title: Msn2DBD_Gal4AD_H04_1


title: Msn2DBD_Gal4AD_G02_1

status: Public on Dec 19 2023

type: SRA

city: Rehovot

first: Naama

last: Barkai

state: HaMerkaz

address: Herzl 234

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

library_source: transcriptomic

data_processing:
Demultiplexing with AdapterRemoval, --trim3p 0 21.
Identification of UMI with umi_tools extract, --bc-pattern=NNNNNNNNN.
Mapping the reads with bowtie2, -p8 --local --very-sensitive --trim-to 30 -x.
Sorting and indexing with samtools.
Deduplication of UMI with umi_tools dedup.
Calculation of coverage with bedtools coverage -counts -s -a.
Assembly: GCA_000146045.2 (R64)
Supplementary files format and content: *.txt: Processed data files contain counts mapped with bedtools coverage in format of (chromosome, chromosome location (start), chromosome location (stop), systemic name, number, strand, counts).

molecule: total RNA

organism: Saccharomyces cerevisiae BY4741

source_name: cultured yeast cells

growth_protocol: Overnight cultures from fresh colonies were diluted (>1:10000) and grown to OD 0.4 in SC medium with glucose.

extract_protocol:
RNA-seq: Modified protocol of the nucleospin 96 RNA kit (Macherey-Nagel, Duren, Germany). Specifically, cell lysis was done in a 96 deep-well plate by adding 450 μl of lysis buffer containing 1 M sorbitol (Sigma-Aldrich), 100 mM EDTA, and 0.45 μl lyticase (10 IU/μl). The plate was incubated at 30°C for 30 minutes in order to break the cell wall and then centrifuged for 10 minutes at 2,500 rpm, and the supernatant was removed. From this point, extraction proceeded as in the protocol of nucleospin 96 RNA kit, only substituting β-mercaptoethanol with DTT 1M.
RNA libraries were created as described before (Chapal et al., 2019).

