title: Kasumi-1_parental_2 [RNA-seq]

value: Parental


title: NT, WA1WA1, 1DPC, REP4

status: Public on Mar 01 2023

type: SRA

city: Memphis

first: Colleen

middle: Beth

last: Jonsson

state: TN

address: 858 Madison Avenue

country: USA

institute: University of Tennessee Health Science Center

library_source: transcriptomic

data_processing:
CLC Genomics Workbench v 22.0
Sequence reads were trimmed  and filter using default parameters in CLC Genomic Workbench
Trimmed and filter sequence reads were mapped to GRCm39/SARS-CoV-2 Wuhan-Hu-1 concatinated genome using default parameters in CLC Genomic Workbench
Read count results were collected in  CLC Genomic Workbench
Read count were normalized and fold change calculated using DESeq2
Assembly: GRCM39 concatinated with SARS-CoV-2 Wuhan-Hu-1 reference genome
Supplementary files format and content: tab-delimited text files include total counts for each sample

molecule: total RNA

organism: Mus musculus

source_name: Nasal turbinate

extract_protocol:
RNA was extracted from homogenized tissue samples using Magmax mirvana RNA isolation kit on Kingfisher instrument.
Libraries were constructed using NEB NEBNext Ultra II RNA Kits

tag: tissue

value: Nasal turbinate

tag: genotype

tag: treatment

value: Infected with WA1


title: No treatment SAM24387821

city: South San Francisco

first: Jason

middle: A

last: Hackney

state: CA

address: 1 DNA Way

department: Department of Bioinformatics and Computational Biology

institute: Genentech, Inc.

description: No treatment

data_processing:
HTSeqGenie 4.2.1
Reads were aligned to the GRCh38 reference genome using GSNAP (version 2013-11-01)
Aligned reads within exons defined by GENCODE (v27) were counted using the countFeatures method from HTSeqGenie
Assembly: GRCh38
Supplementary files format and content: bam alignment files
Supplementary files format and content: tsv count matrices

organism: Homo sapiens

source_name: skin

growth_protocol: Primary keratinocytes (Thermo Fischer, cat C-020-5C) were cultured in basal medium (Thermo Fischer, cat 17005042)

extract_protocol:
Cells were lysed with RLT buffer and RNA was isolated using RNAeasy mini Kit (Qiagen, 74106) in accordance to standard manufacturer's instructions including DNase treatment procedure.
Libraries were prepared using the Illumina TruSeq Stranded Total RNA Library Prep Kit.

treatment_protocol: Cells were plated at 1.5E5 cells per well in the 24-Well TC plate (Costar, 2524) the day before the experiment. The cells were then treated with recombinant produced human active KLK5 at 6 µg/mL (200 nM of 30 kDa MW), human active KLK7 at 5 µg/mL (208 nM of 24 kDa MW), anti-KLK5/7 bispecific antibody at 180 µg/mL (1200 nM of 150 kDa MW) for 4 h.

value: skin

tag: cell line

value: primary

tag: cell type

value: neonatal keratinocytes

value: untreated


title: Kasumi-1_parental_1 [RNA-seq]

city: Nashville

first: Scott

middle: W

last: Hiebert

address: 512 B Preston Research Building

department: Biochemistry

institute: Vanderbilt University

data_processing:
Adaptors were trimmed using TrimmomaticPE LLUMINACLIP:TruSeq3-PE-2.fa:2:30:7
Trimmed reads were aligned to the human genome (hg19) with TopHat v2.0.11.
Differential gene expression was determined using Cuffdiff v.2.1.1.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Cuffdiff differential gene expression output; tab-delimited text files.

molecule: polyA RNA

source_name: Kasumi-1 cells

growth_protocol: Kasumi-1 cells were grown in RPMI +20% FBS +50 U/ml penicillin, 50 μg/ml streptomycin, and 2mM L-glutamine.

extract_protocol:
Total RNA was extracted by Trizol according to the manufacturer's protocol and precipitated with isopropanol.
Libraries were constructed on polyA selected transcript using standard Illumina protocol.

treatment_protocol: Cells were treated with 500 nM dTAG-47 for the indicated timepoints.

tag: genotype/variation

value: Untreated


title: CRC0719LMX0A02001TUMR01000, LMX_BASALE, bio rep 1, QC ok

city: Candiolo

first: Livio

last: Trusolino

state: Turin

address: Strada Provinciale, 142 -KM 3.95

department: Oncology

country: Italy

institute: IRCCS Istituto Candiolo

data_processing:
Align with STAR on hybrid mm/hs genome
Assign counts to genes with FeatureCounts
Consider only human genes to normalize with DESeq2
QC based on evidence of lymphomatous infiltration
https://github.com/molinerisLab/StromaDistiller, https://github.com/vodkatad/RNASeq_biod_metadata
Assembly: GRCh38_GRCm38
Supplementary files format and content: merged_hs_mm.tsv.gz: raw counts for human and murine genes
Supplementary files format and content: vsd.tsv.gz: normalized expression values for human genes

source_name: Colorectal Cancer

growth_protocol: Please check the linked publication

extract_protocol:
total RNA extraction
PolyA enriched
Forward Stranded

treatment_protocol: Please check the linked publication

value: Colorectal Cancer

value: X

value: LM

value: WT


title: CRC0718LMX0A02001TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: NT, WA1WA1, 1DPC, REP2


title: HepG2_MonoCul_FA.rep3

city: Higashi-Osaka

first: Kei

last: IIDA

state: Osaka

address: Kowakae 3-4-1

country: Japan

institute: Kindai University

description: mRNA-seq (polyA+) data from HepG2 cells with treatments of free fatty acids (1 mM), replicate 3

data_processing:
mRNA-seq reads mapped to the rRNA, tRNA, or mitochondrial genome sequences with bowtie (v.2.1.0).
The seuqence data was mapped to the genome sequence with STAR ver. 2.7.1a .
Genome_build: GRCh38.fa
Supplementary_files_format_and_content: Expression values of Ensemble GRCh38.98 gene models were calculated with RSEM ver. 1.3.0.

source_name: Hep G2 Cell Line

growth_protocol: CaCO2 and HepG2 cells were maintained a microfluidic device with Dulbecco’s modified Eagle medium, supplemented with 10%(v/v) fetal bovine serum, 1%(v/v) non-essential amino acids and 1%(v/v) penicillin/streptomycin in a humidified incubator at 37°C with 5%(v/v) CO2.

extract_protocol:
Total RNA was extracted from differentiated primary myoblasts using the RNeasy mini kit (QIAGEN).
SMART-seq (SMART-Seq v4 Ultra Low Input RNA Kit, Takara Bio)

treatment_protocol: Free fatty acids (total 1 mM of palmitic acid and oleic acid with 1:2 molecular ratio) in 0.5% fetal bovine serum in Dulbecco’s modified Eagle medium and subjected to sample preparation after 1 day.

tag: condition

value: Treatments with free fatty acid (1 mM)

tag: derived tissue

value: Human hepatocellular carcinoma


title: KLK7 +antiKLK5/7 SAM24387819

description: KLK7 +antiKLK5/7

value: KLK7 +antiKLK5/7


title: HepG2_MonoCul_FA.rep2

description: mRNA-seq (polyA+) data from HepG2 cells with treatments of free fatty acids (1 mM), replicate 2


title: CRC0717LMX0A02002TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: HepG2_MonoCul_FA.rep1

description: mRNA-seq (polyA+) data from HepG2 cells with treatments of free fatty acids (1 mM), replicate 1


title: KLK7 SAM24387818


title: NT, WA1WA1, 1DPC, REP1


title: Lung, WA1Delta, 1DPC, REP4

source_name: Lung

value: Lung

value: Infected with Delta


title: KLK5 SAM24387822


title: KLK5 SAM24387816


title: Lung, WA1Delta, 1DPC, REP3


title: CRC0716LMX0B02002TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: HepG2_MonoCul_Cont.rep3

description: mRNA-seq (polyA+) data from HepG2 cells without treatments of free fatty acids, replicate 3

value: No treatments with free fatty acid


title: No treatment SAM24387815

description: No treatment


title: HepG2_MonoCul_Cont.rep2

description: mRNA-seq (polyA+) data from HepG2 cells without treatments of free fatty acids, replicate 2


title: CRC0714PRX0A01001TUMR01000, PRX_BASALE, bio rep 1, QC ok

value: PR


title: CRC0714PRH0000000000R02000, PRH, bio rep 1, QC failed

value: H


title: Lung, WA1Delta, 1DPC, REP2


title: Lung, WA1Delta, 1DPC, REP1


title: KLK5+KLK7 SAM24387820

value: skin


title: HepG2_CoCul_FA.rep3

description: mRNA-seq (polyA+) data from HepG2 cells co-cultured with CaCO2 cells with treatments of free fatty acids (1 mM), replicate 3

value: Co-cultured with CaCO2 cells. Treatment with free fatty acid (1 mM)


title: CRC0708LMX0A02003TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: KLK5+antiKLK5/7 SAM24387817

value: primary

value: neonatal keratinocytes


title: NT, WA1WA1, 1DPC, REP3

value: Nasal turbinate

value: Infected with WA1


title: HepG2_MonoCul_Cont.rep1

description: mRNA-seq (polyA+) data from HepG2 cells without treatments of free fatty acids, replicate 1


title: s36_KODIV34C

city: Cardiff

first: Lucia

middle: Fernandez

last: Cardo

state: Wales

address: maindy road

country: United Kingdom

institute: Cardiff University

description:
WTCHG_368686_244147
processed data file: ko.div34_vs_h7.div34.txt

data_processing:
Reads were mapped to the human genome (GRCh38) using Burrows-Wheeler Aligner algorithms
individual gene read counts calculated using featureCounts
DeSeq2 was used to calculate differential gene expression with a cut-off of adjusted p-value<0.1, FDR of 10% and a FC>1.5
Genome_build: GRCh38
Supplementary_files_format_and_content: DeSeq2

source_name: neurons

growth_protocol: For differentiation, hESCs were pre-plated on growth factor-reduced matrigel in TeSR-E8.  When cells reached >80% confluence, neural differentiation was initiated by switching TeSR-E8 to DMEM-F12/Neurobasal (2:1) supplemented with N2 and B27. For the first 10 days, cultures were supplemented with SB431542 (10µM, Tocris) and LDN-193189 (100nM, StemGene). Cultures were passaged using EDTA firstly on day 10, day 20-21 and day 30. Retinol-free B27 was used for the first 25 days, followed by normal B27 from day 26 onwards.

extract_protocol:
RNA was extracted and purified using the PureLink RNA Mini Kit (Thermofisher Scientific)
Libraries were prepared using the TruSeq Stranded mRNA kit (Illumina) from 1µg RNA

value: hESC-derived neurons

tag: differentiation days


title: NT, WA1Alpha, 1DPC, REP1

value: Infected with Alpha


title: CRC0707PRX0A01001TUMR09000, PRX_BASALE, bio rep 1, QC ok

value: Colorectal Cancer

value: X

value: WT


title: Lung, WA1Alpha, 1DPC, REP4


title: HepG2_CoCul_FA.rep2

description: mRNA-seq (polyA+) data from HepG2 cells co-cultured with CaCO2 cells with treatments of free fatty acids (1 mM), replicate 2

value: Human hepatocellular carcinoma


title: s34_KODIV34A

description:
WTCHG_368686_242123
processed data file: ko.div34_vs_h7.div34.txt


title: CRC0707PRH0000000000R01000, PRH, bio rep 1, QC ok


title: s35_KODIV34B

description:
WTCHG_368686_243135
processed data file: ko.div34_vs_h7.div34.txt


title: Lung, WA1Alpha, 1DPC, REP2

value: Lung


title: HepG2_CoCul_FA.rep1

description: mRNA-seq (polyA+) data from HepG2 cells co-cultured with CaCO2 cells with treatments of free fatty acids (1 mM), replicate 1


title: HepG2_CoCul_Cont.rep3

description: mRNA-seq (polyA+) data from HepG2 cells co-cultured with CaCO2 cells without treatments of free fatty acids, replicate 3

value: Co-cultured with CaCO2 cells. No treatments with free fatty acid


title: CRC0706LMX0A02001TUMR01000, LMX_BASALE, bio rep 1, QC ok

value: LM


title: s32_H7DIV34B

description:
WTCHG_368686_240194
processed data file: ko.div34_vs_h7.div34.txt


title: Lung, WA1Alpha, 1DPC, REP1


title: s33_H7DIV34C

description:
WTCHG_368686_241111
processed data file: ko.div34_vs_h7.div34.txt


title: Lung, WA1WA1, 1DPC, REP4


title: s31_H7DIV34A

description:
WTCHG_368686_239182
processed data file: ko.div34_vs_h7.div34.txt


title: HepG2_CoCul_Cont.rep1

description: mRNA-seq (polyA+) data from HepG2 cells co-cultured with CaCO2 cells without treatments of free fatty acids, replicate 1


title: CRC0705LMX0A02001TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: CRC0691LMX0A02002TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: HepG2_CoCul_Cont.rep2

description: mRNA-seq (polyA+) data from HepG2 cells co-cultured with CaCO2 cells without treatments of free fatty acids, replicate 2


title: s30_KODIV21C

description:
WTCHG_368686_238170
processed data file: ko.div21_vs_h7.div21.txt

source_name: neural progenitor cells

value: hESC-derived neural progenitors


title: Lung, WA1WA1, 1DPC, REP2


title: Caco2_MonoCul_FA.rep3

description: mRNA-seq (polyA+) data from CaCO2 cells with treatments of free fatty acids (1 mM), replicate 3

source_name: Caco-2  Cell Line

value: Treatments with free fatty acid (1 mM)

value: Human intestine


title: CRC0689PRX0A01001TUMR01000, PRX_BASALE, bio rep 1, QC ok

value: PR


title: s29_KODIV21B

description:
WTCHG_368686_237158
processed data file: ko.div21_vs_h7.div21.txt


title: Lung, WA1WA1, 1DPC, REP3


title: s28_KODIV21A

description:
WTCHG_368686_236146
processed data file: ko.div21_vs_h7.div21.txt


title: Lung, WA1Alpha, 1DPC, REP3


title: CRC0689PRH0000000000R01000, PRH, bio rep 1, QC ok

value: H


title: Caco2_MonoCul_FA.rep1

description: mRNA-seq (polyA+) data from CaCO2 cells with treatments of free fatty acids (1 mM), replicate 1


