

value: ANTI-FLAG®(sigma #F7429)


title: M_FGC_17W_embryo1_sc14

description: bisulfite treated  genomic DNA


title: P8 NSC Dam