title: DNA-methylation array data_202915420104_R06C01

value: Male


title: Sample 6: wild type, root, biol rep 2

status: Public on Feb 24 2025

type: SRA

city: Poznan

first: Zofia

last: Szweykowska-Kulinska

address: Umultowska 89

department: Departemnt of Gene Expression

country: Poland

institute: Adam Mickiewicz University in Poznan

library_source: transcriptomic

data_processing:
The adapter sequence was removed from the obtained raw reads with Cutadapt
The reads shorten than 18 nt and longer that 28 nt were removed using Cutadapt
Clean fastq reads were collapsed to fasta files using fastx_collapser from FASTX_toolkit
Supplementary files format and content: fasta format, raw read counts for each molecule in the libraries

molecule: total RNA

organism: Hordeum vulgare

source_name: Root

extract_protocol:
Two week-old barley plants were collected in three biological replicates. The extraction of total RNA was performed using Direct-zol RNA Mini Prep Kit (Zymo Research) according to the manufacturer’s protocol.
Libraries were constructed using the TruSeq SmallRNA Library Preparation Kit (Illumina) as described in the manual.

tag: tissue

value: Root

tag: cultivar

value: Golden Promise

tag: genotype

value: wild type


title: MT16 [methylation]

type: genomic

city: Ann Arbor

first: Lana

last: Garmire

state: Michigan

address: 1600 Huron Parkway

country: USA

institute: University of Michigan

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using High Scan SQ using standard recommended Illumina scanner setting

data_processing:
Preprocessed, normalized, and batch removed with ChAMP (version  2.16.2) in R
*processed value definition: Average beta

label: Cy3 and Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: umbilical cord blood

label_protocol: Standard Illumina protocol

extract_protocol: DNA and RNA were extracted simultaneously using the AllPrep DNA/RNA extraction kit (Qiagen)

value: umbilical cord blood

tag: cell type

value: CD34+/CD38-/Lin- Hematopoietic stem cell

value: obese


title: DNA-methylation array data_205689110012_R06C01

city: Berlin

first: Philipp

last: Euskirchen

address: Charitéplatz 1

country: Germany

institute: Charité - Universitätsmedizin Berlin

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation 850k or 935k Beadchip, respectively, using standard Illumina protocol.

scan_protocol: Arrays were scanned on the iscan instument acording to standarad protocol.

data_processing:
IDAT files were preprocessed using R/minfi.
*processed value definition: Average beta value

label: Cy3, Cy5

source_name: tumor

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and purified from human tumor samples using Maxwell RSC FFPE Plus DNA Purification Kit (Promega, USA) according to standard instructions.

value: tumor

tag: tumor type

value: Pleomorphic xanthoastrocytoma

tag: age

tag: Sex

tag: beadchip name


title: Female, ad. Libitum fed, batch 1

city: Houston

first: Jonathan

middle: Carter

last: Bean

state: TX

address: 1100 Bates Ave

department: Pediatrics

institute: Baylor College of Medicine

description: Library name: F_Fed_B1

library_source: transcriptomic single cell

data_processing:
STARsolo v2.7.10a
SoupX v1.6.2
scDblFnd v1.18.0
Seurat v4.4.0
Assembly: Genome assembly GRCm39
Supplementary files format and content: Seurat object, RDS compressed

molecule: polyA RNA

organism: Mus musculus

source_name: arcuate nucleus of hypothalamus

extract_protocol:
dissection followed by nuclei isolation and FAC sorting
Chromium GEM-X Single Cell 3' Kit v3

value: arcuate nucleus of hypothalamus

value: Female

tag: treatment

value: ad. lib. Fed

tag: batch


title: bio replicate 2, gene expression [L6b]

city: Worcester

first: Samuel

middle: M

last: Behar

address: 55 Lake Ave N

department: Microbiology and Physiological Systems (MaPS)

institute: UMass Chan Medical School

description:
Illumina NextSeq 500 and NovaSeq 6000
10x Genomics

data_processing:
Demultiplexing, aligning, barcode processing, gene counting, V(D)J annotation, and aggregation were done using Cell Ranger v6.0
Assembly: mm10
Supplementary files format and content: Tab-separated values, comma-separated values, and matrix files

source_name: Lung

extract_protocol:
TCR⍺ KO mice were injected intravenously (IV) with ESAT-6 specific (C7 and C24) TCR transgenic T-cells and infected with Mtb Erdman 24 hours post-IV. At 26 wpi, mice were IV injected with anti-CD45 antibody 2 minutes before euthanizing with CO2. Lungs were then perfused and removed 3 minutes after anti-CD45 injection. Lung single cell suspensions were prepared by homogenizing lungs using a GentleMACS tissue dissociator, digesting with collagenase at 37C for 30 minutes, followed by a second run of dissociation using the GentleMACS. Suspensions were then filtered through 70 µm strainers and incubated with 1 mL ACK Lysis Buffer (GIBCO) for 1 minute at room temperature (25C). The cells were resuspended in D-PBS and filtered through 40 µm filters. The resulting single cell suspensions were stained with flow antibodies to sort for total live, parenchymal T-cells (CD45 IV Negative, TCR[b] and CD3 double positive) using the BD FACS Aria.
Library construction was performed according to the manufacturer's instructions (single cell 5' v2 protocols, 10x Genomics).

value: Lung

value: T-cells

tag: strain

value: Mtb infected TCRalpha KO mice


title: MT13 [methylation]


title: Sample 4: mutant 33210, root, biol rep 1

value: mutant 33210


title: Female, 28 hours fasted, batch 1

description: Library name: F_Fast_B1

value: 28 hours fasted


title: DNA-methylation array data_207015200146_R01C01

value: Male


title: DNA-methylation array data_202013790058_R07C01

value: High-grade astrocytoma with piloid features


title: DNA-methylation array data_204958100038_R03C01

value: Central neurocytoma


title: MT27 [methylation]

value: control


title: 41 wpi, replicate 2, gene expression

description: 10x Genomics

extract_protocol:
C57Bl/6 mice were injected intravenously (IV) with ESAT-6 specific (C7) TCR transgenic T-cells and infected with Mtb Erdman 24 hours post-IV. At 6 and 41 wpi, mice were IV injected with anti-CD45 antibody 2 minutes before euthanizing with CO2. Lungs were then perfused and removed 3 minutes after anti-CD45 injection. Lung single cell suspensions were prepared by homogenizing lungs using a GentleMACS tissue dissociator, digesting with collagenase at 37C for 30 minutes, followed by a second run of dissociation using the GentleMACS. Suspensions were then filtered through 70 µm strainers and incubated with 1 mL ACK Lysis Buffer (GIBCO) for 1 minute at room temperature (25C). The cells were resuspended in D-PBS and filtered through 40 µm filters. The resulting single cell suspensions were stained with flow antibodies to sort for total live, parenchymal T-cells (CD45 IV Negative, TCR[b] and CD3 double positive) using the BD FACS Aria.
Library construction was performed according to the manufacturer's instructions (single cell 5' v1 and v2 protocols, 10x Genomics).

tag: mouse strain

tag: weeks post-infection


title: Sample 11: mutant 33210, shoot, biol rep 3

source_name: Shoot

value: Shoot

value: Golden Promise


title: Sample 12: mutant 33210, root, biol rep 3

value: Root


title: Sample 2: wild type, root, biol rep 1

value: wild type


title: Sample 9: mutant 33210, shoot, biol rep 1


title: bio replicate 1, gene expression [L5a]


title: 6 wpi, replicate 2, VDJ

description: 10x Genomics


title: MT22 [methylation]

value: umbilical cord blood

value: CD34+/CD38-/Lin- Hematopoietic stem cell


title: 41 wpi, replicate 1, gene expression

description: 10x Genomics


title: DNA-methylation array data_202790040027_R08C01

value: tumor

value: Female


title: 41 wpi, replicate 2, VDJ

description: 10x Genomics

value: Lung


title: DNA-methylation array data_202123800098_R08C01

value: Pleomorphic xanthoastrocytoma


title: Sample 1: wild type, shoot, biol rep 1


title: Tet3cKO_LZ_21

status: Public on Feb 23 2025

city: Beijing

first: Jinmin

last: Yang

address: Yiheyuan Road 5

department: School of life science

country: China

institute: Peking University

description:
5hmC
Chemical labeled genomic DNA

library_source: genomic

data_processing:
*library strategy: schmC-CATCH
rawdata was trimmed by trim-galore to cut adaptor and low quality bases  (parameters: --phred33 --stringency 3 --length 40 --quality 20)
Removing the fixed sequence by cutadapt( -g GGGGGGGGGGGGGGGGGGG -a CTGTCTCTTATACACATCT -m 40)
Alignment was performed by bowtie2 with local default parameters to mouse reference genome(mm10)
5hmC sites were called by customed scripts
Assembly: mm10
Supplementary files format and content: Processed bed files contain chromosome, start position, endposition, reference genotype,regular CpG ("0") or 5hmCpG ("1")

source_name: Zygote

extract_protocol:
Single cells were isolated into lysis buffer and then heat for 30min at 75℃. After that, the DNA was treated with protease.
Cells were lysed and treated by protease. Then naked DNA was tagmented by indexed Tn5 at 55 °C for 15 min (Vazyme Biotech).Pool 8 cell lysate into one tube, denature transposons at 72℃. T4 DNA ligase buffer and 1μL Exo I were added and lysate incubate at 37℃ for 60 min.DNA were purified with the 2× AMPure (Beckman) beads with 500ng carrier RNA (thermo).dC-tailing was performed according to previous protocol.Potassium perruthenate (Sigma-Aldrich,334537) solution was prepared according to published protocol.To obtain the 5hmC profiles from the single cells, the 5hmC labeled DNA was subjected to multiple rounds of primer extension to record the 5hmC-to-T transition signal.Primer extension mix (8 µL of 5× KAPA 2G buffer, 0.8 µL of 10 mM dNTPs, 0.8 µL of 10 µM P5G9H primer, 0.6 µL KAPA2G Robust HS DNA polymerase (Roche, KK5023)) was added.Add 8 µL of KAPA HiFi buffer, 2 µL of 500nM P5-short, 2 µL of 500nM P7-short 1.6 µL Kapa HF Hotstart DNA polymerase directly to the linear amplification mixture. PCR was performed to amplify the library for 11-15 cycles.After the PCR reaction, libraries were purified with the 0.8× AMPure beads.

value: Zygote


title: DNA-methylation array data_205814880164_R06C01


title: MT12 [methylation]


title: 41 wpi, replicate 1, VDJ

description: 10x Genomics

value: T-cells


title: Sample 5: wild type, shoot, biol rep 2


title: Tet3cKO_LZ_18

description:
5hmC
Chemical labeled genomic DNA


title: Tet3cKO_LZ_17

description:
5hmC
Chemical labeled genomic DNA


title: Tet3cKO_LZ_15

description:
5hmC
Chemical labeled genomic DNA


title: Tet3cKO_LZ_14

description:
5hmC
Chemical labeled genomic DNA


title: Tet3cKO_LZ_13

description:
5hmC
Chemical labeled genomic DNA


title: Tet3cKO_LZ_11

description:
5hmC
Chemical labeled genomic DNA


title: Tet3cKO_LZ_10

description:
5hmC
Chemical labeled genomic DNA


title: Tet3cKO_LZ_07

description:
5hmC
Chemical labeled genomic DNA


title: Tet3cKO_LZ_08

description:
5hmC
Chemical labeled genomic DNA


title: DNA-methylation array data_205310760115_R06C01


title: MT14 [methylation]


title: Tet3cKO_LZ_01

description:
5hmC
Chemical labeled genomic DNA


title: 6 wpi, replicate 1, gene expression

description: 10x Genomics


title: Tet3cKO_EZ_16

description:
5hmC
Chemical labeled genomic DNA


title: DNA-methylation array data_204081560059_R02C01


title: MT11 [methylation]