title: Lung, WA1WA1, 1DPC, REP1


title: s27_H7DIV21C

description:
WTCHG_368686_235134
processed data file: ko.div21_vs_h7.div21.txt


title: CRC0687LMX0A02001TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: CRC0692LMX0A02004TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: CRC0683PRX0A01001TUMR01000, PRX_BASALE, bio rep 1, QC ok


title: Caco2_MonoCul_Cont.rep3

description: mRNA-seq (polyA+) data from CaCO2 cells without treatments of free fatty acids, replicate 3

value: No treatments with free fatty acid


title: s25_H7DIV21A

description:
WTCHG_368686_233110
processed data file: ko.div21_vs_h7.div21.txt


title: s26_H7DIV21B

description:
WTCHG_368686_234122
processed data file: ko.div21_vs_h7.div21.txt


title: Caco2_MonoCul_Cont.rep2

description: mRNA-seq (polyA+) data from CaCO2 cells without treatments of free fatty acids, replicate 2


title: NT, Delta, 3DPI, REP2

value: Nasal turbinate

value: Infected with Delta


title: NT, Delta, 3DPI, REP1


title: Caco2_MonoCul_FA.rep2

description: mRNA-seq (polyA+) data from CaCO2 cells with treatments of free fatty acids (1 mM), replicate 2


title: Caco2_MonoCul_Cont.rep1

description: mRNA-seq (polyA+) data from CaCO2 cells without treatments of free fatty acids, replicate 1


title: NT, Delta, 3DPI, REP3


title: CRC0682PRX0A01001TUMR01000, PRX_BASALE, bio rep 1, QC ok


title: s23_KODIV15B

description:
WTCHG_368686_231181
processed data file: ko.div15_vs_h7.div15.txt


title: CRC0683PRH0000000000R01000, PRH, bio rep 1, QC ok


title: NT, Alpha, 3DPI, REP4


title: CRC0682PRH0000000000R05000, PRH, bio rep 1, QC ok


title: s22_KODIV15A

description:
WTCHG_368686_230169
processed data file: ko.div15_vs_h7.div15.txt


title: NT, Alpha, 3DPI, REP3


title: Caco2_CoCul_FA.rep3

description: mRNA-seq (polyA+) data from CaCO2 cells co-cultured with HepG2 cells with treatments of free fatty acids (1 mM), replicate 3

value: Co-cultured with HepG2 cells. Treatments with free fatty acid (1 mM)


title: CRC0671PRX0A02002TUMR01000, PRX_BASALE, bio rep 1, QC ok


title: Caco2_CoCul_FA.rep2

description: mRNA-seq (polyA+) data from CaCO2 cells co-cultured with HepG2 cells with treatments of free fatty acids (1 mM), replicate 2


title: Caco2_CoCul_FA.rep1

description: mRNA-seq (polyA+) data from CaCO2 cells co-cultured with HepG2 cells with treatments of free fatty acids (1 mM), replicate 1


title: s21_H7DIV15C

description:
WTCHG_368686_229157
processed data file: ko.div15_vs_h7.div15.txt


title: NT, Alpha, 3DPI, REP2

value: Infected with Alpha


title: CRC0670LMX0A02002TUMR01000, LMX_BASALE, bio rep 1, QC ok

value: Colorectal Cancer


title: s20_H7DIV15B

description:
WTCHG_368686_228145
processed data file: ko.div15_vs_h7.div15.txt


title: CRC0666PRX0A01001TUMR01000, PRX_BASALE, bio rep 1, QC ok

value: X


title: NT, Alpha, 3DPI, REP1


title: s24_KODIV15C

description:
WTCHG_368686_232193
processed data file: ko.div15_vs_h7.div15.txt


title: Caco2_CoCul_Cont.rep2

description: mRNA-seq (polyA+) data from CaCO2 cells co-cultured with HepG2 cells without treatments of free fatty acids, replicate 2

value: Co-cultured with HepG2 cells. No treatments with free fatty acid


title: CRC0666PRH0000000000R01000, PRH, bio rep 1, QC ok

value: WT


title: Caco2_CoCul_Cont.rep1

description: mRNA-seq (polyA+) data from CaCO2 cells co-cultured with HepG2 cells without treatments of free fatty acids, replicate 1


title: NT, Delta, 3DPI, REP4


title: NT, WA1, 3DPI, REP3

value: Infected with WA1


title: s19_H7DIV15A

description:
WTCHG_368686_227133
processed data file: ko.div15_vs_h7.div15.txt


title: s18_KODIV34C

description:
WTCHG_365099_244147
processed data file: ko.div34_vs_h7.div34.txt

value: hESC-derived neurons


title: NT, WA1, 3DPI, REP2


title: s17_KODIV34B

description:
WTCHG_365099_243135
processed data file: ko.div34_vs_h7.div34.txt


title: CRC0625LMX0A02002TUMR01000, LMX_BASALE, bio rep 1, QC ok

value: LM


title: NT, WA1, 3DPI, REP1


title: CRC0624LMX0A02002TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: s15_H7DIV34C

description:
WTCHG_365099_241111
processed data file: ko.div34_vs_h7.div34.txt


title: CRC0626LMX0A02002TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: pEF1s(orig), dox 13d, low expr

city: Pasadena

first: Yitong

last: Ma

address: 1200 E California Blvd

department: Division of Biology and Biological Engineering

institute: Caltech

library_source: genomic

data_processing:
Trim Galore!
Bismark methylation extractor
Assembly: Reference plasmid map (submitted the plasmid maps to addgene (addgene.org/plasmids/articles/28233817/))
Supplementary files format and content: txt file of CpG methylation calls
Library strategy: EM-seq

molecule: genomic DNA

organism: Cricetulus griseus

source_name: CHO

growth_protocol: Standard CHO condition

extract_protocol:
DNeasy Blood & Tissue Kits, Qiagen
NEBNext Enzymatic Methyl-seq Conversion Module, NEB; Nextera XT Library Prep protocol, Illumina
Enzymatic Methyl-seq

treatment_protocol: doxycycline 1ug/ml

value: CHO

value: Chinese hamster ovary cells

value: dox 13d, low expr


title: s16_KODIV34A

description:
WTCHG_365099_242123
processed data file: ko.div34_vs_h7.div34.txt


title: CRC0622PRX0A01001TUMR01000, PRX_BASALE, bio rep 1, QC ok

value: PR


title: Lung, Delta, 3DPI, REP3

value: Lung


title: pEF1s(orig), dox 13d, med expr

value: dox 13d, med expr


title: Lung, Delta, 3DPI, REP2


title: s14_H7DIV34B

description:
WTCHG_365099_240194
processed data file: ko.div34_vs_h7.div34.txt


title: CRC0622PRH0000000000R01000, PRH, bio rep 1, QC ok

value: H


title: clean_self_LW1

city: Yangling

first: bo

last: wang

state: Shaanxi

address: No. 3 Taicheng Road

country: China

institute: Northwest A&F University

data_processing:
Sequenced reads were trimmed for adaptor sequence, masked for low-complexity or low-quality sequence, then mapped to the predicted gene models of B. dothidea PG45 genome (GenBank accession no. NNRO00000000)
A gene expression profile was created using DESeq R package after transcripts per million (TPM) normalization
miRNAs with a significant P-value (< 0.05) and a greater than threefold change (log2) in transcript level were considered to be differently expressed. All P-values were corrected for false discoveries resulting from multiple hypothesis testing using the Benjamini-Hochberg procedure.
Genome_build: reference genome deposited at DDBJ/EMBL/GenBank under the accession NNRO00000000
Supplementary_files_format_and_content: tab-delimited text files include expression profiles

organism: Botryosphaeria dothidea

source_name: mycelium

extract_protocol:
Total RNA was extracted according to the instruction manual of the Trizol Reagent (Life technologies, California, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: mycelium


title: clean_self_LW6


title: clean_self_LW0


title: pEF1s(orig), dox 13d, high expr

value: dox 13d, high expr


title: s13_H7DIV34A

description:
WTCHG_365099_239182
processed data file: ko.div34_vs_h7.div34.txt


title: CRC0619LMX0B02001TUMR01000, LMX_BASALE, bio rep 1, QC failed


title: pEF1s(orig), dox 8d, high expr

value: dox 8d, high expr


title: Lung, Delta, 3DPI, REP1

value: Infected with Delta


title: CRC0618LMX0A02001TUMR01000, LMX_BASALE, bio rep 1, QC ok

value: Colorectal Cancer

value: X


title: Lung, Delta, 3DPI, REP4


title: CRC0616LMX0A02002TUMR01000, LMX_BASALE, bio rep 1, QC ok

value: WT


title: Lung, Alpha, 3DPI, REP4

value: Infected with Alpha


title: Lung, Alpha, 3DPI, REP3


title: pEF1s(orig), dox 3d, med expr

value: dox 3d, med expr


title: pEF1s(orig), dox 3d, high expr

value: dox 3d, high expr


title: s11_KODIV21B

description:
WTCHG_365099_237158
processed data file: ko.div21_vs_h7.div21.txt

value: hESC-derived neural progenitors


title: s12_KODIV21C

description:
WTCHG_365099_238170
processed data file: ko.div21_vs_h7.div21.txt


title: CRC0612PRX0A01001TUMR01000, PRX_BASALE, bio rep 1, QC ok


title: CRC0610LMX0A02002TUMR01000, LMX_BASALE, bio rep 1, QC ok

value: LM


title: Inset(low)-pEF1s(orig), dox 8d, med expr

value: CHO

value: Chinese hamster ovary cells

value: dox 8d, med expr


title: s9_H7DIV21C

description:
WTCHG_365099_235134
processed data file: ko.div21_vs_h7.div21.txt


title: Lung, Alpha, 3DPI, REP1

value: Lung


title: Lung, Alpha, 3DPI, REP2


title: Inset(low)-pEF1s(orig), dox 8d, high expr


title: Lung, WA1, 3DPI, highdose, REP4

value: Infected with WA1


title: Inset(low)-pEF1s(orig), dox 3d, med expr


title: CRC0607LMX0A02002TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: CRC0609LMX0A02002TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: Lung, WA1, 3DPI, highdose, REP3


title: Lung, WA1, 3DPI, highdose, REP2


title: s6_KODIV15C

description:
WTCHG_365099_232193
processed data file: ko.div15_vs_h7.div15.txt


title: s7_H7DIV21A

description:
WTCHG_365099_233110
processed data file: ko.div21_vs_h7.div21.txt


title: CRC0604LMX0A02001TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: s5_KODIV15B

description:
WTCHG_365099_231181
processed data file: ko.div15_vs_h7.div15.txt


title: Inset(low)-pEF1s(orig), no dox

value: no dox


title: CRC0602LMX0B02004TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: Inset(high)-pEF1s(orig), dox 8d, high expr, repeat


title: Lung, WA1, 3DPI, highdose, REP1


title: CRC0601PRH0000000000R06000, PRH, bio rep 1, QC ok

value: H

value: PR


title: s4_KODIV15A

description:
WTCHG_365099_230169
processed data file: ko.div15_vs_h7.div15.txt


title: Lung, WA1, 3DPI, lowdose, REP3


title: Inset(high)-pEF1s(orig), dox 3d, high expr


title: s10_KODIV21A

description:
WTCHG_365099_236146
processed data file: ko.div21_vs_h7.div21.txt


title: s8_H7DIV21B

description:
WTCHG_365099_234122
processed data file: ko.div21_vs_h7.div21.txt


title: Inset(high)-pEF1s(orig), dox 8d, high expr

value: dox 8d, high expr


title: s2_H7DIV15B

description:
WTCHG_365099_228145
processed data file: ko.div15_vs_h7.div15.txt


title: s1_H7DIV15A

description:
WTCHG_365099_227133
processed data file: ko.div15_vs_h7.div15.txt


title: Lung, WA1, 3DPI, lowdose, REP2


title: CRC0600LMX0B02003TUMR01000, LMX_BASALE, bio rep 1, QC ok

value: Colorectal Cancer


title: Inset(high)-pEF1s(orig), dox 8d, med expr


title: CRC0598LMX0A02002TUMR02000, LMX_BASALE, bio rep 1, QC ok

value: X


title: Inset(high)-pEF1s(orig), dox 6d, low expr

value: dox 6d, low expr


title: Inset(low)-pEF1s(orig), dox 3d, high expr


title: Inset(high)-pEF1s(orig), dox 3d, med expr


title: NT, Delta, 1DPI, REP4

value: Nasal turbinate

value: Infected with Delta


title: NT, Delta, 1DPI, REP3


title: CRC0596PRX0A02001TUMR05000, PRX_BASALE, bio rep 1, QC ok

value: WT


title: CRC0597LMX0A02001TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: siNC_Rep4

city: san francisco

first: Lili

last: Zhu

address: 1650 owens street

institute: Gladstone Institutes

data_processing:
Basecalls performed usding Illumina Real Time Analysis
Alignment of the provided samples to the reference genome was performed using STAR 2.5.2a
Reads were aligned to the human hg19 reference assembly
we used rMATS  to model the counts mapping across splice junctions and the pairing of samples in our experiments
Genome_build: hg19
Supplementary_files_format_and_content: rMATS_output

source_name: Cardiac progenitor cells

growth_protocol: Cardiac progenitors cells were differentiated from Wtc11 hiPS lines by the WNT modulation protocol.  In brief,  6 uM CHIR were added for 48hours, followed by 5 uM IWP4 for 48 hours. Day5, cells ere replated and grow in RPMI with B27 supplement minus insulin.

extract_protocol:
Total RNA was extracted using Zymo Direct-zol RNA kit (Zymo Research, #R2051) with on-column DNase I digestion according to the manufacturer’s instruction
The RNA libraries were prepared with the NuGEN Ovation Ultralow System V2 (Tecan, # 0344NB) according to the manufacturer’s instruction.

treatment_protocol: D5 hCPCs were transfected with siNC or siGATA4. Cells were collect 48 hours after transfection.

