title: GFAP_Positive_Astrocytes [411O.AAGAGGCA_CTAGTCGA]

description: Sorted Astroyctes

source_name: Astrocytes


title: GFAP_Positive_Microglia [411O.ATCTCAGG_AGCTAGAA]

status: Public on Nov 09 2023

type: SRA

city: Boston

first: Zhaorong

last: Li

address: 60 Fenwood Road

country: USA

institute: Dana Farber Cancer Institute

description: Sorted Microglia

library_source: transcriptomic

data_processing:
The sample is aligned to GRCm38 reference genome using STAR, and then quantified using RSEM
Genome_build: GRCm38
Supplementary_files_format_and_content: .isoforms.results files from RSEM

molecule: total RNA

organism: Mus musculus

source_name: Microglia

extract_protocol:
N/A
Libraries were prepared by the Broad Institute according to the SMARTseq 2 protocol as described (Trombetta et al 2014).

tag: strain

tag: Sex

value: Female

tag: age

value: Adults


title: GFAP_Negative_Microglia [411O.TAAGGCGA_AGCTAGAA]

description: Sorted Microglia


title: GFAP_Positive_Astrocytes [411O.CGAGGCTG_CTAGTCGA]

description: Sorted Astroyctes


title: GFAP_Positive_Astrocytes [411O.CTCTCTAC_CTAGTCGA]

description: Sorted Astroyctes


title: GFAP_Negative_Astrocytes [411O.TCCTGAGC_CTAGTCGA]

description: Sorted Astroyctes


title: GFAP_Positive_Astrocytes [411O.TAGGCATG_CTAGTCGA]

description: Sorted Astroyctes


title: GFAP_Negative_Astrocytes [411O.AGGCAGAA_CTAGTCGA]

description: Sorted Astroyctes


title: GFAP_Positive_Astrocytes [411O.GCTCATGA_CTAGTCGA]

description: Sorted Astroyctes


title: GFAP_Negative_Astrocytes [411O.CGTACTAG_CTAGTCGA]

description: Sorted Astroyctes


title: GFAP_Positive_Astrocytes [411O.GTAGAGGA_CTAGTCGA]

description: Sorted Astroyctes


title: blood_SJWLM069401_G1

type: genomic

city: Birmingham

first: Changde

last: Cheng

state: AL

address: 1824 6th Ave S, Wallace Tumor Institute 520A

department: Medicine

institute: University of Alabama at Birmingham

hyb_protocol: bisulfite converted DNA was amplified, fragmented and hybridized according to Illumina's standard protocol

scan_protocol: Arrays were imaged using BeadArray reader

data_processing:
R library minfi
Processed data file contains: Average Beta

label: Cy5, Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: Blood

label_protocol: Standard Illumina protocol

extract_protocol: DNA isolation using DNA QIAamp FFPE Tissue Kit

tag: diagnosis

value: Wilms tumor

tag: tissue

value: Blood sample


title: blood_SJWLM069400_G2


title: tumor_SJWLM069400_D1

source_name: Tumor

value: Tumor sample


title: tumor_SJWLM069401_D1


title: GFAP_Positive_Astrocytes [411O.ATCTCAGG_CTAGTCGA]

description: Sorted Astroyctes


title: GFAP_Negative_Astrocytes [411O.GGACTCCT_CTAGTCGA]

description: Sorted Astroyctes


title: tumor_SJWLM069399_D2


title: blood_SJWLM069399_G2


title: cancer donor 2

city: Kiel

first: Thomas

middle: F.

last: Meyer

address: Schwanenweg 20, Haus U27, 2 OG

department: Infektion Onkologie

country: Germany

institute: IKMB

data_processing:
Reads were aligned to human genome GRCh38 using STAR v2.7
Mapped reads were assigned to transcripts annotate in Gencode Release 27 using FeatureCounts v2.0.1 and summarized at gene level
Assembly: GRCh38
Supplementary files format and content: raw_counts.tsv (tab delimited file with raw counts per gene output of featureCounts. EntrezID as identifier column)

molecule: polyA RNA

source_name: Cervix Epithela

growth_protocol: Organoids were derived from tissue resection as previously described (Chumduri et al., 2021;Gurumurthy et al., 2022;Koster et al., 2022). In short, biopsies were washed and cells were isolated by mincing and enzymatic digestion with 0.5 mg/mL collagenase type II for 2.5 h at 37°C. Afterwards, cells were pelleted at 100 x g for 5 min (4°C) and then again digested with TrypLE Express Enzyme (Gibco, 12604013) for 15 min at 37°C. Cells were then expanded in collagen-coated T25 tissue culture flasks in cervical organoid medium (Advanced DMEM/F-12 (Gibco, 12634) supplemented with 10 mM HEPES (Capricorn, HEP-B), 1% GlutaMax (Gibco, 35050061), 1x NCS21 Neuronal Supplement (Capricorn, C21-H), 1x N2 (Capricorn, N2-K), 10 ng/mL human EGF (Peprotech, AF-100-15), 0.5 μg/mL hydrocortisone (Sigma, H0888), 100 ng/mL human noggin (Peprotech, 120-10C), 100 ng/mL human FGF-10 (Peprotech, 100-26-25), 1.25 mM N-acetyl-L-cysteine (Sigma, A9165), 2 μM TGF-β receptor kinase Inhibitor IV (A83-01, Cayman Chemicals, Cay9001799), 10 μM ROCK inhibitor (Y-27632, Cayman Chemicals, Cay10005583), 10 mM nicotinamide (Sigma, N0636), 10 μM forskolin (Sigma, F6886)) until reaching 70-80% confluency. After successful establishment, cells were harvested and ~20.000 cells were seeded into 50 µl Matrigel domes (Corning, 11543550). Organoids were maintained by passaging every 1-2 weeks at a 1:2-1:5 ratio using enzymatic digestion with TrypLE followed by mechanical singularization of cells using a syringe with an 18G needle (BD medical, BDAM303129) as described earlier (Gurumurthy et al., 2022).

extract_protocol:
Total RNA was extracted using Direct Zoll RNAseq Mini-prep (Zymo, R2050) according to manufacturer and eluted in Nuclease Free Water
Illumina standard mRNA ibraries were prepared according to manufacturer instrictions

value: Cervix Epithela

tag: cell line

value: Cervix Organoids

tag: cell type

value: Primary cells

tag: individual

value: cancer donor


title: cancer donor 3


title: control donor 2

value: control donor


title: control donor 3


title: cancer donor 1


title: HPV donor 1

value: HPV donor


title: HPV donor 3


title: GFAP_Negative_Astrocytes [411O.TAAGGCGA_CTAGTCGA]

description: Sorted Astroyctes


title: HPV donor 2


title: CNE1_LV5_rep1

type: RNA

city: Dongguan

first: Guoliang

last: Huang

address: No.1 Xincheng Avenue, Songshan Lake High-tech Park (Guangdong Medical University)

country: China

institute: Graduate School of Guangdong Medical University

description: Gene expression in CNE1 cells transfected with LV5

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions。

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, 20bit. Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US).

data_processing: Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

source_name: CNE1, LV5, replicate 1

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp WT Labeling Kit ( Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (QIAGEN, GmBH, Germany).

extract_protocol: Total RNA was extracted using TRIzol Reagent (Life technologies, Carlsbad, CA, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

treatment_protocol: CNE1-ATF1 was designated as the CNE1 cells stably expressing ATF1, and CNE1-control as the negative control. NP69-ATF1 was the NP69 cells stably expressing ATF1, while NP69-control as the negative control. Cells (5×105) were inoculated in a 60 mm culture dish for 2 days

value: nasopharynx


title: NP69_ATF1_rep1

description: Gene expression in NP69 cells  transfected with ATF1

source_name: NP69, ATF1, replicate 1


title: blood_SJWLM069398_G2


title: blood_SJWLM069399_G1


title: tumor_SJWLM069399_D1


title: NP69_LV5_rep1

description: Gene expression in NP69 cells transfected with LV5

source_name: NP69, LV5, replicate 1


title: CNE1_ATF1_rep1

description: Gene expression in CNE1 cells transfected with ATF1

source_name: CNE1, ATF1, replicate 1


title: blood_SJWLM069398_G1


title: tumor_SJWLM069398_D1


title: control donor 1


title: tumor_SJWLM069397_D1


title: blood_SJWLM069397_G2


title: tumor_SJWLM069396_D2


title: blood_SJWLM069397_G1


title: blood_SJWLM069400_G1


title: tumor_SJWLM069396_D1


title: blood_SJWLM069396_G1


title: tumor_SJWLM069394_D2


title: tumor_SJWLM069395_D1


title: blood_SJWLM069395_G1


title: tumor_SJWLM069394_D1


title: tumor_SJWLM066792_D3


title: tumor_SJWLM069392_D1


title: blood_SJWLM066792_G2


title: tumor_SJWLM069393_D1


title: blood_SJWLM066789_G2


title: blood_SJWLM069392_G2


title: blood_SJWLM069394_G1


title: blood_SJWLM069393_G1


title: blood_SJWLM069391_G1


title: blood_SJWLM069392_G1


title: tumor_SJWLM069391_D2


title: blood_SJWLM069390_G2


title: blood_SJWLM069389_G2


title: tumor_SJWLM069390_D1


title: blood_SJWLM069390_G1


title: blood_SJWLM069389_G1


title: tumor_SJWLM069388_D1


title: tumor_SJWLM069387_D1


title: blood_SJWLM066784_G3


title: blood_SJWLM069387_G1


title: blood_SJWLM066776_G2


title: tumor_SJWLM069386_D1


title: tumor_SJWLM066778_D3


title: tumor_SJWLM066776_D3


title: blood_SJWLM069386_G2


title: tumor_SJWLM069391_D1


title: blood_SJWLM069386_G1


title: blood_SJWLM066776_G3


title: blood_SJWLM069385_G2


title: tumor_SJWLM069389_D1


title: tumor_SJWLM066784_D3


title: blood_SJWLM069384_G1


title: tumor_SJWLM069383_D1


title: blood_SJWLM069388_G1


title: blood_SJWLM069385_G1


title: tumor_SJWLM069384_D1


title: blood_SJWLM069383_G2


title: blood_SJWLM069383_G1


title: blood_SJWLM069382_G2


title: blood_SJWLM069382_G1


title: blood_SJWLM069381_G1


title: tumor_SJWLM069380_D1


title: tumor_SJWLM069381_D1


title: blood_SJWLM069380_G1


title: tumor_SJWLM069379_D1


title: blood_SJWLM069381_G2


title: blood_SJWLM069379_G1


title: tumor_SJWLM069385_D1


title: blood_SJWLM069378_G1


title: blood_SJWLM066797_G1


title: blood_SJWLM066797_G2


title: tumor_SJWLM066797_D1


title: tumor_SJWLM066796_D1


title: blood_SJWLM066796_G1


title: tumor_SJWLM069378_D1


title: blood_SJWLM066796_G2


title: blood_SJWLM066794_G2


title: tumor_SJWLM066793_D1


title: blood_SJWLM066792_G1


title: tumor_SJWLM066795_D1


title: blood_SJWLM066791_G1


title: tumor_SJWLM066794_D1


title: tumor_SJWLM066791_D1


title: blood_SJWLM066789_G1


title: blood_SJWLM066790_G1


title: tumor_SJWLM069382_D1


title: tumor_SJWLM066789_D1


title: blood_SJWLM066788_G1


title: tumor_SJWLM066788_D1


title: blood_SJWLM066795_G1


title: tumor_SJWLM066789_D2


title: tumor_SJWLM066790_D1


title: blood_SJWLM066793_G1


title: tumor_SJWLM066792_D1


title: blood_SJWLM066787_G1


title: tumor_SJWLM066787_D1


title: blood_SJWLM066794_G1


title: blood_SJWLM066786_G2


title: blood_SJWLM066786_G1


title: tumor_SJWLM066786_D1


title: blood_SJWLM066785_G1


title: blood_SJWLM066785_G2


title: blood_SJWLM066790_G2


title: tumor_SJWLM066785_D1


title: blood_SJWLM066784_G1


title: blood_SJWLM066784_G2


title: blood_SJWLM066782_G1


title: tumor_SJWLM066784_D1


title: blood_SJWLM066781_G1


title: tumor_SJWLM066781_D1


title: Infant 11 day 0

city: Memphis

first: Zhaohui

last: Xu

state: TN

address: 262 Danny Thomas Place

department: Infectious Diseases

institute: St. Jude Children's Research Hospital

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with lumi in R

label: biotin

source_name: Human Whole blood

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: Total RNA was isolated with Tempus Spin RNA Isolation Kit and globin mRNA from total RNA was removed with GLOBINclear Whole Blood Globin Reduction Kit. Quality control was performed with Agilent Bioanalyser.

