title: STZ+HFD model, 52w, treated with control vehicle for 11 weeks, biological replication 2

description:
rawcount_allsamples_mouse.txt
Batch8_STZHFD52w_Vehicle_11w_2

value: 52 weeks


title: STZ+HFD model, 52w, treated with control vehicle for 11 weeks, biological replication 4

status: Public on Jun 16 2024

type: SRA

city: Songpa-Gu

first: Byung-Kwan

last: Jeong

state: Seoul

address: 88, Olympic-ro 43-gil

department: Pathology

country: South Korea

institute: Asan Medical Center

description:
rawcount_allsamples_mouse.txt
Batch8_STZHFD52w_Vehicle_11w_4

library_source: transcriptomic

data_processing:
Raw RNA-sequencing data obtained from mouse were mapped to mouse genome build mm10 (GRCm38) and those from human mapped to human genome build 38 (GRCh38) using STAR (version 020201).
Count matrices were generated using RSEM (v1.3.1)
Assembly: mm10, human genome build 38 (GRCh38)
Supplementary files format and content: tab-delimited text files include raw expected count generated by RNA-seq for each sample

molecule: total RNA

organism: Mus musculus

source_name: Liver

growth_protocol: Mice were housed in climate-controlled, specific pathogen-free barrier facilities under a 12 h light-dark cycle and provided diet and water ad libitum. They were fed standard chow diet (SCD) (Teklad Global 18% Protein Rodent Diet 2018; Harlan Teklad, WI, USA), 18% fat  or HFD (Research Diet (New Brunswick, NJ, USA) D12492, 60% fat) from 8 weeks of age.

extract_protocol:
Total RNA was isolated using a RNeasy Mini kit (Qiagen, Hilden, Germany; 74104) in keeping with the manufacturer’s instructions.
The RNA sequencing library was prepared using a NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England BioLabs, Ipswitch, MA, USA; E7760).

treatment_protocol: Vehicle (HyClone DPBS, Cytiva, Germany) or tirzepatide (109.5 nmol/kg, CPC, Hanzhou, China) dissolved in vehicle was administered via subcutaneous injection to ad libitum-fed STZ+HFD mice 1-2 hours prior to the onset of the dark cycle every 2 days for 10 to 11 weeks.

tag: tissue

value: Liver

tag: strain

tag: age

tag: streptozotocin treatment

value: Treated

tag: diet

value: HFD

tag: Sex

value: Male

tag: genotype

value: WT

tag: drug treatment

value: Vehicle


title: STZ+HFD model, 52w, treated with tirzepatide (109.5 nmol/kg) for 11 weeks, biological replication 2

description:
rawcount_allsamples_mouse.txt
Batch8_STZHFD52w_Tirzepatide_11w_2

value: Tirzepatide


title: HA-PKR w/ PACT Input biol rep 2

city: Boston

first: Sun

last: Hur

state: MA

address: 3 Blackfan St,

country: USA

institute: Howard Hughes Medical Institute and Program in Cellular and Molecular Medicine

data_processing:
Fastq files were trimmed by trimmomatic (v0.36), aligned to RNA45SN1 and RNA5SN1, and the leftover reads were mapped to human genome.
In order to normalize different sequencing depths among samples, all groups were normalized to 1M total non-rRNA reads mapped. They were named as "*PM.bedgraph" (per million bedgraph) individually.
The bedgraph files can be readily opened in IGV using Grch38.p14 human genome.
Assembly: Grch38.p14
Supplementary files format and content: PM (per million) bedgraph files: the alignment file of indivual groups after normalizing to 1M total non-rRNA reads mapped.

organism: Homo sapiens

source_name: Mammary gland

extract_protocol:
RNA was phenol:chloroform extracted and isopropanol precipitated
cDNA library wa prepared using SMARTer Stranded Total RNA-Seq Kit v3 - Pico Input Mammalian using manufacturer's guidelines
CLIP-seq

value: Mammary gland

tag: cell line

tag: cell type

value: epithelial breast cancer


title: HA-PKR w/o PACT Input biol rep 1


title: DKO fCLIP (HA) biol rep 3


title: STZ+HFD model, 38w, treated with tirzepatide (109.5 nmol/kg) for 10 weeks, biological replication 2

description:
rawcount_allsamples_mouse.txt
Batch7_STZHFD38w_Tirzepatide10w_2

value: 38 weeks


title: STZ+HFD model, 38w, treated with tirzepatide (109.5 nmol/kg) for 10 weeks, biological replication 4

description:
rawcount_allsamples_mouse.txt
Batch7_STZHFD38w_Tirzepatide10w_4


title: HA-PKR w/ PACT Input biol rep 1


title: STZ+HFD model, 38w, treated with tirzepatide (109.5 nmol/kg) for 10 weeks, biological replication 1

description:
rawcount_allsamples_mouse.txt
Batch7_STZHFD38w_Tirzepatide10w_1


title: DKO (HA-PKR) Input biol rep 3


title: DKO (HA-PKR) fCLIP (HA) biol rep 1


title: HFD fed mice without STZ treatment, 32w, batch 9, biological replication 1

data_processing:
Raw RNA-sequencing data obtained from mouse were mapped to mouse genome build mm10 (GRCm38) and those from human mapped to human genome build 38 (GRCh38) using STAR (version 020201).
Count matrices were generated using RSEM (v1.3.1)
Assembly: mm10
Supplementary files format and content: rawcounts_newsamples_mouse.txt: raw expected count generated by RNA-seq for each sample

growth_protocol: Mice were housed in climate-controlled, specific pathogen-free barrier facilities under a 12 h light-dark cycle and provided diet and water ad libitum. They were fed standard chow diet (SCD) (Teklad Global 18% Protein Rodent Diet 2018; Harlan Teklad, WI, USA), 18% fat or HFD (Research Diet (New Brunswick, NJ, USA) D12492, 60% fat) from 8 weeks of age.

value: 32 weeks

value: Untreated


title: DKO (HA-PKR) fCLIP (HA) biol rep 2


title: DKO (HA-PKR) Input biol rep 2


title: NIP(WT) m6A-IP shoot Rep.3

city: Beijing

first: Zhe

last: Liang

address: No12 Zhongguancun South Street

department: Biotechnology Research Institute

country: China

institute: Chinese Academy of Agricultural Sciences

description: Os.RNAseq.TPM.csv.gz

data_processing:
The raw reads were trimmed using TrimGalore-0.6.6
The trimmed reads were aligned to the Oryza_sativa.IRGSP-1.0.55 reference genome using STAR (2.7.2a)
Expression levels were estimated using featureCounts (v1.6.3)
Peak calling was performed using MACS2 (2.2.7.1)
Assembly: Oryza_sativa.IRGSP-1.0.55
Supplementary files format and content: csv files include TPM values for each Sample
Library strategy: m6A-seq2

molecule: polyA RNA

organism: Oryza sativa

source_name: 21 day shoot

extract_protocol:
The total RNA was extracted using RNAprep Pure Plant Kit (Tiangen) following the manufacturer’s procedure.
m6A-seq2 was performed as Dierks et al., 2021. The input was used as RNA-Seq&Input.

value: 21 day shoot

tag: cultivar

value: Nipponbare

tag: treatment

value: 28degreeC, light/dark=16h/8h


title: NIP(WT) m6A-IP shoot Rep.1

description: Os.RNAseq.TPM.csv.gz


title: NIP(WT) RNA-Seq&Input shoot Rep.3

description: Os.RNAseq.TPM.csv.gz

data_processing:
The raw reads were trimmed using TrimGalore-0.6.6
The trimmed reads were aligned to the Oryza_sativa.IRGSP-1.0.55 reference genome using STAR (2.7.2a)
Expression levels were estimated using featureCounts (v1.6.3)
Peak calling was performed using MACS2 (2.2.7.1)
Assembly: Oryza_sativa.IRGSP-1.0.55
Supplementary files format and content: csv files include TPM values for each Sample


title: STZ+HFD model, 52w, treated with control vehicle for 11 weeks, biological replication 1

description:
rawcount_allsamples_mouse.txt
Batch8_STZHFD52w_Vehicle_11w_1


title: STZ+HFD model, 38w, treated with tirzepatide (109.5 nmol/kg) for 10 weeks, biological replication 3

description:
rawcount_allsamples_mouse.txt
Batch7_STZHFD38w_Tirzepatide10w_3


title: DKO fCLIP (HA) biol rep 2


title: DKO fCLIP (HA) biol rep 1


title: NIP(WT) m6A-IP shoot Rep.2

description: Os.RNAseq.TPM.csv.gz


title: NIP(WT) RNA-Seq&Input shoot Rep.1

description: Os.RNAseq.TPM.csv.gz


title: DKO (HA-PKR) Input biol rep 1


title: NIP(WT) RNA-Seq&Input shoot Rep.2

description: Os.RNAseq.TPM.csv.gz


title: STZ+HFD model, 38w, treated with control vehicle for 10 weeks, biological replication 3

description:
rawcount_allsamples_mouse.txt
Batch7_STZHFD38w_Vehicle10w_3


title: DKO Input biol rep 3


title: STZ+HFD model, 38w, treated with control vehicle for 10 weeks, biological replication 2

description:
rawcount_allsamples_mouse.txt
Batch7_STZHFD38w_Vehicle10w_2


title: med18 m6A-IP shoot Rep.3

description: Os.RNAseq.TPM.csv.gz


title: med18 m6A-IP shoot Rep.1

description: Os.RNAseq.TPM.csv.gz


title: DKO Input biol rep 2


title: med18 RNA-Seq&Input shoot Rep.2

description: Os.RNAseq.TPM.csv.gz


title: med18 m6A-IP shoot Rep.2

description: Os.RNAseq.TPM.csv.gz


title: STZ+HFD model, 38w, treated with control vehicle for 10 weeks, biological replication 4

description:
rawcount_allsamples_mouse.txt
Batch7_STZHFD38w_Vehicle10w_4


title: STZ+HFD model, 38w, treated with control vehicle for 10 weeks, biological replication 1

description:
rawcount_allsamples_mouse.txt
Batch7_STZHFD38w_Vehicle10w_1


title: med18 RNA-Seq&Input shoot Rep.3

description: Os.RNAseq.TPM.csv.gz


title: STZ+HFD model, 32w, treated with tirzepatide (109.5 nmol/kg) for 11 weeks, biological replication 5

description:
rawcount_allsamples_mouse.txt
Batch6_STZHFD32w_Tirzepatide11w_5


title: med18 RNA-Seq&Input shoot Rep.1

description: Os.RNAseq.TPM.csv.gz


title: DKO Input biol rep 1


title: Rice m6A-IP Seed III Rep.2

description:
Os.RNAseq.TPM.csv.gz
IP2_A14_2

data_processing:
The raw reads were trimmed using TrimGalore-0.6.6
The trimmed reads were aligned to the Oryza_sativa.IRGSP-1.0.55 reference genome using STAR (2.7.2a)
Expression levels were estimated using featureCounts (v1.6.3)
Peak calling was performed using MACS2 (2.2.7.1)
Assembly: Oryza_sativa.IRGSP-1.0.55
Supplementary files format and content: bw file, csv file includes TPM values for each Sample

source_name: Seed III

value: Seed III

value: Planting in the field

tag: rip antibody

value: anti-m6A antibody


title: STZ+HFD model, 32w, treated with tirzepatide (109.5 nmol/kg) for 11 weeks, biological replication 4

description:
rawcount_allsamples_mouse.txt
Batch6_STZHFD32w_Tirzepatide11w_4

value: Liver

value: Treated


title: Rice m6A-IP Seed II Rep.1

description:
Os.RNAseq.TPM.csv.gz
IP2_A13_1

source_name: Seed II

value: Seed II


title: w/o Flag-PACT fCLIP (Flag) biol rep 2


title: Rice m6A-IP Seed III Rep.3

description:
Os.RNAseq.TPM.csv.gz
IP2_A14_3

value: WT


title: Rice m6A-IP Seed I Rep.3

description:
Os.RNAseq.TPM.csv.gz
IP2_A12_3

source_name: Seed I

value: Seed I


title: STZ+HFD model, 32w, treated with tirzepatide (109.5 nmol/kg) for 11 weeks, biological replication 3

description:
rawcount_allsamples_mouse.txt
Batch6_STZHFD32w_Tirzepatide11w_3

value: HFD

value: Male

value: Tirzepatide


title: Rice m6A-IP Seed II Rep.2

description:
Os.RNAseq.TPM.csv.gz
IP2_A13_2


title: STZ+HFD model, 32w, treated with tirzepatide (109.5 nmol/kg) for 11 weeks, biological replication 2

description:
rawcount_allsamples_mouse.txt
Batch6_STZHFD32w_Tirzepatide11w_2


title: Rice m6A-IP Seed II Rep.3

description:
Os.RNAseq.TPM.csv.gz
IP2_A13_3


title: STZ+HFD model, 32w, treated with tirzepatide (109.5 nmol/kg) for 11 weeks, biological replication 1

description:
rawcount_allsamples_mouse.txt
Batch6_STZHFD32w_Tirzepatide11w_1


title: w/o Flag-PACT fCLIP (Flag) biol rep 1

value: Mammary gland

value: epithelial breast cancer


title: Rice m6A-IP Seed I Rep.2

description:
Os.RNAseq.TPM.csv.gz
IP2_A12_2


title: w/ Flag-PACT Input biol rep 2


title: Rice m6A-IP Seed I Rep.1

description:
Os.RNAseq.TPM.csv.gz
IP2_A12_1


title: Rice m6A-IP pollen Rep.3

description:
Os.RNAseq.TPM.csv.gz
IP2_A11_3

source_name: Pollen

value: Pollen


title: STZ+HFD model, 32w, treated with control vehicle for 11 weeks, biological replication 5