value: d7 hiPSC-derived cardiac progenitor cells

value: siNC control


title: CRC0601PRX0A01001TUMR01000, PRX_BASALE, bio rep 1, QC ok


title: siGATA4_Rep3


title: CRC0594LMX0A02001TUMR01000, LMX_BASALE, bio rep 1, QC ok

value: LM


title: Inset(high)-pEF1s(orig), dox 1d, high expr

value: CHO

value: Chinese hamster ovary cells

value: dox 1d, high expr


title: Lung, WA1, 3DPI, lowdose, REP4

value: Lung

value: Infected with WA1


title: Inset(high)-pEF1s(orig), dox 1d, low expr

value: dox 1d, low expr


title: siNC_Rep3


title: NT, Delta, 1DPI, REP2


title: siGATA4_Rep2


title: s3_H7DIV15C

description:
WTCHG_365099_229157
processed data file: ko.div15_vs_h7.div15.txt

value: hESC-derived neural progenitors


title: NT, Delta, 1DPI, REP1


title: CRC0592PRX0B01001TUMR01000, PRX_BASALE, bio rep 1, QC ok

value: PR


title: CRC0593LMX0A02001TUMR01000, LMX_BASALE, bio rep 1, QC ok

value: Colorectal Cancer


title: NT, Alpha, 1DPI, REP4

value: Infected with Alpha


title: siGATA4_Rep4


title: NT, Alpha, 1DPI, REP3


title: Lung, WA1, 3DPI, lowdose, REP1


title: Inset(high)-pEF1s(orig), no dox

value: no dox


title: NT, Alpha, 1DPI, REP2

value: Nasal turbinate


title: siGATA4_Rep1


title: CRC0583PRX0A02001TUMR01000, PRX_BASALE, bio rep 1, QC ok

value: X


title: siNC_Rep2


title: siNC_Rep1


title: CRC0581LMX0A02004TUMR01000, LMX_BASALE, bio rep 1, QC ok

value: WT


title: NT, Alpha, 1DPI, REP1


title: Input_Rep3

data_processing:
library strategy: eCLIP-seq
The trimmed reads longer than 18 nt were mapped to hg19 reference using STAR version 2.5.2b
Reads were aligned to the human hg19 reference assembly
omniCLIP version 0.1.0 (with the optional argument --bck-var) was used to call peaks of mapped reads in a CLIP sample with respect to its matched input.
The peaks that had fewer than 10 mapped fragments in total, which were counted using featureCounts v1.5.1 (with optional arguments -p -O) were removed
peaks overlapping in at least 2 out of 3 replicates are used for further analysis
Genome_build: hg19
Supplementary_files_format_and_content: bed

extract_protocol:
Lysates were clarified from sonicated cells and GATA4-RNA complexes were isolated with antibody.
The libraries were prepared according to the eCLIP protocol(PMID: 27018577)

treatment_protocol: D7 hCPCs were UV crosslinked and used for eCLIP

value: d7 hiPSC-derived cardiac progenitor cells

value: Input


title: NT, WA1, 1DPI, REP4


title: CRC0580LMX0B02002TUMR01000, LMX_BASALE, bio rep 1, QC ok

value: LM


title: CRC0578LMX0A03005TUMR02000, LMX_cetux_6w, bio rep 1, QC ok

value: CET


title: GATA4_eCLIP_Rep3


title: Input_Rep2


title: NT, WA1, 1DPI, REP2


title: NT, WA1, 1DPI, REP1


title: CRC0591LMX0A02002TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: CRC0578LMX0A02002TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: NT, WA1, 1DPI, REP3


title: GATA4_eCLIP_Rep2


title: Input_Rep1


title: Lung, Delta, 1DPI, REP4

value: Infected with Delta


title: CRC0578LMO0A05020002R01000, LMO_BASALE, bio rep 2, QC ok

value: O


title: P12-Bone Marrow-GATA2 mutant

type: genomic

city: Esplugues de Llobregat

first: Maximiliano

last: Distefano

state: Barcelona

address: Passeig de Sant Joan de Déu, 2

department: Department of Hematology and Oncology

country: Spain

institute: Hospital Sant Joan de Deu

description: GATA2 deficiency with susceptibility to MDS/AML

hyb_protocol: Illumina protocol

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

data_processing: shinyÉPICo v1.0.0

label: Cy5 and Cy3

source_name: Bone Marrow, GATA2 mutant

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from bone marrow and peripheral blood samples using Qiagen DNeasy Kit according to standard instructions

tag: "sex"

value: Male

tag: "age"


title: P11-Bone Marrow-GATA2 mutant


title: P6-Bone Marrow-GATA2 mutant

value: Female


title: P13-Bone Marrow-GATA2 mutant


title: Lung, Delta, 1DPI, REP3

value: Lung


title: CRC0578LMO0A04018001R01000, LMO_BASALE, bio rep 1, QC ok


title: P5-Bone Marrow-GATA2 mutant


title: HD1-Bone Marrow-wild type genotype

description: Healthy donor

source_name: Bone Marrow, wild type genotype


title: GATA4_eCLIP_Rep1


title: Lung, Delta, 1DPI, REP2


title: CRC0577PRX0B01001TUMR05000, PRX_BASALE, bio rep 1, QC failed


title: CRC0578LMX0A03001TUMR02000, LMX_cetux_6w_NT, bio rep 1, QC ok

value: NT


title: Lung, Delta, 1DPI, REP1


title: CRC0577PRH0000000000R01000, PRH, bio rep 1, QC ok

value: H

value: PR


title: P10-Bone Marrow-GATA2 mutant


title: P16-Peripheral Blood-GATA2 mutant

source_name: Peripheral Blood, GATA2 mutant


title: P17-Peripheral Blood-GATA2 mutant


title: placenta_OBLA_223

city: Boston

first: Perrie

last: O’Tierney-Ginn

state: MA

address: 800 Washington Street #394

department: Mother Infant Research Institute

institute: Tufts Medical Center

data_processing:
FastQ files of the miRNA-seq libraries were aligned to GRCh38 reference human genome using Bowtie.
Aligned reads were intersected with the genome coordinates of mature miRNAs based on miRBase v21.
The count of an miRNA is defined as the number of reads intersecting with that miRNA
If a read intersected with multiple miRNAs, a fraction of one count was assigned to each miRNA.
The total count of each miRNA was rounded.
Genome_build: GRCh38
Supplementary_files_format_and_content: comma separated file for miRNA count

source_name: whole placenta

extract_protocol:
Whole placenta tissue was flash frozen in liquid nitrogen within 30 min of cesarean delivery. Total RNA was harvested using Trizol reagent. Total RNA was quantified using a NanoDrop Spectrophotometer ND-1000 (NanoDrop Technologies, Inc.) and its integrity was assessed using a 2100 Bioanalyzer (Agilent Technologies). Libraries were generated from 1000 ng of total RNA using the TruSeq® Small RNA Sample Prep Kit (Illumina), as per the manufacturer’s recommendations. cDNA construct purification has been performed on a Pippin Prep instrument (SAGE Science). Final libraries were quantified using the Kapa Illumina GA with Revised Primers-SYBR Fast Universal kit (Kapa Biosystems). Average size fragment was determined using a LabChip GX (PerkinElmer) instrument.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: placenta

tag: gestational age

tag: pregravid bmi

tag: neonatal %bodyfat

tag: maternal race

value: cauc

tag: neonatal sex

value: female


title: placenta_LELA_3

value: male


title: CRC0576LMX0B02004TUMR02000, LMX_BASALE, bio rep 1, QC ok

value: Colorectal Cancer

value: X

value: WT


title: P1-Peripheral Blood-GATA2 mutant


title: Lung, Alpha, 1DPI, REP3

value: Infected with Alpha


title: CRC0574LMX0A04011TUMR01000, LMX_cetux_6w_NT, bio rep 2, QC ok

value: LM


title: Lung, Alpha, 1DPI, REP4


title: HD12-Peripheral Blood-wild type genotype

description: Healthy donor

source_name: Peripheral Blood, wild type genotype


title: placenta_LELA_378


title: CRC0574LMX0A04007TUMR01000, LMX_cetux_6w_NT, bio rep 1, QC ok


title: HD11-Peripheral Blood-wild type genotype

description: Healthy donor


title: placenta_OBHA_270


title: placenta_LEHA_333

value: aa


title: HD10-Peripheral Blood-wild type genotype

description: Healthy donor


title: CRC0574LMX0A04005TUMR03000, LMX_cetux_6w, bio rep 2, QC ok

value: CET


title: Lung, Alpha, 1DPI, REP1


title: Lung, Alpha, 1DPI, REP2


title: placenta_OBLA_331


title: Lung, WA1, 1DPI, REP4

value: Infected with WA1


title: CRC0574LMX0A04001TUMR05000, LMX_cetux_6w, bio rep 1, QC ok


title: HD9-Peripheral Blood-wild type genotype

description: Healthy donor

value: Female


title: HD8-Peripheral Blood-wild type genotype

description: Healthy donor

value: Male


title: Lung, WA1, 1DPI, REP3

value: Lung


title: placenta_LELA_328


title: P9-Peripheral Blood-GATA2 mutant


title: placenta_OBHA_34


title: CRC0574LMX0A02004TUMR02000, LMX_BASALE, bio rep 2, QC ok


title: Lung, WA1, 1DPI, REP2


title: placenta_OBLA_258


title: CRC0574LMH0000000000R01000, LMH, bio rep 1, QC ok

value: H


title: Lung, WA1, 1DPI, REP1


title: placenta_OBLA_407


title: P3-Bone Marrow-GATA2 mutant


title: CRC0572LMX0B02001TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: P8-Peripheral Blood-GATA2 mutant


title: placenta_LEHA_26


title: P7-Peripheral Blood-GATA2 mutant


title: CRC0571PRX0A02001TUMR01000, PRX_BASALE, bio rep 1, QC ok

value: PR


title: sham-SSC-2.control

city: wuhan

first: Jianfei

last: Liang

address: No. 237, Luoyu Road, Hongshan District,

institute: wuhan university

data_processing:
Trim_Galore (v.0.6.6).
Sequence reads were trimmed for adaptor sequence using Trim_Galore (v.0.6.6).
Trimmed sequence reads were mapped to GrCM38.
Read count extraction and normalization were performed using featureCounts (v.2.0.1).
Assembly: mm10
Supplementary files format and content: cleancount.txt: Tab-delimited text file includes raw counts for each Sample.

source_name: skeletal stem cells

extract_protocol:
RNA was harvested using TRIzol reagent (Takara 9109).
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol:
mSSC were derived from metaphysis of long bone digested with collagenase type 2 (Sigma) for 2 hours.
mSSC were derived from cell suspension stained by CD45, Ter119, Tie2, CD51, CD90, 6C3, CD105 and CD200.
Freshly sorted mSSC by fluorescence-activated cell sorting.

value: skeletal stem cells

value: sham

tag: time


title: CRC0572LMO0A02003001R01000, LMO_BASALE, bio rep 1, QC ok

tag: tissue

value: O


title: placenta_LEHA_448

value: placenta

value: cauc

value: male


title: P4-Peripheral Blood-GATA2 mutant


title: placenta_OBHA_353

value: female


title: CRC0574LMX0A02001TUMR02000, LMX_BASALE, bio rep 1, QC ok

value: Colorectal Cancer

value: X

tag: genotype

value: WT


title: placenta_LELA_9


title: sham-SSC-1.control

tag: treatment


title: CRC0570LMX0A02004TUMR01000, LMX_BASALE, bio rep 1, QC ok

tag: cell line

value: LM


title: placenta_OBLA_476


title: P13-Peripheral Blood-GATA2 mutant


title: CRC0569LMX0A02002TUMR05000, LMX_BASALE, bio rep 1, QC ok

tag: cell type


title: HD7-Bone Marrow-wild type genotype

description: Healthy donor


title: CRC0568LMX0A02002TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: HD6-Bone Marrow-wild type genotype

description: Healthy donor


title: Mouse intestinal Pgfra+ cells from adult male C57BL/6J (8 weeks old), untreated, scRNA-seq

city: New York

first: Timothy

middle: Cragin

last: Wang

state: New York

address: 1130 Saint Nicholas Avenue, ICRC

institute: Columbia University

library_source: transcriptomic single cell

data_processing:
Samples were aligned to the mm10 genome using 10x Genomics Cell Ranger 3.0.2 using default parameters
Assembly: mm10

source_name: Small intestine

extract_protocol:
Pdgfra+ stromal cells were harvested from 1 adult (8 weeks old) male  c57b6/j mouse. Briefly, 10 cm of intestinal Jejunum were dissected, flushed with cold DPBS and open longitudinally. Next tissue was cut into small pieces and incubated in cold DPBS+10mM EDTA to promote epithelial cells dissociation as previously described. The remaining tissue fragments were then enzymatically digested using Collagenase XI (Sigma, C7657) and Dispase II (Sigma, D4693) for 30’ at 37®C. Filtered single cells were stained with CD140a-Ab (Biolegend, APA5) for 20’ on ice. Alive(DAPI-)CD31-CD140a+ cells were sorted using a BD FACS Aria and processed for 10x Chromium library preparation.
Single Cell 3′ V3.1 assay (10X Genomics).

value: Small intestine

value: Mesenchymal cells

value: Whole Pdgfra+ cells

tag: strain

tag: developmental stage

value: adult

tag: Sex


title: placenta_OBLA_280


title: Sudachitin treated mouse at ZT18 rep2 [S3_3CT18]

city: Tokushima-City

first: KAZUAKI

last: MAWATARI

state: Tokushima

address: 3-18-15 KUROMOTO-CHO

institute: Tokushima University

data_processing:
The original fluorescence images obtained from high throughput sequencing platforms are transformed to short reads by base calling. These short reads are recorded in FASTQ format, which contains base information (reads) and corresponding sequencing quality information.
After adaptor sequence trimming using Trimmomatic (version 0.39),  the sequence reads were mapped to the mouse genome (GRCm38/mm10) using STAR (2.7.2a). To obtain reliable alignments, the reads with a mapping quality of less than 10 were removed by SAM tools (version 1.7). The University of Clifornia, Santa Cruz (UCSC) known canonical gene set (55,421) was used for annotation, and the reads mapped to the exons were quantified using Homer.
Assembly: mm10
Supplementary files format and content: bigWig and tab-delimited text files containing gene read counts and FPKM values for each sample.