tag: subject

value: Whole blood

tag: time point

value: day 0


title: tumor_SJWLM066783_D1


title: blood_SJWLM066782_G2


title: tumor_SJWLM066780_D2


title: blood_SJWLM066780_G1


title: blood_SJWLM066783_G1


title: blood_SJWLM066780_G2


title: tumor_SJWLM066780_D1


title: blood_SJWLM066779_G1


title: blood_SJWLM066781_G2


title: tumor_SJWLM066779_D1


title: tumor_SJWLM066779_D2


title: tumor_SJWLM066782_D1


title: blood_SJWLM066779_G2


title: blood_SJWLM066778_G2


title: blood_SJWLM066778_G1


title: tumor_SJWLM066778_D1


title: tumor_SJWLM066777_D2


title: blood_SJWLM066777_G1


title: blood_SJWLM066776_G1


title: tumor_SJWLM066777_D1


title: tumor_SJWLM066776_D1


title: blood_SJWLM066775_G1


title: blood_SJWLM066774_G1


title: blood_SJWLM066773_G1


title: tumor_SJWLM066773_D2


title: tumor_SJWLM066774_D1


title: tumor_SJWLM066773_D1


title: blood_SJWLM066772_G1


title: blood_SJWLM066772_G2


title: tumor_SJWLM066770_D1


title: blood_SJWLM066770_G1


title: tumor_SJWLM066772_D1


title: blood_SJWLM066771_G1


title: tumor_SJWLM066771_D1


title: tumor_SJWLM066775_D1


title: tumor_SJWLM066771_D2


title: tumor_SJWLM066770_D2


title: Sorted CD4 cells_PMA_Ionomycin_24h_Donor_MRC015

city: Beerse

first: Filmon

last: Eyassu

address: Turnhoutseweg 30

country: Belgium

institute: Janssen Pharmaceutica

hyb_protocol: Biotin-labeled target samples were hybridized to the Clariom GO Screen (ThermoFisher, #952361) containing probes for over 20,000 genes. Target hybridization was performed on the GeneTitan Multi-Channel Instrument (ThermoFisher, #00-0373) according to manufacturer’s instructions provided for Expression Array Plates.

scan_protocol: Images were analyzed using the GeneChip Command Console (GCC) Software (ThermoFisher).

data_processing: All microarray data were processed using the statistical computing program R (R version 3.2.2) and Bioconductor packages. The microarray dataset was background corrected and normalized with robust multiarray analysis and summarized with the metadata package GO_Screen_hu. Quality assessment was performed with arrayQualityMetrics [52].

label_protocol: Amplification and biotin labelling of total RNA were performed using the GeneChip PICO Reagent Kit following the manufacturer’s instructions (ThermoFisher, #902790).

growth_protocol: Following a 6h or 24h--stimulation of bulk CD4 T cells with the LRAs of interest and in presence of antiretroviral drugs, 10,000 cells were transferred to a tube containing 100 μL of Buffer RLT (Qiagen, #1015762) supplemented with 1% 2-mercaptoethanol (Sigma-Aldrich, #M3148). Cells were stored at -80 °C until further processing.

extract_protocol: RNA extraction was done using the RNeasy plus mini kit (Qiagen, #74181).

tag: donor id

value: Sorted CD4 Tcells

tag: treatment


title: Sorted CD4 cells_PMA_Ionomycin_24h_Donor_MRC008

treatment_protocol: Following a 6h or 24h--stimulation of bulk CD4 T cells with the LRAs of interest and in presence of antiretroviral drugs, 10,000 cells were transferred to a tube containing 100 μL of Buffer RLT (Qiagen, #1015762) supplemented with 1% 2-mercaptoethanol (Sigma-Aldrich, #M3148). Cells were stored at -80 °C until further processing.


title: Sorted CD4 cells_TatL2 + Panobinistat_24h_Donor_MRC001

value: TatL2 + Panobinistat_24h


title: Sorted CD4 cells_PMA_Ionomycin_6h_Donor_MRC004


title: Sorted CD4 cells_TatL2 + Panobinistat_24h_Donor_MRC004


title: Sorted CD4 cells_Panobinistat_24h_Donor_MRC015


title: Sorted CD4 cells_TatL2 + Panobinistat_6h_Donor_MRC004

value: TatL2 + Panobinistat_6h


title: Sorted CD4 cells_PMA_Ionomycin_6h_Donor_MRC008


title: Sorted CD4 cells_TatL2 + Panobinistat_6h_Donor_MRC008


title: Sorted CD4 cells_Panobinistat_6h_Donor_MRC001


title: Sorted CD4 cells_Panobinistat_24h_Donor_MRC004


title: Sorted CD4 cells_Panobinistat_24h_Donor_MRC008


title: Sorted CD4 cells_TatL2_24h_Donor_MRC001

source_name: Sorted CD4 cells_TatL2_24h_Donor_MRC001


title: Sorted CD4 cells_Panobinistat_6h_Donor_MRC008


title: Sorted CD4 cells_Panobinistat_24h_Donor_MRC001


title: Sorted CD4 cells_TatL2 + Panobinistat_24h_Donor_MRC015


title: Sorted CD4 cells_PMA_Ionomycin_24h_Donor_MRC001


title: Sorted CD4 cells_TatL2 + Panobinistat_6h_Donor_MRC001


title: Sorted CD4 cells_TatL2 + Panobinistat_24h_Donor_MRC008


title: Sorted CD4 cells_PMA_Ionomycin_6h_Donor_MRC015


title: Sorted CD4 cells_Panobinistat_6h_Donor_MRC004


title: Sorted CD4 cells_TatL2_24h_Donor_MRC004

source_name: Sorted CD4 cells_TatL2_24h_Donor_MRC004


title: Sorted CD4 cells_PMA_Ionomycin_24h_Donor_MRC004


title: Sorted CD4 cells_TatL2_24h_Donor_MRC008

source_name: Sorted CD4 cells_TatL2_24h_Donor_MRC008


title: Sorted CD4 cells_TatL2_24h_Donor_MRC015

source_name: Sorted CD4 cells_TatL2_24h_Donor_MRC015


title: Sorted CD4 cells_TatL2 + Panobinistat_6h_Donor_MRC015


title: Sorted CD4 cells_PMA_Ionomycin_6h_Donor_MRC001


title: Sorted CD4 cells_Panobinistat_6h_Donor_MRC015


title: Sorted CD4 cells_TatL2_6h_Donor_MRC008

source_name: Sorted CD4 cells_TatL2_6h_Donor_MRC008


title: Sorted CD4 cells_TatL2_6h_Donor_MRC004

source_name: Sorted CD4 cells_TatL2_6h_Donor_MRC004


title: Sorted CD4 cells_TatL2_6h_Donor_MRC001

source_name: Sorted CD4 cells_TatL2_6h_Donor_MRC001


title: Sorted CD4 cells_TatL2_6h_Donor_MRC015

source_name: Sorted CD4 cells_TatL2_6h_Donor_MRC015


title: Sorted CD4 cells_HA L2_24h_Donor_MRC004

source_name: Sorted CD4 cells_HA L2_24h_Donor_MRC004

value: HA L2_24h


title: Sorted CD4 cells_HA L2_24h_Donor_MRC015

source_name: Sorted CD4 cells_HA L2_24h_Donor_MRC015


title: DNA mehtylation of mouse Dendric cells

city: Shinagawa-ku

first: Hideyuki

last: Takeshima

state: Tokyo

department: Institute for Advanced Life Sciences

country: Japan

institute: Hoshi University

hyb_protocol: Standard Illumina Protocol

scan_protocol: The array was scanned with an iScan System

data_processing:
The data were analyzed using GenomeStudio Methylation Module Software.
The matrix_processed.txt contains Average Beta

label: Cy5 and Cy3

source_name: Mouse leukocyte

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted using QIAamp DNA Mini Kit (Qiagen).

value: Dendric cells


title: DNA mehtylation of mouse Neutrophil

value: Neutrophil


title: Sorted CD4 cells_HA L2_24h_Donor_MRC008

source_name: Sorted CD4 cells_HA L2_24h_Donor_MRC008


title: Sorted CD4 cells_HA L2_24h_Donor_MRC001

source_name: Sorted CD4 cells_HA L2_24h_Donor_MRC001


title: DNA mehtylation of mouse NK cells

value: NK cells


title: DNA mehtylation of mouse Macrophage

value: Macrophage


title: Sorted CD4 cells_NS_24h_Donor_MRC001

source_name: Sorted CD4 cells_NS_24h_Donor_MRC001


title: Sorted CD4 cells_DMSO_24h_Donor_MRC008

source_name: Sorted CD4 cells_DMSO_24h_Donor_MRC008


title: Sorted CD4 cells_HA L2_6h_Donor_MRC004

source_name: Sorted CD4 cells_HA L2_6h_Donor_MRC004

value: HA L2_6h


title: Sorted CD4 cells_DMSO_6h_Donor_MRC001

source_name: Sorted CD4 cells_DMSO_6h_Donor_MRC001


title: Sorted CD4 cells_NS_6h_Donor_MRC004

source_name: Sorted CD4 cells_NS_6h_Donor_MRC004


title: Sorted CD4 cells_DMSO_6h_Donor_MRC004

source_name: Sorted CD4 cells_DMSO_6h_Donor_MRC004


title: Sorted CD4 cells_DMSO_24h_Donor_MRC004

source_name: Sorted CD4 cells_DMSO_24h_Donor_MRC004


title: Sorted CD4 cells_HA L2_6h_Donor_MRC008

source_name: Sorted CD4 cells_HA L2_6h_Donor_MRC008


title: Sorted CD4 cells_HA L2_6h_Donor_MRC015

source_name: Sorted CD4 cells_HA L2_6h_Donor_MRC015


title: Sorted CD4 cells_NS_6h_Donor_MRC008

source_name: Sorted CD4 cells_NS_6h_Donor_MRC008


title: Sorted CD4 cells_DMSO_6h_Donor_MRC008

source_name: Sorted CD4 cells_DMSO_6h_Donor_MRC008


title: Sorted CD4 cells_NS_24h_Donor_MRC015

source_name: Sorted CD4 cells_NS_24h_Donor_MRC015


title: Sorted CD4 cells_DMSO_24h_Donor_MRC001

source_name: Sorted CD4 cells_DMSO_24h_Donor_MRC001


title: Sorted CD4 cells_DMSO_24h_Donor_MRC015

source_name: Sorted CD4 cells_DMSO_24h_Donor_MRC015


title: Sorted CD4 cells_NS_24h_Donor_MRC008

source_name: Sorted CD4 cells_NS_24h_Donor_MRC008


title: Sorted CD4 cells_DMSO_6h_Donor_MRC015

source_name: Sorted CD4 cells_DMSO_6h_Donor_MRC015


title: DNA mehtylation of mouse Cd8+ T cells

source_name: Mouse leukocyte

value: Cd8+ T cells


title: Sorted CD4 cells_NS_6h_Donor_MRC001

source_name: Sorted CD4 cells_NS_6h_Donor_MRC001


title: Sorted CD4 cells_NS_6h_Donor_MRC015

source_name: Sorted CD4 cells_NS_6h_Donor_MRC015


title: Sorted CD4 cells_HA L2_6h_Donor_MRC001

source_name: Sorted CD4 cells_HA L2_6h_Donor_MRC001


title: DNA mehtylation of mouse Cd4+ T cells

value: Cd4+ T cells


title: Sorted CD4 cells_NS_24h_Donor_MRC004

source_name: Sorted CD4 cells_NS_24h_Donor_MRC004


title: DNA mehtylation of mouse B cells

value: B cells


title: SC-RTL1 seedling

city: Versailles

first: Filipe

last: Borges

address: Route de St-Cyr (RD10)

country: France

institute: Institut Jean-Pierre Bourgin - INRAE

description: processed files not available at the time of submission due to server maintenance (will be added later)

library_source: genomic

data_processing:
Pre-processed high quality reads were mapped to the TAIR10 genome using bismark (Krueger and Andrews 2011, Bioinformatics) with default settings for paired-end libraries, and all downstream analysis were performed using custom R scripts
Assembly: TAIR10
Supplementary files format and content: wig files with cytosine methylation values (CG,CHG,CHH)

organism: Arabidopsis thaliana

source_name: Seedlings

growth_protocol: Seeds were germinated on MS plates for 2 weeks, and plants were grown in greenhouse long-day conditions to complete the life cycle (16h photoperiod).

extract_protocol:
Genomic DNA was isolated pollen or pooled seedlings using the Edwards method (Edwards et al. 1991, NAR 19:1349).
Whole genome bisulfite sequencing was performed by BGI Genomics (Hong Kong). Genomic DNA was fragmented by sonication, end-repaired and ligated to methylated adaptors. After bisulfite treatment, bisulfite-treated fragments were PCR amplified and sequenced as paired-end 100bp reads (PE100) with DNBSEQ technology (BGI).

value: Seedlings

tag: ecotype

tag: genotype


title: VC-RTL1 seedling


title: RNAseq_Nd38_EZH2i_4uM_REP3

city: New York

first: Richard

last: Koche

state: New York

institute: Memorial Sloan Kettering Cancer Center

data_processing:
RNA-seq reads were filtered for quality and 3' trimmed for adapter sequences.
Reads were aligned to human genome assembly hg19 using STAR (v2.4) with default parameters.
Read count tables were created using HTSeq v0.6.1.
Normalization and differential expression analysis were performed with DESeq2.
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: hPSC-derived neuronal cells

growth_protocol: WA09 (H9 ) human pluripotent stem cell (hPSC) line was cultured in Essential 8 on Vitronectin coated dishes and expanded by dissociation with 0.5mM EDTA. Neural induction was completed using the dual SMAD inhibition protocol and WNT inhibition on Matrigel coated dishes. hPSC for differentiation and neuronal progenitors were dissociated using Accutase. Neurons were maintained on poly-L-ornithine and Laminin/ Fibronectin coated plates in Neurobasal medium supplemented with B27, L-glutamine. DAPT was added to the neuronal maintenance medium from day 20 to day 30 of differentiation. BDNF, GDNF, cAMP, and AA were added starting at day 30.

extract_protocol:
Total RNA from hPSC-derived samples was isolated by chloroform phase separation using Phase Lock Gel-Heavy tubes, precipitated with EtOH, and purified using RNeasy Mini Kit (Qiagen) with on-column DNA digestion step.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq RNA Sample Preparation Kit

treatment_protocol: Treatment of cortical neural progenitor cells (NPCs) with small molecules inhibitors of chromatin regulators was performed from day 12 to 20 of differentiation. Small molecules were dissolved in DMSO and added to the N2/B27 media. Small molecules were washed out before the induction of synchronized neurogenesis and neurons derived from all the treatments were maintained in the same conditions.