description:
rawcount_allsamples_mouse.txt
Batch6_STZHFD32w_Vehicle11w_5

value: 32 weeks

value: Vehicle


title: Rice m6A-IP pollen Rep.2

description:
Os.RNAseq.TPM.csv.gz
IP2_A11_2

value: Nipponbare


title: Rice m6A-IP Seed III Rep.1

description:
Os.RNAseq.TPM.csv.gz
IP2_A14_1

value: Seed III


title: w/ Flag-PACT Input biol rep 1


title: STZ+HFD model, 32w, treated with control vehicle for 11 weeks, biological replication 4

description:
rawcount_allsamples_mouse.txt
Batch6_STZHFD32w_Vehicle11w_4


title: w/ Flag-PACT fCLIP(Flag) biol rep 1


title: w/ Flag-PACT fCLIP(Flag) biol rep 2


title: Rice m6A-IP pollen Rep.1

description:
Os.RNAseq.TPM.csv.gz
IP2_A11_1

value: Planting in the field


title: STZ+HFD model, 32w, treated with control vehicle for 11 weeks, biological replication 3

description:
rawcount_allsamples_mouse.txt
Batch6_STZHFD32w_Vehicle11w_3


title: Rice m6A-IP pistil Rep.3

description:
Os.RNAseq.TPM.csv.gz
IP2_A10_3

source_name: Pistil

value: Pistil

value: anti-m6A antibody


title: w/o Flag-PACT Input biol rep 2


title: STZ+HFD model, 32w, treated with control vehicle for 11 weeks, biological replication 1

description:
rawcount_allsamples_mouse.txt
Batch6_STZHFD32w_Vehicle11w_1

value: Liver

value: Treated


title: w/o Flag-PACT Input biol rep 1


title: Rice m6A-IP mature spikelet Rep.3

description:
Os.RNAseq.TPM.csv.gz
IP2_A9_3

source_name: Mature spikelet (MS)

value: Mature spikelet (MS)

value: WT


title: STZ+HFD model, 32w, treated with control vehicle for 11 weeks, biological replication 2

description:
rawcount_allsamples_mouse.txt
Batch6_STZHFD32w_Vehicle11w_2

value: HFD


title: Rice m6A-IP mature spikelet Rep.2

description:
Os.RNAseq.TPM.csv.gz
IP2_A9_2


title: STZ+HFD model, 50w, dietary change to SCD for 18 weeks, biological replication 4

description:
rawcount_allsamples_mouse.txt
Batch5_Dietchange50w_4

value: 50 weeks

value: HFD for 24 weeks, then changed to SCD for 18 weeks

value: Male

value: Untreated


title: Rice m6A-IP mature spikelet Rep.1

description:
Os.RNAseq.TPM.csv.gz
IP2_A9_1


title: Rice m6A-IP spike neck Rep.3

description:
Os.RNAseq.TPM.csv.gz
IP2_A8_3

source_name: Spike neck (SN)

value: Spike neck (SN)


title: Rice m6A-IP leaf blade Rep.3

description:
Os.RNAseq.TPM.csv.gz
IP1_A7_3

source_name: Leaf blade (LB)

value: Leaf blade (LB)


title: Rice m6A-IP leaf blade Rep.2

description:
Os.RNAseq.TPM.csv.gz
IP1_A7_2


title: Rice m6A-IP spike neck Rep.1

description:
Os.RNAseq.TPM.csv.gz
IP2_A8_1


title: STZ+HFD model, 50w, dietary change to SCD for 18 weeks, biological replication 2

description:
rawcount_allsamples_mouse.txt
Batch5_Dietchange50w_2


title: STZ+HFD model, 50w, dietary change to SCD for 18 weeks, biological replication 3

description:
rawcount_allsamples_mouse.txt
Batch5_Dietchange50w_3


title: Rice m6A-IP pistil Rep.2

description:
Os.RNAseq.TPM.csv.gz
IP2_A10_2


title: Rice m6A-IP spike neck Rep.2

description:
Os.RNAseq.TPM.csv.gz
IP2_A8_2


title: I8A1

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 101-base single-end mode.
Illumina RTA v3.4.4 software was used for base calling.
Generated reads were mapped to the human (hg19) reference genome using TopHat v2.1.1 in combination with Bowtie2 ver. 2.2.8 and SAMtools ver. 0.1.18.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffdiff 2.2.1 with parameter -max-bundle-frags 50000000.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: RD

extract_protocol:
RNA was harvested using ISOGEN II (Nippon Gene) according to the manufacturer’s protocol.
Library preparation was performed using the TruSeq Stranded mRNA sample prep kit (Illumina, San Diego, CA), according to the manufacturer’s instructions.

value: RD

value: human embryo rhabdomyosarcoma cell line

value: RD cells expressing 3A-I8A


title: Rice m6A-IP leaf blade Rep.1

description:
Os.RNAseq.TPM.csv.gz
IP1_A7_1

value: Nipponbare

value: Planting in the field


title: I8A2


title: WT2

value: RD cells expressing wild type 3A protein


title: I10A1

value: RD cells expressing 3A-I10A


title: STZ+HFD model, 50w, dietary change to SCD for 18 weeks, biological replication 1

description:
rawcount_allsamples_mouse.txt
Batch5_Dietchange50w_1

value: Liver

value: Treated


title: Rice m6A-IP auricle, ligule and lamina joint Rep.3

description:
Os.RNAseq.TPM.csv.gz
IP1_A6_3

source_name: Auricle, ligule and lamina joint (ALLJ)

value: Auricle, ligule and lamina joint (ALLJ)

value: WT

value: anti-m6A antibody


title: Rice m6A-IP auricle, ligule and lamina joint Rep.2

description:
Os.RNAseq.TPM.csv.gz
IP1_A6_2


title: Rice m6A-IP leaf sheath Rep.3

description:
Os.RNAseq.TPM.csv.gz
IP1_A5_3

source_name: Leaf sheath (LS)

value: Leaf sheath (LS)


title: Rice m6A-IP auricle, ligule and lamina joint Rep.1

description:
Os.RNAseq.TPM.csv.gz
IP1_A6_1


title: WT1


title: Rice m6A-IP pistil Rep.1

description:
Os.RNAseq.TPM.csv.gz
IP2_A10_1

value: Pistil


title: STZ+HFD model, 50w, without dietary intervention, biological replication 3

description:
rawcount_allsamples_mouse.txt
Batch5_STZHFD50w_3

value: 50 weeks

value: HFD

value: Male

value: Untreated


title: STZ+HFD model, 50w, without dietary intervention, biological replication 4

description:
rawcount_allsamples_mouse.txt
Batch5_STZHFD50w_4


title: Rice m6A-IP leaf sheath Rep.2

description:
Os.RNAseq.TPM.csv.gz
IP1_A5_2


title: Rice m6A-IP leaf sheath Rep.1

description:
Os.RNAseq.TPM.csv.gz
IP1_A5_1


title: Mock2

value: RD

value: human embryo rhabdomyosarcoma cell line

value: RD cells


title: Mock1


title: STZ+HFD model, 50w, without dietary intervention, biological replication 2

description:
rawcount_allsamples_mouse.txt
Batch5_STZHFD50w_2


title: Rice m6A-IP stem Rep.3

description:
Os.RNAseq.TPM.csv.gz
IP1_A4_3

source_name: Stem

value: Stem

value: Nipponbare

value: Planting in the field


title: Rice m6A-IP stem Rep.1

description:
Os.RNAseq.TPM.csv.gz
IP1_A4_1


title: STZ+HFD model, 50w, without dietary intervention, biological replication 1

description:
rawcount_allsamples_mouse.txt
Batch5_STZHFD50w_1

value: Liver


title: Rice m6A-IP stem Rep.2

description:
Os.RNAseq.TPM.csv.gz
IP1_A4_2


title: I10A2

value: RD cells expressing 3A-I10A


title: Rice m6A-IP culm and leaves Rep.1

description:
Os.RNAseq.TPM.csv.gz
IP1_A3_1

source_name: 7day culm and leaves (CL)

value: 7day culm and leaves (CL)

value: 22 degrees C,  light/dark=14h/10h


title: STZ+HFD model, 26w, dietary change to SCD for 6 weeks, biological replication 4

description:
rawcount_allsamples_mouse.txt
Batch4_Dietchange26w_4

value: 26 weeks

value: Treated

value: HFD for 12 weeks, then changed to SCD for 6 weeks

value: WT


title: Rice m6A-IP whole root Rep.3

description:
Os.RNAseq.TPM.csv.gz
IP1_A2_3

source_name: 7day root (WR)

value: 7day root (WR)

value: anti-m6A antibody


title: Rice m6A-IP culm and leaves Rep.3

description:
Os.RNAseq.TPM.csv.gz
IP1_A3_3


title: Rice m6A-IP culm and leaves Rep.2

description:
Os.RNAseq.TPM.csv.gz
IP1_A3_2


title: STZ+HFD model, 26w, dietary change to SCD for 6 weeks, biological replication 3

description:
rawcount_allsamples_mouse.txt
Batch4_Dietchange26w_3

source_name: Liver

value: Male

value: Untreated


title: Rice m6A-IP whole root Rep.2

description:
Os.RNAseq.TPM.csv.gz
IP1_A2_2


title: induced Treg donor#2 day14 by AMRT

city: Kyoto

first: Shin

last: Kaneko

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

department: Department of Cell Growth and Differentiation

institute: Center for iPS Cell Research and Application (CiRA), Kyoto University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Sequenced reads were aligned to human GRCh38 genome reference and quantified gene tag counts as the UMI counts using Cell Ranger v7.0.1.
Assembly: human GRCh38 genome reference
Supplementary files format and content: Tab-separated values file files and matrix files

source_name: induced Treg donor#2 day14 by AMRT

extract_protocol:
Naive CD4+T cells (CD4+CD8-CD25-CD45RA+CCR7+) and CD25+CD127-Treg (CD4+CD8a-CD25highCD127low) were sorted by FACS using CD4+T cells which werer negatively isolated by MACS from purchased frozen PBMCs. iPSC-derived CD4+T cells were differeniated from iPSC-derived hematopoietic progenitor cells by ATO method, and 8 weeks after ATO culture CD4+CD8-CD25- cells were sorted by FACS. The cells were cultured for 7 or 14 days with anti-CD3/28 antibody stimulation in the presence of AMT or AMRT, and library for scRNA-seq was prepared from each sample using Chromium Next GEM Single Cell 3ʹReagent Kits v3.1 (10X Genomics) according to manufacturer instructions.
Library was performed according to manufactur's instruction (10xChromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (Dual Index))

value: induced Treg donor#2 day14 by AMRT


title: Rice m6A-IP root tip Rep.3

description:
Os.RNAseq.TPM.csv.gz
IP1_A1_3

source_name: 7day root tip (RT)

value: 7day root tip (RT)


title: STZ+HFD model, 26w, dietary change to SCD for 6 weeks, biological replication 2

description:
rawcount_allsamples_mouse.txt
Batch4_Dietchange26w_2


title: iCD4+Treg-like day14 by AMRT

description: 10x Genomics

source_name: iPSC-derived CD4+T day14 by AMRT

value: iPSC-derived CD4+T day14 by AMRT


title: iCD4+Treg-like day7 by AMRT

description: 10x Genomics

source_name: iPSC-derived CD4+T day7 by AMRT

value: iPSC-derived CD4+T day7 by AMRT


title: Rice m6A-IP root tip Rep.2

description:
Os.RNAseq.TPM.csv.gz
IP1_A1_2

value: Nipponbare


title: STZ+HFD model, 26w, dietary change to SCD for 6 weeks, biological replication 1

description:
rawcount_allsamples_mouse.txt
Batch4_Dietchange26w_1

value: Liver


title: Rice m6A-IP root tip Rep.1

description:
Os.RNAseq.TPM.csv.gz
IP1_A1_1


title: iPSC-derived CD4+T day0

description: 10x Genomics

source_name: iPSC-derived CD4+T day0

value: iPSC-derived CD4+T day0


title: primary CD25+CD127-Treg donor#1 day14 by AMT

description: 10x Genomics


title: STZ+HFD model, 26w, without dietary intervention, biological replication 3

description:
rawcount_allsamples_mouse.txt
Batch4_STZHFD26w_3

value: HFD


title: primary CD25+CD127-Treg donor#2 day14 by AMT

description: 10x Genomics


title: Rice RNA-Seq&Input Seed III Rep.1

description:
Os.RNAseq.TPM.csv.gz
Input2_A14_1

source_name: Seed III

value: Seed III

value: Planting in the field


title: Rice RNA-Seq&Input Seed II Rep.3

description:
Os.RNAseq.TPM.csv.gz
Input2_A13_3

source_name: Seed II

value: Seed II


title: Rice RNA-Seq&Input Seed III Rep.2

description:
Os.RNAseq.TPM.csv.gz
Input2_A14_2


title: Rice RNA-Seq&Input Seed II Rep.1

description:
Os.RNAseq.TPM.csv.gz
Input2_A13_1


title: induced Treg donor#1 day14 by AMRT

description: 10x Genomics

source_name: induced Treg donor#1 day14 by AMRT

value: induced Treg donor#1 day14 by AMRT


title: Rice RNA-Seq&Input Seed II Rep.2

description:
Os.RNAseq.TPM.csv.gz
Input2_A13_2

value: WT


title: Rice RNA-Seq&Input Seed III Rep.3

description:
Os.RNAseq.TPM.csv.gz
Input2_A14_3


title: STZ+HFD model, 26w, without dietary intervention, biological replication 2

description:
rawcount_allsamples_mouse.txt
Batch4_STZHFD26w_2

value: 26 weeks

value: Treated


title: Rice m6A-IP whole root Rep.1

description:
Os.RNAseq.TPM.csv.gz
IP1_A2_1

value: 7day root (WR)

value: 22 degrees C,  light/dark=14h/10h

value: anti-m6A antibody


title: STZ+HFD model, 26w, without dietary intervention, biological replication 1

description:
rawcount_allsamples_mouse.txt
Batch4_STZHFD26w_1

value: Male

value: Untreated


title: Rice RNA-Seq&Input Seed I Rep.1

description:
Os.RNAseq.TPM.csv.gz
Input2_A12_1

source_name: Seed I

value: Seed I


title: HFD fed mice without STZ treatment, 20w, biological replication 5

description:
rawcount_allsamples_mouse.txt
Batch2_HFDonly20w_5

value: 20 weeks


title: primary CD25+CD127-Treg donor #2 day0

description: 10x Genomics

source_name: primary CD25+CD127-Treg donor #2 day0

value: primary CD25+CD127-Treg donor #2 day0


title: Rice RNA-Seq&Input pollen Rep.3

description:
Os.RNAseq.TPM.csv.gz
Input2_A11_3

source_name: Pollen

value: Pollen

value: Nipponbare


title: primary CD25+CD127-Treg donor #1 day0

description: 10x Genomics

source_name: primary CD25+CD127-Treg donor #1 day0

value: primary CD25+CD127-Treg donor #1 day0


title: Rice RNA-Seq&Input Seed I Rep.3

description:
Os.RNAseq.TPM.csv.gz
Input2_A12_3

value: Planting in the field


title: BeWo,input

city: Xiamen

first: wanshan

last: zheng

state: Fujian

address: Xiang'an Road

department: School of Medicine,

institute: Xiamen University

library_source: genomic

data_processing:
Sequencing was performed using an Illumina NovaSeq 6000. The Illumina Genome Analysis pipeline was used for data processing, and the human genome (hg38) was used as the reference genome. Only reads aligned once were saved, and peak calling was performed using MACS v2.2.6 with default settings.
Assembly: hg38
Supplementary files format and content: TDF, narrowPeak

molecule: genomic DNA

source_name: BeWo

growth_protocol: BeWo cells (ATCC, #CCL-98) were maintained in DMEM/F12 Medium (Gibco, #C11330500BT) supplemented with 10% FBS under a stable environment (at 37 °C and 5% CO2).