source_name: Liver

extract_protocol:
Tissue samples were collected from 30-week old mice at the indicated circadian times (ZT6 and ZT18). Total RNAs were isolated using PureXtract RNAsol® reagent (GenDEPOT)
Two micrograms of extracted RNA from liver (RNA Integrity Number > 9.0, measured by an Agilent 2100 Bioanalyzer) was used for library construction and poly(A)-enriched non-stranded RNA sequencing was carried out by Novogene (Sacramento, CA, USA) on Illumina NovaSeq 6000 with 150-bp paired-end reads

treatment_protocol: Four-week old male C57BL/6J mice were purchased from the Jackson Laboratory (Bar Harbor, ME, USA). After four weeks of acclimation, the mice were fed with 45 cal% high-fat diet (HFD) (Research Diets, New Brunswick, NJ, USA) ad libitum and treated with either vehicle (PBS, n = 11) or Sudachitin (100 mg/kg body weight, n = 12) via oral gavage during ZT8-10 every other day. Body weight and food intake were monitored weekly.

value: Liver

value: Sudachitin treated


title: Ovx-SSC-1.control

value: skeletal stem cells

value: ovariectomy


title: placenta_LELA_361


title: HD5-Bone Marrow-wild type genotype

description: Healthy donor

value: Male


title: Sudachitin treated mouse at ZT6 rep2 [S2_3CT06]


title: placenta_OBHA_19

value: placenta


title: Sudachitin treated mouse at ZT6 rep1 [S2_1CT06]


title: CRC0566PRH0000000000R01000, PRH, bio rep 1, QC ok

source_name: Colorectal Cancer

value: H

value: PR


title: Ovx-SSC-2.control


title: HD4-Bone Marrow-wild type genotype

description: Healthy donor


title: CRC0561LMX0A02003TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: CRC0560LMX0A02001TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: HD3-Bone Marrow-wild type genotype

description: Healthy donor

value: Female


title: Control mouse at ZT6 rep2 [C3_3CT06]

value: male

value: Control


title: Sudachitin treated mouse at ZT18 rep1 [S1_1CT18]


title: CRC0566PRX0B01001TUMR01000, PRX_BASALE, bio rep 1, QC ok

value: Colorectal Cancer

value: X

value: WT


title: HD2-Bone Marrow-wild type genotype

description: Healthy donor


title: placenta_OBHA_43

value: cauc


title: placenta_LEHA_252

description:
The sample was cleaned-up with an RNA clean-up kit. Not used in analysis
samp.21_7

value: aa


title: Control mouse at ZT6 rep1 [C3_1CT06]


title: CRC0559LMX0B02004TUMR06000, LMX_BASALE, bio rep 1, QC ok

value: LM


title: P1-Bone Marrow-GATA2 mutant


title: CRC0558LMX0A02003TUMR05000, LMX_BASALE, bio rep 1, QC ok


title: placenta_OBHA_272


title: Control mouse at ZT18 rep2 [C2_0CT18]

value: Liver


title: Control mouse at ZT18 rep1 [C1_2CT18]


title: ANF_ID35

city: Hamburg

first: Catena

last: Kresbach

address: Martinistrasse 52

country: Germany

institute: Research Institute Children‘s Cancer Center Hamburg

description: Sample 35

hyb_protocol: 100-500 ng DNA were used for bisulfite conversion with the EZ DNA Methylation Kit (Zymo Research). Afterwards, the DNA Clean & Concentrator-5 (Zymo Research) and the Infinium HD FFPE DNA Restore Kit (Illumina) were used to clean and restore the converted DNA.

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

data_processing:
R (v4.1.2)
Average Beta

source_name: biopsy

extract_protocol: DNA was isolated from FFPE tissue using the ReliaPrep™ FFPE gDNA Miniprep System (Promega) according to manufacturer’s instructions.

tag: material

value: FFPE

tag: array type

value: epic

tag: age

tag: clinical nf1 syndrome

tag: initial histological diagnosis

value: ANNUBP

tag: revised histological diagnosis (who 2021)


title: placenta_LEHA_100

tag: gestational age

tag: pregravid bmi

tag: neonatal %bodyfat

tag: maternal race


title: CRC0557LMX0A02001TUMR01000, LMX_BASALE, bio rep 1, QC ok

tag: tissue

tag: genotype


title: placenta_LEHA_267

tag: neonatal sex

value: female


title: CRC0555LMX0A02002TUMR01000, LMX_BASALE, bio rep 1, QC ok

tag: cell line

tag: cell type

tag: treatment


title: placenta_OBLA_473

value: placenta


title: CGN, DIV7, Zic, CUT&RUN, Rep 3

city: Durham

first: Anne

middle: E

last: West

state: NC

address: 311 Research Dr

department: Neurobiology

institute: Duke University

description: S-Prime 50bp

data_processing:
CUT&RUN raw fastq read files were analyzed with FastQC and processed with Trimmomatic 0.38 for quality control and adapter trimming
Trimmed reads were then aligned to the mm10 reference genome using STAR 2.7.2b. Duplicates were filtered from the resulting alignments with macs2 2.1 filterdup keeping only one duplicate
Genome coverage was calculated using bedtools v2.25.0 genomecov.
Peak calling was performed with the genome coverage file using SEACR 1.3 stringent with a numeric cutoff that returned the 0.01 fraction of peaks with top signal. A union peak file was obtained with the union function from GenomicRanges 1.48.0  R package. Raw reads were counted using this union peak file as reference with the regionCounts function from the csaw 1.30.1 R package.
DESeq2 1.36.0 was used to obtain differentially bound peaks between timepoints, using an adjusted p value cutoff of 0.05. Log2 fold change estimates were shrinked using lfcShrink function from DESeq2, and the ashr method.
Assembly: mm10
Supplementary files format and content: bed
Library strategy: CUT&RUN

source_name: Cerebellar granule neuron

growth_protocol: Neurobasal, 2% Calf Serum, 1x glutamine, 1x penicillin/streptomycin, 1x B27. Cells were cultured at 37C at 10% CO2.

extract_protocol:
Cells were scraped into 1X PBS + Protease Inhibitor, pelleted and washed in the same buffer, after which intact nuclei were pelleted and CUT and RUN was performed according to the Epicypher CUT and RUN kit (#14-1408) as per manufacturer guidelines
CUT and RUN libraries were prepared using the NEB Ultra II DNA Library Prep Kit for Illumina (NEB #R7645L) and NEBNext Multiplex Oligos for Illumina (NEB #E6440S). Library Cleanup was performed prior to and after PCR amplification (as noted in Epicypher CUT and RUN Kit, #14-1408), using 0.8X Kapa Hyperpure beads (Roche #08963851001)

treatment_protocol: Cells were treated with 1 uM Cytosine Arabinoside (Arac) at DIV2

value: Cerebellar granule neuron

tag: div

tag: antibody

value: Zic1/2 C terminus (PMID:24413398)


title: ANF_ID33

description: Sample 33

tag: material

tag: array type

tag: Sex

value: PN


title: ANF_ID30

description: Sample 30

source_name: biopsy, multiple

tag: age

tag: clinical nf1 syndrome

tag: initial histological diagnosis

value: Atypical neurofibroma


title: ANF_ID31

description: Sample 31

source_name: biopsy, spine

value: male

tag: revised histological diagnosis (who 2021)


title: placenta_OBHA_459

tag: gestational age

tag: pregravid bmi

tag: neonatal %bodyfat


title: CGN, DIV7, Zic, CUT&RUN, Rep 1

description: S-Prime 50bp


title: placenta_OBHA_269

tag: tissue

tag: maternal race


title: placenta_LEHA_356

tag: neonatal sex


title: CGN, DIV5, Zic, CUT&RUN, Rep 3

description: S-Prime 50bp

tag: cell type


title: CRC0553PRX0A01001TUMR05000, PRX_BASALE, bio rep 1, QC ok

value: Colorectal Cancer

tag: cell line

value: PR

tag: genotype

tag: treatment


title: ANF_ID34

description: Sample 34

source_name: biopsy, Th12/L1

tag: material


title: ANF_ID36

description: Sample 36

source_name: biopsy, thigh

tag: array type

value: lg MPNST


title: CGN, DIV5, Zic, CUT&RUN, Rep 2

description: S-Prime 50bp

tag: div

tag: antibody


title: placenta_LELA_86


title: CRC0554LMX0A02002TUMR01000, LMX_BASALE, bio rep 1, QC ok

value: X

value: WT


title: ANF_ID29

description: Sample 29

source_name: biopsy, arm

tag: age

tag: Sex

tag: clinical nf1 syndrome

value: sporadic


title: CRC0552LMX0A02001TUMR01000, LMX_BASALE, bio rep 1, QC ok

value: LM


title: CGN, DIV7, Zic, CUT&RUN, Rep 2

description: S-Prime 50bp


title: placenta_OBLA_1

tag: gestational age

value: aa


title: CRC0556LMX0B02004TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: O_IDH_mut_1

city: Seoul

first: Kwanghoon

last: Lee

address: 103, Daehak-ro, Jongno-gu

department: Pathology

country: South Korea

institute: Seoul National University

hyb_protocol: Bisulfite converted DNA was amplified, fragmented, and hybridized to Illumina Infinium EPIC 850k Human DNA Methylation Beadchips using standard Illumina protocol

scan_protocol: Arrays were imaged using the Illumina iScan instrument following standard recommended Illumina scanner setting

data_processing: A preprocessing procedure was conducted for raw methylation intensity signals using the R package, “methylationArrayAnalysis” (version 1.14.0)

source_name: Brain tumor

label_protocol: Standard Illumina protocol

growth_protocol: Primary human tumor tissue was used as the source of genomic DNA for all patients at time of initial diagnosis before any radiation or chemotherapy had been administered. No ex vivo culture or xenografting was performed.

extract_protocol: DNA was extracted from FFPE tumor samples using a Maxwell RSC FFPE Plus DNA Kit (AS1135; Promega)

treatment_protocol: Primary human tumor tissue was used as the source of genomic DNA for all patients. No ex vivo culture or xenografting was performed.

tag: gender

value: Male

tag: tissue type

value: oligodendroglioma

tag: grade

value: IDH-mutant and 1p/19q-codeleted (O_IDH_mut)


title: placenta_OBHA_131

tag: tissue

value: placenta

tag: pregravid bmi

tag: neonatal %bodyfat

tag: maternal race


title: A_IDH_mut

value: astrocytoma

tag: genotype

value: IDH-mutant (A_IDH_mut)


title: CGN, DIV5, Zic, CUT&RUN, Rep 1

description: S-Prime 50bp

tag: cell type

value: Cerebellar granule neuron

value: Zic1/2 C terminus (PMID:24413398)


title: ANF_ID28

description: Sample 28

tag: material

value: FFPE

value: epic

value: male

tag: initial histological diagnosis

value: Atypical neurofibroma

tag: revised histological diagnosis (who 2021)

value: ANNUBP


title: CGN, DIV3, Zic, CUT&RUN, Rep 3

description: S-Prime 50bp

tag: div

tag: antibody


title: placenta_LELA_198

tag: neonatal sex

value: female


title: CGN, DIV3, Zic, CUT&RUN, Rep 2

description: S-Prime 50bp


title: ANF_ID27

description: Sample 27

tag: array type

tag: age

tag: Sex

tag: clinical nf1 syndrome

value: sporadic


title: O_IDH_mut_2

tag: gender

tag: tissue type

tag: grade


title: CRC0549PRX0A02002TUMR01000, PRX_BASALE, bio rep 1, QC failed

tag: tissue

value: Colorectal Cancer

tag: cell line

value: X

value: PR

value: WT

tag: treatment


title: CRC0549LMX0B02001TUMR01000, LMX_BASALE, bio rep 1, QC ok

tag: cell type

value: LM

tag: genotype


title: CRC0551LMX0A02004TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: ANF_ID26

description: Sample 26

tag: material

tag: initial histological diagnosis

value: lg MPNST


title: CRC0547PRX0B02001TUMR03000, PRX_BASALE, bio rep 1, QC ok


title: CGN, DIV3, Zic, CUT&RUN, Rep 1

description: S-Prime 50bp

tag: div


title: CRC0549LMH0000000000R02000, LMH, bio rep 1, QC ok

value: H


title: ANF_ID25

description: Sample 25

source_name: biopsy, N. ulnaris

tag: revised histological diagnosis (who 2021)


title: placenta_LELA_481

value: placenta

tag: gestational age

tag: pregravid bmi

tag: neonatal %bodyfat

tag: maternal race

value: cauc

tag: neonatal sex


title: CGN, DIV1, Zic, CUT&RUN, Rep 3

description: S-Prime 50bp

value: Cerebellar granule neuron

tag: antibody

value: Zic1/2 C terminus (PMID:24413398)


title: placenta_LEHA_323


title: ANF_ID24

description: Sample 24

value: FFPE

tag: array type

value: epic

tag: age

tag: Sex

tag: clinical nf1 syndrome


title: CGN, DIV1, Zic, CUT&RUN, Rep 2

description: S-Prime 50bp


title: CGN, DIV1, Zic, CUT&RUN, Rep 1

description: S-Prime 50bp


title: CRC0547PRH0000000000R03000, PRH, bio rep 1, QC ok

tag: tissue

tag: cell line

tag: treatment


title: placenta_OBHA_227

description:
The sample was cleaned-up with an RNA clean-up kit. Not used in analysis
samp.7_P


title: ANF_ID17

description: Sample 17

source_name: biopsy, intramedullary, HWK1/2

tag: material

value: male

value: Atypical neurofibroma

value: PN


title: CRC0544LMX0A02001TUMR02000, LMX_BASALE, bio rep 1, QC ok

tag: cell type

tag: genotype


title: placenta_OBLA_193

description:
The sample was cleaned-up with an RNA clean-up kit. Not used in analysis
samp.6_P


title: placenta_LELA_441

value: aa

value: female


title: CRC0544LMO0C05018001R01000, LMO_BASALE, bio rep 2, QC ok

value: Colorectal Cancer

value: O


title: ANF_ID15

description: Sample 15

source_name: biopsy, shoulder

tag: initial histological diagnosis

tag: revised histological diagnosis (who 2021)


title: placenta_LELA_363

source_name: whole placenta

tag: gestational age

tag: pregravid bmi


title: Mouse 698 Non-Loaded (left) Limb

city: Philadelphia

first: Ryan

last: Tomlinson

state: PA

address: 1015 Walnut Street

department: Orthopaedic Surgery

institute: Thomas Jefferson University

data_processing:
Raw FASTQ sequencing reads were aligned to the mouse genome version GRCm38 with Gencode M19 transcript annotations using the RSEM-STAR pipeline.
Total read counts were obtained using RSEM’s calculate-expression function.
Assembly: GRCm38
Supplementary files format and content: Comma-delimited text files for each sample include raw counts for each gene

source_name: Ulna (middle third)

extract_protocol:
Bone was harvested, placed in RNAlater, pulverized in Trizol using liquid nitrogen mill, and RNA was harvested using Qiagen RNeasy (74104).
Takara Bio SMARTer Stranded Total RNA-Seq Kit (#634837)  was used to prepare libraries using 4 ng of total RNA, following the manufacturer’s protocol.