value: hPSC-derived neuronal cells

tag: developmental stage

value: day 38

value: EZH2 inhibitor GSK343

tag: concentration


title: RNAseq_Nd38_EZH2i_4uM_REP2


title: RNAseq_Nd38_EZH2i_4uM_REP1


title: RNAseq_Nd38_EZH2i_2uM_REP3


title: RNAseq_Nd38_EZH2i_2uM_REP2


title: RNAseq_Nd38_EHMTsi_4uM_REP3

value: EHMT1/2 inhibitor UNC0638


title: RNAseq_Nd38_EHMTsi_4uM_REP2


title: RNAseq_Nd38_EHMTsi_2uM_REP2


title: RNAseq_Nd38_EHMTsi_2uM_REP3


title: RNAseq_Nd38_EHMTsi_4uM_REP1


title: RNAseq_Nd38_DOT1Li_2uM_REP3

value: DOT1L inhibitor EPZ004777


title: RNAseq_Nd38_DOT1Li_4uM_REP2


title: RNAseq_Nd38_DOT1Li_4uM_REP3


title: RNAseq_Nd38_DMSO_4uM_REP1

value: DMSO


title: RNAseq_Nd38_DMSO_2uM_REP3


title: RNAseq_Nd38_DMSO_2uM_REP2


title: RNAseq_Nd38_DMSO_2uM_REP1


title: RNAseq_Nd38_DOT1Li_2uM_REP2


title: LMS_non_responder.3

city: 3601 Spruce Street

first: Yan

last: Zhou

state: PA

address: 333 Cottman Ave

department: Bioinformatics

institute: Fox Chase Cancer Center

data_processing:
Raw reads were aligned to hg38 genome using tophat
Cufflinks algorithm was implemented to assemble transcripts and estimate their abundance. Cuffdiff was used to statistically assess expression changes in quantified genes across different conditions.
Supplementary files format and content: fpkm value in tab-delimited format

source_name: leiomyosarcoma (LMS)

extract_protocol:
RNA was extracted from FFPE tissue samples and RNA-seq was performed by Novogene (https://en.novogene.com) using the Illumina TrueSeq RNA exome pipeline.
RNA sequence library was contructed using NEBNext Ultra II Directional RNA library prep kit.

value: leiomyosarcoma (LMS)

value: sarcoma


title: LMS_non_responder.2


title: LMS_non_responder.1


title: RNAseq_Nd38_DOT1Li_2uM_REP1


title: LMS_non_responder.0


title: RNAseq_Nd38_DOT1Li_4uM_REP1


title: LMS_responder.0


title: RNAseq_Nd38_EZH2i_2uM_REP1


title: hsa_24_KA_A

city: Duarte

first: Hsun

middle: Teresa

last: Ku

state: CA

address: 1500 E. Duarte Road

department: Translational Research and Cellular Therapeutics

institute: City of Hope

data_processing:
RNA-Seq reads were trimmed to remove sequencing adapters using Trimmomatic and polyA tails using FASTP.
The processed reads were mapped to the human genome hg19 using STAR (v. 2.6.0.a), and gene expression levels were summarized by HTSeq-count v.0.11.1.
Gene expression raw counts were normalized using TMM normalization method and differential expression analysis was conducted using log likelihood ratio test implemented in “edgeR”.
Assembly: Assembly: hg38
Supplementary files format and content: Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Cell line

growth_protocol: The cell lines MV4-11, KG-1a were maintained in IMEM (Iscove's Modified Dulbecco's Medium) containing 10% Fetal Bovine Serum (FBS) and 100 U/mL penicillin/streptomycin at 37 °C with 5% CO2.

extract_protocol: QIAGEN RNeasy Micro Kit

value: Cell line

value: acute myeloid leukemia (AML)

value: WT

value: 24h 1uM 8-amino-adenosine


title: hsa_24_KA_B


title: hsa_24_KC_A

value: 24h 1uM 8-chloro-adenosine


title: hsa_24_KN_B

value: no treatment


title: hsa_24_KN_A


title: RNAseq_Nd38_EHMTsi_2uM_REP1


title: RNAseq_Nd38_DMSO_4uM_REP2


title: hsa_24_MA_B


title: RNAseq_Nd38_DMSO_4uM_REP3


title: hsa_24_MA_A


title: hsa_24_MN_B


title: hsa_24_MC_A


title: hsa_24_MC_B


title: hsa_8_KA_B

value: 8h 1uM 8-amino-adenosine


title: hsa_8_KA_A


title: hsa_8_KC_A

value: 8h 1uM 8-chloro-adenosine


title: hsa_8_MA_B


title: hsa_8_KN_A


title: hsa_24_MN_A


title: hsa_8_KC_B


title: hsa_8_MA_A


title: hsa_8_MC_A


title: hsa_8_MC_B


title: hsa_8_KN_B


title: hsa_24_KC_B


title: hsa_8_MN_B


title: hsa_8_MN_A


title: RNA_MSK_SRF001_iPSCs_d37_EZH2i_rep2

data_processing:
RNA-seq reads were filtered for quality and 3' trimmed for adapter sequences.
Reads were aligned to human genome assembly hg19 using STAR (v2.4) with default parameters.
Read count tables were created using HTSeq v0.6.1.
Normalization and differential expression analysis were performed with DESeq2.
Genome build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes raw counts for each sample

value: day 37


title: RNA_MSK_SRF001_iPSCs_d37_EZH2i_rep3

value: hPSC-derived neuronal cells


title: RNA_MSK_SRF001_iPSCs_d37_EZH2i_rep1


title: RNA_MSK_SRF001_iPSCs_d37_EZH2iDOT1Li_rep2

value: combination EPZ004777 and GSK343


title: RNA_MSK_SRF001_iPSCs_d37_EHMTi_rep3


title: RNA_MSK_SRF001_iPSCs_d37_EHMTi_rep2


title: RNA_MSK_SRF001_iPSCs_d37_EHMTi_rep1


title: RNA_MSK_SRF001_iPSCs_d37_DOT1Li_rep3


title: RNA_MSK_SRF001_iPSCs_d37_EZH2iDOT1Li_rep3


title: RNA_MSK_SRF001_iPSCs_d37_EZH2iDOT1Li_rep1


title: RNA_MSK_SRF001_iPSCs_d37_DOT1Li_rep2


title: RNA_MSK_SRF001_iPSCs_d37_DMSO_rep3


title: RNA_MSK_SRF001_iPSCs_d37_DOT1Li_rep1


title: RNA_MSK_SRF001_iPSCs_d37_DMSO_rep2

growth_protocol: MSK_SRF001_iPSCs human pluripotent stem cell (hPSC) line was cultured in Essential 8 on Vitronectin coated dishes and expanded by dissociation with 0.5mM EDTA. Neural induction was completed using the dual SMAD inhibition protocol and WNT inhibition on Matrigel coated dishes. hPSC for differentiation and neuronal progenitors were dissociated using Accutase. Neurons were maintained on poly-L-ornithine and Laminin/ Fibronectin coated plates in Neurobasal medium supplemented with B27, L-glutamine, BDNF, GDNF, cAMP, AA. DAPT was added to the neuronal maintenance medium from day20 to day30 of differentiation.


title: RNA_180_d35_EZH2iDOT1Li_rep3

growth_protocol: WA09 (H9 ) human pluripotent stem cell (hPSC) line was cultured in Essential 8 on Vitronectin coated dishes and expanded by dissociation with 0.5mM EDTA. Neural induction was completed using the dual SMAD inhibition protocol and WNT inhibition on Matrigel coated dishes. hPSC for differentiation and neuronal progenitors were dissociated using Accutase. Neurons were maintained on poly-L-ornithine and Laminin/ Fibronectin coated plates in Neurobasal medium supplemented with B27, L-glutamine, BDNF, GDNF, cAMP, AA. DAPT was added to the neuronal maintenance medium from day20 to day30 of differentiation.

value: day 35


title: RNA_MSK_SRF001_iPSCs_d37_DMSO_rep1


title: RNA_180_d35_EZH2i_rep3

value: EZH2 inhibitor GSK343


title: RNA_178_d50_EZH2i_rep1

value: day 50


title: RNA_178_d50_EHMTi_rep1

value: EHMT1/2 inhibitor UNC0638


title: RNA_178_d50_DOT1Li_rep2

value: DOT1L inhibitor EPZ004777


title: RNA_178_d50_EHMTi_rep2


title: RNA_178_d50_EZH2i_rep3


title: RNA_178_d50_EHMTi_rep3


title: RNA_178_d50_EZH2iDOT1Li_rep2


title: RNA_178_d50_EZH2iDOT1Li_rep1


title: RNA_180_d35_EZH2iDOT1Li_rep2


title: RNA_178_d50_DOT1Li_rep3


title: RNA_178_d50_EZH2i_rep2


title: RNA_178_d50_DOT1Li_rep1


title: RNA_178_d50_DMSO_rep1

value: DMSO


title: RNA_178_d50_EZH2iDOT1Li_rep3


title: RNA_178_d50_DMSO_rep2


title: RNA_178_d35_EZH2i_rep3


title: RNA_178_d35_EZH2i_rep1


title: RNA_178_d35_EZH2iDOT1Li_rep2


title: RNA_178_d35_EHMTi_rep2


title: RNA_178_d35_DMSO_rep3


title: RNA_178_d35_DOT1Li_rep1


title: RNA_178_d35_EHMTi_rep3


title: RNA_178_d25_EZH2i_rep3

value: day 25


title: RNA_178_d35_DMSO_rep2


title: RNA_178_d25_EZH2iDOT1Li_rep3


title: RNA_178_d25_EZH2iDOT1Li_rep2


title: RNA_178_d25_EHMTi_rep3


title: RNA_178_d50_DMSO_rep3


title: RNA_178_d25_DMSO_rep2


title: RNA_178_d25_EHMTi_rep1


title: RNA_178_d25_DOT1Li_rep3


title: RNA_178_d25_EZH2iDOT1Li_rep1


title: RNA_178_d25_DOT1Li_rep1


title: RNA_178_d25_DMSO_rep1


title: CnR_EZH2inh_noab_rep1

data_processing:
Raw sequencing reads were trimmed and filtered for quality (Q>15) and adapter content using version 0.4.5 of TrimGalore and running version 1.15 of cutadapt and version 0.11.5 of FastQC.
Version 2.3.4.1 of bowtie2 was employed to align reads to human assembly hg19 and alignments were deduplicated using MarkDuplicates in Picard Tools v2.16.0.
Enriched regions were discovered using MACS2 with a p-value setting of 0.001 using the no-antibody control as background and then filtered for blacklisted regions.
The BEDTools suite was used to create normalized bigwig files.
Genome build: hg19
Supplementary_files_format_and_content: normalized bigwigs

source_name: hPSC-derived neural progenitor cells

extract_protocol:
50,000 cells were freshly harvested and bound to concanavalin A-coated magnetic beads after an 8min incubation at RT on a rotator. Cell membranes were permeabilized with digitonin and the different antibodies were incubated overnight at 4°C on a rotator. Beads were washed and incubated with pA-MN. Ca2+-induced digestion occurred on ice for 30min and stopped by chelation. DNA was finally isolated using an extraction method with phenol and chloroform as described in Skene et al., 2018
Libraries were prepared for sequencing using standard Illumina protocols

value: hPSC-derived neural progenitor cells

tag: antibody


title: RNA_178_d25_DOT1Li_rep2


title: RNA_178_d25_DMSO_rep3


title: CnR_EZH2inh_noab_rep2


title: RNA_178_d35_EHMTi_rep1


title: RNA_178_d35_DOT1Li_rep3


title: RNA_178_d25_EZH2i_rep2


title: RNA_178_d25_EZH2i_rep1


title: RNA_178_d25_EHMTi_rep2


title: CnR_EHMTinh_H3K4me3_rep2

value: rabbit anti-H3K4me3 (aab8580, abcam)


title: CnR_EZH2inh_H3K27me3_rep1

value: rabbit anti-H3K27me3 (9733, Cell Signaling Technologies)


title: CnR_EHMTinh_H3K4me3_rep1


title: CnR_EHMTinh_H3K27me3_rep2


title: CnR_EHMTinh_noab_rep2


title: CnR_EZH2inh_H3K4me3_rep1


title: CnR_EHMTinh_noab_rep1


title: CnR_EZH2inh_H3K27me3_rep2


title: CnR_EZH2inh_H3K4me3_rep2


title: CnR_DOT1Linh_noab_rep2


title: CnR_DOT1Linh_H3K4me3_rep2


title: CnR_DOT1Linh_noab_rep1


title: CnR_EHMTinh_H3K27me3_rep1


title: CnR_DOT1Linh_H3K4me3_rep1


title: CnR_DOT1Linh_H3K27me3_rep2


title: CnR_DMSO_H3K4me3_rep2


title: CnR_DMSO_H3K4me3_rep1


title: CnR_DMSO_H3K27me3_rep2


title: CnR_DMSO_noab_rep1


title: CnR_DOT1Linh_H3K27me3_rep1


title: hTSC, GCM1 KO, ST, day2, clone 2

city: Sendai

first: Eri

middle: H

last: Kobayashi

state: Miyagi

address: 2-1 Seiryo-machi, Aobaku

department: Medical Biochemistry

institute: Tohoku University Graduate School of Medicine

data_processing:
Libraries were sequenced on an Illumina NovaSeq 6000 platform with 150 bp paired-end reads (Rhelixa).
Sequenced reads were trimmed for quality control using TrimGalore v0.6.7 and aligned to the reference genome (UCSC hg38) using STAR v2.7.10a with the RefSeq gene annotation.
The expression levels (TPM) of RefSeq genes were calculated using RSEM v1.3.1.
Assembly: UCSC hg38
Supplementary files format and content: tab-delimited text file including count data and TPM.

source_name: trophoblast stem cells

growth_protocol: hTSCs were maintained in hTSC medium [DMEM/F12 (FUJIFILM Wako #048-29785) supplemented with 1% knockout serum replacement (KSR) (Thermo Fisher Scientific #10828028), 0.5% penicillin-streptomycin (Thermo Fisher Scientific #15140122), 0.15% bovine serum albumin (BSA) (FUJIFILM Wako #017-22231), 1% ITS-X supplement (FUJIFILM Wako #094-06761), 200 µM L-ascorbic acid (FUJIFILM Wako #013-12061), 25 ng/ml EGF (FUJIFILM Wako #053-07871), 2 μM CHIR99021 (FUJIFILM Wako #038-23101), 5 μM A83-01 (FUJIFILM Wako #035-24113), 0.8 mM valproic acid (FUJIFILM Wako #227-01071), and 2.5 μM Y27632 (FUJIFILM Wako #257-00511)] at 37°C in 95% air and 5% CO2. When hTSCs reached sub-confluence, they were dissociated with TrypLE Express (Thermo Fisher Scientific #12604021) diluted with PBS at a 1:1 ratio for 10-15 min at 37°C. Dissociated cells were seeded in hTSC medium supplemented with 0.5 µg/ml iMatrix-511 (Nippi #892011). hTSCs were typically passaged every two days at a split ratio of 1:4 to 1:8. For CRISPR screening and gene KO, 10 ng/ml BMP4 (R&D Systems #314-BP) was added to the hTSC medium to ameliorate the toxicity of gene transfection and antibiotic selection.