tag: cell type

value: cultured yeast cells

tag: type

tag: fusion

tag: loci

value: HO

tag: delta native tf

value: FALSE

tag: promoter


title: Msn2DBD_Gal4AD_A11_1


title: Msn2DBD_Gcn4AD_lib_nativeloc_E11_2

value: native

value: TRUE

value: synthetic


title: Msn2DBD_Gal4AD_H08_1


title: Msn2DBD_Gal4AD_B11_1


title: BY_32

value: Control


title: Rpn4DBD_Gal4AD_TEF_2


title: BY_33


title: Abf1DBD_Gal4AD_TEF_2


title: Pdr8DBD_Gal4AD_TEF_3


title: Nrg2DBD_Gal4AD_TEF_2


title: Msn2DBD_Gal4AD_lib_nativeloc_B10_2


title: BY_34


title: BY_35


title: Rpn4DBD_Gal4AD_TEF_3


title: Vhr1DBD_Gal4AD_TEF_3


title: Abf1DBD_Gal4AD_TEF_3


title: Nrg2DBD_Gal4AD_TEF_3


title: Vhr1DBD_Gal4AD_TEF_2


title: Abf1DBD_Gcn4AD_TEF_2


title: BY_36


title: BY_37


title: Rpn4DBD_Gcn4AD_TEF_2


title: BY_39


title: BY_38


title: Nrg2DBD_Gcn4AD_TEF_2


title: Pdr8DBD_Gcn4AD_TEF_3


title: Abf1DBD_Gcn4AD_TEF_3


title: Msn2DBD_Gcn4AD_lib_nativeloc_A12_2


title: Pdr8DBD_Gcn4AD_TEF_4


title: Gln3DBD_Gal4AD_TEF_2


title: BY_41


title: Cst6DBD_Gal4AD_TEF_2


title: Sko1DBD_Gal4AD_TEF_3


title: Reb1DBD_Gal4AD_TEF_3


title: BY_43


title: Pdr8DBD_Gal4AD_TEF_4


title: Gln3DBD_Gal4AD_TEF_3


title: Sko1DBD_Gal4AD_TEF_2


title: Reb1DBD_Gal4AD_TEF_2


title: Cst6DBD_Gal4AD_TEF_3


title: Met31DBD_Gcn4AD_TEF_2


title: BY_44


title: BY_42


title: BY_45


title: BY_40


title: Cst6DBD_Gcn4AD_TEF_2


title: Nrg2DBD_Gcn4AD_TEF_3


title: Sko1DBD_Gcn4AD_TEF_2


title: Gln3DBD_Gcn4AD_TEF_2


title: Sko1DBD_Gcn4AD_TEF_3


title: Met31DBD_Gcn4AD_TEF_3


title: BY_46


title: Mig3Full_lib_HOdMig3_H05_1


title: Gln3DBD_Gcn4AD_TEF_3


title: Mig3Full_lib_HOdMig3_F01_1


title: Mig3Full_lib_HOdMig3_A02_1


title: Mig3Full_lib_HOdMig3_G09_1


title: Mig3Full_lib_HOdMig3_H08_1


title: Mig3Full_lib_HOdMig3_D03_1


title: Mig3Full_lib_HOdMig3_A10_1


title: Mig3Full_lib_HOdMig3_A12_1


title: Mig3Full_lib_HOdMig3_F12_1


title: Mig3Full_lib_HOdMig3_B06_1


title: Mig3Full_lib_HOdMig3_G02_1


title: Mig3Full_lib_HOdMig3_D05_1


title: Mig3Full_lib_HOdMig3_A08_1


title: Mig3Full_lib_HOdMig3_TEF_1


title: Mig3Full_lib_HOdMig3_B02_1


title: Mig3Full_lib_HOdMig3_D08_1


title: Mig3Full_lib_HOdMig3_C02_1


title: Mig3Full_lib_HOdMig3_H02_1


title: BY_47


title: Mig3Full_lib_HOdMig3_B01_1


title: Mig3Full_lib_HOdMig3_D11_1


title: BY_48


title: Mig3Full_lib_HOdMig3_C05_1


title: Mig3Full_lib_HOdMig3_E06_1


title: BY_49


title: Cst6DBD_Gcn4AD_TEF_3


title: BY_50


title: Mig3Full_lib_HOdMig3_E02_1


title: Mig3Full_lib_HOdMig3_H11_1


title: Mig3Full_lib_HOdMig3_E09_1


title: Mig3Full_lib_HOdMig3_E07_1


title: Gcn4Full_lib_HOdGcn4_F11_1


title: Gcn4Full_lib_HOdGcn4_H01_1


title: Gcn4Full_lib_HOdGcn4_H06_1


title: Mig3Full_lib_HOdMig3_A04_1


title: Gcn4Full_lib_HOdGcn4_A03_1


title: Mig3Full_lib_HOdMig3_F10_1


title: Gcn4Full_lib_HOdGcn4_E04_1


title: Gcn4Full_lib_HOdGcn4_F04_1


title: Gcn4Full_lib_HOdGcn4_F02_1


title: Gcn4Full_lib_HOdGcn4_E08_1


title: Gcn4Full_lib_HOdGcn4_F06_1


title: Gcn4Full_lib_HOdGcn4_C04_1


title: Gcn4Full_lib_HOdGcn4_F10_1