title: Tet3cKO_EZ_12

description:
5hmC
Chemical labeled genomic DNA


title: Tet3cKO_EZ_10

description:
5hmC
Chemical labeled genomic DNA


title: Tet3cKO_EZ_09

description:
5hmC
Chemical labeled genomic DNA


title: 6 wpi, replicate 2, gene expression

description: 10x Genomics


title: Tet3cKO_EZ_08

description:
5hmC
Chemical labeled genomic DNA


title: Tet3cKO_EZ_06

description:
5hmC
Chemical labeled genomic DNA


title: Tet3cKO_LZ_03

description:
5hmC
Chemical labeled genomic DNA


title: Tet3cKO_LZ_20

description:
5hmC
Chemical labeled genomic DNA


title: Tet3cKO_EZ_05

description:
5hmC
Chemical labeled genomic DNA


title: Tet3cKO_EZ_04

description:
5hmC
Chemical labeled genomic DNA


title: Tet3cKO_LZ_19

description:
5hmC
Chemical labeled genomic DNA


title: Sample 3: mutant 33210, shoot, biol rep 1

value: mutant 33210


title: Tet3cKO_EZ_02

description:
5hmC
Chemical labeled genomic DNA


title: Tet3cKO_EZ_01

description:
5hmC
Chemical labeled genomic DNA


title: Tet3cKO_2C_35

description:
5hmC
Chemical labeled genomic DNA


title: Tet3cKO_2C_30

description:
5hmC
Chemical labeled genomic DNA


title: Tet3cKO_2C_28

description:
5hmC
Chemical labeled genomic DNA


title: Tet3cKO_2C_27

description:
5hmC
Chemical labeled genomic DNA


title: Tet3cKO_2C_26

description:
5hmC
Chemical labeled genomic DNA


title: Tet3cKO_2C_25

description:
5hmC
Chemical labeled genomic DNA


title: Tet3cKO_LZ_16

description:
5hmC
Chemical labeled genomic DNA


title: Tet3cKO_2C_23

description:
5hmC
Chemical labeled genomic DNA


title: Tet3cKO_2C_29

description:
5hmC
Chemical labeled genomic DNA


title: Tet3cKO_LZ_12

description:
5hmC
Chemical labeled genomic DNA


title: Tet3cKO_LZ_09

description:
5hmC
Chemical labeled genomic DNA


title: Tet3cKO_2C_18

description:
5hmC
Chemical labeled genomic DNA


title: Tet3cKO_2C_13

description:
5hmC
Chemical labeled genomic DNA


title: Tet3cKO_LZ_06

description:
5hmC
Chemical labeled genomic DNA


title: Tet3cKO_LZ_05

description:
5hmC
Chemical labeled genomic DNA


title: Tet3cKO_2C_14

description:
5hmC
Chemical labeled genomic DNA


title: Tet3cKO_LZ_04

description:
5hmC
Chemical labeled genomic DNA


title: Tet3cKO_LZ_02

description:
5hmC
Chemical labeled genomic DNA


title: Tet3cKO_2C_10

description:
5hmC
Chemical labeled genomic DNA


title: Tet3cKO_EZ_17

description:
5hmC
Chemical labeled genomic DNA


title: Tet3cKO_EZ_13

description:
5hmC
Chemical labeled genomic DNA


title: Tet3cKO_EZ_14

description:
5hmC
Chemical labeled genomic DNA


title: Tet3cKO_2C_08

description:
5hmC
Chemical labeled genomic DNA


title: Tet3cKO_EZ_11

description:
5hmC
Chemical labeled genomic DNA


title: Tet3cKO_2C_05

description:
5hmC
Chemical labeled genomic DNA


title: Tet3cKO_2C_09

description:
5hmC
Chemical labeled genomic DNA


title: Tet3cKO_2C_07

description:
5hmC
Chemical labeled genomic DNA


title: Morula_71

description:
5hmC
Chemical labeled genomic DNA

data_processing:
rawdata was trimmed by trim-galore to cut adaptor and low quality bases  (parameters: --phred33 --stringency 3 --length 40 --quality 20)
Removing the fixed sequence by cutadapt( -g GGGGGGGGGGGGGGGGGGG -a CTGTCTCTTATACACATCT -m 40)
Alignment was performed by bowtie2 with local default parameters to mouse reference genome(mm10)
5hmC sites were called by customed scripts
Assembly: mm10
Supplementary files format and content: Processed bed files contain chromosome, start position, endposition, reference genotype,regular CpG ("0") or 5hmCpG ("1")
Library strategy: schmC-CATCH