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit and RNase-Free DNase (QIAGEN #74536 and #79254).
RNA-Seq libraries were constructed using NEBNext UltraII Directional RNA Library Prep Kit (NEB).

treatment_protocol: To induce EVT differentiation, hTSCs were cultured in EVT medium [DMEM/F12 supplemented with 0.5% penicillin-streptomycin, 0.15% BSA, 1% ITS-X supplement, 50 ng/ml NRG1 (Cell Signaling #5218SC or #26941), 7.5 μM A83-01, 2.5 μM Y-27632, and 4% KSR] supplemented with 2% Matrigel (Corning #354263) for three days. The culture medium was then replaced with EVT medium without NRG1. Fro ST diffirentiation, hTSCs were cultured on plates coated with 1 µg/ml Col IV (Corning #354233) using ST medium [DMEM/F12 supplemented with 0.5% penicillin-streptomycin, 0.15% BSA, 1% ITS-X supplement, 2.5 μM Y-27632, 2 μM forskolin, and 4% KSR]. Genetically unmodified hTSCs were differentiated into EVTs for five days and STs for four days. WT, DLX3 KO, and GCM1 KO clones were differentiated into EVTs for three days and STs for two days.

value: trophoblast stem cells

value: GCM1 knockout

value: ST differentiation

tag: time

value: Day 2


title: hTSC, WT, EVT, day3, clone empty-2

value: WT

value: EVT differentiation

value: Day 3


title: hTSC, WT, undifferentiated, clone empty-1

value: undiffirentiated

value: Day 0


title: hTSC, WT, EVT, day3, clone empty-1


title: hTSC, WT, undifferentiated, clone empty-2


title: hTSC, WT, ST, day2, clone empty-2


title: hTSC, WT, ST, day2, clone empty-1


title: hTSC, GCM1 KO, EVT, day3, clone 2


title: hTSC, GCM1 KO, undifferentiated, clone 2


title: CnR_DMSO_H3K27me3_rep1


title: hTSC, GCM1 KO, ST, day2, clone 1


title: hTSC, DLX3 KO, EVT, day3, clone 2

value: DLX3 knockout


title: hTSC, DLX3 KO, undifferentiated, clone 2


title: hTSC, GCM1 KO, undifferentiated, clone 1


title: hTSC, GCM1 KO, EVT, day3, clone 1


title: hTSC, DLX3 KO, EVT, day3, clone 1


title: hTSC, WT, ST, day2, clone AAVS-2


title: hTSC, unmodified, ST, day2, clone CT27


title: hTSC, WT, undifferentiated, clone AAVS-1


title: hTSC, WT, ST, day2, clone AAVS-1


title: hTSC, DLX3 KO, ST, day2, clone 1


title: hTSC, DLX3 KO, ST, day2, clone 2


title: hTSC, WT, EVT, day3, clone AAVS-1


title: hTSC, WT, EVT, day3, clone AAVS-2


title: hTSC, DLX3 KO, undifferentiated, clone 1


title: hTSC, unmodified, EVT, day5, clone CT27

value: Day 5


title: hTSC, unmodified, ST, day4, clone CT27

value: Day 4


title: hTSC, unmodified, ST, day4, hypoxia, clone CT27


title: hTSC, unmodified, ST, day4, clone B31


title: hTSC, unmodified, ST, day2, clone B31


title: hTSC, unmodified, undifferentiated, clone B31


title: hTSC, unmodified, EVT, day5, clone B31


title: hTSC, unmodified, EVT, day5, hypoxia, clone B31


title: hTSC, unmodified, undifferentiated, clone CT27


title: hTSC, ST, day4, Hypoxia,  H3K4me3, clone CT27, HiChIP, replicate4

data_processing:
HiChIP reads were mapped to the reference genome (UCSC hg38) using the HiC-Pro pipeline with default settings, and data from replicates were merged.
Significant long-range (>20 kb) chromatin interactions were calculated using FitHiChIP. H3K4me3 ChIP-Seq data from hTSCs, hTSC-derived STs, and hTSC-derived EVTs were used as inputs for FitHiChIP. Only interactions with at least one end overlapping the H3K4me3 ChIP-Seq peaks were retained.
Assembly: UCSC hg38
Supplementary files format and content: bedpe
Library strategy: HiChIP

extract_protocol:
Approximately 10 million cells were fixed in 1% PFA for 10 min and 3 mM disuccinimidyl glutarate for 40 min as previously described. Fixed NIH3T3 cells were added to the cross-linked cells as spike-in controls. The cell mixtures were lysed in HiC Lysis Buffer [10 mM Tris-HCl (pH 7.5), 10 mM NaCl, and 0.2% IGEPAL CA-630], and the isolated nuclei were resuspended in 0.5% sodium dodecyl sulfate (SDS) and permeabilized at 62°C for 10 min. Next, a 3.3-fold volume of 1.5% Triton X-100 was added and incubated at 37°C for 15 min. In situ digestion with DpnII (NEB #R0543) was performed at 37°C for 60 min, and the enzyme was heat-inactivated at 62°C for 20 min. Overhangs were biotin-labeled using DNA Polymerase I large (Klenow) Fragment (NEB #M0210) at 37°C for 60 min in the presence of biotin-14-dATP (Thermo Fisher Scientific #19524016), dTTP, dCTP, and dGTP. Proximity ends were ligated with 13.3 units/µl of T4 DNA ligase (NEB #M0202) at 23°C for 4 h. The nuclei were pelleted and treated with 0.5 units/µL of Exonuclease III (NEB #M0206S) for 5 min at 37°C, resuspended in Nuclear Lysis Buffer [50 mM Tris (pH7.5), 10 mM EDTA, and 1% SDS], and sonicated using Covaris M220 (M&S Instruments Inc.) to 300-700 bp length. Sonicated DNA was diluted 1:10 with ChIP Dilution Buffer [50 mM Tris (pH 7.5), 165 mM NaCl, 1.1% Triton X-100, and 0.01% SDS] and clarified by centrifugation. An anti-H3K4me3 antibody (Merck Millipore, Clone #CMA304) was added to the fragmented DNA at 1:500 dilution, and the mixture was rotated at 4 °C for 60 min. The IP complex was captured using Dynabeads M280 anti-mouse (Life technologies #11201D), and the beads were washed four times with High-Salt Wash Buffer [20 mM Tris (pH 7.5), 500 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS, and 0.1% sodium deoxycholate] and twice with 10 mM Tris-HCl (pH7.5). The washed beads were suspended in Extraction Buffer [10 mM Tris (pH8.0), 350 mM NaCl, 0.1 mM EDTA, and 1% SDS] supplemented with 5% volume of proteinase K (Takara, #9034), and incubated at 55°C for 1 h and 67°C for 2 h to reverse the crosslinks. ChIPed DNA was purified using MinElute PCR Purification Kit (QIAGEN #28004). For biotin pull-down, 5 µl of Dynabeads MyOne Streptavidin C1 beads (Life Technologies #65001) were suspended in 2x Biotin Binding Buffer [10 mM Tris-HCl (pH 7.5), 1 mM EDTA, and 2 M NaCl] and mixed with an equal volume of ChIPed DNA. After 50 min of rotation at room temperature, the beads were washed with Tween Wash Buffer [5 mM Tris-HCl (pH 7.5), 0.5 mM EDTA, 1 M NaCl, 0.05% Tween-20] and NEB T4 Ligase Buffer (NEB # B0202), and resuspended in 10 mM Tris-HCl (pH 8.0).
HiChIP libraries were constructed using KAPA Hyper Prep Kit (NIPPON Genetics #7962312001) and TruSeq-compatible duplex Y adapter (IDT). After PCR amplification, the amplicon was size-selected using Ampure XP (Beckman Coulter #A63880).

treatment_protocol: To induce EVT differentiation, hTSCs were cultured in EVT medium [DMEM/F12 supplemented with 0.5% penicillin-streptomycin, 0.15% BSA, 1% ITS-X supplement, 50 ng/ml NRG1 (Cell Signaling #5218SC or #26941), 7.5 μM A83-01, 2.5 μM Y-27632, and 4% KSR] supplemented with 2% Matrigel (Corning #354263) for three days. The culture medium was then replaced with EVT medium without NRG1. Fro ST diffirentiation, hTSCs were cultured on plates coated with 1 µg/ml Col IV (Corning #354233) using ST medium [DMEM/F12 supplemented with 0.5% penicillin-streptomycin, 0.15% BSA, 1% ITS-X supplement, 2.5 μM Y-27632, 2 μM forskolin, and 4% KSR].


title: hTSC, ST, day4, Hypoxia, H3K4me3, clone CT27, HiChIP, replicate3


title: hTSC, WT, undifferentiated, clone AAVS-2


title: hTSC, ST, day4, H3K4me3, clone CT27, HiChIP, replicate4


title: hTSC, unmodified, EVT, day5, hypoxia, clone CT27


title: hTSC, ST, day4, H3K4me3, clone CT27, HiChIP, replicate1


title: hTSC, ST, day4, Hypoxia, H3K4me3, clone CT27, HiChIP, replicate1


title: hTSC, ST, day4, Hypoxia, H3K4me3, clone CT27, HiChIP, replicate2


title: hTSC, ST, day4, H3K4me3, clone CT27, HiChIP, replicate2


title: hTSC, EVT, day5, H3K4me3, clone CT27, HiChIP, replicate2


title: hTSC, EVT, day5, H3K4me3, clone CT27, HiChIP, replicate4


title: hTSC, EVT, day5, H3K4me3, clone CT27, HiChIP, replicate3


title: hTSC, EVT, day5, H3K4me3, clone CT27, HiChIP, replicate1


title: hTSC, undifferentiated, H3K4me3, clone CT27, HiChIP, replicate6

value: undifferentiated


title: hTSC, undifferentiated, H3K4me3, clone CT27, HiChIP, replicate5


title: hTSC, ST, DLX3, clone CT27, ChIP

data_processing:
ChIP-Seq reads were trimmed for quality control using TrimGalore v0.6.7 and mapped to the reference genome (UCSC hg38) using Bowtie 2 v2.2.5.
Assembly: UCSC hg38
Supplementary files format and content: BigWig

extract_protocol:
Cells were fixed with 1% PFA for 10 min. After quenching and cell lysis, chromatin was sonicated.
ChIP-Seq libraries of TFs were constructed using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB # E7645) with two custom adaptors: Adapter-T and Adapter-C. Adapter-T with a 3′-T overhang was prepared by annealing (5′-CTA CAC GAC GCT CTT CCG ATC TT-3′) and (5′-AGA TCG GAA GAG CAC ACG TCT GAA-3′; 5′ phosphorylated). Adapter-C with a 3′-C overhang was prepared by annealing (5′- CTA CAC GAC GCT CTT CCG ATC TC-3′) and (5′-AGA TCG GAA GAG CAC ACG TCT GAA-3′; 5′ phosphorylated). Adapter-C was added to increase the ligation efficiency.