extract_protocol:
2× 107 BeWo were crosslinked with 1% formaldehyde (CST, #12606) diluted in PBS for 10 minutes at room temperature with rotation followed by 0.125 M Glycine treatment to quench the fixation. First, the cell nuclei were sequentially lysed, pelleted, and resuspended.2× 107 BeWo were crosslinked with 1% formaldehyde (CST, #12606) diluted in PBS for 10 minutes at room temperature with rotation followed by 0.125 M Glycine treatment to quench the fixation. First, the cell nuclei were sequentially lysed, pelleted, and resuspended
ChIP-seq libraries were built using the KAPA DNA HyperPrep Kit (Roche, #KK8502) following the manufacturer's instructions.

value: BeWo


title: Rice RNA-Seq&Input pollen Rep.2

description:
Os.RNAseq.TPM.csv.gz
Input2_A11_2


title: STZ+HFD model, 26w, without dietary intervention, biological replication 4

description:
rawcount_allsamples_mouse.txt
Batch4_STZHFD26w_4

value: Liver

value: HFD


title: HFD fed mice without STZ treatment, 20w, biological replication 3

description:
rawcount_allsamples_mouse.txt
Batch2_HFDonly20w_3

value: WT


title: HFD fed mice without STZ treatment, 20w, biological replication 4

description:
rawcount_allsamples_mouse.txt
Batch2_HFDonly20w_4


title: Rice RNA-Seq&Input pollen Rep.1

description:
Os.RNAseq.TPM.csv.gz
Input2_A11_1


title: NAFLD patient, NAFLD activity score 4-7, fibrosis stage 4, biological replication 5

description:
rawcount_allsamples_human.txt
Human_NAFLD_27

value: Female


title: BeWo,TFEB ChIP seq

value: Tfeb(CST, #D2O7D)


title: Rice RNA-Seq&Input pistil Rep.3

description:
Os.RNAseq.TPM.csv.gz
Input2_A10_3

source_name: Pistil

value: Pistil


title: Rice RNA-Seq&Input pistil Rep.2

description:
Os.RNAseq.TPM.csv.gz
Input2_A10_2


title: Rice RNA-Seq&Input mature spikelet Rep.2

description:
Os.RNAseq.TPM.csv.gz
Input2_A9_2

source_name: Mature spikelet (MS)

value: Mature spikelet (MS)


title: NAFLD patient, NAFLD activity score 4-7, fibrosis stage 4, biological replication 3

description:
rawcount_allsamples_human.txt
Human_NAFLD_25


title: STZ+ SCD mice, 20w, biological replication 2

description:
rawcount_allsamples_mouse.txt
Batch2_STZSCD20w_2

value: Treated

value: SCD

value: Male


title: HFD fed mice without STZ treatment, 20w, biological replication 2

description:
rawcount_allsamples_mouse.txt
Batch2_HFDonly20w_2

value: 20 weeks

value: Untreated


title: Rice RNA-Seq&Input Seed I Rep.2

description:
Os.RNAseq.TPM.csv.gz
Input2_A12_2

value: Seed I


title: NAFLD patient, NAFLD activity score 4-7, fibrosis stage 4, biological replication 2

description:
rawcount_allsamples_human.txt
Human_NAFLD_24


title: NAFLD patient, NAFLD activity score 4-7, fibrosis stage 4, biological replication 6

description:
rawcount_allsamples_human.txt
Human_NAFLD_28


title: HFD fed mice without STZ treatment, 20w, biological replication 1

description:
rawcount_allsamples_mouse.txt
Batch2_HFDonly20w_1


title: NAFLD patient, NAFLD activity score 4-7, fibrosis stage 4, biological replication 4

description:
rawcount_allsamples_human.txt
Human_NAFLD_26


title: NAFLD patient, NAFLD activity score 4-7, fibrosis stage 4, biological replication 1

description:
rawcount_allsamples_human.txt
Human_NAFLD_23


title: Rice RNA-Seq&Input mature spikelet Rep.3

description:
Os.RNAseq.TPM.csv.gz
Input2_A9_3

value: Nipponbare


title: STZ+ SCD mice, 20w, biological replication 3

description:
rawcount_allsamples_mouse.txt
Batch2_STZSCD20w_3


title: Rice RNA-Seq&Input spike neck Rep.3

description:
Os.RNAseq.TPM.csv.gz
Input2_A8_3

source_name: Spike neck (SN)

value: Spike neck (SN)


title: Rice RNA-Seq&Input pistil Rep.1

description:
Os.RNAseq.TPM.csv.gz
Input2_A10_1

value: Planting in the field


title: NAFLD patient, NAFLD activity score 5-6, fibrosis stage 3, biological replication 6

description:
rawcount_allsamples_human.txt
Human_NAFLD_22

source_name: Liver


title: dmv11

type: RNA

city: Akita

first: Takako

last: Ohnuma

state: Akita

department: ARGG

institute: Akita University

hyb_protocol: After complementary RNA had been fragmented to sizes ranging from 35 to 200 bases by heating(35 min at 95℃), 10μg of RNA fragments were hybridized (16h at 45℃) to the Affimetrix Mouse Clariom S Array which interrogates over 20800 well annotated genes.

scan_protocol: The gene chips were automatically washed and stained with streptavidin-phycoerythrin bythe GeneCip Fluidis Statio 450.The chips were scannedusing the GeneChip Scanner 300 7G.

data_processing:
Primary data analysis was performed with the Affymetrix Transcriptome Analysis Console(TAC) software and normalized and following the TAC user guide.
Each analysis of varoance was perpormed by one-way ANOVA. To determine the significance of differentially expressed genes, a cut-off for the fold change value±1.5 and p-value＜0.05 was applied.

label: biotin

source_name: tissue

label_protocol: Doublw stranded cDNA synthesis and biotin-labeled cRNA was performed with GeneChip WT Plus Kit.

extract_protocol: Mouse muscle tissues were used as samples. Total RNA was isolated with QIAGEN Rnesy Lipid Tissue Mini kit.

value: Triceps muscles

value: 5 weeks of Unmodulated 40 Hz stimulation


title: Rice RNA-Seq&Input spike neck Rep.2

description:
Os.RNAseq.TPM.csv.gz
Input2_A8_2


title: Control SCD fed mice without STZ treatment, 20w, biological replication 4

description:
rawcount_allsamples_mouse.txt
Batch2_SCDonly20w_4

value: Liver


title: Control SCD fed mice without STZ treatment, 20w, biological replication 3

description:
rawcount_allsamples_mouse.txt
Batch2_SCDonly20w_3

value: WT


title: con8

value: control


title: dmv4


title: dmv10


title: Rice RNA-Seq&Input spike neck Rep.1

description:
Os.RNAseq.TPM.csv.gz
Input2_A8_1


title: Control SCD fed mice without STZ treatment, 20w, biological replication 1

description:
rawcount_allsamples_mouse.txt
Batch2_SCDonly20w_1


title: DP bb 5

city: Denver

first: Philippa

last: Marrack

state: CO

address: 1400 Jackson St

department: Immunology & Genomic Medicine

institute: National Jewish Health

data_processing:
MKION VDJ sequence analysis v 1.0
Sequence reads were trimmed for short and long reads (>100nt, <800nt)
Out-of-frame sequences were recovered by repairing the TRAJ segment by mapping back to germline
Organize by clonotype and reformat columns into immunarch format
Assembly: mm9
Supplementary files format and content: Comma-separated text file including ranked TCR clonotype counts for each Sample
Library strategy: TCR-Seq

source_name: Tymus

extract_protocol:
Mice were euthanized, and axillary, brachial, inguinal, mesenteric, lumbar, and caudal lymph nodes were collected and filtered through a sterile 100µM filter. Cells were resuspended and washed 3x in BSS in a 15 ml conical tube. Cells were counted and resuspended in BSS supplemented with 1% BSA and anti-mouse CD16/CD32 (Clone: 2.4G2), as a pre-treatment reagent to block non-antigen-specific interactions of immunoglobulins to the FcγIII and FcγII, and possibly FcγI. Lymphocytes were stained with antibodies specific to TCRβ, CD45R, CD4, CD8, CD44, CD62L, and CD25 for 30 mins, washed 3x in BSS wash buffer. Cells were resuspended at 107/ml and fluorescently sorted for naïve lymphocytes on an iCyt Synergy.
RNA was isolated from purified naïve CD4 T cells using the RNeasy Kit (Invitrogen).  cDNA was made using the SuperScript VILO Kit (Invitrogen). For sequencing of TCR α-chains, a two-step PCR was done which added the machine oligonucleotides as well as barcodes for the sequencing runs. The first PCR included a reverse oligonucleotide in the constant region of the α-chain and a mixture of forward oligonucleotides that together cover all the different TCRα family members. The sequence or sequences for each TRAV family are as follows: TRAV01: GAGGGAACCTTTGCTCGGGTC; TRAV02: TATGAAGGGCAAGAAGTGAAC; TRAV03: CArGTCTTCAGTTGCTTATGA; TRAV04: TGCTCTGAGATGCAATTTTwC; TRAV05a: GGTGGAACAGCTCCCTTCCTC; TRAV05b: ATGGCTGCAGCTGGATGGGA; TRAV06a: GGACAAGGTCCACAGCTCCT; TRAV06b: GGAGAAGGTCCACAGCTCCTC; TRAV06c: GTCCAATATCCTGGAGAAGG; TRAV07: AGCAGAGCCCAGAATCCCTCA; TRAV08: AAAGAGCCAATGGGGAGAAG; TRAV08, GAATAGTCAACTAGCAGAAG; TRAV09: AGCTGAGATGCAAsTATTCCT; TRAV10: ACTTACACAGATACTGCyTCA; TRAV11: CACAGGCAAAGGTCTTGTGTC; TRAV12: GCTGAACTGCACCTATCAGA; TRAV13: TGGTTCTGCAGGAGGGGGArA; TRAV14: GTCCCCAATCTCTGACAGTCT; TRAV15: ACTGTTCATATrAGACAAGT; TRAV16: TGGAGAAGACAACGGTGACA; TRAV17: GTTATTCATACAGTGCAGCAC; TRAV18: ACCGCACGCTGCAGCTCCTCA; TRAV19: TACCCTGACAACAGCCCCACA; TRAV21: GTAGCCACGCCACAATCAGTG. The second PCR included just one forward oligonucleotide to add the machine oligonucleotide and a reverse oligonucleotide to add the barcode. For TCR β-chains, one PCR was done that contained a forward oligonucleotide priming all three TRBV13 family members at an identical region, the sequencing machine oligonucleotide CCACTACGCCTCCGCTTTCCTCTCTATGGGCAGTCGGTGATGCTGAGGCTGATCCATTA, and a reverse oligonucleotide that primed the Cβ region and contained the machine oligonucleotide and the barcode, CCATCTCATCCCTGCGTGTCTCCGACTCAGCTAAGGTAACGATCTTGGGTGGAGTCACATTTCTC.