title: Gcn4Full_lib_HOdGcn4_TEF_1


title: Mig3Full_lib_HOdMig3_D04_1


title: BY_51


title: Gcn4Full_lib_HOdGcn4_A05_1


title: Gcn4Full_lib_HOdGcn4_D05_1


title: Gcn4Full_lib_HOdGcn4_G03_1


title: Gcn4Full_lib_HOdGcn4_C09_1


title: Gcn4Full_lib_HOdGcn4_C06_1


title: Gcn4Full_lib_HOdGcn4_C05_1


title: Gcn4Full_lib_HOdGcn4_TEF_2


title: Gcn4Full_lib_HOdGcn4_C07_1


title: Gcn4Full_lib_HOdGcn4_E01_1


title: Gcn4Full_lib_HOdGcn4_E09_1


title: Gcn4Full_lib_HOdGcn4_C11_1


title: Gcn4Full_lib_HOdGcn4_G06_1


title: Gcn4Full_lib_HOdGcn4_D11_1


title: Gcn4Full_lib_HOdGcn4_TEF_3


title: Gcn4Full_lib_HOdGcn4_B06_1


title: Gcn4Full_lib_HOdGcn4_E10_1


title: BY_53


title: Gcn4Full_lib_HOdGcn4_E07_1


title: BY_52


title: Gcn4Full_lib_HOdGcn4_C10_1


title: Gcn4Full_lib_HOdGcn4_H09_1


title: Gcn4Full_lib_HOdGcn4_C12_1


title: Gcn4Full_lib_HOdGcn4_B01_1


title: Gcn4Full_lib_HOdGcn4_B10_1


title: Gcn4Full_lib_HOdGcn4_D10_1


title: Gcn4Full_lib_HOdGcn4_B04_1


title: BY_55


title: BY_54


title: Gcn4Full_lib_HOdGcn4_H12_1


title: BY_56


title: Gcn4Full_lib_HOdGcn4_B07_1


title: Gcn4Full_lib_HOdGcn4_H07_1


title: Gcn4Full_lib_HOdGcn4_D02_1


title: BY_57


title: Mig3DBD_Gcn4AD_lib_HOdMig3_G04_1


title: Mig3DBD_Gcn4AD_lib_HOdMig3_B09_1


title: Mig3DBD_Gcn4AD_lib_HOdMig3_H04_1


title: Mig3DBD_Gcn4AD_lib_HOdMig3_TEF_1


title: BY_58


title: BY_59


title: Mig3DBD_Gal4AD_lib_HOdMig3_TEF_1


title: Mig3DBD_Gal4AD_lib_HOdMig3_H02_1


title: Mig3DBD_Gal4AD_lib_HOdMig3_B02_1


title: Mig3DBD_Gcn4AD_lib_HOdMig3_H11_1


title: Mig3DBD_Gcn4AD_lib_HOdMig3_H12_1


title: Mig3DBD_Gcn4AD_lib_HOdMig3_F02_1


title: BY_60


title: Mig3DBD_Gcn4AD_lib_HOdMig3_E06_1


title: Mig3DBD_Gcn4AD_lib_HOdMig3_A08_1


title: Mig3DBD_Gal4AD_lib_HOdMig3_C07_1


title: Mig3DBD_Gal4AD_lib_HOdMig3_F08_1


title: Mig3DBD_Gal4AD_lib_HOdMig3_D08_1


title: Mig3DBD_Gal4AD_lib_HOdMig3_H01_1


title: Mig3DBD_Gal4AD_lib_HOdMig3_D02_1


title: Mig3DBD_Gal4AD_lib_HOdMig3_H06_1


title: Mig3DBD_Gal4AD_lib_HOdMig3_D07_1


title: Gcn4Full_lib_HOdGcn4_G12_1


title: Mig3DBD_Gcn4AD_lib_HOdMig3_E09_1


title: Mig3DBD_Gcn4AD_lib_HOdMig3_E02_1


title: Mig3DBD_Gcn4AD_lib_HOdMig3_H02_1


title: Mig3DBD_Gcn4AD_lib_HOdMig3_G01_1


title: Mig3DBD_Gcn4AD_lib_HOdMig3_G08_1


title: Postransplant lymphoproliferative disorder (PTLD) 10

type: genomic

city: Barcelona

first: Itziar

last: Salaverria

address: Rossello 153

country: Spain

institute: Hospital Clínic

description: Hybridized to Affymetrix OncoScan FFPE Assay

hyb_protocol: Samples were hybridized onto OncosCan Array for 16h at 49º using Affymetrix Hybridization oven.

scan_protocol: Affymetrix® GeneChip® Scanner 3000G to detect target bound to Oncoscan array after staining with Biotin.

data_processing:
Nexus biodiscovery software
Gains and losses were evaluated with visual inspection by 2 different observers using Nexus Biodiscovery software (Biodiscovery, Hawthorne CA, USA). The CNAs with a minimum size of 100kb were considered real. Loss of heterozigosity regions where considered when size was >5Mb.