title: hTSC, ST, GCM1, clone CT27, ChIP


title: hTSC, undifferentiated, H3K4me3, clone CT27, HiChIP, replicate2


title: hTSC, undifferentiated, H3K4me3, clone CT27, HiChIP, replicate1


title: hTSC, undifferentiated, H3K4me3, clone CT27, HiChIP, replicate3


title: hTSC, unmodified, ST, day4, hypoxia, clone B31


title: hTSC, EVT, DLX3, clone CT27, ChIP


title: hTSC, ST, DLX3, clone B31, ChIP


title: hTSC, EVT, GCM1, clone B31, ChIP


title: hTSC, ST, GCM1, clone B31, ChIP


title: hTSC, EVT, DLX3, clone B31, ChIP


title: hTSC, undifferentiated, clone B31, Input


title: Tumor BOB13352_4

first: Kornelia

last: Polyak

state: MA

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description: Bulk RNA from FFPE of the breast cancer diagnosed patients

data_processing:
FFPE Tumor Bulk RNA fastq files have been processed using RIMA pipeline. In RIMA the raw reads are aligned to a reference genome (hg38) from GDC using STAR (Spliced Transcripts Alignment to a Reference) tool. This tool converts the fastq to BAM files.
The BAM files are used an input for the Salmon tool to calculate the transcript per million counts for genes within in each samples and saved. The quant.sf files from salmon are merged into a final rawcounts.csv file with 16 samples
Assembly: Hg38
Supplementary files format and content: transcript per million csv files

source_name: mammary gland

extract_protocol: Total RNA was extracted from 40 μm scroll of FFPE specimens by MagMAX™ FFPE DNA/RNA Ultra Kit (Thermo Fisher Scientific) based on the manufacturer’s protocol

value: breast

tag: experiment

value: bulk RNA sequencing

tag: tumor status

value: Tumor present


title: Tumor BOB13250_4


title: hTSC, ST, day4, H3K4me3, clone CT27, HiChIP, replicate3


title: Tumor BOB12691_2


title: hTSC, EVT, day5, H3K4me3, clone CT27, HiChIP, replicate5


title: Tumor BOB12560_2


title: hTSC, undifferentiated, H3K4me3, clone CT27, HiChIP, replicate4


title: Tumor BOB12339_2


title: Tumor BOB12540_4


title: Tumor BOB11940_4


title: Tumor BOB12090_4


title: Tumor BOB12371_4


title: Tumor BOB11738_2


title: Tumor BOB11117_2


title: Tumor BOB11390_2


title: Tumor BOB11228_2


title: Tumor BOB10991_5


title: Tumor BOB10852_2


title: Tumor BOB11031_5


title: BOB9211_3

description: Bulk RNA from peripheral blood of the breast cancer diagnosed patients

data_processing:
Blood Bulk RNA fastq files have been processed using RIMA pipeline. In RIMA the raw reads are aligned to a reference genome (hg38) from GDC using STAR (Spliced Transcripts Alignment to a Reference) tool. This tool converts the fastq to BAM files.
The BAM files are used an input for the Salmon tool to calculate the transcript per million counts for genes within in each samples and saved. The quant.sf files from salmon are merged into a final rawcounts.txt file with 93 samples and xx no of genes
Assembly: Hg38
Supplementary files format and content: transcript per million csv files

source_name: Peripheral Blood

extract_protocol:
N/A
Bulk RNA: . Library preparation was done using KAPA mRNA HyperPrep Kit. The concentrations and fragment size of library were measured by Agilent TapeStation 2200 according to the manufacturer’s protocols.


title: Tumor BOB10582_3


title: BOB9205_2


title: BOB9475_2


title: BOB9084_2


title: BOB9135_3


title: BOB8916_3


title: BOB29024WB_1


title: BOB43089BC_1


title: BOB8905_2


title: Tumor BOB12075_4


title: BOB8927_2


title: BOB2888_1_2


title: BOB26524WB_1


title: BOB25995WB_1


title: BOB25601WB_1


title: BOB27710WB_1


title: BOB25183WB_1


title: BOB24000WB_1


title: BOB25569WB_1


title: BOB27302WB_1


title: BOB23865WB_1


title: BOB23838WB_1


title: BOB9262_2


title: BOB23984WB_1


title: BOB23664WB_2


title: BOB22745WB_1


title: BOB22606WB_1


title: BOB22600WB_1


title: BOB22543WB_2


title: BOB22190WB_1


title: BOB22048WB_1


title: BOB21695WB_1


title: BOB22461WB_1


title: BOB21581WB_1


title: BOB21401WB_1


title: BOB26804WB_1


title: BOB21321WB_2


title: BOB21287WB_1


title: BOB24060WB_1


title: BOB20722WB_2


title: BOB20812WB_1


title: BOB20101_4


title: BOB18762_4


title: BOB23854WB_1


title: BOB18535_2


title: BOB17932_2


title: BOB200148_2


title: BOB17730_4


title: BOB17704_2


title: BOB17103_4


title: BOB17502_4


title: BOB17208_2


title: BOB17481_4


title: BOB16460_2


title: BOB16346_2


title: BOB21170WB_1


title: BOB16450_2


title: BOB17012_4


title: BOB16300_2


title: BOB15650_2


title: BOB176892_2


title: BOB15800_2


title: BOB16273_2


title: BOB20533WB_2


title: BOB15272_4


title: BOB16201_4


title: BOB14897_4


title: BOB16124_4


title: BOB14400_2


title: BOB17448_2


title: BOB14224_4


title: BOB14552_4


title: BOB14638_2


title: BOB13703_5


title: BOB13497_3


title: BOB13692_3


title: BOB12540_4


title: BOB12371_4


title: BOB12560_2


title: BOB13352_4


title: BOB12339_2


title: BOB13250_4


title: BOB11738_2


title: BOB12090_4


title: BOB11940_4


title: BOB11117_2


title: BOB11228_2


title: BOB10582_3


title: BOB10991_5


title: BOB11390_2


title: BOB10852_2


title: MM.2S cells, KD2_input

city: Xi'an

first: Yachun

last: Jia

state: None Selected

address: No. 157#, The West 5th Road

institute: xian jiaotong university

description: processed data 2 m6A-seq.xls

data_processing:
fastp software (https://github.com/OpenGene/fastp) was used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. And sequence quality of IP and Input samples were verified using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and RseQC (http://rseqc.sourceforge.net/).
Then we used HISAT2 (http://daehwankimlab.github.io/hisat2) to map reads to the reference genomeHomo sapiens(Ensembl Version: v101,GRCh38).
Peak calling and diff peak analysis were performed by R package exomePeak2 (https://bioconductor.org/packages/release/bioc/html/exomePeak2.html), and peaks were annotated by intersection with gene architecture using R package ANNOVAR (http://www.openbioinformatics.org/annovar/). MEME (http://meme-suite.org) and HOMER (http://homer.ucsd.edu/homer/motif) were used for de novo and known motif finding followed by localization of the motif with respect to peak summit.
And StringTie (https://ccb.jhu.edu/software/stringtie) was used to perform expression level for all transcripts and genes from input libraries by calculating FPKM (total exon fragments /mapped reads (millions) × exon length (kB)).
The differentially expressed transcripts and genes were selected with log2 (fold change) ≥ 1 or log2 (fold change) ≤ -1 and p value < 0.05 by R package edgeR (https://bioconductor.org/packages/edgeR).
Assembly: GRCh38（hg38）
Supplementary files format and content: Excel files include peak  information for each group

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100（Agilent, CA, USA）with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel. Poly (A) RNA is purified from 50μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification.
Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 86℃ 7min. The cleaved RNA fragments were incubated for 2h at 4℃ with m6A-specific antibody (No. 202003, Synaptic Systems, Germany) in IP buffer (50 mM Tris-HCl, 750 mM NaCl and 0.5% Igepal CA-630). The IP RNA was reverse-transcribed to cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which was next used to synthesise U-labeled second-stranded DNAs withE. coliDNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base was added to the blunt ends of each strand, preparing for ligation to the indexed adapters. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. At last, we performed paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 platform(LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: human multiple myeloma cells

value: PRMT1 knockdown

tag: rip antibody


title: MM.3S cells, KD2_IP

description: processed data 2 m6A-seq.xls

value: m6A-specific antibody (No. 202003, Synaptic Systems, Germany)


title: MM.1S cells, KD1_IP

description: processed data 2 m6A-seq.xls


title: MM.1S cells, Control2_IP

description: processed data 1 m6A-seq.xls

value: control


title: BOB12691_2


title: MM.1S cells, KD1_input

description: processed data 2 m6A-seq.xls


title: MM.1S cells, Control2_input

description: processed data 1 m6A-seq.xls


title: MM.1S cells, Control1_IP

description: processed data 1 m6A-seq.xls


title: MM.1S cells, Control1_input

description: processed data 1 m6A-seq.xls


title: MM.1S cells, KD rep3

description: KD 3

data_processing:
(1)Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence;
(2)paired-end clean reads were aligned to the reference genome usinghisat2 (v2.0.5)；
(3)featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample.

extract_protocol:
RNA was harvested using Trizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols


title: MM.1S cells, KD rep2

description: KD 2


title: MM.1S cells, KD rep1

description: KD 1


title: BOB12075_4


title: MM.1S cells, Control rep3

description: Control 3


title: MM.1S cells, Control rep1

description: Control 1


title: MM.1S cells, Control rep2

description: Control 2


title: BOB11031_5


title: HeLa cells,  T343A (dIDR)-2

city: Wuhan

first: Wei

last: Wang

state: Hubei

address: 13 Hangkong Road

institute: Huazhong University of Science and Technology Tongji Medical College

data_processing:
The raw reads were quality-controlled and trimmed using Fastp (v0.20.1) with default parameters.
The resulting Clean RNA-seq reads were aligned to the human reference genome (GRCh38) using Hisat2 (v2.2.1), sorted and indexed using Samtools (v1.14).
The number of reads (raw_counts) per gene was determined using featureCounts (v2.0.1)
Assembly: Homo sapiens
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

source_name: HeLa

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

extract_protocol:
Total RNA was isolated using the Trizol Reagent.
Three micrograms of RNA were used as input material for the RNA sample preparations. Sequencing libraries were generated according to the following steps. Firstly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in fragmentation buffer. First strand strand was synthesized by random hexamers, and the second cDNA strand was synthesized by adding buffer, dNTPs, RNase H and DNA polymerase I. Double stranded cDNA was repaired and A was added to the 3 'end. Hieff NGS® DNA Selection Beads were used for purification and fragment Selection. After purification and fragment selection, the products were amplified and enriched by PCR. Qubit was used for quantitative . The target region library of the duplex was denatured, cycled, and digested to yield a single-stranded circular DNA. Single-stranded circular DNA is amplified by a rolling circle amplification (RCA), known as DNA nano balls (DNB). After library construction, Qubit was used for quantitative.

value: HeLa

value: T343A (dIDR)

value: Untreated


title: HeLa cells (dIDR control),  GFP-3

value: Control


title: HeLa cells,  T343A (dIDR)-3


title: HeLa cells,  T343A (dIDR)-1


title: HeLa cells (dIDR control),  GFP-1


title: DGC-2

source_name: DGC

growth_protocol: The GSC456  were cultured in Neurobasal™-A supplemented with B27 , 20 ng/ml EGF, and 20 ng/ml bFGF . The cells were cultured in 10% FBS containing DMEM media for the differentiation process.  All cells were incubated at 37 °C in a humidified 5% CO2 incubator.

value: DGC


title: DGC-3


title: DGC-1


title: GSC-3

source_name: GSC

value: GSC


title: HeLa cells,HS-WT-1

value: CLK2 (WT)

value: Heat shock


title: GSC-2


title: HeLa cells, HS-WT-2


title: HeLa cells, HS-WT-3


title: HeLa cells, HS-GFP-2


title: HeLa cells (HS control),   WT-1


title: HeLa cells, HS-GFP-3


title: HeLa cells,HS-GFP-1


title: HeLa cells (HS control),  GFP-3


title: HeLa cells (HS control),  WT-3


title: GSC-1


title: HeLa cells (HS control),  WT-2


title: HeLa cells (HS control),  GFP-2


title: HeLa cells (HS control),  GFP-1


title: HeLa cells, T343A-3

data_processing:
The raw reads were quality-controlled and trimmed using Fastp (v0.20.1) with default parameters.
The resulting Clean RNA-seq reads were aligned to the human reference genome (GRCh38) using Hisat2 (v2.2.1), sorted and indexed using Samtools (v1.14).
The number of reads (raw_counts) per gene was determined using featureCounts (v2.0.1)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

extract_protocol:
Total RNA was isolated using the Trizol Reagent.
Three micrograms of RNA were used as input material for the RNA sample preparations. Sequencing libraries were generated according to the following steps. Firstly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in fragmentation buffer. First strand strand was synthesized by random hexamers, and the second cDNA strand was synthesized by adding buffer, dNTPs, RNase H and DNA polymerase I. Double stranded cDNA was repaired and A was added to the 3 'end. Hieff NGS® DNA Selection Beads were used for purification and fragment Selection. After purification and fragment selection, the products were amplified and enriched by PCR. Qubit was used for quantitative .  The target region library of the duplex was denatured, cycled, and digested to yield a single-stranded circular DNA. Single-stranded circular DNA is amplified by a rolling circle amplification (RCA), known as DNA nano balls (DNB). After library construction, Qubit was used for quantitative.


title: HeLa cells, T343A-2


title: HeLa cells (dIDR control),  GFP-2


title: HeLa cells, WT-1


title: HeLa cells, WT-2


title: HeLa cells, GFP-3


title: HeLa cells, GFP-2


title: HeLa cells, GFP-1


title: Podocytes HG control rep2

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

data_processing:
Trimming with preprocessReads from the systemPipeR package in R (Parameter: cutoff=20, low_quality_rate=0.4, batchsize=100000)
Aligment:tophat v2.1.1 bowtie v2.2.9 Parameter: -g 1 --segment-length 25 -i 30 -I 3000
Read Counts: summarizeOverlaps from the GenomicsAlignments package in R Parameter: mode=Union, ignore.strand=TRUE, inter.feature=FALSE, singleEnd=TRUE
RPKM Normalization with the returnRPKM function from systemPipeR package in R
Assembly: hg19
Supplementary files format and content: RPKM values and raw counts generated with tophat

source_name: Kidney

growth_protocol: 50 000 podocytes/well were seeded on top of polycarbonate membrane inserts of 6-well transwell chambers with 0.4 µm pores and left for four days under proliferation conditions (33 °C), followed by 14 days of differentiation at 37 °C. The podocytes were then combined with differentiated glomerular endothelial cells seeded on the surface of 6-well chambers and grown in RPMI-1640 medium with 10% FBS, 1 g/l glucose, 2 g/l sodium hydrogen carbonate, insulin-transferrin-selenium and 200 U/ml penicillin/streptomycin.