source_name: Morula

value: Morula

value: C57BL/6J X DBA/2N


title: Morula_69

description:
5hmC
Chemical labeled genomic DNA


title: Morula_67

description:
5hmC
Chemical labeled genomic DNA


title: Tet3cKO_2C_02

description:
5hmC
Chemical labeled genomic DNA


title: Tet3cKO_EZ_03

description:
5hmC
Chemical labeled genomic DNA


title: Tet3cKO_EZ_15

description:
5hmC
Chemical labeled genomic DNA


title: Morula_63

description:
5hmC
Chemical labeled genomic DNA


title: Morula_62

description:
5hmC
Chemical labeled genomic DNA


title: Morula_61

description:
5hmC
Chemical labeled genomic DNA


title: Tet3cKO_2C_34

description:
5hmC
Chemical labeled genomic DNA


title: Tet3cKO_2C_32

description:
5hmC
Chemical labeled genomic DNA


title: Tet3cKO_2C_33

description:
5hmC
Chemical labeled genomic DNA


title: Tet3cKO_EZ_07

description:
5hmC
Chemical labeled genomic DNA


title: Tet3cKO_2C_24

description:
5hmC
Chemical labeled genomic DNA


title: Tet3cKO_2C_22

description:
5hmC
Chemical labeled genomic DNA


title: Tet3cKO_2C_21

description:
5hmC
Chemical labeled genomic DNA


title: Morula_58

description:
5hmC
Chemical labeled genomic DNA


title: Tet3cKO_2C_19

description:
5hmC
Chemical labeled genomic DNA


title: Tet3cKO_2C_31

description:
5hmC
Chemical labeled genomic DNA


title: Tet3cKO_2C_17

description:
5hmC
Chemical labeled genomic DNA


title: Tet3cKO_2C_16

description:
5hmC
Chemical labeled genomic DNA


title: Tet3cKO_2C_15

description:
5hmC
Chemical labeled genomic DNA


title: Morula_57

description:
5hmC
Chemical labeled genomic DNA

value: C57BL/6J X DBA/89N


title: Morula_55

description:
5hmC
Chemical labeled genomic DNA

value: C57BL/6J X DBA/87N


title: Morula_54

description:
5hmC
Chemical labeled genomic DNA

value: C57BL/6J X DBA/86N


title: Morula_51

description:
5hmC
Chemical labeled genomic DNA

value: C57BL/6J X DBA/83N


title: Morula_50

description:
5hmC
Chemical labeled genomic DNA

value: C57BL/6J X DBA/82N


title: Morula_49

description:
5hmC
Chemical labeled genomic DNA

value: C57BL/6J X DBA/81N


title: Tet3cKO_2C_12

description:
5hmC
Chemical labeled genomic DNA


title: Tet3cKO_2C_20

description:
5hmC
Chemical labeled genomic DNA


title: Morula_52

description:
5hmC
Chemical labeled genomic DNA

value: C57BL/6J X DBA/84N


title: Morula_48

description:
5hmC
Chemical labeled genomic DNA

value: C57BL/6J X DBA/80N


title: Morula_47

description:
5hmC
Chemical labeled genomic DNA

value: C57BL/6J X DBA/79N


title: Tet3cKO_2C_11

description:
5hmC
Chemical labeled genomic DNA


title: Morula_45

description:
5hmC
Chemical labeled genomic DNA

value: C57BL/6J X DBA/77N


title: Morula_43

description:
5hmC
Chemical labeled genomic DNA

value: C57BL/6J X DBA/75N


title: Tet3cKO_2C_06

description:
5hmC
Chemical labeled genomic DNA


title: Tet3cKO_2C_04

description:
5hmC
Chemical labeled genomic DNA


title: Morula_42

description:
5hmC
Chemical labeled genomic DNA

value: C57BL/6J X DBA/74N


title: Morula_38

description:
5hmC
Chemical labeled genomic DNA

value: C57BL/6J X DBA/70N


title: Tet3cKO_2C_01

description:
5hmC
Chemical labeled genomic DNA


title: Morula_70

description:
5hmC
Chemical labeled genomic DNA


title: Morula_68

description:
5hmC
Chemical labeled genomic DNA


title: Tet3cKO_2C_03

description:
5hmC
Chemical labeled genomic DNA


title: Morula_32

description:
5hmC
Chemical labeled genomic DNA

value: C57BL/6J X DBA/64N


title: Morula_31

description:
5hmC
Chemical labeled genomic DNA

value: C57BL/6J X DBA/63N


title: Morula_66

description:
5hmC
Chemical labeled genomic DNA

value: Morula


title: Morula_27

description:
5hmC
Chemical labeled genomic DNA

value: C57BL/6J X DBA/59N


title: Morula_26

description:
5hmC
Chemical labeled genomic DNA

value: C57BL/6J X DBA/58N


title: Morula_65

description:
5hmC
Chemical labeled genomic DNA

value: C57BL/6J X DBA/2N


title: Morula_25

description:
5hmC
Chemical labeled genomic DNA

value: C57BL/6J X DBA/57N


title: Morula_37

description:
5hmC
Chemical labeled genomic DNA

value: C57BL/6J X DBA/69N


title: Morula_64

description:
5hmC
Chemical labeled genomic DNA


title: Morula_60

description:
5hmC
Chemical labeled genomic DNA


title: Morula_59

description:
5hmC
Chemical labeled genomic DNA


title: Morula_24

description:
5hmC
Chemical labeled genomic DNA

value: C57BL/6J X DBA/56N


title: Morula_23

description:
5hmC
Chemical labeled genomic DNA

value: C57BL/6J X DBA/55N


title: Morula_56

description:
5hmC
Chemical labeled genomic DNA

value: C57BL/6J X DBA/88N


title: Morula_53

description:
5hmC
Chemical labeled genomic DNA

value: C57BL/6J X DBA/85N


title: Morula_41

description:
5hmC
Chemical labeled genomic DNA

value: C57BL/6J X DBA/73N


title: Morula_40

description:
5hmC
Chemical labeled genomic DNA

value: C57BL/6J X DBA/72N


title: Morula_20

description:
5hmC
Chemical labeled genomic DNA

value: C57BL/6J X DBA/52N


title: Morula_39

description:
5hmC
Chemical labeled genomic DNA

value: C57BL/6J X DBA/71N


title: Morula_18

description:
5hmC
Chemical labeled genomic DNA

value: C57BL/6J X DBA/50N


title: Morula_36

description:
5hmC
Chemical labeled genomic DNA

value: C57BL/6J X DBA/68N


title: Morula_34

description:
5hmC
Chemical labeled genomic DNA

value: C57BL/6J X DBA/66N


title: Morula_46

description:
5hmC
Chemical labeled genomic DNA

value: Morula

value: C57BL/6J X DBA/78N


title: Morula_33

description:
5hmC
Chemical labeled genomic DNA

value: C57BL/6J X DBA/65N


title: Morula_17

description:
5hmC
Chemical labeled genomic DNA

value: C57BL/6J X DBA/49N


title: Morula_44

description:
5hmC
Chemical labeled genomic DNA

value: C57BL/6J X DBA/76N


title: Morula_16

description:
5hmC
Chemical labeled genomic DNA

value: C57BL/6J X DBA/48N


title: Morula_12

description:
5hmC
Chemical labeled genomic DNA

value: C57BL/6J X DBA/44N


title: Morula_30

description:
5hmC
Chemical labeled genomic DNA

value: C57BL/6J X DBA/62N


title: Morula_13

description:
5hmC
Chemical labeled genomic DNA

value: C57BL/6J X DBA/45N


title: Morula_29

description:
5hmC
Chemical labeled genomic DNA

value: C57BL/6J X DBA/61N


title: Morula_10

description:
5hmC
Chemical labeled genomic DNA

value: C57BL/6J X DBA/42N


title: Morula_28

description:
5hmC
Chemical labeled genomic DNA

value: C57BL/6J X DBA/60N


title: Morula_07

description:
5hmC
Chemical labeled genomic DNA

value: C57BL/6J X DBA/39N


title: Morula_05

description:
5hmC
Chemical labeled genomic DNA

value: C57BL/6J X DBA/37N


title: Morula_35

description:
5hmC
Chemical labeled genomic DNA

value: C57BL/6J X DBA/67N


title: Morula_22

description:
5hmC
Chemical labeled genomic DNA

value: C57BL/6J X DBA/54N


title: Morula_02

description:
5hmC
Chemical labeled genomic DNA

value: C57BL/6J X DBA/34N


title: Morula_19

description:
5hmC
Chemical labeled genomic DNA

value: Morula

value: C57BL/6J X DBA/51N


title: Morula_14

description:
5hmC
Chemical labeled genomic DNA

value: C57BL/6J X DBA/46N


title: Morula_21

description:
5hmC
Chemical labeled genomic DNA

value: C57BL/6J X DBA/53N


title: Morula_15

description:
5hmC
Chemical labeled genomic DNA

value: C57BL/6J X DBA/47N


title: Morula_11

description:
5hmC
Chemical labeled genomic DNA

value: C57BL/6J X DBA/43N


title: PN5_04

description:
5hmC
Chemical labeled genomic DNA

value: Zygote

value: C57BL/6J X DBA/29N


title: PN5_02

description:
5hmC
Chemical labeled genomic DNA

value: C57BL/6J X DBA/27N


title: PN5_01

description:
5hmC
Chemical labeled genomic DNA

value: C57BL/6J X DBA/26N


title: PN4_01

description:
5hmC
Chemical labeled genomic DNA

value: C57BL/6J X DBA/21N


title: Morula_09

description:
5hmC
Chemical labeled genomic DNA

value: C57BL/6J X DBA/41N


title: Morula_08

description:
5hmC
Chemical labeled genomic DNA

value: C57BL/6J X DBA/40N


title: PN3_04

description:
5hmC
Chemical labeled genomic DNA

value: C57BL/6J X DBA/20N


title: PN3_02

description:
5hmC
Chemical labeled genomic DNA

value: C57BL/6J X DBA/18N


title: Morula_04

description:
5hmC
Chemical labeled genomic DNA

value: C57BL/6J X DBA/36N


title: Morula_01

description:
5hmC
Chemical labeled genomic DNA

value: C57BL/6J X DBA/33N


title: PN5_07

description:
5hmC
Chemical labeled genomic DNA

value: C57BL/6J X DBA/32N


title: PN5_06

description:
5hmC
Chemical labeled genomic DNA

value: C57BL/6J X DBA/31N


title: Morula_03

description:
5hmC
Chemical labeled genomic DNA

value: Morula

value: C57BL/6J X DBA/35N


title: PN2_04

description:
5hmC
Chemical labeled genomic DNA

value: C57BL/6J X DBA/13N


title: PN2_03

description:
5hmC
Chemical labeled genomic DNA

value: C57BL/6J X DBA/12N


title: PN5_03

description:
5hmC
Chemical labeled genomic DNA

value: Zygote

value: C57BL/6J X DBA/28N


title: PN5_05

description:
5hmC
Chemical labeled genomic DNA

value: C57BL/6J X DBA/30N


title: PN4_05

description:
5hmC
Chemical labeled genomic DNA

value: C57BL/6J X DBA/25N


title: PN4_03

description:
5hmC
Chemical labeled genomic DNA

value: C57BL/6J X DBA/23N


title: PN4_02

description:
5hmC
Chemical labeled genomic DNA

value: C57BL/6J X DBA/22N


title: Morula_06

description:
5hmC
Chemical labeled genomic DNA

value: C57BL/6J X DBA/38N


title: PN1_02

description:
5hmC
Chemical labeled genomic DNA

value: C57BL/6J X DBA/3N


title: PN1_04

description:
5hmC
Chemical labeled genomic DNA

value: C57BL/6J X DBA/5N


title: PN1_01

description:
5hmC
Chemical labeled genomic DNA

value: C57BL/6J X DBA/2N


title: PN4_04

description:
5hmC
Chemical labeled genomic DNA

value: C57BL/6J X DBA/24N


title: Blast_78

description:
5hmC
Chemical labeled genomic DNA

data_processing:
library strategy: schmC-CATCH
rawdata was trimmed by trim-galore to cut adaptor and low quality bases  (parameters: --phred33 --stringency 3 --length 40 --quality 20)
Removing the fixed sequence by cutadapt( -g GGGGGGGGGGGGGGGGGGG -a CTGTCTCTTATACACATCT -m 40)
Alignment was performed by bowtie2 with local default parameters to mouse reference genome(mm10)
5hmC sites were called by customed scripts
Assembly: mm10
Supplementary files format and content: Processed bed files contain chromosome, start position, endposition, reference genotype,regular CpG ("0") or 5hmCpG ("1")