label: Biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: intestine

label_protocol: Affymetrix OncoScan™ FFPE Assay kit /GPL18602

extract_protocol: DNA from formalin-fixed paraffin-embedded (FFPE)  was extracted using AllPrep DNA/RNA FFPE Qiagen extraction kit (Qiagen, Hilden, Germany)

tag: disease state

value: PTLD

tag: morphology

value: Monomorphic PTLD

tag: diagnosis

value: DLBCL

tag: gender

value: female

tag: tissue preparation

value: FFPE


title: STZ_retina_1

city: Montreal

first: Mike

last: Sapieha

state: Quebec

address: 5415 Boul. L'Assomption

country: Canada

institute: Hôpital Maisonneuve-Rosemont

data_processing:
Analysis was performed using the Torrent Suite software v5.4 (Thermo Fisher) and the RNASeqAnalysis plugins (Thermo Fisher)
The RNASeqAnalysis plugins aligns reads on mouse reference genome (mm10) using STAR, and then unmapped reads are aligned using Bowtie2 and merged together.
Gene level expression is calculated using HTSeq and Picard to report raw read counts and FPKM (fragment per kilobase of transcript per million).
Assembly: mm10

organism: Mus musculus

source_name: STZ diabetic retina lysate

extract_protocol:
Total RNA was isolated from freshly dissected retina lysates using the RNeasy Mini Kit (QIAGEN). The mRNA was then purified from 1μg of total RNA using the Dynabeads® mRNA DIRECT™ Micro Kit (Thermo Fisher). Whole transcriptome libraries were prepared using the Ion Total RNA-seq Kit v2. The yield and size distribution of the amplified libraries were assessed with an Agilent Bioanalyzer using a DNA 1000 Kit. Sequencing was performed on an Ion Chef™ Instrument (Ion Torrent™, Thermo Fisher).
Analysis was performed using the Torrent Suite software v5.4.0 (Thermo Fisher Scientific) and the RNASeqAnalysis plugins (Thermo Fisher Scientific). The RNASeqAnalysis plugins aligns reads on mouse reference genome (mm10) using STAR, and then unmapped reads are aligned using Bowtie2 and merged together. Gene level expression is calculated using HTSeq and Picard to report raw read counts and FPKM (fragment per kilobase of transcript per million).

treatment_protocol: Mice were injected daily intraperitoneally with streptozotocin (50mg/kg) for 5 consecutive days at 6 weeks of age. 10 days after, animals were monitored to confirm hyperglycemia (>25mM). Controls were injected with citrate buffer. All animals were kept with free access to water and food up to 18 weeks old, when retina were collected and analyzed.

tag: strain

tag: genotype

value: Wildtype

tag: treatment

value: streptozotocin-induced

tag: organ

value: Retina


title: Mig3DBD_Gal4AD_lib_HOdMig3_B11_1


title: Control_retina_2

source_name: Citrate control retina lysate

value: Citrate control


title: Mig3DBD_Gal4AD_lib_HOdMig3_TEF_3


title: Mig3DBD_Gal4AD_lib_HOdMig3_TEF_2


title: RMS9_DMEM_2D_P1 [methylation]

city: Lyon

first: Thomas

last: Diot

address: 28 Rue Laennec

country: France

institute: Cancer Research Center of Lyon

hyb_protocol: 100 to 500 ng of gDNA was hybridized to Illumina Infinium HumanMethylationEPIC BeadChip (850K) arrays at the International Agency for Research on Cancer (IARC), in collaboration with the team of Z. Herceg (IARC, Lyon), according to the manufacturer’s protocol recommendations.

data_processing: Methylation data were analyzed using minfi (R library v.1.44.0). Normalization was performed for all samples using functional normalization (FunNorm) with default parameters. Filtering was performed to remove (1) poor performing probes, i.e. detection p-value above 0.01 in one or more samples, (2) probes located on sex chromosomes, (3) probes known to have common SNPs at the CpG site using dropLociWithSnps function; and (4) cross-reactive probes published by Chen et al. (2013) and Pidsley et al. (2016). Beta values were extracted using the getBeta function from minfi with default parameters.

label: Cy3 and Cy5

source_name: RMS9 cell line

growth_protocol: Culture medium was changed twice a week, and RMS_O were split every 2 weeks on average. Finally, culture medium was changed 24 to 48 h before extraction.

extract_protocol: genomic DNA (gDNA) from both RMS tissues and matched in vitro models cultured in 2D or 3D conditions with DMEM, M3 and M5 media were extracted using the Allprep DNA/RNA/miRNA universal kit (Qiagen, cat. no. 80224), following manufacturer’s instructions.