value: Tymus

value: preselection thymocyte

value: bb


title: con1


title: NAFLD patient, NAFLD activity score 5-6, fibrosis stage 3, biological replication 5

description:
rawcount_allsamples_human.txt
Human_NAFLD_21


title: con6


title: Rice RNA-Seq&Input mature spikelet Rep.1

description:
Os.RNAseq.TPM.csv.gz
Input2_A9_1

value: Mature spikelet (MS)


title: STZ+HFD model, 56w, hepatic tumor ID 25

description:
rawcount_allsamples_mouse.txt
Batch1_STZHFD56w_T25

source_name: Liver (tumor)

value: Liver (tumor)

value: 56 weeks

value: Treated

value: HFD


title: STZ+ SCD mice, 20w, biological replication 1

description:
rawcount_allsamples_mouse.txt
Batch2_STZSCD20w_1

value: 20 weeks

value: SCD

value: Male

value: Untreated


title: NAFLD patient, NAFLD activity score 5-6, fibrosis stage 3, biological replication 4

description:
rawcount_allsamples_human.txt
Human_NAFLD_20


title: CD8 g7g7 3

source_name: Peripheral lymph nodes

value: Peripheral lymph nodes

value: naive CD8 T cell


title: NAFLD patient, NAFLD activity score 5-6, fibrosis stage 3, biological replication 3

description:
rawcount_allsamples_human.txt
Human_NAFLD_19

value: Liver


title: Rice RNA-Seq&Input leaf blade Rep.3

description:
Os.RNAseq.TPM.csv.gz
Input1_A7_3

source_name: Leaf blade (LB)

value: Leaf blade (LB)

value: Nipponbare

value: WT

value: Planting in the field


title: Control SCD fed mice without STZ treatment, 20w, biological replication 2

description:
rawcount_allsamples_mouse.txt
Batch2_SCDonly20w_2


title: DP bb 4

value: Tymus

value: preselection thymocyte

value: bb


title: NAFLD patient, NAFLD activity score 5-6, fibrosis stage 3, biological replication 2

description:
rawcount_allsamples_human.txt
Human_NAFLD_18


title: DP bb 6


title: CD8 g7g7 1


title: STZ+HFD model, 56w, hepatic tumor ID 22

description:
rawcount_allsamples_mouse.txt
Batch1_STZHFD56w_T22

value: Liver (tumor)

value: 56 weeks


title: NAFLD patient, NAFLD activity score 5-6, fibrosis stage 3, biological replication 1

description:
rawcount_allsamples_human.txt
Human_NAFLD_17

value: Female


title: NAFLD patient, NAFLD activity score 5-6, fibrosis stage 2, biological replication 5

description:
rawcount_allsamples_human.txt
Human_NAFLD_16


title: STZ+HFD model, 56w, hepatic tumor ID 24

description:
rawcount_allsamples_mouse.txt
Batch1_STZHFD56w_T24

value: Treated

value: HFD


title: Rice RNA-Seq&Input auricle, ligule and lamina joint Rep.3

description:
Os.RNAseq.TPM.csv.gz
Input1_A6_3

source_name: Auricle, ligule and lamina joint (ALLJ)

value: Auricle, ligule and lamina joint (ALLJ)


title: CD8 ff 3

value: ff


title: Rice RNA-Seq&Input auricle, ligule and lamina joint Rep.2

description:
Os.RNAseq.TPM.csv.gz
Input1_A6_2


title: Rice RNA-Seq&Input leaf blade Rep.2

description:
Os.RNAseq.TPM.csv.gz
Input1_A7_2


title: CD8 g7g7 2

value: Peripheral lymph nodes


title: NAFLD patient, NAFLD activity score 5-6, fibrosis stage 2, biological replication 4

description:
rawcount_allsamples_human.txt
Human_NAFLD_15


title: CD8 ff 2

value: naive CD8 T cell


title: CD8 ff 1


title: STZ+HFD model, 56w, hepatic tumor ID 14

description:
rawcount_allsamples_mouse.txt
Batch1_STZHFD56w_T14

value: Male

value: Untreated


title: Rice RNA-Seq&Input auricle, ligule and lamina joint Rep.1

description:
Os.RNAseq.TPM.csv.gz
Input1_A6_1

value: Nipponbare


title: Rice RNA-Seq&Input leaf blade Rep.1

description:
Os.RNAseq.TPM.csv.gz
Input1_A7_1

value: Leaf blade (LB)

value: WT


title: NAFLD patient, NAFLD activity score 5-6, fibrosis stage 2, biological replication 2

description:
rawcount_allsamples_human.txt
Human_NAFLD_13

value: Liver


title: STZ+HFD model, 56w, hepatic tumor ID 13

description:
rawcount_allsamples_mouse.txt
Batch1_STZHFD56w_T13


title: CD8 bb 2


title: Rice RNA-Seq&Input leaf sheath Rep.3

description:
Os.RNAseq.TPM.csv.gz
Input1_A5_3

source_name: Leaf sheath (LS)

value: Leaf sheath (LS)

value: Planting in the field


title: STZ+HFD model, 50w, hepatic tumor ID 11

description:
rawcount_allsamples_mouse.txt
Batch1_STZHFD50w_T11

value: Liver (tumor)

value: 50 weeks


title: CD8 bb 1

value: bb


title: NAFLD patient, NAFLD activity score 5-6, fibrosis stage 2, biological replication 1

description:
rawcount_allsamples_human.txt
Human_NAFLD_12


title: STZ+HFD model, 50w, hepatic tumor ID 10

description:
rawcount_allsamples_mouse.txt
Batch1_STZHFD50w_T10

value: Treated


title: NAFLD patient, NAFLD activity score 5-6, fibrosis stage 1, biological replication 5

description:
rawcount_allsamples_human.txt
Human_NAFLD_11


title: CD4 ss 4

value: naive CD4 T cell

value: ss


title: Rice RNA-Seq&Input stem Rep.3

description:
Os.RNAseq.TPM.csv.gz
Input1_A4_3

source_name: Stem

value: Stem


title: Rice RNA-Seq&Input stem Rep.2

description:
Os.RNAseq.TPM.csv.gz
Input1_A4_2


title: CD4 ss 2

value: Peripheral lymph nodes


title: STZ+HFD model, 50w, hepatic tumor ID 09

description:
rawcount_allsamples_mouse.txt
Batch1_STZHFD50w_T09

value: HFD


title: NAFLD patient, NAFLD activity score 5-6, fibrosis stage 1, biological replication 4

description:
rawcount_allsamples_human.txt
Human_NAFLD_10

value: Male


title: CD4 g7g7 3


title: STZ+HFD model, 56w, hepatic tumor ID 18

description:
rawcount_allsamples_mouse.txt
Batch1_STZHFD56w_T18

value: 56 weeks

value: Untreated


title: STZ+HFD model, 50w, hepatic tumor ID 07

description:
rawcount_allsamples_mouse.txt
Batch1_STZHFD50w_T07


title: NAFLD patient, NAFLD activity score 5-6, fibrosis stage 2, biological replication 3

description:
rawcount_allsamples_human.txt
Human_NAFLD_14


title: Rice RNA-Seq&Input stem Rep.1

description:
Os.RNAseq.TPM.csv.gz
Input1_A4_1

value: Nipponbare


title: NAFLD patient, NAFLD activity score 5-6, fibrosis stage 1, biological replication 2

description:
rawcount_allsamples_human.txt
Human_NAFLD_08


title: STZ+HFD model, 44w, hepatic tumor ID 06

description:
rawcount_allsamples_mouse.txt
Batch1_STZHFD44w_T06

value: 44 weeks

value: WT


title: NAFLD patient, NAFLD activity score 5-6, fibrosis stage 1, biological replication 1

description:
rawcount_allsamples_human.txt
Human_NAFLD_07

value: Liver


title: Rice RNA-Seq&Input culm and leaves Rep.3

description:
Os.RNAseq.TPM.csv.gz
Input1_A3_3

source_name: 7day culm and leaves (CL)

value: 7day culm and leaves (CL)

value: 22 degrees C,  light/dark=14h/10h


title: Rice RNA-Seq&Input leaf sheath Rep.2

description:
Os.RNAseq.TPM.csv.gz
Input1_A5_2

value: Leaf sheath (LS)

value: Planting in the field


title: Rice RNA-Seq&Input leaf sheath Rep.1

description:
Os.RNAseq.TPM.csv.gz
Input1_A5_1


title: Rice RNA-Seq&Input culm and leaves Rep.2

description:
Os.RNAseq.TPM.csv.gz
Input1_A3_2


title: CD4 g7g7 1


title: STZ+HFD model, 44w, hepatic tumor ID 04

description:
rawcount_allsamples_mouse.txt
Batch1_STZHFD44w_T04

value: Liver (tumor)

value: Treated


title: CD4 ff 6

value: naive CD4 T cell

value: ff


title: NAFLD patient, NAFLD activity score 2-3, fibrosis stage 1, biological replication 6

description:
rawcount_allsamples_human.txt
Human_NAFLD_06


title: Rice RNA-Seq&Input culm and leaves Rep.1

description:
Os.RNAseq.TPM.csv.gz
Input1_A3_1


title: NAFLD patient, NAFLD activity score 2-3, fibrosis stage 1, biological replication 5

description:
rawcount_allsamples_human.txt
Human_NAFLD_05


title: NAFLD patient, NAFLD activity score 5-6, fibrosis stage 1, biological replication 3

description:
rawcount_allsamples_human.txt
Human_NAFLD_09


title: STZ+HFD model, 44w, hepatic tumor ID 03

description:
rawcount_allsamples_mouse.txt
Batch1_STZHFD44w_T03


title: Rice RNA-Seq&Input whole root Rep.3

description:
Os.RNAseq.TPM.csv.gz
Input1_A2_3

source_name: 7day root (WR)

value: 7day root (WR)


title: STZ+HFD model, 56w, biological replication 6

description:
rawcount_allsamples_mouse.txt
Batch1_STZHFD56w_6

value: HFD


title: CD4 ff 4

value: Peripheral lymph nodes


title: STZ+HFD model, 44w, hepatic tumor ID 05

description:
rawcount_allsamples_mouse.txt
Batch1_STZHFD44w_T05

value: Male


title: NAFLD patient, NAFLD activity score 2-3, fibrosis stage 1, biological replication 4

description:
rawcount_allsamples_human.txt
Human_NAFLD_04


title: CD4 ff 1


title: CD4 g7g7 2


title: STZ+HFD model, 56w, biological replication 5

description:
rawcount_allsamples_mouse.txt
Batch1_STZHFD56w_5

value: 56 weeks

value: Untreated


title: STZ+HFD model, 56w, biological replication 4

description:
rawcount_allsamples_mouse.txt
Batch1_STZHFD56w_4


title: Rice RNA-Seq&Input whole root Rep.1

description:
Os.RNAseq.TPM.csv.gz
Input1_A2_1

value: Nipponbare


title: NAFLD patient, NAFLD activity score 2-3, fibrosis stage 1, biological replication 3

description:
rawcount_allsamples_human.txt
Human_NAFLD_03


title: CD4 bxg7 4


title: NAFLD patient, NAFLD activity score 2-3, fibrosis stage 1, biological replication 2

description:
rawcount_allsamples_human.txt
Human_NAFLD_02


title: CD4 bxg7 3


title: CD4 bxg7 2


title: STZ+HFD model, 56w, biological replication 3

description:
rawcount_allsamples_mouse.txt
Batch1_STZHFD56w_3

value: WT


title: NAFLD patient, NAFLD activity score 2-3, fibrosis stage 1, biological replication 1

description:
rawcount_allsamples_human.txt
Human_NAFLD_01

value: Liver


title: Healthy liver donor, biological replication 4

description:
rawcount_allsamples_human.txt
Human_Healthy_04


title: CD4 ff 5


title: STZ+HFD model, 56w, biological replication 1

description:
rawcount_allsamples_mouse.txt
Batch1_STZHFD56w_1


title: Rice RNA-Seq&Input root tip Rep.1

description:
Os.RNAseq.TPM.csv.gz
Input1_A1_1

source_name: 7day root tip (RT)

value: 7day root tip (RT)


title: CD4 bxg7 1


title: STZ+HFD model, 56w, biological replication 2

description:
rawcount_allsamples_mouse.txt
Batch1_STZHFD56w_2


title: Rice RNA-Seq&Input root tip Rep.2

description:
Os.RNAseq.TPM.csv.gz
Input1_A1_2

value: 22 degrees C,  light/dark=14h/10h


title: Rice RNA-Seq&Input whole root Rep.2

description:
Os.RNAseq.TPM.csv.gz
Input1_A2_2


title: STZ+HFD model, 50w, biological replication 4

description:
rawcount_allsamples_mouse.txt
Batch1_STZHFD50w_4

value: 50 weeks


title: Healthy liver donor, biological replication 3

description:
rawcount_allsamples_human.txt
Human_Healthy_03


title: CD4 bxf 6

value: bxf


title: Healthy liver donor, biological replication 2

description:
rawcount_allsamples_human.txt
Human_Healthy_02


title: STZ+HFD model, 50w, biological replication 3

description:
rawcount_allsamples_mouse.txt
Batch1_STZHFD50w_3


title: CD4 bxf 5


title: Rice RNA-Seq&Input root tip Rep.3

description:
Os.RNAseq.TPM.csv.gz
Input1_A1_3


title: CD4 bxf 4


title: STZ+HFD model, 50w, biological replication 2

description:
rawcount_allsamples_mouse.txt
Batch1_STZHFD50w_2


title: STZ+HFD model, 50w, biological replication 1

description:
rawcount_allsamples_mouse.txt
Batch1_STZHFD50w_1


title: Micro-C_MOLM13_Tet2Delta

city: Houston

first: Jia

last: Li

state: Texas

address: 2121 W HOLCOMBE BLVD

department: CEDP

institute: Guangzhou Medical University

data_processing:
RNA-seq data were mapped to the hg19 or mm10 genome assembly using STAR (version=2.7.10a) with default parameters. DESeq2 was used to call significantly differentially expressed genes (DEGs; log2 fold change >= 1 or <= -1, q-value < = 0.05) between MOLM13 expression TET2CD and TET2CDΔLCI.
Raw WGBS fastq files were mapped to the hg19/mm10 genome assembly using the bsmap-2.89 software with “-v 6 -n 1 -q 3 -r 1” parameters. The bisulfite conversion ratios were estimated using unmethylated lambda DNA. Mcall modual in MOABS (56) was used to call the mCG/CG ratios for each CpG site. Mcomp modual was used to call DMRs with parameter “–minNominalDif = 0.2–minDmcsInDmr 3–maxDistConsDmcs 500”. The CpGs with coverage > = 5 was used for downstream analysis.
Raw DamID fastq data were aligned to mm10 genome assembly using bowtie2.4.5 with default parameters. Mapped DamID data were analyzed by damidseq_pipeline (55). Specifically, sequencing fragments located on GATC sites were counted, normalized and bedGraph file with DamID-fusion / DamID-only log2ratio were generated. Find_peaks perl script in damidseq_pipeline was used to call significant peaks. The genome was splitted into 5k bins and the mean signals of mESC Flag-Tet2 ChIP, Dam-fusion with Tet2CD/Dam-only ratios, mESC H3K27ac and mESC H3K9me3 on each 5k bin were calculated. The pearson correlation coefficient among them were calculated and plotted. IGV was used to visualize the tracks.
Raw CMS-IP fastq data were mapped to the mm10/hg19 genome assembly using bsmap-2.89 with default parameters. After duplication removal, CMS peaks were called by using macs2 with default parameters. Bedtools merge was used to generate merged peaks for all samples. Reads numbers in each peak were counted if there was >1 bp overlap between reads location and peak region. The raw counts file with row as each peak, column as samples was used as input to DESeq2 and differentially significantly CMS peaks (q value < = 0.05) between the control and TET2CD or control and TET2CDΔLCI groups were called. Volcano plots were plotted using the R package ggplot2.
For Micro-C data analysis, we used Micro-C data analysis pipeline in https://micro-c.readthedocs.io/en/latest/ to process Micro-C data. Specifically, we used bwa-mem (0.7.17) algorithm to map raw fastqs on hg19 version genome with the following command: bwa mem -5SP -T0 -t16 hg38.fasta MicroC_2M_R1.fastq MicroC_2M_R2.fastq -o aligned.sam. PCR duplicates were removed. Pairtools pipeline was used to identify ligation event from mapping results and the validate pairs was extracted for downstream analysis. Juice box tools (57) was used to generate contact matrix (*.hic) data which can be visualize in Juicebox. runHiCpca.pl in Homer was used to calculate PCA1 value (A/B comparment) for 50k bins and the PCA1 value was corrected by using MOLM13 H3K27ac data (GSM2136938).
Assembly: mm10/hg19
Library strategy: Micro-C