extract_protocol:
Total RNA was prepared using an RNeasy mini kit (Qiagen) according to the manufacturer’s instructions and eluted in 30 µl nuclease-free water.
RNA libraries were prepared for sequencing using standard BGISeq-500 protocols

treatment_protocol: Treatment with high glucose (25 mM) for 48 hr or 96 hr. The control group contained 5.5 mM glucose and 19.5 mM mannitol as osmotic control.

tag: tissue

value: Kidney

value: Podocytes


title: Podocytes + 96 hr HG rep4

value: 96 hr HG


title: Podocytes + 96 hr HG rep3


title: Podocytes HG control rep3


title: Podocytes HG control rep1


title: A549, AFos Knock-In, plus Dox, RNA-seq, rep2

city: University Park

first: Lu

last: Bai

address: 406 South Frear Building

institute: Penn State University

data_processing:
Basecalls were performed using DRAGEN BCL Convert (v3.8.4).
Paired-end reads were filtered using Cutadapt (Version 4.0) according to default settings.
Filtered reads were aligned to the human reference genome (hg38) using gapped-read mapper RNA STAR (Version 2.7.10b).
Read counts were generated for genomic features from the BAM alignment files using featureCounts (Version 2.0.3).
Differential expression analysis was performed using DESeq2 (Version 2.11.40.7).
Assembly: hg38
Supplementary files format and content: tabular file for featureCounts

growth_protocol: Ham's F-12K (Kaighn's), 10% fetal bovine serum, 1% penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were lysed by Trizol, extracted by 0.2 volume of chloroform, followed by adding equal volume of 100% ethanol. RNeasy kit was then used to purify the RNA. 3 µg of purified RNA was treated with 2 U of RNase-free DNase I, and purified again with RNeasy kit.
Sequencing library was constructed by the Illumina Stranded mRNA Prep kit. 30 million paired-end 50bp reads were obtained for each RNA-seq sample using a NextSeq 2000 instrument.

treatment_protocol: For doxycyline treated cells, doxycyline was added to cell medium a final concentration of 1 μg/mL.

tag: cell line

value: Human lung carcinoma

value: A-Fos integrated into genome with piggyBac

value: Doxycycline (1 μg/mL)


title: A549, AFos Knock-In, plus Dox, RNA-seq, rep1

tag: cell type


title: Podocytes + 96 hr HG rep2


title: HeLa cells, T343A-1


title: Podocytes + 48 hr HG rep4

value: 48 hr HG


title: A549, A-Fos, Dox, FOSL2, ChIP, Biol Rep 1

data_processing:
Basecalls were performed using DRAGEN BCL Convert (v3.8.4).
Paired-end reads were filtered using fastp (Version 0.23.2) according to default settings.
Filtered reads were aligned to the human reference genome (hg38) using BWA-MEM2 (Version 2.2.1)
Resulting BAM files were filtered for MAPQ scores > 20 using SAMtools (Version 1.8)
Read coverage (bigwig file) was obtained separately for input and ChIP samples using deepTools “bamCoverage”, with a bin size of 10 bp (Version 3.5.1). In this step, blacklisted regions were removed (hg38 Version 2, https://doi.org/10.1038/s41598-019-45839-z)
ChIP peaks were called using MACS2 callpeak with the default settings (Version 2.1.1.20160309).
Assembly: hg38
Supplementary files format and content: bigwig for ChIP and input samples
Supplementary files format and content: bed only for ChIP samples

extract_protocol:
Cells were fixed with formaldehyde (1% final concentration) for 10 minutes at room temperature. Crosslinking was quenched with glycine (0.125M final concentration) for 5 minutes ar room temperature. After cell and nuclei lysis, chromatin was fragmented in Diagenode Pico with a circulating water bath at 4°C using the Shear and Go Easy Mode setting for 3 cycles (30 seconds on followed by 30 seconds off).
Sequencing library was constructed by NEBNext ultra II DNA library prep kit (NEB E7103L). 50 million paired-end 50bp reads were obtained for each ChIP and input sample using a NextSeq 2000 instrument.

treatment_protocol: For doxycyline treated cells, doxycyline was added to cell medium a final concentration of 1 μg/mL. Cells were fixed with formaldehyde 48 hours after doxycycline induction.

value: A-Fos integrated with piggyBac

value: Fra2 (Cell Signaling Technology, 19967S)


title: Podocytes + 48 hr HG rep3


title: A549, A-Fos, Input, Rep1


title: Podocytes + 48 hr HG rep2


title: HeLa cells, WT-3

value: HeLa


title: A549, A-Fos, Dox, FOXA1, ChIP, Biol Rep 2

value: FOXA1 (GeneTex, GTX100308)


title: A549, A-Fos, Input, Rep2


title: A549, A-Fos, Dox, FOSL2, ChIP, Biol Rep 2


title: Podocytes + 96 hr HG rep1


title: A549, AFos Knock-In, minus Dox, RNA-seq, rep1

value: No treatment


title: Podocytes + 48 hr HG rep1


title: A549, A-Fos, No Dox, FOXA1, ChIP, Biol Rep 2


title: A549, A-Fos, No Dox, FOSL2, ChIP, Biol Rep 2


title: A549, A-Fos, No Dox, FOSL2, ChIP, Biol Rep 1


title: Podocytes HG control rep4

value: Control


title: A549, A-Fos, Dox, FOXA1, ChIP, Biol Rep 1


title: A549, A-Fos, No Dox, FOXA1, ChIP, Biol Rep 1


title: A549, H3K27me3, ChIP, Biol Rep2

value: WT

value: H3K27me3 (Abcam, ab6002)


title: GECs HG control rep4

growth_protocol: 60 000 glomerular endothelial cells/well were seeded separately on the bottom surface of 6-well chambers for four days under proliferation conditions (33 °C), before switching to differentiation conditions (37 °C) for 4 days. The cells were then combined with differentiated podocytes in polycarbonate membrane inserts with 0.4 µm pores and grown in RPMI-1640 medium with 10% FBS, 1 g/l glucose, 2 g/l sodium hydrogen carbonate, insulin-transferrin-selenium and 200 U/ml penicillin/streptomycin.

value: Glomerular endothelial cells


title: A549, AFos Knock-In, minus Dox, RNA-seq, rep2


title: GECs HG control rep3


title: GECs HG control rep2


title: Donor 3 Gene expression scRNAseq

city: Hamburg

first: Marcus

last: Altfeld

address: Süderfeldstraße

institute: Leibniz Institute of Virology

description:
10x genomics
Donor3_filtered_feature_bc_matrix.h5
Donor3_GEX

library_source: transcriptomic single cell

data_processing:
Barcodes and gene expression libraries were aligned using cellranger 7.0.0
Assembly: GRCh38
Supplementary files format and content: Hierarchical Data Format (HDF).

source_name: Blood

extract_protocol:
PBMC isolation was performed by density centrifugation (500 g, 30 min, 21 °C) using Lymphocyte Separation Media (catalog no. LSM-A, Capricorn, Ebsdorfergrund, Germany). After collection of PBMCs at the interphase of the layers and washes using Hank´s Balanced Salt (catalog no. H6648, Sigma Aldrich, St. Louis, MO, USA), remaining erythrocytes were lysed with ASK Lysing Buffer (catalog no. BP10-548E, Lonza, Basel, Switzerland) for 3 min. Cell counts were determined using the Trypan Blue (catalog no. T8154, Sigma Aldrich) exclusion method on a TC20 Automated Cell Counter (Bio-Rad, Hercules, CA, USA) and aliquots of different proportions were prepared. PBMCs were frozen in heat inactivated fetal bovine serum (FBS, catalog. no S0615, Sigma Aldrich) + 10% dimethyl sulfoxide (catalog no. D85897, Sigma Aldrich) at -80 °C and transferred into liquid nitrogen storage the next day until further processing. For fluorescence-activated cell sorting of pDCs, PBMCs were stained with surface antibodies and a dead stain (NEAR-IR) for 20 minutes at room temperature in the dark.
Cells were loaded onto the 10X Chromium Controller (10X Genomics, Pleasanton, CA, USA). Single-cell libraries were generated using the Chromium Next GEM Single Cell 5' Kit v2 (10X Genomics) according to the manufacturer’s instructions. Libraries were sequenced on an Illumina NovaSeq 6000 system (S4 flow cell) with 150 base pairs and paired-end configurations.

treatment_protocol: Donor received testosterone injections as gender-affirming hormone therapy (GAHT) and blood was collected before and after 6 months of hormone therapy. PBMCs were isolated and stimulated with CL097 for 2hrs, following pDC isolation using fluorescence-activated cell sorting.

value: Blood

value: Plasmacytoid dendritic cells

value: Testosterone, CL097


title: Donor 3 Hashtag scRNAseq

description:
10x genomics
Donor3_filtered_feature_bc_matrix.h5
Donor3_ADT


title: A549, H3K9me3, ChIP, Biol Rep 2

value: H3K9me3 (Abcam, ab8898)


title: A549, H3K27me3, ChIP, Biol Rep1

value: Human lung carcinoma


title: A549, H3K9me3, ChIP, Biol Rep 1


title: GECs HG control rep1

value: Kidney


title: A549, FOXA1, ChIP-ISO input, biol rep 2

data_processing:
Basecalls were performed using DRAGEN BCL Convert (v3.8.4).
Paired-end reads were filtered using fastp (Version 0.23.2) according to default settings.
First three nucleotides were trimmed from each read using cutadapt to remove the 0-3 random nucleotides introduced by the amplicon primers.
Paired-end reads were aligned to a FASTA file containing all ChIP-ISO library sequences in their forward and reverse orientation using BWA-MEM2
BAM alignments containing at least 2 mismatched nucleotides were filtered out using BAMtools
Number of sequences (counts) aligning to each library sequence were determined using the "count occurences of each record" tool in Galaxy
Assembly: hg38
Supplementary files format and content: Raw counts files including sequence ID and number of aligned reads or "counts" in tabular format.
Library strategy: ChIP-ISO

extract_protocol:
Cells were fixed with formaldehyde (1% final concentration) for 10 minutes at room temperature. Crosslinking was quenched with glycine (0.125M final concentration) for 5 minutes at room temperature. After cell and nuclei lysis, chromatin was fragmented in Diagenode Pico with a circulating water bath at 4°C using the Shear and Go Easy Mode setting for 3 cycles (30 seconds on followed by 30 seconds off).
To amplify the integrated ChIP-ISO library sequences while excluding other genomic DNA, including native CCND1e, we performed two rounds of PCR amplification with a BbsI digestion step in between. The primer pairs for the first round of PCR contain regions annealing to the CCND1e (outside the 193bp library sequence) at the 3’-ends, partial Illumina TruSeq adaptor sequences at the 5’-end and 0-3 random nucleotide spacers in between to increase sequence complexity. Primers with different numbers of spacers are mixed in equimolar ratio for the first round of PCR. Preliminary PCR tests were performed to decide the optimal cycle number that keeps the PCR reactions in exponential phase. We used 23-25 cycles for our first round of PCR. For the first round of PCR, 30 μl of ChIP DNA was amplified in a 100 μl PCR reaction using NEBNext Ultra II Q5 master mix. The PCR products were purified with AMPure XP beads with a beads to DNA ratio of 0.9. 15 μL of the purified PCR product was digested with 20 U of BbsI in a 30 μL reaction at 37°C for two hours. The digestion products were purified with AMPure XP beads with a beads to DNA ratio of 0.9, followed by the second round of PCR. The primer pairs for the second round of PCR contain the rest of the Illumina TruSeq adaptor sequences and sample indexes. For the second round of PCR, 2 μl of purified digestion product was amplified in a 50 μl PCR reaction for 8 cycles using NEBNext Ultra II Q5 master mix. The PCR products were purified with AMPure XP beads with a beads to DNA ratio of 0.8. Quality control was conducted with TapeStation (Agilent). 30 million paired-end 150bp reads were obtained for each ChIP-ISO and input sample using a NextSeq 2000 (Illumina) instrument.

value: ISO library integrated at AAVS1


title: A549, FOXA1, ChIP-ISO ChIP, biol rep 2

value: FOXA1 (GeneTex GTX100308)


title: Donor 2 Gene expression scRNAseq

description:
10x genomics
Donor2_filtered_feature_bc_matrix.h5
Donor2_GEX


title: A549, FOXA1, ChIP-ISO input, biol rep 1


title: Donor 2 Hashtag scRNAseq

description:
10x genomics
Donor2_filtered_feature_bc_matrix.h5
Donor2_ADT


title: GECs + 96 hr HG rep4

value: 96 hr HG


title: GECs + 96 hr HG rep3


title: A549, H3K27me3, ChIP-ISO ChIP, biol rep 1

value: H3K27me3 (abcam ab6002)


title: A549, H3K27me3, ChIP-ISO input, biol rep 1


title: Donor 1 Hashtag scRNAseq

description:
10x genomics
Donor1_filtered_feature_bc_matrix.h5
Donor1_ADT


title: GECs + 96 hr HG rep2


title: A549, FOXA1, ChIP-ISO ChIP, biol rep 1


title: Donor 1 Gene expression scRNAseq

description:
10x genomics
Donor1_filtered_feature_bc_matrix.h5
Donor1_GEX


title: A549, H3K9me3, ChIP-ISO ChIP, biol rep 1

value: H3K9me3 (abcam ab8898)


title: A549, H3K9me3, ChIP-ISO input, biol rep 1


title: Hypoxia siRNA-KMT2E 1

city: Pittsburgh

first: Satoshi

last: Okawa

address: 200 Lothrop Street

institute: University of Pittsburgh

data_processing:
The raw fastq reads were mapped against the human genome build hg19 using STAR aligner.
The read counts for each gene were calculated using featureCounts.
Gene expression was normalized by DESeq2 with variance-stabilizing transformation (VST).
The low expression genes with total counts across all samples less than 10 were excluded.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include raw count values for each sample

source_name: Pulmonary arterial endothelial cells

growth_protocol: Primary HPAECs were grown in EBM-2 basal medium supplemented with EGM-2 MV BulletKit (Lonza).