value: Ulna (middle third)

value: Non-Loaded

tag: disease status

value: Tlr4 Conditional Knockout


title: CRC0544LMO0C04018001R01000, LMO_BASALE, bio rep 1, QC ok

value: LM

value: WT


title: ANF_ID14

description: Sample 14

source_name: biopsy, thorax

value: ANNUBP


title: Mouse 698 Loaded (right) Limb

value: Loaded


title: Mouse 693 Non-Loaded (left) Limb


title: CRC0542LMX0B03006TUMR09000, LMX_cetux_h, bio rep 1, QC ok

value: X

value: CET


title: ANF_ID13

description: Sample 13

source_name: biopsy, gluteal

value: FFPE

value: epic


title: placenta_LEHA_341

value: placenta

tag: neonatal %bodyfat

tag: maternal race

value: cauc

tag: neonatal sex


title: Mouse 693 Loaded (right) Limb


title: ANF_ID12

description: Sample 12

source_name: biopsy, foot

tag: array type

tag: age

value: male

value: sporadic

value: Atypical neurofibroma


title: CRC0542LMX0B02004TUMR02000, LMX_BASALE, bio rep 1, QC ok

source_name: Colorectal Cancer

value: Colorectal Cancer


title: Mouse 691 Non-Loaded (left) Limb

value: Ulna (middle third)


title: Mouse 691 Loaded (right) Limb


title: ANF_ID10

description: Sample 10

source_name: biopsy, upper arm

tag: Sex

value: female

tag: clinical nf1 syndrome


title: 9-009 (miRNA)

city: Rochester

first: Daniel

middle: Rothschild

last: OBrien

state: MN

address: 200 First St. SW

institute: The Mayo Clinic

description: uploaded to GSE151496

data_processing:
Bowtie for alignment
miRDeep2 to quantify expression
Genome_build: hg38
Supplementary_files_format_and_content: tsv format containg raw miRNA precursor counts

source_name: Duodenal mucosa (biopsy)

extract_protocol:
RNA was extracted from freshly frozen biopsy tissue with TRIzol (Ambion, Waltham, Massachusetts) and chloroform.  After centrifugation, the aqueous phase was purified with an RNeasy Mini Kit (Qiagen, Valencia, California). The quality of total RNA samples was assessed by using an Agilent bioanalyzer (Santa Clara, CA).
RNA libraries were prepared according to the manufacturer's instructions for the TruSeq Stranded Total RNA Library preparation kit (Illumina, San Diego, CA). Unique indices, included in the standard TruSeq kits were incorporated at the adaptor ligation step for multiplex sample loading on the flow cells. The flow cells were sequenced as 101×2 paired-end reads on an Illumina HiSeq 4000

tag: disease group

value: Healthy Control

tag: tissue

value: Duodenal mucosa (biopsy)


title: Mouse 688 Loaded (right) Limb

tag: treatment

value: Tlr4 Conditional Knockout


title: ANF_ID16

description: Sample 16

source_name: biopsy, Xiphoid

tag: material

value: ANNUBP


title: CRC0542LMO0C02017002R01000, LMO_cetuxi_h, bio rep 2, QC ok

data_processing:
Align with STAR on hybrid mm/hs genome
Assign counts to genes with FeatureCounts
Consider only human genes to normalize with DESeq2
QC based on evidence of lymphomatous infiltration
https://github.com/molinerisLab/StromaDistiller, https://github.com/vodkatad/RNASeq_biod_metadata
Assembly: GRCh38_GRCm38
Supplementary files format and content: merged_hs_mm.tsv.gz: raw counts for human and murine genes
Supplementary files format and content: vsd.tsv.gz: normalized expression values for human genes

extract_protocol:
total RNA extraction
PolyA enriched
Forward Stranded

tag: cell line

value: O

tag: cell type

value: LM

tag: genotype

value: WT


title: placenta_OBLA_307

tag: gestational age

value: aa


title: ANF_ID9

description: Sample 9

source_name: biopsy, galea

value: FFPE

value: epic

tag: initial histological diagnosis

tag: revised histological diagnosis (who 2021)


title: ANF_ID11

description: Sample 11

source_name: biopsy, intrapelvic, m. psoas


title: 9-006 (miRNA)

description: uploaded to GSE151496


title: 9-008 (miRNA)

description: uploaded to GSE151496


title: ANF_ID8

description: Sample 8

source_name: biopsy, lumbal to proximal thigh


title: CRC0542LMO0C03058001R01000, LMO_BASALE, bio rep 1, QC ok


title: 11-004 (miRNA)

description: uploaded to GSE151496


title: Mouse 688 Non-Loaded (left) Limb

value: Non-Loaded

tag: disease status


title: Mouse 699 Non-Loaded (left) Limb

value: Wildtype


title: CRC0542LMO0C02017001R01000, LMO_cetuxi_h_NT, bio rep 2, QC ok

value: NT


title: placenta_LEHA_400

value: placenta

tag: pregravid bmi

tag: neonatal %bodyfat

tag: maternal race


title: CRC0542LMO0C02012003R01000, LMO_cetuxi_h, bio rep 1, QC ok

value: Colorectal Cancer

value: CET


title: CRC0542LMX0B03003TUMR05000, LMX_cetux_h_NT, bio rep 1, QC ok

value: X


title: Mouse 699 Loaded (right) Limb

value: Ulna (middle third)

value: Loaded


title: 9-005 (miRNA)

description: uploaded to GSE151496

value: Healthy Control

value: Duodenal mucosa (biopsy)


title: ANF_ID7

description: Sample 7

source_name: biopsy, retroperitoneal to thigh

tag: array type

tag: age

value: female

value: Atypical neurofibroma

value: ANNUBP


title: 9-004 (miRNA)

description: uploaded to GSE151496


title: ANF_ID6

description: Sample 6

source_name: biopsy, paravertebral

tag: Sex

tag: clinical nf1 syndrome

value: PN


title: ANF_ID5

description: Sample 5

source_name: biopsy, dorsal thigh

value: FFPE


title: CRC0540LMX0A02001TUMR01000, LMX_BASALE, bio rep 1, QC ok

tag: tissue

value: LM

value: WT


title: Mouse 694 Non-Loaded (left) Limb

tag: treatment

value: Non-Loaded

value: Wildtype


title: Mouse 694 Loaded (right) Limb


title: 10-005 (miRNA)

description: uploaded to GSE151496

tag: disease group


title: ANF_ID4

description: Sample 4

source_name: biopsy, abdominal wall

tag: material

value: epic

value: male


title: ANF_ID3

description: Sample 3

source_name: biopsy, cervical


title: 9-002 (miRNA)

description: uploaded to GSE151496


title: Mouse 692 Non-Loaded (left) Limb


title: CRC0539LMX0A02001TUMR02000, LMX_BASALE, bio rep 1, QC ok

value: Colorectal Cancer

tag: cell line

tag: cell type


title: CRC0539LMH0000000000R01000, LMH, bio rep 1, QC ok

value: H

tag: genotype


title: Mouse 692 Loaded (right) Limb

value: Ulna (middle third)


title: 12-006 (miRNA)

description: uploaded to GSE151496


title: ANF_ID2

description: Sample 2

source_name: biopsy, supraclavicular

tag: initial histological diagnosis


title: ANF_ID1

description: Sample 1

source_name: biopsy,thigh

tag: revised histological diagnosis (who 2021)


title: Mouse 690 Non-Loaded (left) Limb

source_name: Ulna (middle third)

tag: disease status


title: 10-004 (miRNA)

description: uploaded to GSE151496


title: 10-003 (miRNA)

description: uploaded to GSE151496


title: Mouse 690 Loaded (right) Limb

value: Loaded


title: CRC0542LMO0C02012002R01000, LMO_cetuxi_h_NT, bio rep 1, QC ok

value: O

value: NT


title: CRC0538LMX0A02003TUMR01000, LMX_BASALE, bio rep 1, QC ok

value: X


title: CRC0537LMX0B02001TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: 12-005 (miRNA)

description: uploaded to GSE151496

value: Healthy Control

value: Duodenal mucosa (biopsy)


title: CRC0536LMX0B02003TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: RNA-seq_CNS-28_KO_memory_T_rep1

city: Bethesda

first: Yaqiang

last: Cao

state: Maryland

address: 9000 Rockville Pike

department: System Biology Center

institute: NHLBI

data_processing:
Raw reads of RNA-seq data were mapped by STAR (v2.7.3a) (Dobin et al., 2013).   Raw reads of  ChIP-seq data were mapped by Bowtie2 (Langmead and Salzberg, 2012). Mapped unique paired-end reads with MAPQ 10 were used for the following analysis.  Raw reads of Hi-TrAC data were process by tracPre2.py in cLoops2 package (Cao et al., 2022).
Assembly: mm10
Supplementary files format and content: BigWig files for RNA-seq and ChIP-seq were provided for visualization in genome browser.  TEXT files for RNA-seq gene expressions were provided. BEDPE files for Hi-TrAC data with high quality uniquely mapped paired-end tags (PETs) were provided.

source_name: memory-T

growth_protocol: Naive CD4+ T cells were tsolated by magnetic selection according to the protocol provided by the manufacturer (Stem Cell, EasySep Mouse CD4+CD62L+ T cell Isolation Kit). Isolated Naïve CD4+ T cells active with plate-bound anti-CD3(Clone: 145-2C11, 1 μg/ml, eBioscience), anti-CD28(Clone: 37.51, 3 μg/ml, eBioscience), then polarized under Th1 condition. The CD4+CD44+CD62L- memory T cell population was purified from spleen and lymph nodes of WT and CNS-28 KO mice by sorting. GATA3 KO Nive CD4 cells sort from Gata3 [fl/fl]JAX 7914- Homo-hCD2Cre mice by CD4+CD25-CD44-CD62L+.