value: Rhabdomyosarcoma

tag: Sex

value: M

value: Embryonal

value: Primary

value: Foot

tag: fresh/cryopreserved

value: fresh

tag: medium

value: DMEM


title: Mig3DBD_Gal4AD_lib_HOdMig3_G10_1

tag: cell type

value: cultured yeast cells

tag: type

value: HO

value: TRUE

value: synthetic


title: RMS7_T1 [methylation]

scan_protocol: 100 to 500 ng of gDNA was hybridized to Illumina Infinium HumanMethylationEPIC BeadChip (850K) arrays at the International Agency for Research on Cancer (IARC), in collaboration with the team of Z. Herceg (IARC, Lyon), according to the manufacturer’s protocol recommendations.

source_name: RMS7 tissue

value: Gluteal


title: RMS9_M5_2D_P3 [methylation]

label_protocol: 100 to 500 ng of gDNA was hybridized to Illumina Infinium HumanMethylationEPIC BeadChip (850K) arrays at the International Agency for Research on Cancer (IARC), in collaboration with the team of Z. Herceg (IARC, Lyon), according to the manufacturer’s protocol recommendations.


title: RMS9_T1 [methylation]

source_name: RMS9 tissue


title: Mig3DBD_Gal4AD_lib_HOdMig3_D04_1

tag: fusion

tag: loci


title: STZ_retina_2


title: RMS2_O_P18* [methylation]

source_name: RMS2 organoid

value: Relapse/metastatic

value: Lung

value: Ischioanal

value: cryopreserved


title: RMS2_O_P7 [methylation]


title: Mig3DBD_Gal4AD_lib_HOdMig3_H08_1

tag: delta native tf

tag: promoter


title: subject OND4 PBMC, stimulated with EBV

city: Houston

first: John

middle: William

last: Lindsey

state: TX

address: 6431 Fannin St, Ste 7.044 MSB, Neurology Dept

country: USA

institute: University of Texas Health Science Center At Houston

data_processing:
data processing done by MedGenome
Supplementary files format and content: excel files with TCR alpha and beta sequences and number of reads
Supplementary files format and content: excel file with TCR beta CDR3 regions aligned for all antigens and conditions for each subject

source_name: other neurologic disease

growth_protocol: CSF and PBMC directly ex vivo, antigen specific cells sorted after 6 days in culture

extract_protocol:
cells were lysed in Trizol and stored at -80.  RNA was extracted from Trizol aqueous phase with Takara Nucleospin RNA XS columns
Takara SMARTer Human TCR a/b Profiling Kit

treatment_protocol: antigens used for stimulation were Epstein-Barr virus, autologuous EBV-infected cell lines, varicella zoster virus, influenza A, candida, or no antigen.

tag: tissue

value: other neurologic disease

tag: cell line

value: PBMC

value: EBV


title: Mig3DBD_Gal4AD_lib_HOdMig3_H07_1


title: Control_retina_1

value: Wildtype

value: Citrate control

value: Retina


title: RMS2_O_P17* [methylation]

value: Rhabdomyosarcoma

value: M

value: Embryonal


title: subject OND4 PBMC, stimulated with autologous LCL

value: LCL


title: Mig3DBD_Gcn4AD_lib_HOdMig3_G07_1

value: cultured yeast cells

value: HO

value: TRUE


title: subject OND4 PBMC, ex vivo


title: subject OND4 PBMC, stimulated with influenza

value: influenza


title: RMS7_DMEM_2D_P5 [methylation]

source_name: RMS7 cell line

value: Primary

value: Gluteal

value: fresh

value: DMEM


title: subject OND4 CSF cells, ex vivo

value: other neurologic disease

value: cerebrospinal fluid


title: RMS2_T [methylation]

source_name: RMS2 tissue

value: Relapse/metastatic

value: Lung

value: Ischioanal


title: Mig3DBD_Gcn4AD_lib_HOdMig3_F10_1

value: synthetic


title: RMS7_M5_2D_P4 [methylation]

value: Rhabdomyosarcoma

value: M


title: RMS7_DMEM_2D_P4 [methylation]

value: Embryonal


title: Mig3DBD_Gcn4AD_lib_HOdMig3_E04_1

value: cultured yeast cells


title: Mig3DBD_Gcn4AD_lib_HOdMig3_E05_1

value: HO


title: Mig3DBD_Gcn4AD_lib_HOdMig3_G03_1

value: TRUE


title: subject OND3 PBMC, stimulated with autologous LCL

value: PBMC

value: LCL


title: RMS9_T2 [methylation]