source_name: Blastocyst

value: Blastocyst


title: Blast_79

description:
5hmC
Chemical labeled genomic DNA


title: Blast_77

description:
5hmC
Chemical labeled genomic DNA


title: Blast_74

description:
5hmC
Chemical labeled genomic DNA


title: PN3_03

description:
5hmC
Chemical labeled genomic DNA

value: C57BL/6J X DBA/19N


title: PN3_01

description:
5hmC
Chemical labeled genomic DNA

value: C57BL/6J X DBA/17N


title: Blast_72

description:
5hmC
Chemical labeled genomic DNA


title: Blast_70

description:
5hmC
Chemical labeled genomic DNA


title: PN2_06

description:
5hmC
Chemical labeled genomic DNA

value: C57BL/6J X DBA/15N


title: PN2_05

description:
5hmC
Chemical labeled genomic DNA

value: C57BL/6J X DBA/14N


title: PN2_07

description:
5hmC
Chemical labeled genomic DNA

value: C57BL/6J X DBA/16N


title: Blast_68

description:
5hmC
Chemical labeled genomic DNA


title: Blast_66

description:
5hmC
Chemical labeled genomic DNA


title: PN2_02

description:
5hmC
Chemical labeled genomic DNA

value: Zygote

value: C57BL/6J X DBA/11N


title: Blast_62

description:
5hmC
Chemical labeled genomic DNA


title: PN2_01

description:
5hmC
Chemical labeled genomic DNA

value: C57BL/6J X DBA/10N


title: PN1_08

description:
5hmC
Chemical labeled genomic DNA

value: C57BL/6J X DBA/9N


title: PN1_07

description:
5hmC
Chemical labeled genomic DNA

value: C57BL/6J X DBA/8N


title: Blast_57

description:
5hmC
Chemical labeled genomic DNA


title: PN1_06

description:
5hmC
Chemical labeled genomic DNA

value: C57BL/6J X DBA/7N


title: Blast_71

description:
5hmC
Chemical labeled genomic DNA


title: PN1_05

description:
5hmC
Chemical labeled genomic DNA

value: C57BL/6J X DBA/6N


title: Blast_53

description:
5hmC
Chemical labeled genomic DNA


title: PN1_03

description:
5hmC
Chemical labeled genomic DNA

value: C57BL/6J X DBA/4N


title: Blast_51

description:
5hmC
Chemical labeled genomic DNA


title: Blast_75

description:
5hmC
Chemical labeled genomic DNA


title: Blast_76

description:
5hmC
Chemical labeled genomic DNA


title: Blast_50

description:
5hmC
Chemical labeled genomic DNA


title: Blast_60

description:
5hmC
Chemical labeled genomic DNA


title: Blast_73

description:
5hmC
Chemical labeled genomic DNA


title: Blast_58

description:
5hmC
Chemical labeled genomic DNA


title: Blast_69

description:
5hmC
Chemical labeled genomic DNA


title: Blast_46

description:
5hmC
Chemical labeled genomic DNA


title: Blast_44

description:
5hmC
Chemical labeled genomic DNA


title: Blast_67

description:
5hmC
Chemical labeled genomic DNA


title: Blast_65

description:
5hmC
Chemical labeled genomic DNA


title: Blast_42

description:
5hmC
Chemical labeled genomic DNA


title: Blast_40

description:
5hmC
Chemical labeled genomic DNA


title: Blast_64

description:
5hmC
Chemical labeled genomic DNA


title: Blast_63

description:
5hmC
Chemical labeled genomic DNA


title: Blast_61

description:
5hmC
Chemical labeled genomic DNA


title: Blast_38

description:
5hmC
Chemical labeled genomic DNA


title: Blast_39

description:
5hmC
Chemical labeled genomic DNA


title: Blast_56

description:
5hmC
Chemical labeled genomic DNA


title: Blast_55

description:
5hmC
Chemical labeled genomic DNA


title: Blast_36

description:
5hmC
Chemical labeled genomic DNA


title: Blast_54

description:
5hmC
Chemical labeled genomic DNA


title: Blast_34

description:
5hmC
Chemical labeled genomic DNA


title: Blast_32

description:
5hmC
Chemical labeled genomic DNA


title: Blast_48

description:
5hmC
Chemical labeled genomic DNA


title: Blast_52

description:
5hmC
Chemical labeled genomic DNA


title: Blast_59

description:
5hmC
Chemical labeled genomic DNA


title: Blast_28

description:
5hmC
Chemical labeled genomic DNA


title: Blast_47

description:
5hmC
Chemical labeled genomic DNA


title: Blast_45

description:
5hmC
Chemical labeled genomic DNA


title: Blast_25

description:
5hmC
Chemical labeled genomic DNA


title: Blast_41

description:
5hmC
Chemical labeled genomic DNA


title: Blast_43

description:
5hmC
Chemical labeled genomic DNA


title: Blast_22

description:
5hmC
Chemical labeled genomic DNA


title: Blast_20

description:
5hmC
Chemical labeled genomic DNA


title: Blast_17

description:
5hmC
Chemical labeled genomic DNA


title: Blast_37

description:
5hmC
Chemical labeled genomic DNA


title: Blast_35

description:
5hmC
Chemical labeled genomic DNA


title: Blast_31

description:
5hmC
Chemical labeled genomic DNA


title: Blast_30

description:
5hmC
Chemical labeled genomic DNA


title: Blast_33

description:
5hmC
Chemical labeled genomic DNA


title: Blast_29

description:
5hmC
Chemical labeled genomic DNA


title: Blast_12

description:
5hmC
Chemical labeled genomic DNA


title: Blast_10

description:
5hmC
Chemical labeled genomic DNA


title: Blast_27

description:
5hmC
Chemical labeled genomic DNA


title: Blast_26

description:
5hmC
Chemical labeled genomic DNA


title: Blast_21

description:
5hmC
Chemical labeled genomic DNA


title: Blast_19

description:
5hmC
Chemical labeled genomic DNA


title: Blast_18

description:
5hmC
Chemical labeled genomic DNA


title: Blast_06

description:
5hmC
Chemical labeled genomic DNA


title: Blast_07

description:
5hmC
Chemical labeled genomic DNA


title: Blast_23

description:
5hmC
Chemical labeled genomic DNA


title: Blast_08

description:
5hmC
Chemical labeled genomic DNA


title: Blast_16

description:
5hmC
Chemical labeled genomic DNA


title: Blast_14

description:
5hmC
Chemical labeled genomic DNA


title: Blast_24

description:
5hmC
Chemical labeled genomic DNA


title: Blast_15

description:
5hmC
Chemical labeled genomic DNA


title: Blast_05

description:
5hmC
Chemical labeled genomic DNA


title: Blast_02

description:
5hmC
Chemical labeled genomic DNA


title: Blast_11

description:
5hmC
Chemical labeled genomic DNA


title: Blast_03

description:
5hmC
Chemical labeled genomic DNA


title: Blast_09

description:
5hmC
Chemical labeled genomic DNA


title: Blast_01

description:
5hmC
Chemical labeled genomic DNA


title: 8C_59

description:
5hmC
Chemical labeled genomic DNA


title: 8C_60

description:
5hmC
Chemical labeled genomic DNA


title: 8C_56

description:
5hmC
Chemical labeled genomic DNA


title: 8C_58

description:
5hmC
Chemical labeled genomic DNA


title: Blast_04

description:
5hmC
Chemical labeled genomic DNA


title: Blast_13

description:
5hmC
Chemical labeled genomic DNA


title: 8C_57

description:
5hmC
Chemical labeled genomic DNA


title: 8C_55

description:
5hmC
Chemical labeled genomic DNA


title: 8C_54

description:
5hmC
Chemical labeled genomic DNA


title: 8C_53

description:
5hmC
Chemical labeled genomic DNA


title: 8C_52

description:
5hmC
Chemical labeled genomic DNA


title: 8C_50

description:
5hmC
Chemical labeled genomic DNA


title: 8C_51

description:
5hmC
Chemical labeled genomic DNA


title: 8C_46

description:
5hmC
Chemical labeled genomic DNA


title: 8C_45

description:
5hmC
Chemical labeled genomic DNA


title: 8C_44

description:
5hmC
Chemical labeled genomic DNA


title: 8C_43

description:
5hmC
Chemical labeled genomic DNA


title: 8C_39

description:
5hmC
Chemical labeled genomic DNA


title: 8C_49

description:
5hmC
Chemical labeled genomic DNA


title: 8C_48

description:
5hmC
Chemical labeled genomic DNA


title: 8C_42

description:
5hmC
Chemical labeled genomic DNA


title: 8C_41

description:
5hmC
Chemical labeled genomic DNA


title: 8C_38

description:
5hmC
Chemical labeled genomic DNA


title: 8C_36

description:
5hmC
Chemical labeled genomic DNA


title: 8C_37

description:
5hmC
Chemical labeled genomic DNA


title: 8C_40

description:
5hmC
Chemical labeled genomic DNA


title: 8C_35

description:
5hmC
Chemical labeled genomic DNA


title: 8C_34

description:
5hmC
Chemical labeled genomic DNA


title: 8C_33

description:
5hmC
Chemical labeled genomic DNA


title: 8C_30

description:
5hmC
Chemical labeled genomic DNA


title: 8C_32

description:
5hmC
Chemical labeled genomic DNA


title: 8C_47

description:
5hmC
Chemical labeled genomic DNA


title: 8C_31

description:
5hmC
Chemical labeled genomic DNA


title: 8C_18

description:
5hmC
Chemical labeled genomic DNA


title: 8C_17

description:
5hmC
Chemical labeled genomic DNA


title: 8C_21

description:
5hmC
Chemical labeled genomic DNA


title: 8C_13

description:
5hmC
Chemical labeled genomic DNA


title: 8C_20

description:
5hmC
Chemical labeled genomic DNA


title: 8C_16

description:
5hmC
Chemical labeled genomic DNA


title: 8C_12

description:
5hmC
Chemical labeled genomic DNA


title: 8C_10

description:
5hmC
Chemical labeled genomic DNA


title: 8C_11

description:
5hmC
Chemical labeled genomic DNA


title: 8C_08

description:
5hmC
Chemical labeled genomic DNA


title: 8C_09

description:
5hmC
Chemical labeled genomic DNA


title: 8C_07

description:
5hmC
Chemical labeled genomic DNA


title: 8C_03

description:
5hmC
Chemical labeled genomic DNA


title: 4C_41

description:
5hmC
Chemical labeled genomic DNA


title: 8C_15

description:
5hmC
Chemical labeled genomic DNA


title: 8C_06

description:
5hmC
Chemical labeled genomic DNA


title: 8C_05

description:
5hmC
Chemical labeled genomic DNA


title: 8C_04

description:
5hmC
Chemical labeled genomic DNA


title: 8C_02

description:
5hmC
Chemical labeled genomic DNA


title: 4C_40

description:
5hmC
Chemical labeled genomic DNA


title: 4C_39

description:
5hmC
Chemical labeled genomic DNA


title: 4C_35

description:
5hmC
Chemical labeled genomic DNA


title: 8C_01

description:
5hmC
Chemical labeled genomic DNA


title: 4C_37

description:
5hmC
Chemical labeled genomic DNA


title: 8C_19

description:
5hmC
Chemical labeled genomic DNA


title: 4C_38

description:
5hmC
Chemical labeled genomic DNA


title: 4C_34

description:
5hmC
Chemical labeled genomic DNA


title: 8C_14

description:
5hmC
Chemical labeled genomic DNA


title: 4C_28

description:
5hmC
Chemical labeled genomic DNA


title: 4C_33

description:
5hmC
Chemical labeled genomic DNA


title: 4C_30

description:
5hmC
Chemical labeled genomic DNA


title: 4C_36

description:
5hmC
Chemical labeled genomic DNA


title: 4C_29

description:
5hmC
Chemical labeled genomic DNA


title: 4C_31

description:
5hmC
Chemical labeled genomic DNA


title: 4C_27

description:
5hmC
Chemical labeled genomic DNA


title: 4C_26

description:
5hmC
Chemical labeled genomic DNA


title: 4C_20

description:
5hmC
Chemical labeled genomic DNA


title: 4C_25

description:
5hmC
Chemical labeled genomic DNA


title: 4C_19

description:
5hmC
Chemical labeled genomic DNA


title: 4C_17

description:
5hmC
Chemical labeled genomic DNA


title: 4C_16

description:
5hmC
Chemical labeled genomic DNA


title: 4C_32

description:
5hmC
Chemical labeled genomic DNA


title: 4C_13

description:
5hmC
Chemical labeled genomic DNA


title: 4C_12

description:
5hmC
Chemical labeled genomic DNA


title: 4C_24

description:
5hmC
Chemical labeled genomic DNA


title: 4C_23

description:
5hmC
Chemical labeled genomic DNA


title: 4C_11

description:
5hmC
Chemical labeled genomic DNA


title: 4C_14

description:
5hmC
Chemical labeled genomic DNA


title: 4C_15

description:
5hmC
Chemical labeled genomic DNA


title: 4C_09

description:
5hmC
Chemical labeled genomic DNA


title: 4C_10

description:
5hmC
Chemical labeled genomic DNA


title: Blast_49

description:
5hmC
Chemical labeled genomic DNA


title: 4C_07

description:
5hmC
Chemical labeled genomic DNA


title: 4C_04

description:
5hmC
Chemical labeled genomic DNA


title: 4C_02

description:
5hmC
Chemical labeled genomic DNA


title: 4C_22

description:
5hmC
Chemical labeled genomic DNA


title: 4C_06

description:
5hmC
Chemical labeled genomic DNA


title: 4C_05

description:
5hmC
Chemical labeled genomic DNA


title: 4C_21

description:
5hmC
Chemical labeled genomic DNA


title: 2C_84

description:
5hmC
Chemical labeled genomic DNA


title: 2C_85

description:
5hmC
Chemical labeled genomic DNA


title: 4C_01

description:
5hmC
Chemical labeled genomic DNA


title: 2C_83

description:
5hmC
Chemical labeled genomic DNA


title: 4C_18

description:
5hmC
Chemical labeled genomic DNA


title: 2C_79

description:
5hmC
Chemical labeled genomic DNA


title: 2C_82

description:
5hmC
Chemical labeled genomic DNA


title: 2C_86

description:
5hmC
Chemical labeled genomic DNA


title: 4C_03

description:
5hmC
Chemical labeled genomic DNA


title: 2C_81

description:
5hmC
Chemical labeled genomic DNA


title: 2C_76

description:
5hmC
Chemical labeled genomic DNA


title: 2C_73

description:
5hmC
Chemical labeled genomic DNA


title: 2C_78

description:
5hmC
Chemical labeled genomic DNA


title: 2C_72

description:
5hmC
Chemical labeled genomic DNA


title: 2C_75

description:
5hmC
Chemical labeled genomic DNA


title: 2C_80

description:
5hmC
Chemical labeled genomic DNA


title: 4C_08

description:
5hmC
Chemical labeled genomic DNA


title: 2C_70

description:
5hmC
Chemical labeled genomic DNA


title: 2C_69

description:
5hmC
Chemical labeled genomic DNA


title: 2C_68

description:
5hmC
Chemical labeled genomic DNA


title: 2C_77

description:
5hmC
Chemical labeled genomic DNA


title: 2C_66

description:
5hmC
Chemical labeled genomic DNA


title: 2C_67

description:
5hmC
Chemical labeled genomic DNA


title: 2C_65

description:
5hmC
Chemical labeled genomic DNA


title: 2C_63

description:
5hmC
Chemical labeled genomic DNA


title: 2C_64

description:
5hmC
Chemical labeled genomic DNA


title: 2C_74

description:
5hmC
Chemical labeled genomic DNA


title: 2C_62

description:
5hmC
Chemical labeled genomic DNA


title: 2C_52

description:
5hmC
Chemical labeled genomic DNA


title: 2C_53

description:
5hmC
Chemical labeled genomic DNA


title: 2C_51

description:
5hmC
Chemical labeled genomic DNA


title: 2C_71

description:
5hmC
Chemical labeled genomic DNA


title: 2C_50

description:
5hmC
Chemical labeled genomic DNA


title: 2C_49

description:
5hmC
Chemical labeled genomic DNA


title: 2C_48

description:
5hmC
Chemical labeled genomic DNA


title: 2C_44

description:
5hmC
Chemical labeled genomic DNA


title: 2C_45

description:
5hmC
Chemical labeled genomic DNA


title: 2C_43

description:
5hmC
Chemical labeled genomic DNA


title: 2C_42

description:
5hmC
Chemical labeled genomic DNA


title: 2C_47

description:
5hmC
Chemical labeled genomic DNA


title: 2C_41

description:
5hmC
Chemical labeled genomic DNA


title: 2C_40

description:
5hmC
Chemical labeled genomic DNA


title: 2C_38

description:
5hmC
Chemical labeled genomic DNA


title: 2C_37

description:
5hmC
Chemical labeled genomic DNA


title: 2C_39

description:
5hmC
Chemical labeled genomic DNA


title: 2C_36

description:
5hmC
Chemical labeled genomic DNA


title: 2C_35

description:
5hmC
Chemical labeled genomic DNA


title: 2C_34

description:
5hmC
Chemical labeled genomic DNA


title: 2C_31

description:
5hmC
Chemical labeled genomic DNA


title: 2C_29

description:
5hmC
Chemical labeled genomic DNA


title: 2C_27

description:
5hmC
Chemical labeled genomic DNA


title: 2C_30

description:
5hmC
Chemical labeled genomic DNA


title: 2C_28

description:
5hmC
Chemical labeled genomic DNA


title: 2C_26

description:
5hmC
Chemical labeled genomic DNA


title: 2C_32

description:
5hmC
Chemical labeled genomic DNA


title: 2C_25

description:
5hmC
Chemical labeled genomic DNA


title: 2C_46

description:
5hmC
Chemical labeled genomic DNA


title: 2C_23

description:
5hmC
Chemical labeled genomic DNA


title: 2C_33

description:
5hmC
Chemical labeled genomic DNA


title: 2C_21

description:
5hmC
Chemical labeled genomic DNA


title: 2C_20

description:
5hmC
Chemical labeled genomic DNA


title: 2C_18

description:
5hmC
Chemical labeled genomic DNA


title: 2C_17

description:
5hmC
Chemical labeled genomic DNA


title: 2C_16

description:
5hmC
Chemical labeled genomic DNA


title: 2C_15

description:
5hmC
Chemical labeled genomic DNA


title: 2C_11

description:
5hmC
Chemical labeled genomic DNA


title: 2C_14

description:
5hmC
Chemical labeled genomic DNA


title: 2C_09

description:
5hmC
Chemical labeled genomic DNA


title: 2C_13

description:
5hmC
Chemical labeled genomic DNA


title: 2C_10

description:
5hmC
Chemical labeled genomic DNA


title: 2C_07

description:
5hmC
Chemical labeled genomic DNA


title: 2C_05

description:
5hmC
Chemical labeled genomic DNA


title: 2C_04

description:
5hmC
Chemical labeled genomic DNA


title: 2C_02

description:
5hmC
Chemical labeled genomic DNA


title: Oocyte_40

description:
5hmC
Chemical labeled genomic DNA

source_name: Oocyte

value: Oocyte


title: 2C_24

description:
5hmC
Chemical labeled genomic DNA

value: C57BL/6J X DBA/2N


title: Oocyte_39

description:
5hmC
Chemical labeled genomic DNA


title: 2C_06

description:
5hmC
Chemical labeled genomic DNA


title: 2C_22

description:
5hmC
Chemical labeled genomic DNA


title: Oocyte_37

description:
5hmC
Chemical labeled genomic DNA


title: Oocyte_34

description:
5hmC
Chemical labeled genomic DNA


title: 2C_01

description:
5hmC
Chemical labeled genomic DNA


title: Oocyte_33

description:
5hmC
Chemical labeled genomic DNA


title: 2C_19

description:
5hmC
Chemical labeled genomic DNA


title: Oocyte_32

description:
5hmC
Chemical labeled genomic DNA


title: Oocyte_36

description:
5hmC
Chemical labeled genomic DNA


title: Oocyte_35

description:
5hmC
Chemical labeled genomic DNA


title: 2C_12

description:
5hmC
Chemical labeled genomic DNA


title: Oocyte_29

description:
5hmC
Chemical labeled genomic DNA


title: 2C_08

description:
5hmC
Chemical labeled genomic DNA


title: Oocyte_31

description:
5hmC
Chemical labeled genomic DNA


title: Oocyte_26

description:
5hmC
Chemical labeled genomic DNA


title: Oocyte_25

description:
5hmC
Chemical labeled genomic DNA


title: Oocyte_27

description:
5hmC
Chemical labeled genomic DNA


title: Oocyte_30

description:
5hmC
Chemical labeled genomic DNA


title: Oocyte_22

description:
5hmC
Chemical labeled genomic DNA


title: Oocyte_28

description:
5hmC
Chemical labeled genomic DNA


title: Oocyte_23

description:
5hmC
Chemical labeled genomic DNA


title: 2C_03

description:
5hmC
Chemical labeled genomic DNA


title: Oocyte_21

description:
5hmC
Chemical labeled genomic DNA


title: Oocyte_38

description:
5hmC
Chemical labeled genomic DNA


title: Oocyte_19

description:
5hmC
Chemical labeled genomic DNA


title: Oocyte_18

description:
5hmC
Chemical labeled genomic DNA


title: Oocyte_16

description:
5hmC
Chemical labeled genomic DNA


title: Oocyte_17

description:
5hmC
Chemical labeled genomic DNA


title: Oocyte_15

description:
5hmC
Chemical labeled genomic DNA


title: Oocyte_14

description:
5hmC
Chemical labeled genomic DNA


title: Oocyte_12

description:
5hmC
Chemical labeled genomic DNA


title: Oocyte_13

description:
5hmC
Chemical labeled genomic DNA


title: Oocyte_06

description:
5hmC
Chemical labeled genomic DNA


title: Oocyte_24

description:
5hmC
Chemical labeled genomic DNA


title: Oocyte_11

description:
5hmC
Chemical labeled genomic DNA


title: Oocyte_10

description:
5hmC
Chemical labeled genomic DNA


title: Oocyte_08

description:
5hmC
Chemical labeled genomic DNA


title: Oocyte_09

description:
5hmC
Chemical labeled genomic DNA


title: Oocyte_04

description:
5hmC
Chemical labeled genomic DNA


title: Oocyte_05

description:
5hmC
Chemical labeled genomic DNA


title: Oocyte_03

description:
5hmC
Chemical labeled genomic DNA


title: Sperm_48

description:
5hmC
Chemical labeled genomic DNA

source_name: Sperm

value: Sperm


title: Sperm_44

description:
5hmC
Chemical labeled genomic DNA


title: Sperm_47

description:
5hmC
Chemical labeled genomic DNA


title: Oocyte_02

description:
5hmC
Chemical labeled genomic DNA


title: Oocyte_07

description:
5hmC
Chemical labeled genomic DNA


title: Oocyte_01

description:
5hmC
Chemical labeled genomic DNA


title: Sperm_46

description:
5hmC
Chemical labeled genomic DNA


title: Sperm_41

description:
5hmC
Chemical labeled genomic DNA


title: Sperm_43

description:
5hmC
Chemical labeled genomic DNA


title: Oocyte_20

description:
5hmC
Chemical labeled genomic DNA


title: Sperm_40

description:
5hmC
Chemical labeled genomic DNA


title: Sperm_39

description:
5hmC
Chemical labeled genomic DNA


title: Sperm_37

description:
5hmC
Chemical labeled genomic DNA


title: Sperm_38

description:
5hmC
Chemical labeled genomic DNA


title: Sperm_36

description:
5hmC
Chemical labeled genomic DNA


title: Sperm_45

description:
5hmC
Chemical labeled genomic DNA


title: Sperm_34

description:
5hmC
Chemical labeled genomic DNA


title: Sperm_35

description:
5hmC
Chemical labeled genomic DNA


title: Sperm_33

description:
5hmC
Chemical labeled genomic DNA


title: Sperm_32

description:
5hmC
Chemical labeled genomic DNA


title: Sperm_31

description:
5hmC
Chemical labeled genomic DNA


title: Sperm_29

description:
5hmC
Chemical labeled genomic DNA


title: Sperm_30

description:
5hmC
Chemical labeled genomic DNA


title: Sperm_28

description:
5hmC
Chemical labeled genomic DNA


title: Sperm_24

description:
5hmC
Chemical labeled genomic DNA


title: Sperm_26

description:
5hmC
Chemical labeled genomic DNA


title: Sperm_25

description:
5hmC
Chemical labeled genomic DNA


title: Sperm_21

description:
5hmC
Chemical labeled genomic DNA


title: Sperm_27

description:
5hmC
Chemical labeled genomic DNA


title: Sperm_22

description:
5hmC
Chemical labeled genomic DNA


title: Sperm_16

description:
5hmC
Chemical labeled genomic DNA


title: Sperm_19

description:
5hmC
Chemical labeled genomic DNA


title: Sperm_23

description:
5hmC
Chemical labeled genomic DNA


title: Sperm_17

description:
5hmC
Chemical labeled genomic DNA


title: Sperm_42

description:
5hmC
Chemical labeled genomic DNA


title: Sperm_18

description:
5hmC
Chemical labeled genomic DNA


title: Sperm_20

description:
5hmC
Chemical labeled genomic DNA


title: Sperm_13

description:
5hmC
Chemical labeled genomic DNA


title: Sperm_12

description:
5hmC
Chemical labeled genomic DNA


title: Sperm_10

description:
5hmC
Chemical labeled genomic DNA


title: Sperm_11

description:
5hmC
Chemical labeled genomic DNA


title: Sperm_09

description:
5hmC
Chemical labeled genomic DNA


title: Sperm_08

description:
5hmC
Chemical labeled genomic DNA


title: Sperm_06

description:
5hmC
Chemical labeled genomic DNA


title: Sperm_07

description:
5hmC
Chemical labeled genomic DNA


title: Sperm_05

description:
5hmC
Chemical labeled genomic DNA


title: Sperm_04

description:
5hmC
Chemical labeled genomic DNA

data_processing:
rawdata was trimmed by trim-galore to cut adaptor and low quality bases  (parameters: --phred33 --stringency 3 --length 40 --quality 20)
Removing the fixed sequence by cutadapt( -g GGGGGGGGGGGGGGGGGGG -a CTGTCTCTTATACACATCT -m 40)
Alignment was performed by bowtie2 with local default parameters to mouse reference genome(mm10)
5hmC sites were called by customed scripts
Assembly: mm10
Supplementary files format and content: Processed bed files contain chromosome, start position, endposition, reference genotype,regular CpG ("0") or 5hmCpG ("1")

extract_protocol:
Single cells were isolated into lysis buffer and then heat for 30min at 75℃. After that, the DNA was treated with protease.
Cells were lysed and treated by protease. Then naked DNA was tagmented by indexed Tn5 at 55 °C for 15 min (Vazyme Biotech).Pool 8 cell lysate into one tube, denature transposons at 72℃. T4 DNA ligase buffer and 1μL Exo I were added and lysate incubate at 37℃ for 60 min.DNA were purified with the 2× AMPure (Beckman) beads with 500ng carrier RNA (thermo).dC-tailing was performed according to previous protocol.Potassium perruthenate (Sigma-Aldrich,334537) solution was prepared according to published protocol.To obtain the 5hmC profiles from the single cells, the 5hmC labeled DNA was subjected to multiple rounds of primer extension to record the 5hmC-to-T transition signal.Primer extension mix (8 µL of 5× KAPA 2G buffer, 0.8 µL of 10 mM dNTPs, 0.8 µL of 10 µM P5G9H primer, 0.6 µL KAPA2G Robust HS DNA polymerase (Roche, KK5023)) was added.Add 8 µL of KAPA HiFi buffer, 2 µL of 500nM P5-short, 2 µL of 500nM P7-short 1.6 µL Kapa HF Hotstart DNA polymerase directly to the linear amplification mixture. PCR was performed to amplify the library for 11-15 cycles.After the PCR reaction, libraries were purified with the 0.8× AMPure beads.
schmC-CATCH


type: RNA

city: Krakow

first: Magdalena

last: Rutkowska-Zapala

address: Wielicka 265

institute: Jagiellonian University Medical College

description:
Human Treg cells from Patient 9 from healthy controls group
H_9_(Clariom_D_Human)

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing:
The Transcriptome Analysis Console (TAC) Software (Affymetrix) was used to analyze raw data for quality, expression patterns of genes, exons and pathways.
The input material used for microarray assays was 50 ng of total RNA. Samples for array hybridization were processed with GeneChip WT PLUS Reagent Kit and GeneChip 3000 instrument system (Affymetrix) in line of protocol. The Transcriptome Analysis Console (TAC) Software (Affymetrix) was used to analyze raw data for quality, expression patterns of genes, exons, lncRNA, and pathways. Gene advanced Robust Multiarray Analysis method with Signal Space Transformation (SST-RMA) summarization was performed by TAC (version 4.0.2.15 for Windows, Waltham, Massachusetts, USA, www.thermofisher.com). The quality of the experiment was assessed based on the values of Pos versus Neg AUC, intensity distribution plots, foreground-to-background plots, MA-plots, and 2D-intensity plots and principal component analysis (PCA).
affymetrix-algorithm-name=gc-correction,scale-intensities,rma-bg,quant-norm.sketch=0.usepm=true.bioc=true,pm-only,med-polish
affymetrix-algorithm-version=1

label: biotin

source_name: Patient 9 from healthy controls group

extract_protocol: the total RNA was extracted from Treg cells samples using RNeasy Micro Kit (Qiagen, Germany) according to the manufacturer’s protocol.

value: Treg cells

value: female

tag: group

value: healthy controls group


title: Sperm_02

description:
5hmC
Chemical labeled genomic DNA


description:
Human Treg cells from Patient 7 from healthy controls group
H_7_(Clariom_D_Human)

hyb_protocol: Samples for array hybridization were processed with GeneChip WT PLUS Reagent Kit and GeneChip 3000 instrument system (Affymetrix) in line of protocol.

source_name: Patient 7 from healthy controls group

value: male


description:
Human Treg cells from Patient 11 from healthy controls group
H_11_(Clariom_D_Human)

source_name: Patient 11 from healthy controls group

label_protocol: Samples for array hybridization were processed with GeneChip WT PLUS Reagent Kit and GeneChip 3000 instrument system (Affymetrix) in line of protocol.


description:
Human Treg cells from Patient 8 from healthy controls group
H_8_(Clariom_D_Human)

source_name: Patient 8 from healthy controls group


description:
Human Treg cells from Patient 10 from healthy controls group
H_10_(Clariom_D_Human)

source_name: Patient 10 from healthy controls group


description:
Human Treg cells from Patient 6 from healthy controls group
H_6_(Clariom_D_Human)

source_name: Patient 6 from healthy controls group


description:
Human Treg cells from Patient 5 from healthy controls group
H_5_(Clariom_D_Human)

source_name: Patient 5 from healthy controls group


description:
Human Treg cells from Patient 3 from healthy controls group
H_3_(Clariom_D_Human)

source_name: Patient 3 from healthy controls group


description:
Human Treg cells from Patient 2 from healthy controls group
H_2_(Clariom_D_Human)

source_name: Patient 2 from healthy controls group


description:
Human Treg cells from Patient 12 from SIgAD group
S_12_(Clariom_D_Human)

source_name: Patient 12 from SIgAD group

value: SIgAD group


description:
Human Treg cells from Patient 1 from healthy controls group
H_1_(Clariom_D_Human)

source_name: Patient 1 from healthy controls group


description:
Human Treg cells from Patient 11 with autoimmune disease from SIgAD group
S_11_a_(Clariom_D_Human)


description:
Human Treg cells from Patient 4 from healthy controls group
H_4_(Clariom_D_Human)

source_name: Patient 4 from healthy controls group


title: Sperm_15

description:
5hmC
Chemical labeled genomic DNA


description:
Human Treg cells from Patient 10 with autoimmune disease from SIgAD group
S_10_a_(Clariom_D_Human)


description:
Human Treg cells from Patient 13 from SIgAD group
S_13_(Clariom_D_Human)

source_name: Patient 13 from SIgAD group


title: Sperm_14

description:
5hmC
Chemical labeled genomic DNA


description:
Human Treg cells from Patient 7 from SIgAD group
S_7_(Clariom_D_Human)

source_name: Patient 7 from SIgAD group


description:
Human Treg cells from Patient 9 with autoimmune disease fromSIgAD group
S_9_a_(Clariom_D_Human)

value: Patient with autoimmune disease fromSIgAD group


description:
Human Treg cells from Patient 5 from SIgAD group
S_5_(Clariom_D_Human)

source_name: Patient 5 from SIgAD group


description:
Human Treg cells from Patient 8 from SIgAD group
S_8_(Clariom_D_Human)

source_name: Patient 8 from SIgAD group


description:
Human Treg cells from Patient 4 from SIgAD group
S_4_(Clariom_D_Human)

source_name: Patient 4 from SIgAD group


description:
Human Treg cells from Patient 6 fromSIgAD group
S_6_(Clariom_D_Human)

source_name: Patient 6 fromSIgAD group


description:
Human Treg cells from Patient 3 from SIgAD group
S_3_(Clariom_D_Human)

source_name: Patient 3 from SIgAD group


description:
Human Treg cells from Patient 13 from CVID group
C_13_(Clariom_D_Human)

source_name: Patient 13 from CVID group

value: CVID group


description:
Human Treg cells from Patient 2 from SIgAD group
S_2_(Clariom_D_Human)

source_name: Patient 2 from SIgAD group


description:
Human Treg cells from Patient 1 from SIgAD group
S_1_(Clariom_D_Human)

source_name: Patient 1 from SIgAD group


title: Sperm_01

description:
5hmC
Chemical labeled genomic DNA

source_name: Sperm


title: Sperm_03

description:
5hmC
Chemical labeled genomic DNA


description:
Human Treg cells from Patient 12 from CVID group
C_12_(Clariom_D_Human)

source_name: Patient 12 from CVID group


description:
Human Treg cells from Patient 11 from CVID group
C_11_(Clariom_D_Human)

source_name: Patient 11 from CVID group


description:
Human Treg cells from Patient 7 from CVID group
C_7_(Clariom_D_Human)

source_name: Patient 7 from CVID group


description:
Human Treg cells from Patient 10 from CVID group
C_10_(Clariom_D_Human)

source_name: Patient 10 from CVID group


description:
Human Treg cells from Patient 8 from CVID group
C_8_(Clariom_D_Human)

source_name: Patient 8 from CVID group


description:
Human Treg cells from Patient 9 from CVID group
C_9_(Clariom_D_Human)

source_name: Patient 9 from CVID group


description:
Human Treg cells from Patient 6 with autoimmune disease from CVID group
C_6_a_(Clariom_D_Human)


description:
Human Treg cells from Patient 5 with autoimmune disease from CVID group
C_5_a_(Clariom_D_Human)


description:
Human Treg cells from Patient 3 from CVID group
C_3_(Clariom_D_Human)

source_name: Patient 3 from CVID group


description:
Human Treg cells from Patient 2 from CVID group
C_2_(Clariom_D_Human)

source_name: Patient 2 from CVID group


description:
Human Treg cells from Patient 1 with autoimmune disease from CVID group
C_1_a_(Clariom_D_Human)

value: patient with autoimmune disease from CVID group


description:
Human Treg cells from Patient 4 from CVID group
C_4_(Clariom_D_Human)

source_name: Patient 4 from CVID group


title: Spleen, Glutoborin

first: Weixuan

last: Wang

address: No. 38 Xueyuan Road, Haidian District

description:
Library name: Glutoborin
10x Genomics

data_processing:
The Cell ranger software pipeline (version 6.0.1) provided by 10xGenomics was used to demultiplex cellular barcodes,map reads to the transcriptome, control quality and generate quantitative matrix.
The R package Seurat (version 4.3.0) was used for generation of Seurat object.
The count matrix was normalized with NormalizeData function.
tSNE and UMAP were performed by R package Seurat (version 4.3.0).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Spleen

extract_protocol:
Single cells were mixed with Gel Beads, Partitioning Oil and glycerol, using for preparation of GEMs with ChromiumTM Next GEM Chip G Single Cell Kit. The GEMs were subjected to RT-PCR, and the products were purified with Dynabeads, followed by cDNA amplification.
RNA libraries were prepared with ChromiumTM Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1 according to the manufacturer's protocol.

treatment_protocol: Mice were intraperitoneally injected with 1 × 10^⁴ iRBCs, and on days 2 and 4 post-infection Vehicle and Glutoborin were administered. On day 5 post-infection spleens from both group were collected to isolate lymphocytes. CD45+ cells were then sorted by flow cytometry for subsequent single-cell sequencing analysis.

value: Spleen

value: WT

value: infection of 1 x 10^4 iRBCs for 5 days, treated with Glutoborin on days 2 and 4


title: Spleen, Vehicle

description:
Library name: Vehicle
10x Genomics

value: infection of 1 x 10^4 iRBCs for 5 days, treated with Vehicle on days 2 and 4


title: KO_2C_2b_b2

city: London

first: Louise

last: Walport

address: 82 Wood Lane

country: United Kingdom

institute: Imperial College London

description: Library name: WIL4940A86_S709_L004

data_processing:
Fastq files were mapped to the GRCm38 genome and converted to gene count files using Nextflow nf-core/rnaseq pipeline (https://nf-co.re/rnaseq/3.11.2/, version 3.11.2) with parameters: aligner = star_rsem, genome = mm10.
Assembly: GRCm38
Supplementary files format and content: rsem.merged.gene_counts.csv (processed gene counts file outputted from Next-flow/rna-seq, csv format).