growth_protocol: MOLM13 cells were maintained in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.0 ug of total RNA was used for the construction of sequencing libraries.Purified genomic DNA (30 ng, spiked in with 5% of unmethylated lambda genomic DNA, Promega) was sheared to 200–500 bp using Covaris M220 (Covaris, MA).
RNA libraries for RNA-seq were prepared using NEBNext Ultra Directional RNA Library Prep Kit (NEB #7760) following manufacturer's protocols. WGBS: The shared genomic DNA were then performed subjected t using EZ DNA methylation-lightning kit (Zymo Research) according to manufacturer’s instructions. The bisulfite treated genomic DNA were further proceeded to library preparation with xGenTM Methyl Seq DNA Library Prep Kit (IDT, CA) following the manufactures’ instructions. DamID:1 µg genomic DNA from mESCs expressing DamID only, TET2CD-Dam or TET2CDΔLCI-Dam is extracted and digested with DpnI (NEB,R0176) for 12 hrs at 37 °C. The digested DNA was purified by QIAquick PCR Purification Kit (Qiagen) to exclude uncut genomic DNA. Adaptors are ligated to the DpnI cutting fragments for PCR amplification. After digested with DpnII (NEB,R0543), DNA was then used as template for a PCR reaction to amplify the methylated fragments. DNA was then purified and sonicated into 200-300 bp for end repair, 3’ end adenylation and sequencing adaptor ligation. The enriched libraries are pooled and subjected to high-throughput sequencing. Micro-C:Micro-C libraries were prepared with Micro-C Kit (Dovetail, CA) following the manufacturer’s instructions. In brief, 1 million cells were resuspended and fixed by freshly made DSG (3 mM) for 15 min and then formaldehyde (1%) for another 10 min at room temperature. The crosslinking reaction was quenched with Tris buffer (pH = 7.5) to the final 0.75 M at room temperature. Fixed cells were washed twice and then subjected to chromatin fragmentation via MNase digestion for 15 min. After end repairing and proximity ligation, DNA were purified with streptavidin beads and adaptor ligation was performed on beads. An optimal PCR cycle for final library amplification was determined by quantification PCR and libraries were pooled and sequenced on Illumina Nova-seq platform with paired-end, 150/8/8/150 mode.

treatment_protocol: TETs expression was induced by treatment of 1ug/ml Doxcyclin (Sigma) 24 or48  hours post 70% confluent cells.

value: Leukemia cell

value: TET2-CD{delta}LCI 48 hours

value: doxcyclin

tag: time


title: CD4 bb&ff 5

value: naive CD4 T cell

value: bb&ff


title: Healthy liver donor, biological replication 1

description:
rawcount_allsamples_human.txt
Human_Healthy_01


title: MOLM13_TET2-CDΔLCI_48h

data_processing:
RNA-seq data were mapped to the hg19 or mm10 genome assembly using STAR (version=2.7.10a) with default parameters. DESeq2 was used to call significantly differentially expressed genes (DEGs; log2 fold change >= 1 or <= -1, q-value < = 0.05) between MOLM13 expression TET2CD and TET2CDΔLCI.
Raw WGBS fastq files were mapped to the hg19/mm10 genome assembly using the bsmap-2.89 software with “-v 6 -n 1 -q 3 -r 1” parameters. The bisulfite conversion ratios were estimated using unmethylated lambda DNA. Mcall modual in MOABS (56) was used to call the mCG/CG ratios for each CpG site. Mcomp modual was used to call DMRs with parameter “–minNominalDif = 0.2–minDmcsInDmr 3–maxDistConsDmcs 500”. The CpGs with coverage > = 5 was used for downstream analysis.
Raw DamID fastq data were aligned to mm10 genome assembly using bowtie2.4.5 with default parameters. Mapped DamID data were analyzed by damidseq_pipeline (55). Specifically, sequencing fragments located on GATC sites were counted, normalized and bedGraph file with DamID-fusion / DamID-only log2ratio were generated. Find_peaks perl script in damidseq_pipeline was used to call significant peaks. The genome was splitted into 5k bins and the mean signals of mESC Flag-Tet2 ChIP, Dam-fusion with Tet2CD/Dam-only ratios, mESC H3K27ac and mESC H3K9me3 on each 5k bin were calculated. The pearson correlation coefficient among them were calculated and plotted. IGV was used to visualize the tracks.
Raw CMS-IP fastq data were mapped to the mm10/hg19 genome assembly using bsmap-2.89 with default parameters. After duplication removal, CMS peaks were called by using macs2 with default parameters. Bedtools merge was used to generate merged peaks for all samples. Reads numbers in each peak were counted if there was >1 bp overlap between reads location and peak region. The raw counts file with row as each peak, column as samples was used as input to DESeq2 and differentially significantly CMS peaks (q value < = 0.05) between the control and TET2CD or control and TET2CDΔLCI groups were called. Volcano plots were plotted using the R package ggplot2.
For Micro-C data analysis, we used Micro-C data analysis pipeline in https://micro-c.readthedocs.io/en/latest/ to process Micro-C data. Specifically, we used bwa-mem (0.7.17) algorithm to map raw fastqs on hg19 version genome with the following command: bwa mem -5SP -T0 -t16 hg38.fasta MicroC_2M_R1.fastq MicroC_2M_R2.fastq -o aligned.sam. PCR duplicates were removed. Pairtools pipeline was used to identify ligation event from mapping results and the validate pairs was extracted for downstream analysis. Juice box tools (57) was used to generate contact matrix (*.hic) data which can be visualize in Juicebox. runHiCpca.pl in Homer was used to calculate PCA1 value (A/B comparment) for 50k bins and the PCA1 value was corrected by using MOLM13 H3K27ac data (GSM2136938).
Assembly: mm10/hg19

value: Human Leukemia cell line


title: STZ+HFD model, 44w, biological replication 5

description:
rawcount_allsamples_mouse.txt
Batch1_STZHFD44w_5

value: 44 weeks

value: Treated

value: HFD


title: STZ+HFD model, 44w, biological replication 4

description:
rawcount_allsamples_mouse.txt
Batch1_STZHFD44w_4

value: Male

value: Untreated


title: MOLM13_TET2-CDΔLCI_24h

value: TET2-CD{delta}LCI 24 hours


title: CD4 bb&ff 4

value: Peripheral lymph nodes


title: CD4 bb&ff 2


title: MOLM13_Tet2CD_48h

value: TET2 CD 48 hours


title: CD4 bb&ff 3


title: Micro-C_MOLM13_Tet2CD


title: AML_compound 9a_rep7

city: paris

first: Jerome

last: Tamburini

address: 22 rue mechain

country: France

institute: Cochin Institute

hyb_protocol: cDNA were hybridized to GeneChip® Clariom S Human (Affymetrix) at 45°C for 17 hours, then washed on the fluidic station FS450 (Affymetrix)

scan_protocol: GCS3000 7G (Thermo Fischer Scientific)

data_processing: Raw fluorescence intensity values were normalized using Robust Multiarray Average (RMA) algorithm in R to generate the normalized data matrix by performing background correction, quantile normalization and log2 transformation of raw fluorescence intensity values of each gene. All quality controls and statistics were performed using Partek® Genomics Suite software (Partek, St. Louis, MO, USA). Data were normalized using custom brainarray CDF files (v20 ENTREZG). To identify differentially expressed genes, we applied a classical analysis of variance (ANOVA) with a FDR permutation-base for each gene. We created a matrix with only the significant ANOVA site and performed Z-scoring of rows. Hierarchical clustering by Pearson's dissimilarity and average linkage and principal components analysis (PCA) were conducted in an unsupervised fashion to control for experimental bias or outlier samples.

source_name: primary AML sample

label_protocol: 100 ng of total RNA was reverse transcribed using the GeneChip® WT Plus Reagent Kit

growth_protocol: Viably frozen samples obtained from patients diagnosed with AML were thawed in 37°C water bath as fast as possible and placed immediately in 20% FCS Iscove's Modified Dulbecco's Medium (Gibco IMDM, Thermo-Fischer Scientific) supplemented with DNASE I. Next, cells were spun at 1,500 rpm for 5 min and re-suspended in complete medium (see below) at 2-5x106 cells/mL. The thawed cells were subsequently cultured in complete medium: IMDM supplemented with 10% fetal bovine serum (FBS) and BIT (bovine serum albumin 4 g/L, insulin 5 µg/mL, and transferrin 60 µg/mL, all from Sigma-Aldrich, Saint Louis, MO, USA). To facilitate optimal cell growth and maintenance, the supplemented medium, known as IMDM-BIT, was prepared with the addition of specific components. The following factors and reagents were incorporated into the IMDM-BIT medium: 50 ng/mL FLT3 ligand, 10 ng/mL IL-6, 50 ng/mL stem cell factor (SCF), 25 ng/mL thrombopoietin (TPO), 10 ng/mL IL-3, and 10 ng/mL granulocyte colony-stimulating factor (G-CSF) (all from Peprotech, Rock Hill, NJ, USA). Additionally, 50 µM β-mercaptoethanol (Sigma-Aldrich) was included in the culture medium.

extract_protocol: RNA was extracted using a RNeasy Mini Kit (Qiagen, Redwood City, CA, USA) and quality was evaluated with a Bioanalyzer 2100 (using Agilent RNA6000 nano chip kit)

treatment_protocol: AML cells were incubated with vehicle or 1mM compound 9a for 24 h and then processed for RNA extraction.