extract_protocol:
Detailed procedures for ChIP-Seq:  1. Three plates (15-cm) of HeLa or SW-13 cells cultured in 20 ml of DMEM containing  10% FCS and antibiotics were stimulated with 500 units/ml of IFN-α for 2 hrs.  2. Add HCHO to 1% of each plate and incubate at 37°C for 10 min; Stop the crosslinking  by aspirating the medium. Wash the cells twice with 10 ml of 1xPBS.  3. Aspirate the buffer (keep 0.5 ml in the plate). Harvest cells by scraping. Wash the  plate once with 0.5% BSA/PBS. Combine the cells from the three plates.  4. Spin down the cells at 3000rpm, 3 min, 4oC.  5. Remove supernatant and resuspend the cells in 2.5 ml of 1 x TE + 1 mM PMSF + 1 x  proteinase inhibitor cocktail. For anti-AcH3 or anti-AcH4 CHIP, add sodium  butyrate to 5 mM. Sonicate 20 x 20 seconds in ice-water bath with power setting at 5  with an Ultrasonic Processor XL (HEAT System) to break chromatin to about 0.3-05  kb.  6. Adjust to RIPA buffer + 200 mM NaCl by adding 0.28 ml of 10% TX100, 28 μl of  10% Na-Deoxycholate, 28 μl of 10% SDS, 110 μl of 5M NaCl. Mix well. Incubate  for 5 min on ice. Spin in a microfuge, 13K rpm, 10 min, 4oC.  7. Collect supernatant.  8. Add 4 μg of the antibodies to 40 μl of Dynabeads protein A beads. Incubate at 4°C 4-  6hrs with rotation. Wash away antibody by 1xPBS.  9. Add 500 μl of the chromatin ( sup.) to the beads+antibody. Incubate at at 4°C  overnight with rotation.  10. Wash the beads twice with RIPA buffer; twice with RIPA buffer (+0.3M NaCl);  twice with LiCl buffer (1xTE, 0.25M LiCl, 0.5% NP40, 0.5% Na-Deoxycholate); and  twice with 1xTE.  11. Resuspend the beads in 100 μl of 1xTE, 2.5 μl of 10% SDS, 5 μl of 10 mg/ml  proteinase K, mix well, incubate at 65oC, overnight. Also treat 100 μl of the input  chromatin in the same way.  12. Collect sup. Wash the beads once with 100 μl of 1xTE. Combine the supernatants.  Extract 1 x with Phenol-CHCl3.  13. Precipitate DNA with 2 μl of 20mg/ml glycogen, 20 μl of 3M NaOAc pH5.2, 500 μl  of ethanol. Incubate 10 min on dry ice. Spin 20 min at 4 °C in a microfuge. Remove  sup, wash pellet 1 x with 70% ethanol, air dry, resuspend in 30 μl of 1 x TE. Use 3 μl  for one PCR reaction.  14. The concentration of the input DNA is determined by spectrophotometer.  For RNA-Seq, five thousand cells were sorted into 700μl of QIAzol Lysis Reagent (miRNAeasy Micro Kit (QIAGEN, Cat#217084). Total RNA was extracted and on-column digestion with DNase (QIAGEN, Cat#79254) was performed, followed by elution with 10μl of RNase-free water. Total RNA from 1K cells was reverse transcribed by SuperScript II (Invitrogen, Cat#18064-014) with oligo-dT and LNA-containing TSO primers in a final reaction volume of 10μl using the condition: 42°C for 90min, 10 cycles of 50°C 2min to 42°C 2min, 70°C for 15min and hold at 4°C. cDNA was pre-amplified by PCR using KAPA HiFi HotStart ReadyMix (KAPABIOSYSTEMS Cat#KK2602) with IS PCR for 12 cycles in 25μl. PCR products were purified by Ampure XP beads (Beckman Coulter, Cat#A63881) and eluted with 17.5μl Nuclease-free water as described for Smart-seq2 method (Picelli et al., 2014). PCR pre-amplified cDNA (40μl) was sonicated to 200~400bps by Bioruptor Pico (Diagenode) for 15 cycles (30″ on and 30″ off). Sonicted cDNA was blunt-ended by End-It DNA-Repair kit (Epicentre, Cat#ER81050), ligated to “Y” adaptor and PCR-amplified for 12 cycles and sequenced as described for the scDNase-seq libraries. For Hi-TrAC, cells were fixed with 1% Formaldehyde at room temperature for 10 minutes, and then incubated with the transposase complex to bridge interacting chromatin at 37 °C for 2 hours. Genomic DNA was purified after reverse cross-linking.
1. Repair DNA ends using the Epicentre DNA END-Repair kit (Cat. No. ER0720, Epicentre Biotechnologies, Tel 800-284-8474)  This step generates blunt-ended DNA.  1-34 ul DNA (0.1 to 5 ug)  5 ul 10x End repair buffer (330 mM Tris-acetate, pH7.8, 660 mM potassium acetate, 100 mM magnesium acetate, 5 mM DTT)  5 ul 2.5 mM each dNTPs  5 ul 10 mM ATP  x ul H2O to adjust the reaction volume to 49 ul  1 ul End-Repair Enzyme mix (T4 DNA Pol + T4 PNK)  Incubate 45 min at room temperature.  Purify the DNA using MinElute Reaction Cleanup Kit and protocol, eluting in 32 ul of EB.  2. Add “A” to 3’ ends  32 ul DNA from above  5 ul 10x Klenow buffer  10 ul 1 mM dATP  3 ul 5 U/ ul Klenow Exo-  Incubate for 30 min at 37°C.  Purify the DNA as before. Eluting in 22 ul of 1x EB.  3. Linker ligation (two mixed linkers).  The oligo mix should contain 10x molar excess of the DNA templates.  23 ul DNA (300ng)  3 ul 10x T4 DNA ligase buffer  1 ul Index PE Adapter Oligo Mix (1:10 diluted)  3 ul T4 DNA ligase (400 units/ul)  2  Incubate for 30 min at room temperature. Purify the DNA as before. Eluting in 20 ul of 1x EB.  4. Size selection-2% E-Gel  Load 20 ul linker ligated DNA onto a 2% E-Gel (Invitrogen).  Cut the gel around 200-400 bp region (DNA will not be visible).  Extract the DNA using MinElute gel extraction kit (every 900ul of QG Buffer add 400ul of 2-Propanol). Elute in 22 ul EB.  (Note: (1) Dissolve gel slices at room temperature with frequent mixing, but not at elevated temperature. This helps to reserve AT-rich DNA that can be easily denatured at higher temperature and gets lost at column binding step. (2) NEVER run PCR-amplified samples of Step 7 with the linker-ligated products of Step 5 together on the same gel because the latter can be contaminated!).  5. Amplify the DNA using Solexa primers and enzyme mix (using half amount of the reagents and run a 25 ul reaction).  18 ul of DNA  20 ul of master mix  1 ul of PCR primer InPE1.0 (2x diluted)  1 ul of PCR Primer Index<#> (2x diluted)  Total volume: 50 ul  Denature at 98°C for 30 sec.  98°C, 10”; 65°C, 30”; 72°C, 30”.  Try 18 cycles first, check 2.5 ul of product on 1.8% gel. If the band is not clearly visible, do 3 more cycles. Check again.  6. Purify the amplified products on 2.5% agarose gel. Excise the band near 220 bp and purify the DNA using QIAquick gel extraction kit. Measure the DNA concentration using Qubit fluorometer. (Note: Dissolve gel slices at room temperature with frequent mixing, but not at elevated temperature. This helps to reserve AT-rich DNA that can be easily denatured at higher temperature and gets lost at column binding step). For Hi-TrAC libraries, gaps in purified genomic DNA was repaired with T4 DNA polymerase. Genomic DNA was digested with MluCI and NlaIII restriction enzymes, and biotin labeled DNA fragments was enriched by streptavidin beads. Perform adapter ligation with T7 ligase on beads, and then run PCR to amplify and add index to libraries.

treatment_protocol: Using DAPI to sort out live cells for Dnase-seq, ChIP-seq, RNA-seq, and Hi-TrAC experiments.

tag: strain

value: mixed C57BL/6 and 129

value: memory-T

value: spleen and lymph nodes


title: RNA-seq_CNS-28_KO_memory_T_rep2


title: CRC0535LMX0B02001TUMR02000, LMX_BASALE, bio rep 1, QC ok

city: Candiolo

first: Livio

last: Trusolino

address: Strada Provinciale, 142 -KM 3.95

institute: IRCCS Istituto Candiolo

value: LM

value: WT


title: CRC0534LMX0A04038TUMR09000, LMX_cetux_h_NT, bio rep 2, QC ok


title: Mouse 686 Non-Loaded (left) Limb

value: Non-Loaded

value: Wildtype


title: RNA-seq_CNS-28_WT_memory_T_rep2


title: 11-003 (miRNA)

description: uploaded to GSE151496


title: 11-001 (miRNA)

description: uploaded to GSE151496


title: CRC0534LMX0A04035TUMR01000, LMX_cetux_h, bio rep 2, QC ok

value: CET


title: 12-001 (miRNA)

description: uploaded to GSE151496


title: Mouse 685 Non-Loaded (left) Limb


title: Mouse 686 Loaded (right) Limb


title: 12-003 (miRNA)

description: uploaded to GSE151496


title: CRC0534LMX0A04026TUMR01000, LMX_cetux_h_NT, bio rep 1, QC ok

value: Colorectal Cancer


title: CRC0534LMX0A04013TUMR01000, LMX_cetux_h, bio rep 1, QC ok


title: CRC0542LMO0C04013001R01000, LMO_BASALE, bio rep 2, QC ok


title: 11-002 (miRNA)

description: uploaded to GSE151496


title: RNA-seq_CNS-28_WT_memory_T_rep1


title: Mouse 687 Loaded (right) Limb


title: 12-002 (miRNA)

description: uploaded to GSE151496


title: Mouse 687 Non-Loaded (left) Limb


title: ChIP-seq_CNS-28_KO_memory_T_H3K4me1_rep1


title: CRC0534LMX0A02001TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: OPC ko pair 6

city: Los Angeles

first: Ye

last: Zhang

address: 635 Charles E Young Dr S

institute: UCLA

data_processing:
STAR alignment, v2.7.8a
HTSeq quantification, v0.13.5
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files of gene counts, labelled with Ensembl gene IDs

source_name: cerebral cortex

extract_protocol:
Mice were perfused for 10 minutes with phosphate buffered saline solution before dissection of the cerebral cortex.  Cortical tissue was roughly chopped then placed in a papain solution (12 units/mL) for enzymatic digestion at 34.5C for 45 minutes. Digested tissue was washed with ovomucoid inhibitor and mechanically digested via trituration.  Cells were spun down and resuspended in PBS with 0.02% bovine serum albumin, then passed through a mesh filter to generate a single cell suspension. The final cell suspension was incubated on various petri dishes (10 min/dish) that were coated with antibodies targeting a desired cell population.  Cells bound to each dish were rinsed with PBS, and RNA was harvested immediately with 700 uL of TRIzol before flash freezing in liquid nitrogen. RNA was purified for sequencing using the miRNeasy kit (Qiagen).
RNA libraries were constructed with the Ovation V2 system (Tecan) and the NEBNext Ultra RNA Library Prep Kit (New England Biolabs)

value: cerebral cortex

value: OPC

value: female


title: 10-002 (miRNA)

description: uploaded to GSE151496


title: OPC control pair 6

value: male


title: ChIP-seq_CNS-28_WT_memory_T_H3K4me1_rep1


title: CRC0534LMO0B03025002R01000, LMO_BASALE, bio rep 2, QC ok

source_name: Colorectal Cancer

value: O


title: CRC0534LMO0B04017001R01000, LMO_BASALE, bio rep 1, QC ok


title: ChIP-seq_CNS-28_KO_memory_T_H3K4me1_rep2


title: OPC ko pair 4


title: RNA-seq_CNS-28_KO_Th1_72h_rep1

value: CD4+ T cells stimulated under Th1 condition

value: Cell Culture

value: CNS-28 KO DAPI-


title: OPC control pair  5


title: 9-001 (miRNA)

description: uploaded to GSE151496

value: Healthy Control

value: Duodenal mucosa (biopsy)


title: CRC0534LMO0B03021006R01000, LMO_cetuxi_h, bio rep 2, QC ok


title: 8-005 (miRNA)

value: Functional Dyspepsia


title: Mouse 685 Loaded (right) Limb

value: Ulna (middle third)

value: Loaded


title: 8-004 (miRNA)


title: ChIP-seq_CNS-28_WT_memory_T_H3K4me1_rep2

value: mixed C57BL/6 and 129

value: memory-T

value: spleen and lymph nodes


title: OPC control pair 4


title: CRC0534LMO0B02018002R01000, LMO_cetuxi_h, bio rep 1, QC ok

value: Colorectal Cancer

value: LM

value: WT

value: CET


title: 8-003 (miRNA)


title: CRC0534LMO0B02018001R01000, LMO_cetuxi_h_NT, bio rep 1, QC ok

value: NT


title: 8-002 (miRNA)


title: RNA-seq_CNS-28_KO_Th1_72h_rep2


title: OPC control pair 3

value: cerebral cortex

value: OPC

value: male


title: OPC ko pair 3


title: OPC ko pair 2

value: female


title: CRC0530LMX0A02001TUMR01000, LMX_BASALE, bio rep 1, QC ok

value: X


title: 12-004 (miRNA)

description: uploaded to GSE151496

value: Healthy Control

value: Duodenal mucosa (biopsy)


title: RNA-seq_CNS-28_KO_Th1_24h_rep2

value: CD4+ T cells stimulated under Th1 condition

value: Cell Culture

value: CNS-28 KO DAPI-


title: RNA-seq_CNS-28_KO_Th1_24h_rep1

value: mixed C57BL/6 and 129


title: OPC control pair 2


title: RNA-seq_CNS-28_WT_Th1_24h_rep2

value: CNS-28 WT DAPI-


title: 8-001 (miRNA)

value: Functional Dyspepsia


title: CRC0529LMX0A02003TUMR02000, LMX_BASALE, bio rep 1, QC ok

value: Colorectal Cancer

value: LM


title: CRC0534LMO0B03021005R01000, LMO_cetuxi_h_NT, bio rep 2, QC ok

value: O

value: WT


title: RNA-seq_CNS-28_WT_Th1_72h_rep2


title: CRC0528LMX0B02004TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: RNA-seq_CNS-28_WT_Th1_24h_rep1


title: 7-004 (miRNA)


title: OPC ko pair 1

value: cerebral cortex


title: CRC0527LMX0B02003TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: OPC control pair 1

value: OPC


title: RNA-seq_CNS-28_KO_Naive_CD4_rep2

source_name: Naive CD4+ T cells

value: Naive CD4+ T cells

value: lymph nodes


title: RNA-seq_CNS-28_WT_Th1_72h_rep1


title: CRC0526LMX0A02001TUMR01000, LMX_BASALE, bio rep 1, QC ok

value: X


title: 7-002 (miRNA)

source_name: Duodenal mucosa (biopsy)


title: RNA-seq_CNS-28_KO_Naive_CD4_rep1


title: 7-001 (miRNA)


title: 6-017 (miRNA)


title: CRC0521LMX0A02001TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: CRC0525LMX0A02003TUMR06000, LMX_BASALE, bio rep 1, QC ok


title: 6-015 (miRNA)


title: RNA-seq_CNS-28_WT_Naive_CD4_rep2


title: RNA-seq_CNS-28_WT_Naive_CD4_rep1


title: 6-014 (miRNA)


title: CRC0518LMX0A02002TUMR05000, LMX_BASALE, bio rep 1, QC ok


title: CRC0520LMX0A02001TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: Oligodendrocyte ko pair 5

value: oligodendrocyte

value: female


title: Oligodendrocyte control pair 5


title: Hi-TrAC_CNS-28_KO_Naive_rep3

data_processing:
Raw reads of RNA-seq data were mapped by STAR (v2.7.3a) (Dobin et al., 2013).   Raw reads of  ChIP-seq data were mapped by Bowtie2 (Langmead and Salzberg, 2012). Mapped unique paired-end reads with MAPQ 10 were used for the following analysis.  Raw reads of Hi-TrAC data were process by tracPre2.py in cLoops2 package (Cao et al., 2022).
Assembly: mm10
Supplementary files format and content: BigWig files for RNA-seq and ChIP-seq were provided for visualization in genome browser.  TEXT files for RNA-seq gene expressions were provided. BEDPE files for Hi-TrAC data with high quality uniquely mapped paired-end tags (PETs) were provided.
Library strategy: Hi-TrAC


title: CRC0517LMX0A02002TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: 6-013 (miRNA)

value: Duodenal mucosa (biopsy)


title: Hi-TrAC_CNS-28_KO_Naive_rep4


title: Oligodendrocyte control pair 3

value: male


title: 6-012 (miRNA)


title: Oligodendrocyte ko pair 6


title: Hi-TrAC_CNS-28_KO_Naive_rep1


title: Hi-TrAC_CNS-28_KO_Naive_rep2


title: Oligodendrocyte ko pair 1


title: CRC0516LMX0B03010TUMR09000, LMX_cetux_h, bio rep 1, QC ok

value: CET


title: Oligodendrocyte control pair 6


title: Hi-TrAC_CNS-28_WT_Naive_rep5

value: mixed C57BL/6 and 129


title: Oligodendrocyte control pair 1


title: CRC0516LMX0B03006TUMR09000, LMX_cetux_h_NT, bio rep 1, QC ok

value: NT


title: Hi-TrAC_CNS-28_WT_Naive_rep4


title: 6-010 (miRNA)

value: Functional Dyspepsia


title: CRC0516LMX0B01001TUMR02000, LMX_BASALE, bio rep 1, QC ok

value: Colorectal Cancer


title: Microglia ko pair 6

value: microglia


title: 7-003 (miRNA)


title: Oligodendrocyte ko pair 3


title: 6-009 (miRNA)


title: Microglia control pair 6


title: Hi-TrAC_CNS-28_WT_Naive_rep3


title: CRC0516LMH0000000000R05000, LMH, bio rep 1, QC ok

value: H

value: LM


title: Hi-TrAC_CNS-28_WT_Naive_rep2


title: 6-008 (miRNA)