source_name: 2-cell Blastomere

extract_protocol:
MII oocytes, zygotes and 2-cell embryo blastomeres were dispensed into 12.5 µL CDS sorting solution from the Takara Smart-SeqHT kit (TakaraBio, #634439) and stored at -80 °C.
Sequencing libraries were prepared using the Takara Smart-SeqHT Kit (Takara Bio, #634439) according to the manufacturer’s instructions. Briefly, cells were lysed and polyadenylated RNA captured in a total volume of 12.5 µL. One-Step first strand synthesis and double stranded cDNA amplification were carried out with 18 PCR cycles. Amplified cDNA was purified via a SPRISelect (Beckman Coulter, #B23317) 1X bead clean-up and eluted in 15 µL Elution Buffer. Nextera Dual Index libraries were prepared with the Nextera XT kit (Illumina, #FC-131-1096). Purified cDNA was normalised to 0.2 ng/µL input and tagmentation was carried out by adding 2.5 µL Tagment DNA Buffer + 1.25 µL Amplicon Tagment mix to 1.25 µL cDNA. The tagmentation reaction was run for 10 min at 55 oC. A final index PCR was performed after adding 2.5 µL Nextera compatible dual indices (at 10 µM) + 3.75 µL NPM PCR Mix. Amplified libraries were purified via a SPRIselect (Beckman Coulter, #B23317) 0.9X bead clean-up. The quality and fragment size distributions of the purified libraries was assessed by a 4200 TapeStation Instrument (Agilent).

value: 2-cell Blastomere


title: KO_2C_2c_b1

description: Library name: WIL4940A87_S710_L004


title: KO_2C_2b_b1

description: Library name: WIL4940A85_S708_L004


title: KO_2C_2c_b2

description: Library name: WIL4940A88_S711_L004


title: C663A_2C_2c_b2

description: Library name: WIL4940A82_S705_L004


title: KO_2C_2a_b1

description: Library name: WIL4940A83_S706_L004


title: C663A_2C_2c_b1

description: Library name: WIL4940A81_S704_L004


title: KO_2C_2a_b2

description: Library name: WIL4940A84_S707_L004


title: C663A_2C_2b_b2

description: Library name: WIL4940A80_S703_L004


title: C663A_2C_2b_b1

description: Library name: WIL4940A79_S702_L004


title: C663A_2C_2a_b1

description: Library name: WIL4940A77_S700_L004


title: C663A_2C_2a_b2

description: Library name: WIL4940A78_S701_L004


title: KO_Zygote_2a

description: Library name: WIL4940A73_S697_L004

source_name: Zygote

value: Zygote


title: KO_Zygote_2b

description: Library name: WIL4940A74_S698_L004


title: KO_Zygote_2c

description: Library name: WIL4940A75_S699_L004


title: KO_2C_1c_b2

description: Library name: WIL4940A70_S696_L004


title: KO_2C_1b_b1

description: Library name: WIL4940A67_S693_L004


title: KO_2C_1a_b2

description: Library name: WIL4940A66_S692_L004


title: KO_2C_1c_b1

description: Library name: WIL4940A69_S695_L004


title: KO_2C_1a_b1

description: Library name: WIL4940A65_S691_L004


title: KO_2C_1b_b2

description: Library name: WIL4940A68_S694_L004


title: WT_2C_2c_b1

description: Library name: WIL4940A61_S689_L004

value: wild-type


title: WT_2C_2c_b2

description: Library name: WIL4940A62_S690_L004


title: WT_2C_2b_b1

description: Library name: WIL4940A59_S687_L004


title: WT_2C_2a_b1

description: Library name: WIL4940A57_S685_L004


title: WT_2C_1c_b2

description: Library name: WIL4940A56_S684_L004


title: WT_2C_2a_b2

description: Library name: WIL4940A58_S686_L004


title: WT_2C_1c_b1

description: Library name: WIL4940A55_S683_L004


title: WT_2C_1b_b2

description: Library name: WIL4940A54_S682_L004


title: C663A_2C_1c_b2

description: Library name: WIL4940A50_S678_L004


title: WT_2C_1a_b1

description: Library name: WIL4940A51_S679_L004


title: C663A_2C_1c_b1

description: Library name: WIL4940A49_S677_L004


title: C663A_2C_1a_b2

description: Library name: WIL4940A46_S674_L004


title: C663A_2C_1a_b1

description: Library name: WIL4940A45_S673_L004


title: C663A_2C_1b_b1

description: Library name: WIL4940A47_S675_L004


title: KO_Oocyte_2c

description: Library name: WIL4940A43_S672_L004

source_name: MII Oocyte

value: MII Oocyte


title: C663A_Oocyte_2b

description: Library name: WIL4940A38_S668_L004


title: WT_Zygote_2c

description: Library name: WIL4940A35_S666_L004


title: C663A_Oocyte_2c

description: Library name: WIL4940A39_S669_L004


title: WT_Zygote_2b

description: Library name: WIL4940A34_S665_L004


title: KO_Oocyte_2a

description: Library name: WIL4940A41_S670_L004


title: WT_2C_2b_b2

description: Library name: WIL4940A60_S688_L004


title: C663A_Oocyte_2a

description: Library name: WIL4940A37_S667_L004


title: WT_Zygote_2a

description: Library name: WIL4940A33_S664_L004


title: WT_Zygote_1c

description: Library name: WIL4940A31_S663_L004


title: KO_Oocyte_1c

description: Library name: WIL4940A23_S657_L004


title: WT_Oocyte_2a

description: Library name: WIL4940A25_S658_L004


title: WT_Zygote_1a

description: Library name: WIL4940A29_S661_L004


title: WT_2C_1b_b1

description: Library name: WIL4940A53_S681_L004


title: WT_Oocyte_2b

description: Library name: WIL4940A26_S659_L004


title: WT_Zygote_1b

description: Library name: WIL4940A30_S662_L004


title: KO_Oocyte_1a

description: Library name: WIL4940A21_S655_L004


title: KO_Oocyte_1b

description: Library name: WIL4940A22_S656_L004


title: WT_2C_1a_b2

description: Library name: WIL4940A52_S680_L004


title: KO_Zygote_1b

description: Library name: WIL4940A18_S653_L004


title: KO_Oocyte_2b

description: Library name: WIL4940A42_S671_L004


title: KO_Zygote_1a

description: Library name: WIL4940A17_S652_L004


title: C663A_Zygote_1c

description: Library name: WIL4940A11_S648_L004


title: C663A_Zygote_2a

description: Library name: WIL4940A13_S649_L004


title: C663A_Zygote_1b

description: Library name: WIL4940A10_S647_L004


title: C663A_Zygote_1a

description: Library name: WIL4940A9_S646_L004


title: C663A_2C_1b_b2

description: Library name: WIL4940A48_S676_L004


title: C663A_Zygote_2c

description: Library name: WIL4940A15_S651_L004


title: WT_Oocyte_1b

description: Library name: WIL4940A6_S644_L004


title: WT_Oocyte_2c

description: Library name: WIL4940A27_S660_L004


title: WT_Oocyte_1a

description: Library name: WIL4940A5_S643_L004


title: C663A_Oocyte_1b

description: Library name: WIL4940A2_S641_L004


title: C663A_Oocyte_1c

description: Library name: WIL4940A3_S642_L004


title: C663A_Oocyte_1a

description: Library name: WIL4940A1_S640_L004


title: Sample10, hypothalamus, fed, 18h

city: Incheon

first: Mi-Ryung

last: Han

address: 265, Harmony-ro, Yeonsu-gu, Incheon, Republic of Korea

country: South Korea

institute: Incheon National University

description: Library name: FED1-Hypo

data_processing:
Raw sequnece reads with low-quality and adapter sequences for the hippocampus were trimmed using Trimmomatic (v0.36) with parameters:PE ILLUMINACLIP: TruSeq3-PE-2.fa:2:30:10:5:true, LEADING:3, TRAILING:3, SLIDINGWINDOW:4:15, MINLEN:36. For the hypothalamus, cutadapt (v3.4) was used with parameters: --minimum-length 20:20 -q 20 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT.
Trimmed reads were mapped to GRCm38 (101 released) using STAR (v.2.7.3a) with parameters: --outFilterType BySJout --outFilterMismatchNmax 999 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMismatchNoverLmax 0.04 --twopassMode Basic.
Assigned reads to genes were calculated using featureCounts (v2.0.1) with parameters: -F GTF -t exon -g gene_id --minOverlap 60 -s 2 -p -B -C -a Mus_musculus.GRCm38.101.chr.gtf.
Assembly: GRCm38
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

source_name: hypothalamus

extract_protocol:
Total RNA was extracted from the hypothalamic and hippocampal tissues from mice.
Libraries for RNA-seq were prepared using Illumina TruSeq Stranded mRNA Sample Prep Kit (Illumina) according to the manufacturer’s instruction.

value: hypothalamus

value: fed, 18h


title: Sample11, hypothalamus, fed, 18h

description: Library name: FED2-Hypo


title: Sample12, hypothalamus, fed, 18h

description: Library name: FED3-Hypo


title: Sample2, hippocampus, fasted, 18h

description: Library name: FASTED2-Hippo

source_name: hippocampus

value: hippocampus

value: fasted, 18h


title: Sample4, hippocampus, fed, 18h

description: Library name: FED1-Hippo


title: Sample9, hypothalamus, fasted, 18h

description: Library name: FASTED3-Hypo


title: Mtr4-cKO-rep3

city: Shanghai

first: Hong

last: Cheng

address: 320 Yue Yang Road

institute: Shanghai Institute of Biochemistry and Cell Biology, CAS

data_processing:
The raw reads were filtered to remove the sequencing adaptors and low-quality bases using Cutadapt (v1.18) with parameters: -a CTGTCTCTTATACACATCTCCGAGCCCACGAGAC -A CTGTCTCTTATACACATCTGACGCTGCCGACGA -m 20 –max-n 5 -q 30. Then, the clean reads were mapped using STAR (v2.7.10a) to the mouse genome with GENCODE gene annotation (vM24) with default parameter. Samtools (v1.9) was used to extract uniquely mapped reads from bam file. RNA-seq signal track were generated by using bam2wig.py provided in RSeQC package (v3.0.0), and visualized in UCSC genome browser with custom track hub.
Gene counts were calculated by featureCounts (v1.6.0) with default parameter. Differentially expressed genes were called by using DESeq2 package (v1.20.0) with following criteria: FDR < 0.05 and at least 1.5-fold change. Functional enrichment analysis was performed on the list of differentially expressed genes by using the clusterProfiler package (v3.14.3) to determine if the genes are enriched for specific terms.
Assembly: mm10
Supplementary files format and content: bw file
Supplementary files format and content: xlsx file

source_name: testis

extract_protocol:
The RNA-seq was performed based on Smart-seq2. The isolated cells were lysed in lysis buffer from Vazyme Single Cell Full Length mRNA-Amplification Kit (N712) for mRNA amplification.
RNA libraries were then prepared for sequencing using the TruePrepTM DNA Library Prep Kit V2 (Vazyme Biotech Co.,Ltd, #TD503).

treatment_protocol: Single-cell suspensions were derived from P8 mice testes. The suspensions were then incubated with anti-CD117 / c-Kit antibody (1:50, eBioscience, 11-1171-82). Flow cytometric analysis was executed employing the FACSAria Fusion (BD) system.

value: testis

value: KIT(+) cell


title: Sample7, hypothalamus, fasted, 18h

description: Library name: FASTED1-Hypo


title: Sample6, hippocampus, fed, 18h

description: Library name: FED3-Hippo


title: Sample8, hypothalamus, fasted, 18h

description: Library name: FASTED2-Hypo


title: Experimental01-72h

city: hangzhou

first: Yanqiu

last: Liu

address: Zijingang Campus, Zhejiang University, Hangzhou, Zhejiang Province, China

institute: Zhejiang University

description: Library name: Experimental01-72h_L1

data_processing:
HTSeq v0.6.1
Assembly: Nonomuraea gerenzanensis L70

organism: Nonomuraea gerenzanensis

source_name: mycelia

growth_protocol: To prepare genomic DNA-free RNA, RNA isolation was performed as follows. Samples were collected from 3 independent biological replicates of YS fermentation at 48 and 72 hours.

extract_protocol:
Mycelia were collected and washed twice with RNase-free TE buffer. Total RNA was then prepared from the mycelia using the EASYspin Plus bacteria RNA extract kit (Aidlab Biotech, Beijing, China).
The preparations were sequenced on an Illumina Novaseq platform (Illumina, San Diego, CA, USA) and 150 bp paired-end reads were generated. HTSeq v0.6.1 was used to count the number of reads mapped to each gene.

value: mycelia

value: total RNA

value: wblA knockout


title: WT_Oocyte_1c

description: Library name: WIL4940A7_S645_L004


title: Sample5, hippocampus, fed, 18h

description: Library name: FED2-Hippo


title: Kidney,SHAM,3

city: Harbin

first: Jiannan

last: Zhang

address: No. 23, Youzheng Street

department: Department of Critical Care Medicine

institute: The First Affiliated Hospital of Harbin Medical University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork(parameters-mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Kidney