extract_protocol:
Cells were harvested for total RNA extraction using Rneasy mini kit (Qiagen) with DNase digestion (Qiagen).
Illumina stranded total RNA library was prepared for the RNA sequencing.  mRNA and lncRNA profiles were generated by deep sequencing, using NextSeq 2000 P3 flow cell (2 x 101bp, 40M reads/sample).

treatment_protocol: Cultured HPAECs were transfected with siRNAs targeting either negative control, KMT2E-AS1 or KMT2E, then exposed to hypoxic stress (0.2% oxygen) for 24 hours.

value: Pulmonary arterial endothelial cells

value: siRNA KMT2E+0.2% oxygen

value: 8 hour siRNA incubation then hypoxia 0.2% oxygen the following day for 24 hours


title: GECs + 96 hr HG rep1


title: single cell multiome for MSCs ATAC

city: Indianapolis

first: Yunlong

last: Liu

state: IN

address: 410 West 10th Street

department: Medical and Molecular Genetics

institute: Indiana University School of Medicine

description: 10x Genomics multiome ATAC

library_source: genomic single cell

data_processing:
cellranger-atac v1.0.0 (http://support.10xgenomics.com/) was utilized to process the raw sequence data generated.
souporcell (v2.0) was used to demultiplex the cells in the pool from different donors.
Signac and Seurat were used to analyze the filtered barcode-peak matrices and fragment file generated from running cellragner-arc.
The gene expression and chromatin accessiblity data were process separately, WNN (weighted nearest neighbor) was used for cell clustering.
Assembly: GRCh38 (from 10X: refdata-cellranger-arc-GRCh38-2020-A-2.0.0)
Supplementary files format and content: 10x Genomics cellranger-arc output files (the files needed for further analysis): filtered_feature_bc_matrix.h5, atac_fragments.tsv.gz, atac_fragments.tsv.gz.tbi, per_barcode_metrics.csv

source_name: cell line

extract_protocol:
trypsin EDTA treat cell to detach from flask
Paired ATAC and gene expression libraries from the same single nuclei were generated from the isolated nuclei following the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide (10X Genomics, Inc).
single-cell multiome (GEX + ATAC)

value: Mesenchymal stem cells


title: GECs + 48 hr HG rep4

value: 48 hr HG


title: Hypoxia siRNA-KMT2E 2


title: Hypoxia siRNA-KMT2E-AS1 3

value: siRNA KMT2E-AS1+0.2% oxygen


title: Hypoxia siRNA-KMT2E-AS1 2


title: GECs + 48 hr HG rep3

value: Glomerular endothelial cells


title: Hypoxia siRNA-Negative control 2

value: siRNA negative control+0.2% oxygen


title: GECs + 48 hr HG rep2


title: Hypoxia siRNA-KMT2E 3


title: single cell multiome for MSCs cDNA

description: 10x Genomics multiome cDNA


title: Hypoxia siRNA-KMT2E-AS1 1


title: Hypoxia siRNA-Negative control 3


title: Con_120min_3; TGFb 120min; si-Con

city: Cheongju

first: Jung-Won

last: Lee

address: 1, Chungdae-ro

department: Department of Biochemistry, School of Medicine

country: South Korea

institute: Institute for Tumor Research

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 whole genome using Tophat
FPKM calculation using Cufflink
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Kidney; Embryo

growth_protocol: HEK293 cells (ATCC, Manassas, VA, USA) were maintained in Dulbecco’s modiﬁed Eagle’s medium (Gibco BRL, Thermo Fisher Scientific, Waltham, MA, USA) supplemented with 10% fetal bovine serum (Gibco BRL) and 1% penicillin/streptomycin (Invitrogen, Carlsbad, CA, USA). Cells were incubated at 37°C with 5% CO2

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using the NEBNext Ultra II Directional RNA-Seq Kit standard protocols.

treatment_protocol: Cells were cultured at low cell density. Before TGFb1 treatment, cells were cultured under serum-free conditions for 1 h and then, treated with 1 ng/ml TGFb1 (Cat# 100-21C, PeproTech, Rocky Hill, USA).

value: Kidney; Embryo

value: HEK 293 cells

value: immortalized human embryonic kidney cells

value: Wild type

value: TGFb 1ng/ml


title: Hypoxia siRNA-Negative control 1


title: human CF PMNs treated with LPS [GEX]

city: New Orleans

first: Guoshun

state: LA

address: CSRB 607, 533 Bolivar Street

institute: Louisiana State University Health Sciences Center

description:
CF_LPSNeu
CFTR mutation
10x Genomics
mRNA

data_processing:
10x Cellranger V.6.0.0 and V.6.1.2 were used to generate Fastq files, perform alignment, filtering, barcode counting, UMI counting and aggregation.
Seurat v4.2.1 for scRNA QC and further analysis.
Assembly: GRCh38
Supplementary files format and content: 10x Genomics output files: filtered_feature_bc_matrix.h5

extract_protocol:
mRNA was extracted from human PMN single cell suspension using the 10X Genomics Chromium™ Single Cell G Chip Kit.
Library was prepared using Chromium Single Cell 3ʹ v3.1 protocol (10x Genomics). Cellular mRNA and antibody-derived oligos were reverse-transcribed and indexed with a shared cellular barcode. mRNA derived cDNA and antibody-derived tagged DNA were constructed to libraries according to the Chromium Single Cell 3’ v3.1 protocol (10x Genomics). mRNA derived cDNA library and antibody-derived tagged library were pooled and sequenced at 4:1 ratio.

value: Blood

value: Primary neutrophils

value: CFTR mutation

tag: disease

value: Cystic fibrosis

value: LPS

tag: library type

value: mRNA

tag: antibodies/tags


title: human CF PMNs treated with LPS [HTO]

description:
CF_LPSNeu
CFTR mutation
10x Genomics

library_source: other

molecule: protein

value: HTO

value: Anti CD298 + Anti β2 microglobulin:Donor 1 -- TotalSeq™-A0251; Donor 2 -- TotalSeq™-A0252; Donor 3 -- TotalSeq™-A0253


title: human healthy PMNs [GEX]

description:
NL_Neu
Healthy Control
10x Genomics
mRNA

value: Control

value: Healthy

value: No treatment


title: human CF PMNs [GEX]

description:
CF_Neu
CFTR mutation
10x Genomics
mRNA


title: Normoxia siRNA-Negative control 2

value: Pulmonary arterial endothelial cells

value: siRNA negative control

value: 8 hour siRNA incubation


title: Con_120min_1; TGFb 120min; si-Con

value: Kidney; Embryo

value: HEK 293 cells

value: immortalized human embryonic kidney cells


title: Normoxia siRNA-Negative control 3


title: human healthy PMNs treated with LPS [GEX]

description:
NL_LPSNeu
Healthy Control
10x Genomics
mRNA

value: Blood


title: Con_0min_2; TGFb 0min; si-Con

value: Wild type

value: TGFb 1ng/ml


title: Normoxia siRNA-Negative control 1


title: Podocytes MGO control rep4

data_processing:
trimmed with trim_galore version 0.6.4. Parameters: --length 26 --phred33
Get raw counts with kallisto quant version 0.4.6.
TPM abundance estimates, generated with kallisto quant 0.4.6
Assembly: hg19
Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.

growth_protocol: Podocytes were seeded at a density of 50 000/well on top of polycarbonate membrane inserts of 6-well transwell chambers with 0.4 µm pores and left for 4 days under proliferation conditions (33°C), followed by 14 days at differentiation conditions (37 °C). While podocytes were differentiating, GECs with a density of 60 000/well were seeded separately on the surface of 6-well chambers for four days under proliferation conditions, before switching to differentiation conditions for 4 days. The inserts with the podocytes were then combined with the wells containing the glomerular endothelial cells and  and grown in RPMI-1640 medium with 10% FBS, 1 g/l glucose, 2 g/l sodium hydrogen carbonate, insulin-transferrin-selenium and 200 U/ml penicillin/streptomycin.

treatment_protocol: Treatment with 200 µM methylglyoxal (MGO). The control group was treated with water.

value: Kidney

value: Podocytes

value: Control (water)


title: Podocytes + 96 hr MGO rep4

value: 200 µM MGO for 96 hr


title: 60nM FOXA1, Shifted Band, Rep 2

data_processing:
Basecalls were performed using DRAGEN BCL Convert (v3.8.4).
Paired-end reads were filtered using fastp (Version 0.23.2) according to default settings.
First three nucleotides were trimmed from each read using cutadapt to remove the 0-3 random nucleotides introduced by the amplicon primers.
Paired-end reads were aligned to a FASTA file containing all EMSA-seq library sequences in their forward and reverse orientation using BWA-MEM2
BAM alignments containing at least 2 mismatched nucleotides were filtered out using BAMtools
Number of sequences (counts) aligning to each library sequence were determined using the "count occurences of each record" tool in Galaxy
Assembly: hg38
Supplementary files format and content: Raw counts files including sequence ID (column 1), nucleotide sequence (column 2), and number of aligned reads or "counts" (column 3) in tabular format.
Library strategy: EMSA-seq

molecule: other

organism: synthetic construct

source_name: FOXA1-bound (shifted) synthetic oligonucleotide library at 60 nM FOXA1

extract_protocol:
Synthetic oligonucleotide library was designed to include 3,203 different sequences, each 229bp in length with 193bp variable regions and 18bp primer-binding regions on the two sides. The synthetic oligo library was ordered from Agilent (Product #G7220A).
To amplify the synthetic oligonucleotide library sequences, we performed two rounds of PCR amplification with a BbsI digestion step in between. The primer pairs for the first round of PCR contain regions annealing to the CCND1e (outside the 193bp library sequence) at the 3’-ends, partial Illumina TruSeq adaptor sequences at the 5’-end and 0-3 random nucleotide spacers in between to increase sequence complexity. Primers with different numbers of spacers are mixed in equimolar ratio for the first round of PCR. Preliminary PCR tests were performed to decide the optimal cycle number that keeps the PCR reactions in exponential phase. We used 23-25 cycles for our first round of PCR. For the first round of PCR, 30 μl of ChIP DNA was amplified in a 100 μl PCR reaction using NEBNext Ultra II Q5 master mix. The PCR products were purified with AMPure XP beads with a beads to DNA ratio of 0.9. 15 μL of the purified PCR product was digested with 20 U of BbsI in a 30 μL reaction at 37°C for two hours. The digestion products were purified with AMPure XP beads with a beads to DNA ratio of 0.9, followed by the second round of PCR. The primer pairs for the second round of PCR contain the rest of the Illumina TruSeq adaptor sequences and sample indexes. For the second round of PCR, 2 μl of purified digestion product was amplified in a 50 μl PCR reaction for 8 cycles using NEBNext Ultra II Q5 master mix. The PCR products were purified with AMPure XP beads with a beads to DNA ratio of 0.8. Quality control was conducted with TapeStation (Agilent). 30 million paired-end 150bp reads were obtained for each sample using a NextSeq 2000 (Illumina) instrument.