title: CRC0515LMX0A03003TUMR05000, LMX_cetux_6w, bio rep 1, QC ok

value: WT


title: CRC0515LMX0A03007TUMR05000, LMX_cetux_6w_NT, bio rep 1, QC ok


title: 6-007 (miRNA)


title: Microglia control pair 5

value: cerebral cortex


title: Hi-TrAC_CNS-28_WT_Naive_rep1

value: Naive CD4+ T cells


title: 6-011 (miRNA)


title: Microglia ko pair 4


title: 6-006 (miRNA)


title: CRC0515LMX0A02002TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: Microglia ko pair 5


title: ChIP-seq_GATA3_KO_Naive_CD4_CTCF_rep2

value: lymph nodes

value: GATA3 KO(CD4+CD25-CD62L+CD44-)


title: Microglia control pair 4


title: 6-005 (miRNA)


title: ChIP-seq_GATA3_KO_Naive_CD4_CTCF_rep1


title: 6-004 (miRNA)


title: CRC0515LMO0A04021002R01000, LMO_cetuxi_h, bio rep 2, QC ok

value: O


title: ChIP-seq_GATA3_WT_Naive_CD4_CTCF_rep2

value: GATA3 WT(CD4+CD25-CD62L+CD44-)


title: Microglia ko pair 3


title: CRC0515LMO0A04021001R01000, LMO_cetuxi_h_NT, bio rep 2, QC ok


title: 6-002 (miRNA)

value: Duodenal mucosa (biopsy)


title: ChIP-seq_GATA3_WT_Naive_CD4_CTCF_rep1


title: CRC0515LMO0A04018002R01000, LMO_cetuxi_h, bio rep 1, QC ok


title: Microglia control pair 3

value: male


title: 6-001 (miRNA)


title: ChIP-seq_GATA3_KO_Naive_CD4_H3K4me1_rep2


title: ChIP-seq_GATA3_KO_Naive_CD4_H3K4me1_rep1


title: 5-013 (miRNA)


title: CRC0515LMO0A04012001R01000, LMO_BASALE, bio rep 2, QC ok


title: Microglia control pair 2

value: female


title: Microglia ko pair 1


title: 5-012 (miRNA)


title: CRC0515LMO0A04011001R01000, LMO_BASALE, bio rep 1, QC ok


title: ChIP-seq_GATA3_WT_Naive_CD4_H3K4me1_rep1

value: mixed C57BL/6 and 129


title: 5-011 (miRNA)


title: CRC0514PRX0A01001TUMR05000, PRX_BASALE, bio rep 1, QC ok

value: X

value: PR


title: Microglia control pair 1


title: 5-010 (miRNA)

value: Functional Dyspepsia


title: Hi-TrAC_MLL4_KO_Naive_CD4_rep6

value: MLL4 KO(CD4+CD8-CD62L+CD44-)


title: Astrocyte ko pair 6

value: astrocyte


title: CRC0512LMX0B02003TUMR02000, LMX_BASALE, bio rep 1, QC ok

value: Colorectal Cancer

value: LM


title: 5-009 (miRNA)


title: Astrocyte control pair 6

value: cerebral cortex


title: Hi-TrAC_MLL4_KO_Naive_CD4_rep5

value: Naive CD4+ T cells


title: CRC0508LMX0A03005TUMR05000, LMX_cetux_6w, bio rep 1, QC ok

value: WT

value: CET


title: 5-008 (miRNA)


title: CRC0515LMO0A04018001R01000, LMO_cetuxi_h_NT, bio rep 1, QC ok

value: O

value: NT


title: Microglia ko pair 2

value: microglia


title: Astrocyte ko pair 5


title: CRC0508LMX0A03002TUMR05000, LMX_cetux_6w_NT, bio rep 1, QC ok


title: Hi-TrAC_MLL4_KO_Naive_CD4_rep3

value: lymph nodes


title: 5-007 (miRNA)

value: Duodenal mucosa (biopsy)


title: Astrocyte control pair 5

value: female


title: ChIP-seq_GATA3_WT_Naive_CD4_H3K4me1_rep2

value: mixed C57BL/6 and 129

value: GATA3 WT(CD4+CD825-CD62L+CD44-)


title: Astrocyte ko pair 4

value: male


title: 5-006 (miRNA)

value: Functional Dyspepsia


title: Hi-TrAC_MLL4_KO_Naive_CD4_rep2

value: MLL4 KO(CD4+CD8-CD62L+CD44-)


title: CRC0508LMX0A02004TUMR09000, LMX_BASALE, bio rep 1, QC ok

value: Colorectal Cancer

value: X


title: Hi-TrAC_MLL4_KO_Naive_CD4_rep1


title: CRC0513LMX0A02002TUMR01000, LMX_BASALE, bio rep 1, QC ok

value: LM


title: CRC0507LMX0A02003TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: Astrocyte ko pair 3

value: cerebral cortex

value: astrocyte


title: 5-004 (miRNA)


title: CRC0506PRX0A01001TUMR01000, PRX_BASALE, bio rep 1, QC ok

value: PR

value: WT


title: Hi-TrAC_MLL4_KO_Naive_CD4_rep4

value: Naive CD4+ T cells


title: CRC0506PRH0000000000R01000, PRH, bio rep 1, QC ok

value: H


title: Hi-TrAC_MLL4_WT_Naive_CD4_rep5

value: lymph nodes

value: MLL4 WT(CD4+CD8-CD62L+CD44-)


title: Hi-TrAC_MLL4_WT_Naive_CD4_rep6


title: 5-003 (miRNA)

value: Duodenal mucosa (biopsy)


title: Astrocyte control pair 3


title: CRC0505LMX0A02004TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: 5-002 (miRNA)


title: Astrocyte ko pair 2

value: female


title: Hi-TrAC_MLL4_WT_Naive_CD4_rep4

value: mixed C57BL/6 and 129


title: 5-001 (miRNA)


title: Astrocyte control pair 2


title: Hi-TrAC_MLL4_WT_Naive_CD4_rep3


title: CRC0504LMX0A03005TUMR03000, LMX_BASALE, bio rep 1, QC ok


title: 5-005 (miRNA)


title: Astrocyte ko pair 1

value: male


title: 9-009 (mRNA)

description: uploaded to GSE151496

data_processing:
TopHat for alignment
FeatureCounts to quantify expression
Genome_build: hg38
Supplementary_files_format_and_content: tsv format containg RPKM normalized expression values

value: Healthy Control


title: CRC0504LMX0A03005TUMR02000, LMX_cetux_6w_NT, bio rep 1, QC ok

value: NT


title: Astrocyte control pair 4


title: Astrocyte control pair 1


title: Hi-TrAC_MLL4_WT_Naive_CD4_rep1


title: Hi-TrAC_MLL4_WT_Naive_CD4_rep2


title: 9-008 (mRNA)

description: uploaded to GSE151496


title: CRC0503LMX0A02001TUMR01000, LMX_BASALE, bio rep 1, QC ok

value: Colorectal Cancer


title: 11-004 (mRNA)

description: uploaded to GSE151496


title: CRC0502LMX0A02001TUMR01000, LMX_BASALE, bio rep 1, QC ok

value: X


title: 9-006 (mRNA)

description: uploaded to GSE151496


title: Spinal cord, unaffected heterozygouse littermates (WT), rep4

city: Oxford

first: Anna

middle: Jolanta

last: Kordala

address: Old Road Campus, Roosevelt Dr, Headington

institute: University of Oxford

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads 1 containing ploy-N and low quality reads from raw data
Mus Musculus (GRCm38/mm10) reference genome was used, index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach.
Quantification of gene expression level Feature Counts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
Supplementary files format and content: tab-delimited text files include gene counts for each Sample

source_name: spinal cord, p7

growth_protocol: Mice were housed and all the procedures were carried out at the Biomedical Services Building, University of Oxford and authorised by the UK Home Office

extract_protocol:
RNA extraction was performed using Maxwell® RSC simply RNA Kit (Promega) following the manufacturer’s instructions
RNA quantification and integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). mRNA was purified using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer. First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform with a coverage of 25 million reads and 150 bp paired-end reads were generated.

treatment_protocol: untreated SMA mice and WT - no treatment, MS023 treated SMA mice - daily (p1-p6) oral MS023, 2 mg/kg, nusinersen treated SMA mice: one subc injection, p0, 30 mg/kg, nusinersen, MS023 and nusinersen treated mice: one subc injection, p0, 30 mg/kg, nusinersen and daily (p1-p6) oral MS023, 2 mg/kg

value: spinal cord, p7

value: no treatment


title: 9-005 (mRNA)

description: uploaded to GSE151496


title: Spinal cord, unaffected heterozygouse littermates (WT), rep3


title: Spinal cord, unaffected heterozygouse littermates (WT), rep2


title: CRC0501PRH0000000000R02000, PRH, bio rep 1, QC ok


title: Spinal cord, unaffected heterozygouse littermates (WT), rep1


title: 9-004 (mRNA)

description: uploaded to GSE151496


title: CRC0501PRX0B02001TUMR02000, PRX_BASALE, bio rep 1, QC failed


title: ChIP-seq_WT_Naive_CD4_T-bet_rep1


title: ChIP-seq_WT_Naive_CD4_GATA3_rep2


title: ChIP-seq_MLL4_KO_Naive_CD4_CTCF_rep3

value: MLL4 KO(CD4+CD8-CD62L+CD44-)


title: CRC0500PRX0A01001TUMR01000, PRX_BASALE, bio rep 1, QC ok

value: PR


title: Spinal cord, MS023 and nusinersen treated SMA mice, rep4

value: one subc injection, p0, 30 mg/kg, nusinersen and daily (p1-p6) oral MS023, 2 mg/kg


title: 10-005 (mRNA)

description: uploaded to GSE151496


title: CRC0504LMX0A03002TUMR02000, LMX_cetux_6w, bio rep 1, QC ok

value: LM

value: WT

value: CET


title: ChIP-seq_MLL4_KO_Naive_CD4_CTCF_rep2

value: Naive CD4+ T cells

value: lymph nodes


title: Spinal cord, MS023 and nusinersen treated SMA mice, rep3


title: CRC0500PRH0000000000R05000, PRH, bio rep 1, QC ok

value: H


title: Spinal cord, MS023 and nusinersen treated SMA mice, rep2


title: ChIP-seq_WT_Th1_GATA3

value: mixed C57BL/6 and 129

value: CD4+ T cells stimulated under Th1 condition

value: Cell Culture

value: WT DAPI-


title: CRC0499LMX0B02001TUMR01000, LMX_BASALE, bio rep 1, QC ok

value: Colorectal Cancer


title: 9-002 (mRNA)

description: uploaded to GSE151496

value: Healthy Control

value: Duodenal mucosa (biopsy)


title: ChIP-seq_MLL4_KO_Naive_CD4_CTCF_rep1


title: ChIP-seq_WT_Naive_CD4_T-bet_rep2


title: 12-006 (mRNA)

description: uploaded to GSE151496


title: 10-004 (mRNA)

description: uploaded to GSE151496


title: CRC0498PRX0B01001TUMR01000, PRX_BASALE, bio rep 2, QC ok

value: X


title: ChIP-seq_MLL4_WT_Naive_CD4_CTCF_rep3

value: MLL4 WT(CD4+CD8-CD62L+CD44-)


title: Spinal cord, MS023 and nusinersen treated SMA mice, rep1

value: spinal cord, p7


title: Spinal cord, nusinersen treated SMA mice, rep4

value: one subc injection, p0, 30 mg/kg, nusinersen


title: ChIP-seq_MLL4_WT_Naive_CD4_CTCF_rep2


title: 10-003 (mRNA)

description: uploaded to GSE151496


title: CRC0498PRX0A01001TUMR01000, PRX_BASALE, bio rep 1, QC ok

value: PR


title: Spinal cord, nusinersen treated SMA mice, rep3


title: CRC0498PRH0000000000R01000, PRH, bio rep 1, QC ok

value: WT


title: 11-003 (mRNA)

description: uploaded to GSE151496


title: Water-stressed 48 h cotton primary root tip replicate 3

city: Columbia

first: Sidharth

last: Sen

state: Missouri

address: Agriculture Bldg, University of Missouri

department: The Division of Plant Sciences and Technology

institute: University of Missouri

data_processing:
Sequencing were performed by MU Genomics Technology Core
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Gossypium hirsutum NAU-NBT v1.1 whole genome using Hisat2 (v1.0).
Read counts were calculated using Htseq-count (v0.6.1), counting how many aligned reads overlap the exon of each gene (Anders et al., 2015).
Assembly: Gossypium hirsutum NAU-NBT v1.1
Supplementary files format and content: Matrix tables for raw counts for all samples

organism: Gossypium hirsutum

source_name: Cotton Primary Root Tip

growth_protocol: Cotton (cv. AU90810) seedlings were cultivated in a vermiculite culture system at well-watered (WW) and water-stressed (WS) treatments. Seedlings were grown at 29 oC and near-saturation humidity in a dark growth chamber until harvest. The root tips of cotton were harvested at 24 h and 48 h after transplanting to well-watered or water-stressed media. Transplanting and harvesting were performed using a green ‘safe’ light. Root tips containing the whole elongation zones of cotton (12 mm for WW; 6 mm for WS) primary roots were collected.

extract_protocol:
Cotton root tip samples (12 mm for WW; 6 mm for WS) were collected from seedlings and immediately frozen in liquid nitrogen and pooled to generate 50-100 mg FW per sample. Total RNA was isolated using Qigen Plant RNeasy mini kit.
RNA libraries for sequencing were prepared using standard Illumina protocols.

treatment_protocol: The media were set at water potentials of -0.02 MPa (well-watered treatments, WW), -1.0 MPa (water-stressed treatments, WS), which were obtained by mixing with certain amounts of 1 mM CaSO4. No further water supplies were added after the transplanting.