tag: disease state

value: patient with AML


title: AML_vehicle_rep7


title: STZ+HFD model, 44w, biological replication 3

description:
rawcount_allsamples_mouse.txt
Batch1_STZHFD44w_3

value: Liver

value: WT


title: STZ+HFD model, 44w, biological replication 2

description:
rawcount_allsamples_mouse.txt
Batch1_STZHFD44w_2


title: CD4 bb&ff 1


title: AML_vehicle_rep8


title: STZ+HFD model, 44w, biological replication 1

description:
rawcount_allsamples_mouse.txt
Batch1_STZHFD44w_1


title: CD4 bb 5

value: bb


title: MOLM13_Tet2CD_24h

value: TET2 CD 24 hours


title: MOLM13_Control

value: doxcyclin


title: AML_vehicle_rep6


title: STZ+HFD model, 32w, biological replication 5

description:
rawcount_allsamples_mouse.txt
Batch1_STZHFD32w_5

value: 32 weeks


title: AML_compound 9a_rep6


title: CD4 bb 4

value: naive CD4 T cell


title: AML_compound 9a_rep5


title: AML_compound 9a_rep8


title: AML_vehicle_rep5


title: MOLM13_TET2-CDΔLCI_48h_rep2

value: Leukemia cell

value: TET2-CD{delta}LCI 48 hours


title: AML_vehicle_rep4


title: STZ+HFD model, 32w, biological replication 4

description:
rawcount_allsamples_mouse.txt
Batch1_STZHFD32w_4

value: Treated


title: MOLM13_TET2-CDΔLCI_48h_rep1


title: CD4 b+/- 3


title: CD4 b+/- 4


title: STZ+HFD model, 32w, biological replication 3

description:
rawcount_allsamples_mouse.txt
Batch1_STZHFD32w_3

value: HFD


title: MOLM13_TET2-CDΔLCI_24h_rep2


title: STZ+HFD model, 32w, biological replication 2

description:
rawcount_allsamples_mouse.txt
Batch1_STZHFD32w_2

value: Male


title: CD4 b+/- 1


title: AML_compound 9a_rep4


title: STZ+HFD model, 32w, biological replication 1

description:
rawcount_allsamples_mouse.txt
Batch1_STZHFD32w_1

value: Untreated


title: MOLM13_Tet2CD_48h_rep2


title: CD4 b+/- 2


title: AML_vehicle_rep3


title: mEsc-WT-Dam-Tet2delta-DamID-2

data_processing:
RNA-seq data were mapped to the hg19 or mm10 genome assembly using STAR (version=2.7.10a) with default parameters. DESeq2 was used to call significantly differentially expressed genes (DEGs; log2 fold change >= 1 or <= -1, q-value < = 0.05) between MOLM13 expression TET2CD and TET2CDΔLCI.
Raw WGBS fastq files were mapped to the hg19/mm10 genome assembly using the bsmap-2.89 software with “-v 6 -n 1 -q 3 -r 1” parameters. The bisulfite conversion ratios were estimated using unmethylated lambda DNA. Mcall modual in MOABS (56) was used to call the mCG/CG ratios for each CpG site. Mcomp modual was used to call DMRs with parameter “–minNominalDif = 0.2–minDmcsInDmr 3–maxDistConsDmcs 500”. The CpGs with coverage > = 5 was used for downstream analysis.
Raw DamID fastq data were aligned to mm10 genome assembly using bowtie2.4.5 with default parameters. Mapped DamID data were analyzed by damidseq_pipeline (55). Specifically, sequencing fragments located on GATC sites were counted, normalized and bedGraph file with DamID-fusion / DamID-only log2ratio were generated. Find_peaks perl script in damidseq_pipeline was used to call significant peaks. The genome was splitted into 5k bins and the mean signals of mESC Flag-Tet2 ChIP, Dam-fusion with Tet2CD/Dam-only ratios, mESC H3K27ac and mESC H3K9me3 on each 5k bin were calculated. The pearson correlation coefficient among them were calculated and plotted. IGV was used to visualize the tracks.
Raw CMS-IP fastq data were mapped to the mm10/hg19 genome assembly using bsmap-2.89 with default parameters. After duplication removal, CMS peaks were called by using macs2 with default parameters. Bedtools merge was used to generate merged peaks for all samples. Reads numbers in each peak were counted if there was >1 bp overlap between reads location and peak region. The raw counts file with row as each peak, column as samples was used as input to DESeq2 and differentially significantly CMS peaks (q value < = 0.05) between the control and TET2CD or control and TET2CDΔLCI groups were called. Volcano plots were plotted using the R package ggplot2.
For Micro-C data analysis, we used Micro-C data analysis pipeline in https://micro-c.readthedocs.io/en/latest/ to process Micro-C data. Specifically, we used bwa-mem (0.7.17) algorithm to map raw fastqs on hg19 version genome with the following command: bwa mem -5SP -T0 -t16 hg38.fasta MicroC_2M_R1.fastq MicroC_2M_R2.fastq -o aligned.sam. PCR duplicates were removed. Pairtools pipeline was used to identify ligation event from mapping results and the validate pairs was extracted for downstream analysis. Juice box tools (57) was used to generate contact matrix (*.hic) data which can be visualize in Juicebox. runHiCpca.pl in Homer was used to calculate PCA1 value (A/B comparment) for 50k bins and the PCA1 value was corrected by using MOLM13 H3K27ac data (GSM2136938).
Assembly: mm10/hg19
Library strategy: DamID

source_name: mouse embryonic stem cells (mESCs)

value: mouse embryonic stem cells (mESCs)


title: AML_compound 9a_rep3


title: MOLM13_Tet2CD_48h_rep1


title: STZ+HFD model, 20w, biological replication 5

description:
rawcount_allsamples_mouse.txt
Batch1_2_STZHFD20w_5

value: 20 weeks


title: AML_vehicle_rep2


title: STZ+HFD model, 20w, biological replication 4

description:
rawcount_allsamples_mouse.txt
Batch1_2_STZHFD20w_4


title: MOLM13_Tet2CD_24h_rep2


title: STZ+HFD model, 20w, biological replication 3

description:
rawcount_allsamples_mouse.txt
Batch1_2_STZHFD20w_3


title: mEsc-WT-Dam-Tet2delta-DamID-1


title: AML_compound 9a_rep2


title: mEsc-WT-Dam-Tet2CD-DamID-2


title: MOLM13_Tet2CD_24h_rep1


title: AML_vehicle_rep1


title: MOLM13_TET2-CDΔLCI_24h_rep1

value: TET2-CD{delta}LCI 24 hours


title: STZ+HFD model, 20w, biological replication 2

description:
rawcount_allsamples_mouse.txt
Batch1_2_STZHFD20w_2


title: MOLM13_Control_rep2


title: AML_compound 9a_rep1

value: patient with AML


title: mEsc-WT-Dam-Tet2CD-DamID-1


title: mEsc-WT-Dam-DamID-2


title: MOLM13_Control_rep1


title: STZ+HFD model, 20w, biological replication 1

description:
rawcount_allsamples_mouse.txt
Batch1_2_STZHFD20w_1

value: Liver


title: case40

first: Lin

last: Shen

state: Beijing

address: Peking University Cancer Hospital & Institute, 52 Fucheng Rd, Haidian District

data_processing:
Illumina bcl2fastq v2.19  software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, and the reads from the original copies of sRNA were distinguished from their amplification products by unique molecularidentifiers (UMIs) , then mapped to GRCh38 whole genome and known miRNA database(miRbase v22) using bowtie v1.2.1.1 with parameters -f -v 0 -p 5 -S.
Transcripts per Megabase of library size(TPM) were calculated using a protocol from Bo Li et al., Bioinformatics, 2009. In miRNA-Seq, read length is longer than miRNA length. One miRNA read count means one transcript.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw miRNA counts for every miRNA and every sample

source_name: gastric cancer patient plasma small extracellular vesicle

extract_protocol:
Peripheral blood samples from individuals were collected in EDTA tubes and centrifugated at 3,000 ×g for 15 min at 4 °C to collect the plasma. The sEVs were isolated by size exclusion chromatography (Exosupur columns, Echobiotech, China) and ultrafiltration (100 kDa molecular weight cut-off Amicon Ultra spin filters, Merck, Germany) methods. Total RNA was extracted and purified from plasma exosome using miRNeasy Serum/Plasma Advanced Kit (Qiagen, cat. No. 217204)
Small RNA libraries were prepared for sequencing using the SMARTer Stranded Total RNA-Seq Kit (Takara Bio USA, Inc.)

tag: metastasis status

tag: disease

value: gastric cancer


title: STZ+HFD model, 14w, biological replication 5

description:
rawcount_allsamples_mouse.txt
Batch1_STZHFD14w_5

tag: tissue

value: 14 weeks

value: WT


title: AML_shNCOA4_rep4

treatment_protocol: Twelve-well plates were coated with 500 µL of retronectin (20 µg/mL in PBS) and incubated overnight at 4°C. Subsequently, the plates were blocked with 1 mL of 2% BSA PBS for 30 minutes at room temperature and washed once with PBS. Next, 600 µL of concentrated lentiviral supernatant was added to each well, and the plates were centrifuged at 4000 rpm for 3 hours at 4°C to enhance virus adhesion to retronectin. Following centrifugation, 0.4 mL of the viral supernatant was replaced with 1 mL of pre-warmed culture medium containing 1-5×106 cells. The plates were then centrifuged at 1500 rpm for 10 minutes at room temperature and incubated at 37°C for 24 hours.


title: mEsc-WT-Dam-DamID-1


title: AML_shCTL_rep4


title: STZ+HFD model, 14w, biological replication 4

description:
rawcount_allsamples_mouse.txt
Batch1_STZHFD14w_4

tag: strain


title: 5hmC of Tet1/2/3 triple KO mESC

data_processing:
For CMS-IP-seq analysis, raw FASTQ files were mapped to mm10 using BSMAP . Only uniquely mapped non duplicated reads were kept as input for MACS2  to call 5hmC enriched regions (peaks). Differential hydroxymethylation regions (DHMRs) were identified using DESeq2 with default parameters. Bam files were transformed to bigwig format, which can be used to visualize 5hmC signals in the UCSC genome browser.. H3K9me3 and H3K9me2 ChIPseq data was aligned on mm10 using bowtie2. The bam files were inputted to EDD (https://github.com/CollasLab/edd) to identify ChIPseq enriched regions.
For the WGBS analysis, raw FASTQ files were mapped to the NCBI Human Reference Genome Build GRCh37 (hg19) using BSMAP. Fastp was used to trim adaptor sequences from fastq data and remove 15 bp from the two ends of the reads based on Swift protocol. MCALL module in MOABS software was used to calculate DNA methylation ratio and coverage for each CpG site. Differentially methylated CpGs and regions were identified using the MCOMP module considering variance among samples (--withVariacne 1) in the MOABS software. Bisulfite conversion efficiencies were estimated using spike-in unmethylated lambda phage DNA. The output bedGraph files from MCALL include single base resolution DNA methylation ratios, which were transformed to a bigwig file format. The bigwig files were uploaded to the UCSC genome browser for visualization.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

source_name: mESC

growth_protocol: mESCs were cultured on MEFs in Knock-out Dulbecco’s Modified Eagle’s Medium (Gibco), supplemented with 15% fetal bovine serum (Omega), 0.5% penicillin-streptomycin (Gibco), 0.1 mM non-essential amino acids (Gibco), 0.1 mM 2-mercaptoetanol (Sigma), and 103 U/mL of leukemia inhibitory factor (Millipore)

extract_protocol:
DNA were purified using Qiagen AllPrep DNA/RNA micro kit.
CMSIP: 5hmC-containing genomic DNA were immunoprecipitated by CMS antibody after being bisulfite treated.  Immunoprecipitated DNA and input were proceed for Library generation by using zymo pico methyl kit.
CMSIP

treatment_protocol: Tet1/2/3 triple knock-out mESCs were generated by the CRISPR/Cas9 technology, FLAG-tagged Tets catalytic domain (TET-CD) or deficient with LCI are transfected to 293T with lipofectimin or transduced to mESC through lentivirus.

value: stem cell


title: case39

institute: Peking University Cancer Hospital & Institute


title: STZ+HFD model, 14w, biological replication 3

description:
rawcount_allsamples_mouse.txt
Batch1_STZHFD14w_3

data_processing:
Raw RNA-sequencing data obtained from mouse were mapped to mouse genome build mm10 (GRCm38) and those from human mapped to human genome build 38 (GRCh38) using STAR (version 020201).
Count matrices were generated using RSEM (v1.3.1)
Assembly: mm10, human genome build 38 (GRCh38)
Supplementary files format and content: tab-delimited text files include raw expected count generated by RNA-seq for each sample

tag: age


title: 5hmC of Tet1/2/3 triple KO mESC transfected with human Tet2 CD domain with replace IDR with Tet1 IDR sequences rep2


title: case38


title: AML_shCTL_rep3


title: AML_shNCOA4_rep3


title: 5hmC of Tet1/2/3 triple KO mESC transfected with human Tet2 CD domain with replace IDR with Tet1 IDR sequences rep1


title: 5hmC of Tet1/2/3 triple KO mESC transfected with human Tet2 CD domain with randomalize aa sequence of IDR rep4


title: STZ+HFD model, 14w, biological replication 2

description:
rawcount_allsamples_mouse.txt
Batch1_STZHFD14w_2

tag: streptozotocin treatment


title: case37


title: STZ+HFD model, 14w, biological replication 1

description:
rawcount_allsamples_mouse.txt
Batch1_STZHFD14w_1

tag: diet


title: AML_shNCOA4_rep2


title: case36


title: 5hmC of Tet1/2/3 triple KO mESC transfected with human Tet2 CD domain with randomalize aa sequence of IDR rep3


title: Acutre streptozotocin-treated state,8w, biological replication 3

description:
rawcount_allsamples_mouse.txt
Batch1_STZSCD08w_3

value: 8 weeks

value: SCD

tag: Sex


title: 5hmC of Tet1/2/3 triple KO mESC transfected with human Tet2 CD domain with randomalize aa sequence of IDR rep2


title: Acutre streptozotocin-treated state,8w, biological replication 2

description:
rawcount_allsamples_mouse.txt
Batch1_STZSCD08w_2

tag: genotype


title: case35


title: 5hmC of Tet1/2/3 triple KO mESC transfected with human Tet2 CD domain with randomalize aa sequence of IDR rep1


title: AML_shCTL_rep1


title: case33


title: case34


title: Acutre streptozotocin-treated state,8w, biological replication 1

description:
rawcount_allsamples_mouse.txt
Batch1_STZSCD08w_1

tag: drug treatment


title: AML_quiescent fraction_rep4_(Clariom_S_Human)

treatment_protocol: For the identification and sorting of human AML cells, hCD33 and hCD45 staining were employed on an Astrios cell sorter (Beckman Coulter). Then quiescent and cycling leukemic cells were sorted based on their quiescent (Pyronin Y low) or cycling (Pyronin Y high) status.


title: Healthy control,7w, biological replication 5

description:
rawcount_allsamples_mouse.txt
Batch1_Control07w_5

value: 7 weeks


title: 5hmC of Tet1/2/3 triple KO mESC transfected with human Tet2 CD domain with deletion of IDR rep4


title: case32


title: Healthy control,7w, biological replication 4

description:
rawcount_allsamples_mouse.txt
Batch1_Control07w_4


title: AML_cycling fraction_rep4_(Clariom_S_Human)


title: AML_shCTL_rep2


title: AML_quiescent fraction_rep3_(Clariom_S_Human)


title: case31


title: 5hmC of Tet1/2/3 triple KO mESC transfected with human Tet2 CD domain with deletion of IDR rep3


title: AML_shNCOA4_rep1


title: Healthy control,7w, biological replication 3

description:
rawcount_allsamples_mouse.txt
Batch1_Control07w_3


title: AML_quiescent fraction_rep2_(Clariom_S_Human)


title: case30


title: Healthy control,7w, biological replication 2

description:
rawcount_allsamples_mouse.txt
Batch1_Control07w_2


title: 5hmC of Tet1/2/3 triple KO mESC transfected with human Tet2 CD domain with deletion of IDR rep2


title: 5hmC of Tet1/2/3 triple KO mESC transfected with human Tet2 CD domain with deletion of IDR rep1


title: AML_cycling fraction_rep2_(Clariom_S_Human)


title: Healthy control,7w, biological replication 1

description:
rawcount_allsamples_mouse.txt
Batch1_Control07w_1


title: case29


title: 5hmC of Tet1/2/3 triple KO mESC transfected with human Tet2 CD domain rep4


title: case28


title: KO-FSK-24h, bio rep 1

data_processing:
The raw reads were first aligned to the genome hg38 with STAR version 2.7.9a, and then gene counts were acquired from the number of uniquely and unambiguously aligned reads by Subread:featureCount (version 2.0.1). The variation analysis was conducted by DESeq2 to the DEGs and the corresponding adjusted p-values in the Benjamini and Hochberg correction. The DEGs were identified using the setting: |fold change| >2 for mice and >1.5 for cell samples with adjusted p-value < 0.05.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: BeWo

growth_protocol: BeWo cells were maintained in DMEM/F12 supplemented with 10% FBS under a stable environment (at 37 °C and 5% CO2).