value: not applicable

value: 60 nM FOXA1

tag: emsa band

value: Shifted Band


title: Con_15min_1; TGFb 15min; si-Con

tag: treatment


title: Con_15min_2; TGFb 15min; si-Con


title: human healthy PMNs [HTO]

description:
NL_Neu
Healthy Control
10x Genomics

value: Primary neutrophils

value: Control

value: Healthy

value: No treatment

value: HTO

value: Anti CD298 + Anti β2 microglobulin:Donor 1 -- TotalSeq™-A0251; Donor 2 -- TotalSeq™-A0252; Donor 3 -- TotalSeq™-A0253


title: Con_120min_2; TGFb 120min; si-Con

value: Kidney; Embryo

value: HEK 293 cells

value: immortalized human embryonic kidney cells


title: human CF PMNs [HTO]

description:
CF_Neu
CFTR mutation
10x Genomics

value: Blood

value: CFTR mutation

value: Cystic fibrosis


title: Podocytes MGO control rep2

value: Kidney

value: Podocytes

value: Control (water)


title: Podocytes + 96 hr MGO rep3

value: 200 µM MGO for 96 hr


title: Podocytes MGO control rep3


title: Con_0min_3; TGFb 0min; si-Con

value: Wild type

value: TGFb 1ng/ml


title: Podocytes MGO control rep1


title: GECs + 48 hr HG rep1

value: Glomerular endothelial cells

value: 48 hr HG


title: human healthy PMNs treated with LPS [HTO]

description:
NL_LPSNeu
Healthy Control
10x Genomics

value: Primary neutrophils

value: Control

value: Healthy

value: LPS


title: 60nM FOXA1, Free Band, Rep 2

source_name: FOXA1-unbound (free) synthetic oligonucleotide library at 60 nM FOXA1

value: not applicable

value: 60 nM FOXA1

value: Free Band


title: Con_15min_3; TGFb 15min; si-Con

value: Kidney; Embryo

value: HEK 293 cells

value: immortalized human embryonic kidney cells


title: Con_0min_1; TGFb 0min; si-Con


title: 60nM FOXA1, Shifted Band, Rep 1

value: Shifted Band


title: YAP1_120min_3; TGFb 120min; YAP1 Knock-down

value: YAP1 Knock-down


title: 60nM FOXA1, Free Band, Rep 1


title: YAP1_120min_2; TGFb 120min; YAP1 Knock-down


title: Podocytes + 96 hr MGO rep1

value: Kidney

value: Podocytes

value: 200 µM MGO for 96 hr


title: GECs MGO control rep4

value: Glomerular endothelial cells

value: Control (water)


title: 30nM FOXA1, Shifted Band, Rep 1

source_name: FOXA1-bound (shifted) synthetic oligonucleotide library at 30 nM FOXA1

value: 30 nM FOXA1


title: 30nM FOXA1, Shifted Band, Rep 2


title: 30nM FOXA1, Free Band, Rep 1

source_name: FOXA1-unbound (free) synthetic oligonucleotide library at 30 nM FOXA1


title: YAP1_120min_1; TGFb 120min; YAP1 Knock-down

value: TGFb 1ng/ml


title: 20nM FOXA1, Shifted Band, Rep 2

source_name: FOXA1-bound (shifted) synthetic oligonucleotide library at 20 nM FOXA1

value: 20 nM FOXA1


title: GECs MGO control rep3


title: 30nM FOXA1, Free Band, Rep 2


title: GECs MGO control rep2


title: 20nM FOXA1, Shifted Band, Rep 1


title: 10nM FOXA1, Shifted Band, Rep 2

source_name: FOXA1-bound (shifted) synthetic oligonucleotide library at 10 nM FOXA1

value: 10 nM FOXA1


title: YAP1_15min_3; TGFb 15min; YAP1 Knock-down


title: 10nM FOXA1, Free Band, Rep 2

source_name: FOXA1-unbound (free) synthetic oligonucleotide library at 10 nM FOXA1

value: not applicable


title: 20nM FOXA1, Free Band, Rep 2

source_name: FOXA1-unbound (free) synthetic oligonucleotide library at 20 nM FOXA1


title: YAP1_15min_1; TGFb 15min; YAP1 Knock-down


title: 10nM FOXA1, Shifted Band, Rep 1


title: YAP1_0min_3; TGFb 0min; YAP1 Knock-down


title: 3nM FOXA1, Shifted Band, Rep 2

source_name: FOXA1-bound (shifted) synthetic oligonucleotide library at 3 nM FOXA1

value: 3 nM FOXA1


title: GECs + 96 hr MGO rep4


title: GECs MGO control rep1


title: YAP1_15min_2; TGFb 15min; YAP1 Knock-down


title: GECs + 96 hr MGO rep3


title: 3nM FOXA1, Free Band, Rep 2

source_name: FOXA1-unbound (free) synthetic oligonucleotide library at 3 nM FOXA1

value: Free Band


title: Podocytes + 96 hr MGO rep2


title: 20nM FOXA1, Free Band, Rep 1


title: YAP1_0min_2; TGFb 0min; YAP1 Knock-down

value: Kidney; Embryo


title: GECs + 96 hr MGO rep2


title: 1nM FOXA1, Shifted Band, Rep 2

source_name: FOXA1-bound (shifted) synthetic oligonucleotide library at 1 nM FOXA1

value: 1 nM FOXA1


title: 3nM FOXA1, Free Band, Rep 1


title: 3nM FOXA1, Shifted Band, Rep 1


title: GECs + 96 hr MGO rep1


title: RUNX3_120min_3; TGFb 120min; RUNX3 Knock-down

value: HEK 293 cells

value: immortalized human embryonic kidney cells

value: RUNX3 Knock-down


title: 1nM FOXA1, Free Band, Rep 2

source_name: FOXA1-unbound (free) synthetic oligonucleotide library at 1 nM FOXA1


title: 10nM FOXA1, Free Band, Rep 1


title: 1nM FOXA1, Free Band, Rep 1


title: CB cells, efnA5-FC, Rep 6

city: Aachen

first: Geraldine

middle: Marion

last: Zimmer-Bensch

state: NRW

address: Worringer Weg 3

department: Neuroepigenetic

institute: RWTH Aachen

description: 1200 ng gNDa bisulfite converted using the Zymo EZ-96 DNA Methylation kit (Zymo Research, Irine, CA, USA)

hyb_protocol: according to instructions

scan_protocol: Illumina iScan System

data_processing: Differentially methylated regions (DMRs) were detected using the R packages Enmix (Xu et al., 2016), sva (Leek, 2007) and minfi (Aryee et al., 2014). The raw idat files were loaded by Enmix::readidat() together with Illumina’s Infinium mouse-methylation manifest file (v.1.0). For background correction, dye bias correction, inter-array normalization and probe type bias correction we applied Enmix::mpreprocess() on the raw idat data setting the parameters qc and impute to TRUE. It returns a matrix of preprocessed methylation beta values. As a second preprocessing step we used sva::ComBat() to mitigate the batch effect contained in these beta values which was introduced by different experiment runs under inevitably different conditions. The experiment run ID was set as the batch variable. Eventually, DMRs were identified by calling minfi::dmpFinder() on the preprocessed beta values. The parameter pheno was set to the respective cell conditions (for each sample either ctrl-Fc or efnA5-Fc) and the parameter type to =”categorical”. CpGs for which the dmpFinder result indicates a p-value of 0.05 or smaller were considered significant DMRs. If not indicated otherwise, default parameters have been passed to the applied R functions.

source_name: cell culture 24 post treatment

label_protocol: according to instructions

growth_protocol: Cerebellar granule (CB) cells (Fossale et al., 2004) were cultured as previously described (Pensold et al., 2021). Briefly, CB cells were incubated in Dulbecco’s modified Eagle medium (DMEM) with high glucose (#11965084, Gibco), supplemented with 10% fetal bovine serum (FBS) (#S1810, Biowest), 1× GlutaMAX™ (#35050038, Thermo Scientific) and 24 mM KCl at 33℃, 5% CO2 and 95% relative humidity. Upon thawing, the medium was additionally supplemented with 100 U/mL penicillin and 100 µg/mL streptomycin until the first passage.

extract_protocol: 24 h after ephrinA5-Fc or control Fc stimulation, CB cells were harvested and their DNA was extracted using the PureLink® Genomic DNA Mini Kit (#K1820, Invitrogen). The samples were then treated with proteinase K and RNase A supplied in the kit.

treatment_protocol: Cells were stimulated with 5 µg/mL of either the recombinant ephrinA5-Fc (#374-EA, Biotechne) or Fc protein (#109-1103, Rockland) as control, both pre-clustered with 10 µg/mL Alexa488-conjugated anti-human IgG (#A11013, Invitrogen) for 30 min at RT.

value: cerebellar granule (CB) cells

value: 5 ug/mL efnA5-FC


title: RUNX3_120min_2; TGFb 120min; RUNX3 Knock-down


title: CB cells, ctrl-FC, Rep 6

description: 1200 ng gDNA bisulfite converted using the Zymo EZ-96 DNA Methylation kit (Zymo Research, Irine, CA, USA)

value: 5 ug/mLFC


title: 1nM FOXA1, Shifted Band, Rep 1

value: Shifted Band


title: CB cells, efnA5-FC, Rep 5


title: RUNX3_120min_1; TGFb 120min; RUNX3 Knock-down


title: CB cells, ctrl-FC, Rep 5


title: RUNX3_15min_3; TGFb 15min; RUNX3 Knock-down


title: ChIP-Seq_ClpX-HA_Caulobacter_crescentus_UG22115_PYE+Nal20

city: Geneva 4

first: Patrick

middle: H.

last: Viollier

address: Rue Michel Servet 1

department: Dept.  Microbiology and Molecular Medicine

country: Switzerland

institute: University of Geneva, Faculty of Medicine / CMU

data_processing:
Base calling: NextSeq Control Software 4.0.2.7, RTA2.11.3, bcl2fastq2.17 v2.17.1.14
Read Quality: FastQC (Galaxy Version 0.73+galaxy0), FASTQ Trimmer (Galaxy Version 1.1.5)
Alignment: Bowtie2 (Galaxy Version 2.4.2+galaxy0)
Peak calling: MACS2 (Galaxy Version 2.1.1.20160309.6 , No broad regions option) relative to the total input DNA samples. The q-value (false discovery rate, FDR) cut-off for called peaks was 0.05.
Motif-based sequence analysis: http://meme-suite.org/
ChIP-Seq profiles RPM normalized and annotation: SeqMonk Software v1.47.2 (Braham Bionformatics Institute)
Assembly: Caulobacter crescentus NA1000 (NC_011916.1)
Supplementary files format and content: The xlsx file reporting DjlA-HA, DnaJ12345-HA and ClpX-HA ChIP-Seq RPM normalized profiles was generated by SeqMonk software. The sheet is organized in columns as follows: column 1: Start (bp); column 2: End (bp); column 3: Feature strand; column 4: Feature Type; column 5: Feature Name; column 6: Description; column 7 to 18: DjlA-HA, DnaJ12345-HA and ClpX-HA ChIP-Seq profiles (normalized Read Per Million unit, RPM)

organism: Caulobacter vibrioides

growth_protocol: Overnight cultures in PYE of C. crescentus were freshly restarted (starting O.D.660nm~0.05) in 80ml of PYE supplemented with Xylose 0,3% and incubated at 30°C under agitation. Nalidixic acid treated culture was supplemented with 20 μg/mL of antibiotic 30 minutes before being fixed.

extract_protocol:
After resuspension of the cells in TES buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA, 100 mM NaCl) containing 10 mM of DTT, the cell resuspensions were incubated in the presence of Ready-Lyse lysozyme solution (Epicentre, Madison, WI) for 10 minutes at 37°C, according to the manufacturer's instructions. Lysates were sonicated (Bioruptor® Pico) at 4°C using 15 bursts of 30 seconds to shear DNA fragments to an average length of 0.2-0.5 kbp and cleared by centrifugation at 14,000 rpm for 2 min at 4°C. The volume of the lysates was then adjusted (relative to the protein concentration) to 1 mL using ChIP buffer (0.01% SDS, 1.1% Triton X-84 100, 1.2 mM EDTA, 16.7 mM Tris-HCl [pH 8.1], 167 mM NaCl) containing protease inhibitors (Roche) and pre-cleared with 80 μl of Protein-A agarose (Roche, www.roche.com) and 100 μg BSA. 5% of each pre-cleared lysate were reserved as total input samples (negative control samples). The pre-cleared lysates were then incubated overnight at 4°C with monoclonal rabbit antibodies Anti-HA (1:250 dilution) (Clone 114-2C-7, Merck Millipore). The immuno-complexes were captured after incubation with Protein-A agarose beads (pre-saturated with BSA) during a 4 h incubation at 4°C and then, washed subsequently with low salt washing buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.1, 150 mM NaCl), with high salt washing buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.1, 500 mM NaCl), with LiCl washing buffer (0.25 M LiCl, 1% NP-40, 1% deoxycholate, 1 mM EDTA, 10 mM Tris-HCl pH 8.1) and finally twice with TE buffer (10 mM Tris-HCl pH 8.1, 1 mM EDTA). The immuno-complexes were eluted from the Protein-A agarose beads with two times 250 μL elution buffer (SDS 1%, 0.1 M NaHCO3, freshly prepared) and then, just like total input samples, incubated overnight with 300 mM NaCl at 65°C to reverse the crosslinks. The samples were then treated with 2 μg of Proteinase K for 2 hours at 45°C in 40 mM EDTA and 40 mM Tris-HCl (pH 6.5). DNA was extracted using phenol:chloroform:isoamyl alcohol (25:24:1), ethanol-precipitated using 20 μg of glycogen as a carrier and resuspended in 50 μL of DNAse/RNAse free water.
Immunoprecipitated chromatins were used to prepare sample libraries used for deep sequencing at Fasteris SA (Geneva, Switzerland). ChIP-Seq libraries were prepared using the DNA Sample Prep Kit (Illumina) following manufacturer instructions. Single-end run was performed on an Illumina Next-Generation DNA sequencing instruments (NextSeq High), 50 cycles were performed and yielded several million reads per sequenced samples.

treatment_protocol: Cultures of exponentially growing cells (O.D.660nm of 0.5) were supplemented with 10 μM sodium phosphate buffer (pH 7.6) and then treated with formaldehyde (1% final concentration) at RT for 10 minutes to achieve crosslinking. Subsequently, the cultures were incubated for an additional 30 minutes on ice and washed three times in phosphate buffered saline (PBS, pH 7.4). The resulting cell pellets were stored at -80°C.

tag: strain

value: Medium supplemented with 0,3% Xylose and treated with Nalidixic acid (20µg/ml) 30 min prior fixation

tag: chip antibody

value: Anti-HA (Merck Millipore, Clone114-2C-7)


title: RUNX3_15min_2; TGFb 15min; RUNX3 Knock-down

tag: genotype

value: TGFb 1ng/ml


title: RUNX3_15min_1; TGFb 15min; RUNX3 Knock-down


title: ChIP-Seq_DnaJ4-HA_Caulobacter_crescentus_UG22111_PYE+Nal20


title: ChIP-Seq_DjlA-HA_Caulobacter_crescentus_UG22388(tipR::Tn)_PYE+Nal20

value: {delta}bla (CCNA_02223) tipR::Tn xyl::Pxyl-djlA-HA


title: Totalinput_DjlA-HA_Caulobacter_crescentus_UG14074_PYE+Nal20


title: ChIP-Seq_DnaJ5-HA_Caulobacter_crescentus_UG22113_PYE+Nal20