value: Root


title: 12-005 (mRNA)

description: uploaded to GSE151496


title: CRC0498LMX0B02001TUMR01000, LMX_BASALE, bio rep 2, QC ok

value: LM


title: Spinal cord, nusinersen treated SMA mice, rep2


title: CRC0498LMX0A02002TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: Spinal cord, nusinersen treated SMA mice, rep1


title: Water-stressed 48 h cotton primary root tip replicate 1


title: Water-stressed 48 h cotton primary root tip replicate 2


title: 12-001 (mRNA)

description: uploaded to GSE151496


title: Spinal cord, MS023 treated SMA mice, rep4

value: daily (p1-p6) oral MS023, 2 mg/kg


title: CRC0498LMH0000000000R01000, LMH, bio rep 1, QC failed

value: H


title: Well-watered 48 h cotton primary root tip replicate 3


title: Spinal cord, MS023 treated SMA mice, rep3


title: Well-watered 48 h cotton primary root tip replicate 2


title: 11-002 (mRNA)

description: uploaded to GSE151496


title: 12-003 (mRNA)

description: uploaded to GSE151496


title: CRC0495LMX0B03012TUMR01000, LMX_cetux_h, bio rep 1, QC ok

value: CET


title: Spinal cord, MS023 treated SMA mice, rep2


title: CRC0495LMX0B03007TUMR05000, LMX_cetux_h_NT, bio rep 1, QC ok

value: NT


title: Well-watered 48 h cotton primary root tip replicate 1


title: ChIP-seq_MLL4_WT_Naive_CD4_CTCF_rep1

value: mixed C57BL/6 and 129

value: Naive CD4+ T cells

value: lymph nodes


title: CRC0495LMX0B02003TUMR06000, LMX_BASALE, bio rep 1, QC ok

value: Colorectal Cancer


title: 12-002 (mRNA)

description: uploaded to GSE151496

value: Healthy Control

value: Duodenal mucosa (biopsy)


title: Water-stressed 24 h cotton primary root tip replicate 3


title: 10-002 (mRNA)

description: uploaded to GSE151496


title: Spinal cord, MS023 treated SMA mice, rep1


title: CRC0494LMX0A05016TUMR02000, LMX_cetux_6w_NT, bio rep 1, QC ok

value: X


title: Spinal cord, untreated SMA mice, rep4

value: spinal cord, p7

value: no treatment


title: Water-stressed 24 h cotton primary root tip replicate 2


title: CRC0494LMX0A05032TUMR02000, LMX_cetux_6w, bio rep 1, QC ok


title: Water-stressed 24 h cotton primary root tip replicate 1


title: 12-004 (mRNA)

description: uploaded to GSE151496


title: CRC0494LMX0A02004TUMR06000, LMX_BASALE, bio rep 1, QC ok


title: Spinal cord, untreated SMA mice, rep3


title: 9-001 (mRNA)

description: uploaded to GSE151496


title: Spinal cord, untreated SMA mice, rep2


title: Well-watered 24 h cotton primary root tip replicate 3


title: CRC0493LMX0A03004TUMR05000, LMX_cetux_h_NT, bio rep 1, QC ok


title: Well-watered 24 h cotton primary root tip replicate 2


title: Spinal cord, untreated SMA mice, rep1


title: 8-004 (mRNA)

value: Functional Dyspepsia


title: Well-watered 24 h cotton primary root tip replicate 1


title: 8-003 (mRNA)


title: CRC0493LMX0A02003TUMR05000, LMX_BASALE, bio rep 1, QC ok

value: WT


title: RNA-seq_MLL4KO_Th1_48h

data_processing:
Raw reads of RNA-seq data were mapped by STAR (v2.7.3a) (Dobin et al., 2013).   Raw reads of  ChIP-seq data were mapped by Bowtie2 (Langmead and Salzberg, 2012). Mapped unique paired-end reads with MAPQ  10 were used for the following analysis. H3K4me1 ChIP-seq peaks were called by cLoops2(v0.0.3) (Cao et al., 2022)  to annotate the CNS regions for Ifng.
Assembly: mm10
Supplementary files format and content: BigWig files for RNA-seq and ChIP-seq were provided for visualization in genome browser.

growth_protocol: Naive CD4+ T cells were tsolated by magnetic selection according to the protocol provided by the manufacturer (Stem Cell, EasySep Mouse CD4+CD62L+ T cell Isolation Kit). Isolated Naïve CD4+ T cells active with plate-bound anti-CD3(Clone: 145-2C11, 1 μg/ml, eBioscience), anti-CD28(Clone: 37.51, 3 μg/ml, eBioscience), then polarized under Th1 condition.

extract_protocol:
Detailed procedures for ChIP-Seq analysis was performed as described previously (Hu et al., 2018). For RNA-Seq, 2ng of total RNA were extracted miRNeasy Micro Kit (50) from Qiagen (Cat # 217084).
ChIP DNA were end-repaired using an End-It DNA End-Repair kit (Epicentre), universal adaptors were then ligated. The libraries were amplified using indexed primers with the PCR condition: 98°C, 10”; 67°C, 30”; 72°C, 30” for 16 cycles. The fragments between 180bp to 350bp were isolated on E-gel and subjected to sequencing on Illumina HiSeq2500.

treatment_protocol: Using DAPI to sort out live cells for Dnase-seq, ChIP-seq, and RNA-seq experiments.

value: CD4+ T cells stimulated for 48 h (horizontal axis) under Th1 condition

value: Cell Culture

value: MLL4 KO DAPI-


title: RNA-seq_WT_Th1_48h

value: WT DAPI-


title: 8-002 (mRNA)


title: CRC0493LMH0000000000R05000, LMH, bio rep 1, QC ok

value: H

value: LM


title: RNA-seq_MLL4KO_Th1_6h

value: mixed C57BL/6 and 129

value: CD4+ T cells stimulated for 6 h (horizontal axis) under Th1 condition


title: 11-001 (mRNA)

description: uploaded to GSE151496


title: T47DPRL2

city: Shang hai

first: Jiawei

address: 上海交通大学药学院6号楼202

institute: Shanghai Jiao Tong University

data_processing:
Clean data: Use SOAPnuke (v1.5.6) to screen out reads that contaminated by adapter or containing more than 5% unknown bases.  Parameters: -l 15 -q 0.2 -n 0.05
Genome reference: Use HISAT2 (v2.1.0) to align clean data to genome reference. Parameters: -sensitive --no-discordant --no-mixed -I 1 -X 1000 -p 8 --rna-strandness RF
Gene set reference: Use Bowtie2 (v2.3.4.3) align clean data to gene set reference. Parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant -p 1 -k 200
Assembly: genome version: GCF_000001405.39_GRCh38.p13
Supplementary files format and content: txt file including fpkm, tpm and read counts of each samples

source_name: breast  cancer

growth_protocol: RPMI1640+10&FBS for 2 days

extract_protocol:
trizol
standard Illumina protocols

treatment_protocol: NT

value: breast  cancer

value: luminal

value: Lentivirus PRL


title: T47DPRL3

address: 上海交通大学药学院6号楼202


title: 8-001 (mRNA)

value: Duodenal mucosa (biopsy)


title: CRC0492LMX0B02001TUMR01000, LMX_BASALE, bio rep 1, QC ok

value: Colorectal Cancer

value: X


title: T47DPRL1

address: 上海交通大学药学院6号楼202


title: 7-004 (mRNA)


title: RNA-seq_WT_Th1_6h


title: CRC0491PRX0A01001TUMR01000, PRX_BASALE, bio rep 1, QC failed

value: PR


title: T47DPLVX3

address: 上海交通大学药学院6号楼202

value: Lentivirus control


title: CRC0490LMX0A03009TUMR01000, LMX_cetux_h, bio rep 1, QC ok

value: WT

value: CET


title: RNA-seq_MLL4KO_NaiveCD4

value: Naive CD4+ T cells

value: lymph node

value: MLL4 KO(CD4+CD8-CD62+CD44-)


title: 7-003 (mRNA)

value: Functional Dyspepsia


title: CRC0493LMX0A03003TUMR01000, LMX_cetux_h, bio rep 1, QC ok

value: LM


title: RNA-seq_WT_NaiveCD4

value: mixed C57BL/6 and 129


title: 8-005 (mRNA)


title: CRC0490LMX0A03008TUMR09000, LMX_cetux_h_NT, bio rep 1, QC ok

value: NT


title: ChIP-seq_WT_NaiveCD4_CTCF


title: T47DPLVX1

address: 上海交通大学药学院6号楼202

value: breast  cancer


title: 7-001 (mRNA)


title: 7-002 (mRNA)


title: T47DPLVX2

address: 上海交通大学药学院6号楼202

value: luminal


title: CRC0490LMX0A02002TUMR03000, LMX_BASALE, bio rep 1, QC ok


title: CRC0490LMH0000000000R09000, LMH, bio rep 1, QC ok

value: H


title: S, ConA7

city: Hangzhou

first: Jianing

last: Chen

address: Qingchun Road 79#

institute: Zhejiang university

data_processing:
Library strategy: DNA-seq
Vsearch software (v2.3.4) was used for basecalling
dereplication using DADA2
Chao1, Observed species, Goods coverage, Shannon, Simpsonin our samples were calculated with QIIME2.
Blast was used for sequence alignment
feature sequences were annotated with SILVA database
Supplementary files format and content: otu_table_with_taxonomy.txt (abundance measurements), gene_counts_statistics.txt (raw counts)

organism: feces metagenome

source_name: murine feces

extract_protocol:
Total genome DNA from murine luminal samples from ileocecus was extracted for amplification
The libraries were sequenced on Illumina NovaSeq PE250 platform
DNA V4 region

value: Salm+Con A

value: 49 day

tag: fraction

value: rDNA


title: 6-017 (mRNA)

value: Duodenal mucosa (biopsy)


title: ChIP-seq_WT_Th1_TBX21

value: CD4+ T cells stimulated for 24 h (horizontal axis) under Th1 condition

value: Cell Culture

value: WT DAPI-


title: S, ConA4


title: 6-015 (mRNA)


title: CRC0488LMX0B02002TUMR01000, LMX_BASALE, bio rep 1, QC ok

value: Colorectal Cancer

value: X

value: WT


title: 6-014 (mRNA)

value: Functional Dyspepsia


title: S, ConA3


title: ChIP-seq_CNS-28_Th1_24h_H3K27ac_rep1

value: CNS-28 DAPI-


title: ChIP-seq_CNS-28_Th1_24h_H3K27ac_rep2

value: mixed C57BL/6 and 129


title: 6-013 (mRNA)


title: CRC0484LMX0A02001TUMR02000, LMX_BASALE, bio rep 1, QC ok

value: LM


title: 6-012 (mRNA)


title: ChIP-seq_CNS-28_Th1_24h_H3K4me3_rep1


title: CRC0481PRX0B01001TUMR01000, PRX_BASALE, bio rep 2, QC ok

value: PR


title: S, ConA1


title: S, PBS7

value: Salm Control


title: ChIP-seq_WT_NaiveCD4_GATA3

value: Naive CD4+ T cells

value: lymph node


title: 6-011 (mRNA)


title: CRC0481PRX0A01001TUMR01000, PRX_BASALE, bio rep 1, QC ok


title: S, PBS6

value: 49 day


title: ChIP-seq_CNS-28_Th1_24h_H3K4me1_rep1


title: ChIP-seq_CNS-28_Th1_24h_H3K4me1_rep2


title: CRC0481PRH0000000000R01000, PRH, bio rep 1, QC ok

value: H


title: S, PBS5

value: rDNA


title: CRC0481LMX0B02001TUMR01000, LMX_BASALE, bio rep 2, QC ok


title: 6-009 (mRNA)

value: Duodenal mucosa (biopsy)


title: CRC0486LMX0A02004TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: CRC0481LMX0A03008TUMR01000, LMX_cetux_6w_NT, bio rep 1, QC ok

value: NT


title: S, PBS1


title: S, ConA2

value: Salm+Con A


title: ChIP-seq_CNS-28_Th1_24h_H3K4me3_rep2

value: CD4+ T cells stimulated for 24 h (horizontal axis) under Th1 condition

value: Cell Culture


title: ChIP-seq_WT_Th1_24h_H3K27ac_rep1

value: WT DAPI-


title: 6-007 (mRNA)

value: Functional Dyspepsia


title: CRC0481LMX0A03007TUMR01000, LMX_cetux_6w, bio rep 1, QC ok

value: Colorectal Cancer

value: X

value: WT

value: CET


title: ChIP-seq_WT_Th1_24h_H3K4me3_rep2

value: mixed C57BL/6 and 129


title: P, ConA7

value: PBS+ con A


title: CRC0481LMX0A03006TUMR01000, LMX_cetux_h_NT, bio rep 1, QC ok

value: LM


title: ChIP-seq_WT_Th1_24h_H3K4me3_rep1


title: 6-006 (mRNA)


title: P, ConA5

value: 49 day


title: 6-010 (mRNA)


title: ChIP-seq_WT_Th1_24h_H3K4me1_rep2


title: CRC0481LMX0A03001TUMR01000, LMX_cetux_h, bio rep 1, QC ok


title: 6-005 (mRNA)


title: CRC0481LMX0A02001TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: P, ConA4


title: P, ConA3


title: ChIP-seq_WT_Th1_24h_H3K4me1_rep1


title: S, PBS4

value: Salm Control


title: ChIP-seq_WT_Th1_24h_H3K27ac_rep2


title: CRC0481LMH0000000000R01000, LMH, bio rep 1, QC ok

value: H


title: P, ConA2

value: rDNA


title: 6-008 (mRNA)

value: Duodenal mucosa (biopsy)


title: ChIP-seq_CNS-28_Naive_CD4_H3K27ac_rep2

value: Naive CD4+ T cells

value: lymph node


title: 6-001 (mRNA)


title: P, Ctrl7

value: PBS Control


title: ChIP-seq_CNS-28_Naive_CD4_H3K27ac_rep1


title: P, Ctrl4


title: 5-013 (mRNA)


title: ChIP-seq_CNS-28_Naive_CD4_H3K4me3_rep2


title: CRC0480LMX0B02001TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: 5-012 (mRNA)


title: CRC0477LMX0A02004TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: CRC0475LMX0B02004TUMR02000, LMX_BASALE, bio rep 1, QC ok


title: 6-004 (mRNA)


title: 6-002 (mRNA)


title: P, Ctrl2


title: ChIP-seq_CNS-28_Naive_CD4_H3K4me1_rep1


title: ChIP-seq_CNS-28_Naive_CD4_H3K4me1_rep2


title: ChIP-seq_CNS-28_Naive_CD4_H3K4me3_rep1


title: P, Ctrl1