extract_protocol:
Total RNAs from BeWo cells with DMSO or FSK treatments were extracted by TRIzol and purified by poly-A before subjected to RNA-Seq. 1 μg of  total RNA was used for sequencing libraries.
MGIEasy Fast PCR-FREE FS Library Prep Set

treatment_protocol: For cell fusion experiments, BeWo cells were treated with DMSO or 50 μM Forskolin at 12 or 24h.

tag: cell line

value: BeWo

value: TFEB KO

value: FSK


title: 5hmC of Tet1/2/3 triple KO mESC transfected with human Tet2 CD domain rep3

tag: cell type


title: mESC_hTet2Delta


title: case27


title: case26


title: AML_quiescent fraction_rep1_(Clariom_S_Human)


title: 5hmC of Tet1/2/3 triple KO mESC transfected with human Tet2 CD domain rep2


title: case25


title: AML_cycling fraction_rep3_(Clariom_S_Human)


title: KO-FSK-12h, bio rep 2


title: AML_cycling fraction_rep1_(Clariom_S_Human)


title: 5hmC of Tet1/2/3 triple KO mESC transfected with human Tet2 CD domain rep1


title: KO-FSK-12h, bio rep 1


title: CD4 ss 1

value: Peripheral lymph nodes

value: naive CD4 T cell

value: ss


title: mst2D epe1-deg gcn5D,+TN 120hr -TN 72hr +TN 24hr, input

city: Waltham

first: Ajay

last: Larkin

address: 415 South St

department: MCB

institute: Brandeis University

data_processing:
sequences were trimmed with Trimmomatic, aligned with BWA, and normalized by SES using Deeptools BamCompare to input
Assembly: ASM294v2.29
Supplementary files format and content: bedgraph files

organism: Schizosaccharomyces pombe

growth_protocol: EMMC, grown to log phase at 32C

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 minutes. Cells were lysed with bead beating.
ChIPseq libraries were prepared with NEBNext Ultra II DNA Library Prep Kit for Illumina. 1Ng of DNA was used as starting material

treatment_protocol: +TN cultures were treated with 15mM thiamine and 500mM 1-napthaleneacetic acid

tag: chip antibody

value: ade6::ade6+-adh15prom-skp1-OsTIR1-natMX6-adh15prom-skp1-AtTIR1-2NLS nmt81-epe1-3xFLAG-AID mst2D gcn5D


title: case24


title: mst2D epe1-deg gcn5D,+TN 120hr -TN 72hr +TN 24hr, H3K9me3

tag: treatment


title: KO-DMSO-24h, bio rep 2

value: DMSO


title: KO-FSK-24h, bio rep 2


title: KO-DMSO-24h, bio rep 1


title: DMSOrep2tech1

city: Charlottesville

first: Jeffrey

middle: John

last: Saucerman

state: VA

department: Biomedical Engineering

institute: University of Virginia

data_processing:
Sequence read quality was assessed using the FastQC software (http://www.bioinformatics. babraham.ac.uk/projects/fastqc). All samples at all positions had Phred scores greater than 30. Paired-end reads were mapped to the human reference genome hg38 using the Bowtie2 aligner [66] and gene-level counts were quantified using the featureCounts program [67]. Genes with low counts were removed before normalizing by TMM.
Assembly: Paired-end reads were mapped to the human reference genome hg38 using the Bowtie2 aligner [66]
Supplementary files format and content: GEOreadcounts.csv contains the normalized gene counts from each sample.

source_name: Cellular Dynamics iCell Cardiomyocytes

growth_protocol: manufacturer's instructions

extract_protocol:
Total RNA was isolated from hiPSC-CMs treated for 24 h using the mirVana microRNA Isolation Kit with phenol (Invitrogen) according to the manufacturer’s guidelines. Each sample was run with 3 biological replicates.
RNA sequencing libraries were generated and indexed using 200 ng of total RNA and the TruSeq Stranded mRNA LT Sample Prep Kit - Set B (Illumina) following the protocol provided by the manufacturer.
Resulting libraries were then assessed using the Agilent TapeStation 4200 (Agilent Technologies) and quantified by Qubit 2.0 (Thermo Fisher Scientific). The indexed libraries were pooled at equal molar concentrations and paired-end sequenced with 75 bp per read on the Illumina NextSeq 500 system using NextSeq 500 High Output 150 cycle cartridges (Illumina).

treatment_protocol: Cellular Dynamics iCell Cardiomyocytes were treated with DMSO or 1 of 5 small molecules (C1, C2, C3, C4, C5) for 24 hours. Each condition had 3 replicates.

value: Cellular Dynamics iCell Cardiomyocytes


title: DMSOrep1tech1


title: mESC_hTet2CD

value: mouse embryonic stem cells (mESCs)


title: case23

value: gastric cancer


title: mst2D epe1-deg gcn5D,+TN 120hr -TN 72hr +TN 24hr, H3K9me2


title: KO-DMSO-12h, bio rep 2


title: mst2D epe1-deg gcn5D,+TN 120hr -TN 72hr, input


title: case22


title: C5rep3tech1


title: KO-DMSO-12h, bio rep 1


title: case21


title: mst2D epe1-deg gcn5D,+TN 120hr -TN 72hr, H3K9me3


title: control-FSK-24h, bio rep 2


title: C5rep2tech1


title: mst2D epe1-deg gcn5D,+TN 120hr -TN 72hr, H3K9me2


title: DMSOrep3tech1


title: case20


title: control-FSK-24h, bio rep 1


title: C5rep1tech1


title: mst2D epe1-deg gcn5D,+TN 120hr -TN 48hr +TN 24hr, input


title: case18


title: C4rep3tech1


title: case19


title: mst2D epe1-deg gcn5D,+TN 120hr -TN 48hr +TN 24hr, H3K9me3


title: C4rep2tech1


title: mst2D epe1-deg gcn5D,+TN 120hr -TN 48hr +TN 24hr, H3K9me2


title: control-FSK-12h, bio rep 1


title: C4rep1tech1


title: control-DMSO-24h, bio rep 2


title: case16


title: C3rep3tech1


title: case15


title: control-DMSO-24h, bio rep 1


title: mst2D epe1-deg gcn5D,+TN 120hr -TN 48hr, input


title: case14


title: C3rep2tech1


title: mst2D epe1-deg gcn5D,+TN 120hr -TN 48hr, H3K9me3


title: control-DMSO-12h, bio rep 2


title: mst2D epe1-deg gcn5D,+TN 120hr -TN 48hr, H3K9me2


title: control-FSK-12h, bio rep 2


title: mst2D epe1-deg gcn5D,+TN 120hr -TN 24hr +TN 24hr, input


title: C3rep1tech1


title: case12


title: C2rep3tech1


title: case17


title: mst2D epe1-deg gcn5D,+TN 120hr -TN 24hr +TN 24hr, H3K9me2


title: Root, 24 hours long NaCl stress, replicate 3

city: Bearsden

first: Pawel

last: Herzyk

address: Wolfson Wohl Cancer Research Centre, Garscube Estate

department: College of Medical, Veterinary and Life Sciences

country: United Kingdom

institute: University of Glasgow

data_processing:
Read Pre-processing: Sequence reads were pre-processed in the same way for de-novo transcriptome assembly and RNAseq: First, Reads were subjected to the error correction procedure and the un-correctable reads removal with Rcorrector (version 1.0.3.1) software using k-mer length of 25 (-k 25). Then, reads were trimmed for adaptor sequences and low-quality stretches using -trimmomatic flag within Trinity software.
Reference transcriptome assembly: Pre-processed reads were then assembled de-novo with Trinity (version 2.8.4) for shoot and root tissues separately. Subsequently, likely ORFs were identified with TransDecoder (version 5.5.0) and transcript redundancy removed further with CD-Hit (version 4.8.1) using identity threshold of 0.95 and retaining the longest sequence per cluster. The corresponding sets of nucleotide sequences constituted the non-redundant reference transcriptomes for root and shoot tissues, separately.
RNA-seq analysis: Transcript-specific read counts for each root and shoot sample were generated with Kallisto (version 0.45) against root and shoot reference transcriptomes, respectively. They were further processed with EdgeR (version 3.40.1) to generate lists of differentially expressed transcripts between different conditions. Here, a prefiltering was applied so that only transcripts with CPM > 1 in at least 3 samples were accepted for differential expression analysis.
Assembly: Two separate transcriptomes for Sesuvium portulacastrum (L.) root and shoot tissues, assembled in this study
Supplementary files format and content: matrix containing coma delimited raw read counts for shoot tissue
Supplementary files format and content: matrix containing coma delimited raw read counts for root tissue
Supplementary files format and content: matrix containing coma delimited TMM normalised CPM values for shoot tissue
Supplementary files format and content: matric containing coma delimited TMM normalised CPM values for root tissue

organism: Sesuvium portulacastrum

source_name: Root

growth_protocol: Stem cuttings of S. portulacastrum were collected from Thane creek, near Mumbai (GPS location - 19° 3' 35.28" N, 72° 57' 0" E). Collected stem cuttings were washed with Tween-20 for five minutes followed by five-time washing with water. For studying the rooting response, washed stem cuttings were established under hydroponic conditions (25 ± 2°C under 12 h photoperiod using white tube lights) in half strength MS medium.

extract_protocol:
Total RNA was isolated using PureLink RNA Mini Kit (Invitrogen) and RNA quality check was performed by running on agarose gel and by checking 260/280 and 260/230 ratio.
RNA sequencing libraries were prepared with Illumina-compatible NEBNext® Ultra™ Directional RNA Library Prep Kit (New England BioLabs, MA, USA) following manufacturer's protocol.

treatment_protocol: The 15 days old hydroponically grown seedlings were divided into three sets, (T0) control, where nutrient medium was changed to control medium and then harvested immediately, (T8) and (T24) where nutrient media were changed to 250 mM NaCl and hervested after 8 hours and 24 hours, respectively.

value: Root

value: 24 hours long NaCl stress


title: case11


title: case13


title: C2rep2tech1


title: C2rep1tech1


title: Root, 24 hours long NaCl stress, replicate 1


title: Root, 24 hours long NaCl stress, replicate 2


title: mst2D epe1-deg gcn5D,+TN 120hr -TN 24hr +TN 24hr, H3K9me3


title: case10


title: C1rep3tech1


title: Root, 8 hours long NaCl stress, replicate 3

value: 8 hours long NaCl stress


title: mst2D epe1-deg gcn5D,+TN 120hr -TN 24hr, input


title: control-DMSO-12h, bio rep 1

value: WT


title: mst2D epe1-deg gcn5D,+TN 120hr -TN 24hr, H3K9me2


title: mst2D epe1-deg gcn5D,+TN 120hr -TN 24hr, H3K9me3


title: C1rep2tech1


title: Root, 8 hours long NaCl stress, replicate 2


title: case8


title: TUH102P2 day 7

data_processing:
Single-cell RNA sequencing (scRNA-seq) data output files in bcl2 format were converted to FASTQ format using Cell Ranger v.6.1.1.1 (ref). The resulting count matrices from Cell Ranger were imported into the R programming environment v4.1.2 using the Seurat package v4.1.0 (ref). To ensure data quality, cells with a low number of unique genes (<7500 unique genes) and a high proportion of mitochondrial RNA (>20%) were removed. Gene counts were then normalized using a regularized negative binomial regression method, employing the SCT normalization workflow from the Seurat package (ref). The integration process utilized 30 principal components and 3000 genes. Subsequently, dimensional reduction was performed, summarizing the 30 principal components using UMAP dimensionality reduction. Cell clusters were identified through Louvain clustering within the Seurat workflow, with the resolution parameter set to 0.25. Clustering of co-expressing genes was determined using hierarchical clustering with the nclust package (https://gitlab.com/pwirapati/nclust). Signature values on the SCT-transformed data were computed using the AddModuleScore method from Seurat.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: hematopoietic

extract_protocol:
Purification of hCD45+CD33+ from PDX : After red blood cells lysis with EL buffer (Qiagen, 79217), 10x106 cells from mice bone marrow of PDXs treated with vehicle or GILT were stained with Fixable Viability Stain 510 (BD Biosciences Cat# 564406, RRID:AB_2869572) and the fluorescent conjugated antibodies hCD45-APC (BD Biosciences Cat# 555485, RRID:AB_398600) and hCD33-PE (BD Biosciences Cat# 555450, RRID:AB_395843) in cell staining buffer (Biolegend, BLE420201) following to the manufacturer’s instructions. Viable hCD45+CD33+ were sorted using BD FACSAria Fusion flow cytometer (Becton Dickinson) and gently re-suspended at 1500cells/µL in PBS1X supplemented with 0.04% Ultrapure BSA (Invitrogen, Cat# AM2616).
Up to 10,000 cells per sample were encapsulated using the 10X Chromium controller (10X Genomics) following the Chromium Next GEM Single Cell 3ʹ User Guide v3.1 (10X Genomics). Briefly, cells were encapsulated into oil droplets with barcoded Gel Beads and reagents to convert mRNA into complementary DNA (cDNA). cDNAs were then amplified, fragmented and Illumina adapters were added during ligation. After performing a last index PCR, libraries quality was assessed using Tapestation 2200 (Agilent) and frozen before quantitation and sequencing. Barcoding was done on three levels: cell barcodes allow attribution of each sequence read to its cell of origin; unique molecular identifiers (UMIs) upstream to poly(d)T primers allow tagging of each original molecule to avoid amplification bias; and index allows pooling of different samples. scRNA-seq libraries were quantified with HSD1000 reagents on TapeStation 2200 system (Agilent) and pooled at equimolar concentrations within 200 to 700bp. Pool libraries were sequenced at 1.8pM 1% phiX using a NextSeq 500 sequencer (Illumina), at a sequencing depth of 40,000-50,000 reads per cell. Sequencing were configured Paired-End at 28 cycles for the first read, 91 cycles for the second one and 8 cycles for a single index.