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Kidney

value: Sham (control)


title: C663A_Zygote_2b

description: Library name: WIL4940A14_S650_L004


title: Sample1, hippocampus, fasted, 18h

description: Library name: FASTED1-Hippo


title: Experimental03-72h

description: Library name: Experimental03-72h_L1


title: Kidney,SHAM,2


title: Sample3, hippocampus, fasted, 18h

description: Library name: FASTED3-Hippo


title: Experimental02-48h

description: Library name: Experimental02-48h_L1


title: Experimental02-72h

description: Library name: Experimental02-72h_L1


title: Kidney,SHAM,1


title: Mtr4-WT-rep3


title: Experimental01-48h

description: Library name: Experimental01-48h_L1


title: Control03-72h

description: Library name: Control03-72h_L1

value: WT


title: Kidney,CLP,2

value: Cecal Ligation and Puncture (CLP)


title: Kidney,CLP,3


title: Control02-72h

description: Library name: Control02-72h_L1


title: Control02-48h

description: Library name: Control02-48h_L1


title: Kidney,CLP,1


title: Mtr4-cKO-rep2

data_processing:
The raw reads were filtered to remove the sequencing adaptors and low-quality bases using Cutadapt (v1.18) with parameters: -a CTGTCTCTTATACACATCTCCGAGCCCACGAGAC -A CTGTCTCTTATACACATCTGACGCTGCCGACGA -m 20 –max-n 5 -q 30.  Then, the clean reads were mapped using STAR (v2.7.10a) to the mouse genome with GENCODE gene annotation (vM24) with default parameter.  Samtools (v1.9) was used to extract uniquely mapped reads from bam file.  RNA-seq signal track were generated by using bam2wig.py provided in RSeQC package (v3.0.0), and visualized in UCSC genome browser with custom track hub.
Gene counts were calculated by featureCounts (v1.6.0) with default parameter. Differentially expressed genes were called by using DESeq2 package (v1.20.0) with following criteria: P-value < 0.05 and at least 1.5-fold change. Functional enrichment analysis was performed on the list of differentially expressed genes by using the clusterProfiler package (v3.14.3) to determine if the genes are enriched for specific terms.
Assembly: mm10
Supplementary files format and content: tab-delimited text file
Supplementary files format and content: bw file

treatment_protocol: Single-cell suspensions were derived from P8 mice testes. The suspensions were then incubated with anti-CD117 / c-Kit antibody (1:50, eBioscience, 11-1171-82).  Flow cytometric analysis was executed employing the FACSAria Fusion (BD) system.


title: KELLY BPTF sh2  exp1

city: Madrid

first: Jaime

last: Martinez de Villarreal

state: Madrid

address: Melchor Fernández Almagro, 3

department: Molecular Oncology Programme

country: Spain

institute: CNIO

data_processing:
Analyses were performed using Nextpresso RNA-seq pipeline.
Raw files were aligned to hg19 reference genome using Bowtie and TopHat aligners.
Raw counts were generated using htseq
Assembly: hg19
Supplementary files format and content: text file with gene expression raw counts

source_name: Neuroblastoma

growth_protocol: Infected KELLY cells were grown in RPMI supplemented with 10% FBS tetracycline negative and 1% sodium pyruvate at 37 °C with 5% CO2

extract_protocol:
RNA was extracted using the ReliaPrep RNA kit (Promega, ref. Z6012) following manufacturer’s instructions
Total RNA samples were converted into cDNA sequencing libraries with the "QuantSeq 3‘m RNA-seq Library Prep Kit (FWD) for Illumina" (Lexogen, Cat.No. 015)

treatment_protocol: Doxycycline (1µg/mL) for 48h

value: Neuroblastoma

tag: cell line

value: KELLY

value: Cancer cell

value: BPTF sh2

value: doxycycline (1ug/mL), 48h


title: KELLY sh NT exp2

value: shNT

value: Vehicle


title: mESC_03

description:
5hmC
Chemical labeled genomic DNA

source_name: mESC

value: mESC


title: KO_Zygote_1c

description: Library name: WIL4940A19_S654_L004

value: Zygote


title: Mtr4-cKO-rep1

value: testis

value: KIT(+) cell


title: Mtr4-WT-rep2


title: Experimental03-48h

description: Library name: Experimental03-48h_L1

value: mycelia

value: total RNA


title: ID30

city: Brussels

first: Jean-Pascal

last: Machiels

address: Avenue Hippocrate 10

country: Belgium

institute: Cliniques Universitaires Saint-Luc

description:
Library name: ID30_S3_L001
FFPE spatiale transcriptome sequencing

data_processing:
Visium libraries were sequenced on Illumina NextSeq2000. The sequencing depth was determined by the amount of Visium spots covered by tissue (25.000 reads per spot). Spots corresponding to tumor area were manually selected in the Loupe-Browser (v6.4.1)16. 10x data were processed using SpaceRanger (v2.0.1). Reads were aligned to the human reference sequence GRCh38. Seurat package (v4.3.0)17 was used to analyse the spatial transcriptomic data. Counts were normalized with the SCTransform function of Seurat package and integrated into a single Seurat object.
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv.gz list of spatial barcodes
Supplementary files format and content: matrix.mtx.gz gene expression count
Supplementary files format and content: features.tsv.gz list of genes ID
Supplementary files format and content: V11Y11-322-B1_IDXX.json regions of interest used of analyses
Supplementary files format and content: SlideXAreaX.tiff HE staining of the analysed tissue
Supplementary files format and content: clusters.tsv clusters found in region of interest after t-SNE
Library strategy: Spatial Transcriptomics

source_name: head and neck squamous cell carcinoma

extract_protocol:
Surgical specimens were processed in FFPE in the same way as for conventional pathological analysis.Prior to sectioning, the FFPE blocks were incubated in an ice bath for 10-30 min and 5µm-thick sections were cut using a microtome. Resulting sections were floated for 40 sec in a 42°C water bath until flat and immediately placed onto the Visium slides. Slides containing sections were dried for 3h at 42°C and placed in a desiccator overnight at room temperature to ensure proper drying. They were further stored for a maximum of 1 week before use
Deparaffinization, staining, imaging, decrosslinking and construction of sequencing libraries was done according to the manufacturer’s instructions (Visium Spatial Gene Expression for FFPE – Deparaffinization, H&E staining, Imaging & decrosslinking, CG000409, RevC; Visium Spatial Gene Expression Reagent Kit for FFPE - User Guide, CG000407, RevD) using the Visium Spatial for FFPE Gene Expression Kit, Human Transcriptome (10x Genomics, 1000338).

value: head and neck squamous cell carcinoma

tag: cluster

value: non-EMT

value: afatinib


title: Mtr4-WT-rep1


title: mESC_02

description:
5hmC
Chemical labeled genomic DNA


title: Control01-72h

description: Library name: Control01-72h_L1

value: WT


title: 8C_29

description:
5hmC
Chemical labeled genomic DNA

value: C57BL/6J X DBA/2N


title: ID15

description:
Library name: ID15_S4_L001
FFPE spatiale transcriptome sequencing

value: EMT


title: ID08

description:
Library name: ID08_S2_L001
FFPE spatiale transcriptome sequencing


title: Control03-48h

description: Library name: Control03-48h_L1


title: MTR4-LACEseq-rep3

data_processing:
The adapter sequences and poly(A) tails at the 3′ end of raw reads were removed using Cutadapt (v1.15) with two parameters: -a ATCTCGTATGCCGTCTTCTGCTT  -n 10  --minimum-length 18  -e 0.1, and -f fastq -a A -m 18 -n 2. Clean reads were first aligned to mouse pre-rRNA using Bowtie (v1.0.0) with default parameters,  and the remaining unmapped reads were then aligned to the mouse (mm10) reference genome.
For peak calling,  the mapped reads were first extended 30 nt to 3′ downstream.  Peaks were identified by Piranha (v1.2.1) with parameters: -s -b 20 -p 0.05.
Assembly: mm10
Supplementary files format and content: bedgraph file
Supplementary files format and content: bw file

extract_protocol:
Cells were lysed on ice using 50 μl wash buffer for 10 min. Next, 1 μl SUPERase·In RNase inhibitor (Ambion, AM2696) and 4 μl RQ1 DNase (Promega, M6101) were applied to the lysate and incubated at 37 °C for 3 min.
RNA immunoprecipitation of the samples was performed. The immunoprecipitated RNAs were then fragmented by MNase and dephosphorylated. Then a series of steps were performed to include, reverse transcription, first-strand cDNA capture by streptavidin beads, poly(A) tailing, pre-PCR, IVT, RNA purification, RT, PCR barcoding and deep sequencing.

treatment_protocol: Single-cell suspensions were derived from P8 mice testes. The suspensions were then incubated with anti-CD117 / c-Kit antibody (1:50, eBioscience, 11-1171-82).  Flow cytometric analysis was executed employing the FACSAria Fusion (BD) system, the sorted cells were then irradiated twice with UV-C light on ice at 400 mJ.

tag: antibody


title: 8C_28

description:
5hmC
Chemical labeled genomic DNA


title: KELLY BPTF sh2  exp2

tag: tissue

value: Neuroblastoma

value: KELLY

value: Cancer cell


title: mESC_01

description:
5hmC
Chemical labeled genomic DNA


title: Blood, case, P_17241

city: Sao Paulo

first: Vanessa

middle: Kiyomi

last: Ota

state: SP

address: Rua Botucatu, 740, Ed. Leitao da Cunha, 1o andar

department: Morphology and Genetics

country: Brazil

institute: Universidade Federal de Sao Paulo

description:
Library name: P_17241
P_17241

data_processing:
We downloaded the Fastq files from Illumina Basespace and determined the miRNA counts using miRge3.0, which is implemented in Python, adding the parameters for Qiagen UMI (--qiagenumi -umi 0,12). We chose this pipeline because of its ability to process UMIs to account for PCR duplicates. Briefly, miRge3.0 performs quality control and adapter trimming using Cutadapt (v3.0). Then, it collapses identical reads into a single read and captures the counts in a Pandas data frame. Reads were aligned to miRBase (v22) using Bowtie (v1.3.0), and the output was then imported into R (v4.1.2) for statistical analysis. We performed differential gene expression analysis using the DESeq2 package.
Assembly: miRbase v22
Supplementary files format and content: raw read counts with each miRNA in rows and each sample in columns

source_name: Blood

extract_protocol:
Blood samples were collected from all participants using PAXgene Blood RNA Tubes (BD), and total RNA was isolated using the PAXgene Blood miRNA Kits (Qiagen). All RNA samples had an RNA Integrity Number value above 7.
We prepared the libraries using 100 ng of RNA and the QIAseq miRNA Library Kit (Qiagen), which adds Unique Molecular Identifiers (UMIs) to the sequences, following the manufacturer’s instructions. Library concentrations and quality were measured using Qubit Fluorimeter (Thermo Fisher Scientific), Qubit dsDNA HS Assay Kit, and Agilent 2100 Bioanalyzer (Agilent) with the Agilent High Sensitivity DNA Kit. The libraries were pooled and sequenced (1 × 75) on the NextSeq 500 instrument (Illumina) using the HighOutput kit (75 cycles)

value: Blood

value: Female


title: Blood, case, P_17220

description:
Library name: P_17220
P_17220

value: Male


title: MTR4-LACEseq-rep1


title: Control01-48h

description: Library name: Control01-48h_L1


title: Blood, case, P_17215

description:
Library name: P_17215
P_17215


title: MTR4-LACEseq-rep2


title: KELLY sh NT exp1

value: shNT

value: Vehicle


title: Blood, case, P_17432

description:
Library name: P_17432
P_17432


title: Blood, case, P_16920

description:
Library name: P_16920
P_16920


title: 8C_23

description:
5hmC
Chemical labeled genomic DNA


title: Blood, case, P_17189

description:
Library name: P_17189
P_17189


title: 8C_27

description:
5hmC
Chemical labeled genomic DNA


title: Blood, case, P_17431

description:
Library name: P_17431
P_17431


title: mESC_04

description:
5hmC
Chemical labeled genomic DNA

value: mESC


title: Blood, case, P_17252

description:
Library name: P_17252
P_17252


title: 8C_22

description:
5hmC
Chemical labeled genomic DNA


title: 8C_25

description:
5hmC
Chemical labeled genomic DNA


title: Blood, case, P_15316

description:
Library name: P_15316
P_15316


title: 8C_24

description:
5hmC
Chemical labeled genomic DNA


title: Blood, case, P_14569

description:
Library name: P_14569
P_14569


title: MM.1S cells EGCG 80μM 2

city: Jinan

first: xunqi

last: zhang

address: Bei yuan street N0.247

department: hematology

institute: Shandong University

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit  version 0.0.13 and Perl version 5.8.8
Paired-end sequence files (fq.gz) were mapped to the reference genome GRCh38.108 using Hisat2 (Hierarchical Indexing for Spliced Alignment of Transcripts, version 2.0.5). The output SAM (sequencing alignment/map) files were converted to BAM (binary alignment/map) files and sorted using SAMtools (version 1.3.1).
Gene abundance measurements were generationed and normalized  using Cufflink version 2.0.2.Linux_x86_64 ; The normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM)
Differential expression analysis for mRNA was performed using R package edgeR.
Assembly: GRCh38.108
Supplementary files format and content: tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample

source_name: MM.1S cells multiple myeloma

growth_protocol: MM.1S cells were cultured in RPMI 1640 medium  containing 10% fetal bovine serum and 1% penicillin-streptomycin. Cells were cultured in an incubator with 5% CO2, 37℃ and constant humidity. The medium was changed every other day.

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MM.1S cells were treated with EGCG (0、40μM、80μM ) for 24h

value: MM.1S cells multiple myeloma

value: tumor cells

value: EGCG 80 microM 24h


title: Blood, control, C_17448

description:
Library name: C_17448
C_17448


title: Blood, case, P_15311

description:
Library name: P_15311
P_15311


title: 8C_26

description:
5hmC
Chemical labeled genomic DNA


title: MM.1S cells EGCG 80μM 1


title: tumor DNA from cell line MDA-MB-231

type: other

city: Lund

first: Johan

last: Staaf

address: Medicon Village

country: Sweden

institute: SCIBLU - Swegene Centre for Integrative Biology at Lund University

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to human Infinium MethylationEPIC beadchip (Illumina) using standard Illumina protocol.

scan_protocol: Arrays were imaged using BeadArray Reader (HiScan) and standard recommended Illumina scanner setting.

data_processing: Beta values, representing the level of methylation, were computed using the minfi R package v1.44 function preprocessFunnorm() and next Infinium probe normalized using the approach described by PMID:26923702

molecule: other

source_name: breast cancer

growth_protocol: Cell lines were grown according to recommendations by supplier

extract_protocol: Cell line DNA was extracted using Qiagen AllPrep kit according to manufacturer's instructions.

value: breast cancer

value: human triple negative breast cancer (TNBC) cell line

value: TNBC


title: Blood, control, C_17447

description:
Library name: C_17447
C_17447


title: tumor DNA from cell line MDA-MB-453


title: Blood, control, C_17450

description:
Library name: C_17450
C_17450


title: Blood, case, P_13658

description:
Library name: P_13658
P_13658


title: 2C_61

description:
5hmC
Chemical labeled genomic DNA

value: C57BL/6J X DBA/2N


title: Blood, control, C_17449

description:
Library name: C_17449
C_17449


title: Blood, control, C_17380

description:
Library name: C_17380
C_17380


title: 2C_60

description:
5hmC
Chemical labeled genomic DNA


title: MM.1S cells EGCG 40μM 2

value: EGCG 40 microM 24h


title: 2C_57

description:
5hmC
Chemical labeled genomic DNA


title: Blood, control, C_17376

description:
Library name: C_17376
C_17376


title: tumor DNA from cell line BT549


title: Blood, control, C_17426

description:
Library name: C_17426
C_17426


title: 2C_59

description:
5hmC
Chemical labeled genomic DNA


title: MM.1S cells EGCG 40μM 3


title: tumor DNA from cell line HCC1937


title: Blood, control, C_17419

description:
Library name: C_17419
C_17419


title: Blood, control, C_17377

description:
Library name: C_17377
C_17377


title: 2C_58

description:
5hmC
Chemical labeled genomic DNA


title: tumor DNA from cell line HCC2157


title: Blood, control, C_17378

description:
Library name: C_17378
C_17378


title: Blood, control, C_17371

description:
Library name: C_17371
C_17371


title: 2C_56

description:
5hmC
Chemical labeled genomic DNA


title: 2C_54

description:
5hmC
Chemical labeled genomic DNA


title: MM.1S cells EGCG 40μM 1


title: INPUT_r1

city: Wuhan

first: Ying

address: No.1 Shizishan Street

institute: Huazhong Agricultural University

data_processing:
ChIP-Seq: Analysis was performed using BWA-MEM (v.0.7.15), MACS2 (v2.1.2).
Genome_build: Arabidopsis genome (TAIR10) was obtained from Ensembl (http://plants.ensembl.org/).
Supplementary_files_format_and_content: BigWig, the genome coverage of each sample.

organism: Arabidopsis thaliana

source_name: seedling

growth_protocol: Plants were grown in soil (KEKKILA) in a growth room at 21°C, 45% humidity, and 75 μE m-2 s-1 light with a 12-hr-light/12-hr-dark photoperiod. 14-day-old seedlings were cultured on half-strength Murashige and Skoog (1/2MS) plates containing 1% sucrose and 0.8% agar, and grown under the same condition as above.

extract_protocol: Lysates were clarified from sonicated nuclei, and protein-DNA complexes were isolated with antibody.

value: 14 days

value: seedling

tag: chip antibody


title: tumor DNA from cell line SUM185PE


title: tumor DNA from cell line MDA-MB-468


title: CLP 3h+ACTH 45min 3

status: Public on Feb 22 2025

city: Lexington

first: Xiang-An

last: Li

address: 741 S Limestone

institute: University of Kentucky

description:
Library name: XL6.bam
read count and fkpm

data_processing:
(1) Data quality control: filtering reads containing adapter or with low quality; (2) Statistics analysis of data production of quality; (3) Mapping reads to reference genome (STAR); (4) Gene expression quantification (HTseq); (5) Differential expression analysis (DEseq2/edgeR).
pair-end reads were 150-base-pair ones, output is 9G. NovaSeq 6000 Illumina platform was used
Supplementary files format and content: fpkm
Supplementary files format and content: readcount

source_name: Adrenal

extract_protocol:
Total RNA was isolated by using RNeasy mini kit from Qiagen
Total RNA was sent to Novogen for library construction

value: Adrenal

tag: genotype

value: CLP+ACTH 45min


title: CLP 3h+ACTH 45min 2

description:
Library name: XL5.bam
read count and fkpm


title: MM.1S cells control 3

tag: cell type

value: EGCG 0 microM 24h


title: 2C_55

description:
5hmC
Chemical labeled genomic DNA

data_processing:
library strategy: schmC-CATCH
rawdata was trimmed by trim-galore to cut adaptor and low quality bases  (parameters: --phred33 --stringency 3 --length 40 --quality 20)
Removing the fixed sequence by cutadapt( -g GGGGGGGGGGGGGGGGGGG -a CTGTCTCTTATACACATCT -m 40)
Alignment was performed by bowtie2 with local default parameters to mouse reference genome(mm10)
5hmC sites were called by customed scripts
Assembly: mm10
Supplementary files format and content: Processed bed files contain chromosome, start position, endposition, reference genotype,regular CpG ("0") or 5hmCpG ("1")

extract_protocol:
Single cells were isolated into lysis buffer and then heat for 30min at 75℃. After that, the DNA was treated with protease.
Cells were lysed and treated by protease. Then naked DNA was tagmented by indexed Tn5 at 55 °C for 15 min (Vazyme Biotech).Pool 8 cell lysate into one tube, denature transposons at 72℃. T4 DNA ligase buffer and 1μL Exo I were added and lysate incubate at 37℃ for 60 min.DNA were purified with the 2× AMPure (Beckman) beads with 500ng carrier RNA (thermo).dC-tailing was performed according to previous protocol.Potassium perruthenate (Sigma-Aldrich,334537) solution was prepared according to published protocol.To obtain the 5hmC profiles from the single cells, the 5hmC labeled DNA was subjected to multiple rounds of primer extension to record the 5hmC-to-T transition signal.Primer extension mix (8 µL of 5× KAPA 2G buffer, 0.8 µL of 10 mM dNTPs, 0.8 µL of 10 µM P5G9H primer, 0.6 µL KAPA2G Robust HS DNA polymerase (Roche, KK5023)) was added.Add 8 µL of KAPA HiFi buffer, 2 µL of 500nM P5-short, 2 µL of 500nM P7-short 1.6 µL Kapa HF Hotstart DNA polymerase directly to the linear amplification mixture. PCR was performed to amplify the library for 11-15 cycles.After the PCR reaction, libraries were purified with the 0.8× AMPure beads.


title: IP_Flag_r1

value: FLAG


title: IP_Flag_r2


title: CLP 3h+PBS 45min 1

description:
Library name: XL1.bam
read count and fkpm

value: CLP+PBS 45min


title: Blood, control, C_17373

description:
Library name: C_17373
C_17373

value: Blood

value: Male


title: tumor DNA from cell line HCC1599

value: Female


title: MM.1S cells control 2

value: MM.1S cells multiple myeloma

value: tumor cells


title: INPUT_r2


title: CLP 3h+ACTH 45min 1

description:
Library name: XL4.bam
read count and fkpm


title: CLP 3h+PBS 45min 2

description:
Library name: XL2.bam
read count and fkpm


title: MM.1S cells control 1


title: ctl_3

city: Wenzhou

first: Keqing

last: Shi

address: Fanhaixilu

institute: The First Affiliated Hospital of Wenzou Medical University

description: Library name: ctl_3

data_processing:
Transcriptome sequencing was conducted on the Illumina platform (Illumina NovaSeq 6000)
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
The clean reads were aligned to the reference genome using HISAT2. The FPKM values for each gene were calculated, and the read counts for each gene were obtained using HTSeq-count.
Differential expression analysis was performed using DESeq2. A Q value < 0.05 and fold change > 2 or fold change < 0.5 were set as the criteria for significantly differentially expressed genes (DEGs).
Assembly: GRCm39
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: Matrix table with FPKM values for every gene and every sample

source_name: NIH-3T3 cells, cultured on standard plates

growth_protocol: NIH-3T3 were maintained in DMEM culture medium (Biological Industries, Israel) supplemented with 10% fetal bovine serum (Gemini, USA) and 1% streptomycin and penicillin (Invitrogen Corp., Carlsbad, CA, USA) in a humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
Total RNA was extracted from NIH-3T3 cells cultured on plates or scaffolds using TRIzol reagent (catalog #15596026, Invitrogen, Carlsbad, CA, USA).
The libraries were constructed using NEBNext® Ultra™ RNA Library Prep Kit for Illumina according to the manufacture's instructions

treatment_protocol: NIH-3T3 cells cultured on plates or Nanopore #3 scaffolds

value: embryo

value: fibroblast cell

value: WT

value: cultured on standard plates


title: Nanopore #3_1

description: Library name: Nanopore #3_1

source_name: NIH-3T3 cells, cultured on Nanopore #3 scaffold

value: cultured on Nanopore #3 scaffold


title: ctl_1

description: Library name: ctl_1


title: Nanopore #3_3

description: Library name: Nanopore #3_3


title: ADULT_IFNAR_UI_0h_A62_S94

city: Philadelphia

first: Alison

last: Carey

state: PA

address: 245 N 15th Street

institute: Drexel University College of Medicine

description:
Library name: A62-IFNAR-UI_S94
8-weeks-old

data_processing:
FastQ generation, including base calling, demultiplexing, and adapter trimming were automatically performed after sequencing on Illumina BaseSpace using BCL Convert.
FastQ reads were pseudoaligned to the indexed mm10/GRCm38 transcriptome reference used Salmon v1.8 in ISR mode. Aggregation of transcript-level counts to gene-level counts used tximport v1.22.
Samples which failed quality control assessments (A1, A2, A3, A4, A5, A6, A38, A39, A40, A48, A49, N57, N69, N78, N79, N81, N83) were dropped from final analyses.
Assembly: mm10
Supplementary files format and content: Processed data files .quant.sf were produced using Salmon v1.8 with mm10 as the reference. The five tab-delimited columns are Name (Ensembl ID), Length (total transcript length), EffectiveLength (computed length accounting for sequencing parameters, TPM (estimate of transcripts per million), NumReads ("count" of reads with multiple mappers fractionally split).

source_name: Lung

extract_protocol:
Type II epithelial cells were enriched from homogenized murine lung tissues by filtration for cells <20 microns and antibody depletion of CD45 and CD16/32-expressing cells. Total RNA was isolated using phase-separation with TRIzol following manufacturer recommendations, including DNase treatment. Further purification used RNeasy kits (Qiagen), per manufacturer's instructions. RNA purity was determined by spectrophotometry, concentration by Qbit fluorometry, and quality by Bioanalyzer.
The Illumina TruSeq stranded mRNA kit with selection for polyadenylated trascripts was used to prepare sequencing libraries according to recommended protocols.

treatment_protocol: Adult or neonatal mice of two genotypes (C57/BL6 or an isogenic IFNAR knockout) were infected with flu virus (PR8) or not, and lung tissue was harvested at 1, 2, or 3 days post-infection for isolation of type II epithelial cells.

value: Lung

value: Type II alveolar epithelial cell


title: ADULT_C57_UI_0h_A59_S92

description:
Library name: A59-C57-UI_S92
8-weeks-old


title: CLP 3h+PBS 45min 3

description:
Library name: XL3.bam
read count and fkpm

value: Adrenal


title: ADULT_C57_UI_0h_A58_S91

description:
Library name: A58-C57-UI_S91
8-weeks-old


title: ADULT_IFNAR_UI_0h_A61_S96

description:
Library name: A61-IFNAR-UI_S96
8-weeks-old


title: Wild-type mice undergoing TAC surgery

city: Nanjing

first: Hao

address: Dingjiaqiao 87#, Southeast University, Gulou District, Nanjing, Jiangsu Province, China

institute: Southeast University

description:
Library name: WT_TAC_1
Wild-type mice undergoing TAC surgery

data_processing:
Raw sequencing data were processed using Cell Ranger, with alignment to the Mus musculus reference genome.
Quality control and filtering of low-quality cells were performed using the Seurat R package.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Heart

extract_protocol:
Total RNA was extracted from the hypertrophied left ventricle of mice using a commercial RNA extraction kit.
Single-cell RNA sequencing libraries were constructed using the 10x Genomics Chromium Single Cell 3’ Reagent Kit, following the manufacturer’s instructions.

value: Heart

value: Cardiomyocytes


title: ctl_2

description: Library name: ctl_2