treatment_protocol: Primary AML samples (P0) were utilized to establish patient-derived xenografts (PDX) denoted as P1 samples. Serial transplantation resulted in the generation of P2 samples, which were analyzed at one- or seven-days post-transplantation. Human leukemic cells were isolated using CD33/CD45 staining, and their transcriptomes were comprehensively analyzed at the single-cell level utilizing 10X Genomics technology

value: acute myeloid leukemia

value: hematopoietic


title: case7


title: mst2D epe1-deg gcn5D,+TN 120hr, input

source_name: mst2D epe1-deg gcn5D,+TN 120hr, input


title: C1rep1tech1


title: Root, 0 hours long NaCl stress, replicate 3

value: 0 hours long NaCl stress


title: case9


title: mst2D epe1-deg gcn5D,+TN 120hr, H3K9me2

source_name: mst2D epe1-deg gcn5D,+TN 120hr, H3K9me2


title: TUH84P2 day 7


title: MOLM13-3rd-T2-delta-48h-1

data_processing:
RNA-seq data were mapped to the hg19 or mm10 genome assembly using STAR (version=2.7.10a) with default parameters. DESeq2 was used to call significantly differentially expressed genes (DEGs; log2 fold change >= 1 or <= -1, q-value < = 0.05) between MOLM13 expression TET2CD and TET2CDΔLCI.
Raw WGBS fastq files were mapped to the hg19/mm10 genome assembly using the bsmap-2.89 software with “-v 6 -n 1 -q 3 -r 1” parameters. The bisulfite conversion ratios were estimated using unmethylated lambda DNA. Mcall modual in MOABS (56) was used to call the mCG/CG ratios for each CpG site. Mcomp modual was used to call DMRs with parameter “–minNominalDif = 0.2–minDmcsInDmr 3–maxDistConsDmcs 500”. The CpGs with coverage > = 5 was used for downstream analysis.
Raw DamID fastq data were aligned to mm10 genome assembly using bowtie2.4.5 with default parameters. Mapped DamID data were analyzed by damidseq_pipeline (55). Specifically, sequencing fragments located on GATC sites were counted, normalized and bedGraph file with DamID-fusion / DamID-only log2ratio were generated. Find_peaks perl script in damidseq_pipeline was used to call significant peaks. The genome was splitted into 5k bins and the mean signals of mESC Flag-Tet2 ChIP, Dam-fusion with Tet2CD/Dam-only ratios, mESC H3K27ac and mESC H3K9me3 on each 5k bin were calculated. The pearson correlation coefficient among them were calculated and plotted. IGV was used to visualize the tracks.
Raw CMS-IP fastq data were mapped to the mm10/hg19 genome assembly using bsmap-2.89 with default parameters. After duplication removal, CMS peaks were called by using macs2 with default parameters. Bedtools merge was used to generate merged peaks for all samples. Reads numbers in each peak were counted if there was >1 bp overlap between reads location and peak region. The raw counts file with row as each peak, column as samples was used as input to DESeq2 and differentially significantly CMS peaks (q value < = 0.05) between the control and TET2CD or control and TET2CDΔLCI groups were called. Volcano plots were plotted using the R package ggplot2.
For Micro-C data analysis, we used Micro-C data analysis pipeline in https://micro-c.readthedocs.io/en/latest/ to process Micro-C data. Specifically, we used bwa-mem (0.7.17) algorithm to map raw fastqs on hg19 version genome with the following command: bwa mem -5SP -T0 -t16 hg38.fasta MicroC_2M_R1.fastq MicroC_2M_R2.fastq -o aligned.sam. PCR duplicates were removed. Pairtools pipeline was used to identify ligation event from mapping results and the validate pairs was extracted for downstream analysis. Juice box tools (57) was used to generate contact matrix (*.hic) data which can be visualize in Juicebox. runHiCpca.pl in Homer was used to calculate PCA1 value (A/B comparment) for 50k bins and the PCA1 value was corrected by using MOLM13 H3K27ac data (GSM2136938).
Assembly: mm10/hg19
Library strategy: CMS-IP

value: Leukemia cell

value: TET2-CD{delta}LCI 48 hours

value: doxcyclin


title: case4


title: Root, 0 hours long NaCl stress, replicate 2


title: MOLM13-3rd-T2-delta-24h-2

value: TET2-CD{delta}LCI 24 hours


title: Shoot, 24 hours long NaCl stress, replicate 3

source_name: Shoot

value: Shoot


title: Root, 0 hours long NaCl stress, replicate 1


title: MOLM13-3rd-T2-delta-48h-2


title: case5


title: case3


title: mst2D epe1-deg gcn5D,-TN, H3K9me3

source_name: mst2D epe1-deg gcn5D,-TN, H3K9me3

value: ade6::ade6+-adh15prom-skp1-OsTIR1-natMX6-adh15prom-skp1-AtTIR1-2NLS nmt81-epe1-3xFLAG-AID mst2D gcn5D


title: case2


title: Root, 8 hours long NaCl stress, replicate 1


title: Shoot, 24 hours long NaCl stress, replicate 2


title: mst2D epe1-deg gcn5D,-TN, H3K9me2

source_name: mst2D epe1-deg gcn5D,-TN, H3K9me2


title: case6


title: mst2D epe1-deg gcn5D,+TN 120hr, H3K9me3

source_name: mst2D epe1-deg gcn5D,+TN 120hr, H3K9me3


title: MOLM13-3rd-T2-delta-24h-1


title: Shoot, 24 hours long NaCl stress, replicate 1


title: ATAC-seq of STZ+HFD model, 20w, biological replication 3

data_processing:
Raw ATAC-seq data were trimmed by removing adapters and sequences shorter than 36 base pairs (bp) using TrimGalore (ver. 0.5.0).
Trimmed data were aligned to the mouse genome (mm10, GRCm38) using Bowtie2 (version 2.3.5.1) using the following parameters: -very-sensitive –no-discordant –no-mixed –no-unal.
Mitochondrial reads were subsequently removed using Samtools (version 1.9) and PCR duplicated reads removed using Picard MarkDuplicates tool (Picard version 2.2.2).
Peak calling was performed with MACS2 (version 2.1.1) and ENCODE blacklisted regions for mm10 subtracted with Bedtools intersect (version 2.27.1). Bigwig files were generated using deeptools.
Peaks from MACS2 and sample metadata were inputted into R and read counts for consensus peaksets and overlapping peaks in each sample subsequently counted by R package Diifbind.
Assembly: mm10
Supplementary files format and content: bigWig and bed files containing Peaks generated by ATAC-seq for each sample

source_name: Liver

extract_protocol:
ATAC-seq libraries were prepared from 5 mg of fresh liver tissue.
To prepare ATAC-seq library, nuclei were extracted from liver cells using the Singulator 100 system (S2 Genomics, CA, USA) with an extended nuclear dissociation protocol. 50,000 nuclei were transferred to an EP tube containing 1 mL of ATAC-seq resuspension buffer, then transposition solution was adde, and eluted DNA was purified and amplifired with Nextera DNA Flex kit(Illumina).

value: Liver

value: 20 weeks

value: Treated

value: HFD

value: Male

value: Untreated


title: case1

value: gastric cancer


title: MOLM13-3rd-T2CD-48h-2

value: TET2 CD 48 hours


title: CD8 ff 4

source_name: Peripheral lymph nodes

value: Peripheral lymph nodes

value: naive CD8 T cell

value: ff


title: ATAC-seq of STZ+HFD model, 20w, biological replication 2

value: WT


title: mst2D epe1-deg gcn5D,-TN, input

source_name: mst2D epe1-deg gcn5D,-TN, input


title: MOLM13-3rd-T2CD-24h-2

value: Leukemia cell

value: TET2 CD 24 hours


title: Shoot, 8 hours long NaCl stress, replicate 2

value: 8 hours long NaCl stress


title: ATAC-seq of STZ+HFD model, 20w, biological replication 1


title: CD8 bb 3

value: bb


title: MOLM13-3rd-T2CD-24h-1

value: doxcyclin


title: CD4 g7g7 6

value: naive CD4 T cell


title: MOLM13-3rd-Control-2


title: ATAC-seq of HFD fed mice without STZ treatment, 20w, biological replication 3

value: Liver

value: 20 weeks


title: CD4 g7g7 5


title: Shoot, 0 hours long NaCl stress, replicate 3

value: Shoot

value: 0 hours long NaCl stress


title: ATAC-seq of HFD fed mice without STZ treatment, 20w, biological replication 2

value: Untreated

value: HFD

value: Male


title: Shoot, 8 hours long NaCl stress, replicate 1


title: Shoot, 8 hours long NaCl stress, replicate 3


title: Shoot, 0 hours long NaCl stress, replicate 1


title: Shoot, 0 hours long NaCl stress, replicate 2


title: CD4 bxg7 5

value: Peripheral lymph nodes


title: CD4 g7g7 4


title: ATAC-seq of HFD fed mice without STZ treatment, 20w, biological replication 1


title: ATAC-seq of STZ+ SCD mice, 20w, biological replication 2

value: Treated

value: SCD


title: ATAC-seq of STZ+ SCD mice, 20w, biological replication 3

value: WT


title: MOLM13-3rd-T2CD-48h-1

value: Leukemia cell

value: TET2 CD 48 hours


title: P21 male Wildtype striatum 3

city: New York

first: Deanna

middle: L

last: Benson

state: NY

address: 1470 Madison Avenue, 9-114

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

description:
L-MiniLIMS RNAseq_Strandedx6
7WT

data_processing:
Preprocessing and alignment was performed by Weill Cornell Epigenomics Core. FASTQC was used to analyze the quality of the FASTQ files. We analyzed the presence of adaptors and we trimmed the reads with quality scores below 30. For trimming we used Flexbar.
HISAT2 was used for alignment using the indexed mouse genome obtained from https://ccb.jhu.edu/software/hisat2/manual.shtml.
For converting the obtained SAM files into BAM files we used SAMtools.
Stringtie was used to generate the gene expression matrix
Supplementary files format and content: text file; FPKM data; WT = wildtype and GS = Lrrk2-G2019S KI; # refers to sample number

source_name: dorsal striatum

extract_protocol:
Qiagen miRNeasy mini kit; quantified using Qubit on 01/04/17 by MSSM Biorepository and Pathology Core
TruSeq RNA sample prep kit; Weill Cornell Epigenomics Core

treatment_protocol: postnatal day 21 mice, anesthetized, sac'd, striatum rapidly dissected and placed in RNAlater on 12/21/16

value: dorsal striatum


title: MOLM13-3rd-Control-1


title: CD8 bb 4

value: naive CD8 T cell

value: bb


title: imDC_H2O2_r2

city: Guiyang

first: Dong

middle: mei

last: ling

state: Guizhou

address: Guizhou Medical University

department: School of Basic Medical Sciences

institute: Guizhou Medical University

data_processing:
DNBSEQ
clean reads were compared to the reference genome sequence using HISAT
Bowtie2 was used to compare clean reads to reference gene sequences to obtain comparison results
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: immature dendritic cells

growth_protocol: Male C57BL/6 mice (6 weeks old) were sacrificed after anesthesia, femur and tibia were dissected, bone marrow cells were washed with PBS solution, and red blood cells were removed from cell suspension with red blood cell lysate. Complete media (containing 10% FBS, 20 ng/mL of rmGM-CSF and 10 ng/mL of rmIL-4) were added to re-suspension cell suspensions, and cell suspensions were subpackaged and cultured in six-well plates, and the liquid was changed every other day and half, and immature DCs was obtained on day 6.

extract_protocol:
1×106 cell samples were taken into the grinding and crushing tube with corresponding number. Add 600μL Buffer RLT Plus, homogenize the grinding machine, and let it stand at room temperature for 5 min; At room temperature, centrifuge at 12,000×g for 3 min; All supernatants were transferred to AllPrep DNA spin column; Centrifuge at room temperature of 10,000×g for 30 s, and the liquid in the collection tube was purified and collected for RNA
The DNBs obtained were added to the mesh holes on the chip using high-density DNA nanochip technology, and sequenced by combined probe anchoring polymerization (cPAS)

treatment_protocol: High purity imDCs was obtained after purification by CD11c+ magnetic beads, and H2O2 with concentration of 100 μM was added for 24 h to obtain imDCS-H2O2.

value: immature dendritic cells


title: imDC_H2O2_r1


title: imDC-H2O2


title: P21 male Wildtype striatum 1

description:
L-MiniLIMS RNAseq_Strandedx6
5WT


title: ATAC-seq of control SCD fed mice without STZ treatment, 20w, biological replication 3

value: Liver


title: P21 male Lrrk2G2019S KI striatum 3

description:
L-MiniLIMS RNAseq_Strandedx6
3GS


title: P21 male Wildtype striatum 2

description:
L-MiniLIMS RNAseq_Strandedx6
6WT


title: P21 male Lrrk2G2019S KI striatum 2

description:
L-MiniLIMS RNAseq_Strandedx6
2GS


title: ATAC-seq of STZ+ SCD mice, 20w, biological replication 1

value: 20 weeks


title: ATAC-seq of control SCD fed mice without STZ treatment, 20w, biological replication 1


title: imDC_r2

value: control


title: ATAC-seq of control SCD fed mice without STZ treatment, 20w, biological replication 2