value: Primary

value: Foot


title: Mig3DBD_Gal4AD_lib_HOdMig3_TEF_4


title: RMS1_T1 [methylation]

source_name: RMS1 tissue

value: Relapse

value: Parameningeal


title: subject OND3 PBMC, ex vivo

value: other neurologic disease


title: RMS1_T2 [methylation]


title: Mig3DBD_Gal4AD_lib_HOdMig3_E06_1


title: subject OND3 PBMC, stimulated with influenza

value: influenza


title: RMS2_O_P10* [methylation]

value: Relapse/metastatic

value: Lung

value: cryopreserved


title: subject OND2 PBMC, stimulated with influenza


title: subject OND3 CSF cells, ex vivo

value: cerebrospinal fluid


title: subject OND3 PBMC, stimulated with EBV

value: EBV


title: Mig3DBD_Gal4AD_lib_HOdMig3_A06_1

value: synthetic


title: RMS2_O_P11* [methylation]

value: Rhabdomyosarcoma

value: M

value: Embryonal

value: Ischioanal


title: Mig3DBD_Gal4AD_lib_HOdMig3_A01_1

value: cultured yeast cells

value: HO

value: TRUE


title: subject OND2 PBMC, ex vivo

value: PBMC


title: subject OND2 PBMC, stimulated with autologous LCL

value: LCL


title: subject OND2 CSF cells, ex vivo

value: other neurologic disease


title: Mig3DBD_Gal4AD_lib_HOdMig3_A02_1


title: RMS7_M5_2D_P3 [methylation]

value: Primary

value: Gluteal

value: fresh


title: subject OND2 PBMC, stimulated with EBV


title: subject OND1 PBMC, stimulated with influenza

value: influenza


title: Mig3DBD_Gcn4AD_lib_HOdMig3_G11_1


title: Mig3DBD_Gcn4AD_lib_HOdMig3_G12_1


title: RMS2_O_P6 [methylation]

value: Relapse/metastatic

value: Lung


title: subject OND1 PBMC, stimulated with autologous LCL


title: subject OND1 PBMC, stimulated with EBV

value: EBV


title: subject OND1 PBMC, ex vivo


title: subject OND1 CSF cells, ex vivo

value: cerebrospinal fluid


title: Mig3DBD_Gcn4AD_lib_HOdMig3_F07_1

value: synthetic


title: Mig3DBD_Gcn4AD_lib_HOdMig3_TEF_2


title: RMS1_O_P22* [methylation]

source_name: RMS1 organoid

value: Rhabdomyosarcoma

value: M

value: Embryonal

value: Relapse

value: Parameningeal

value: cryopreserved


title: subject HC4 PBMC, stimulated with influenza, biol rep 2

source_name: healthy control

value: healthy control

value: PBMC


title: RMS9_DMEM_2D_P4 [methylation]

value: Primary

value: Foot

value: DMEM


title: Mig3DBD_Gal4AD_lib_HOdMig3_G09_1

value: cultured yeast cells

value: HO

value: TRUE


title: subject HC4 PBMC, stimulated with VZV

value: VZV


title: Mig3DBD_Gal4AD_lib_HOdMig3_A07_1


title: Mig3DBD_Gal4AD_lib_HOdMig3_C06_1


title: subject HC4 PBMC, stimulated with influenza, biol rep 1

value: influenza


title: RMS1_O_P23* [methylation]


title: subject HC4 PBMC, stimulated with EBV

value: EBV


title: subject HC4 PBMC, stimulated with autologous LCL

value: LCL


title: subject HC4 PBMC, stimulated with candida

value: candida


title: Mig3DBD_Gal4AD_lib_HOdMig3_B07_1

value: synthetic


title: Mig3DBD_Gal4AD_lib_HOdMig3_G04_1


title: subject HC4 PBMC, ex vivo


title: RMS7_T2 [methylation]

value: Rhabdomyosarcoma

value: M

value: Embryonal

value: Gluteal


title: Mig3DBD_Gcn4AD_lib_HOdMig3_A01_1


title: subject HC3 PBMC, stimulated with no antigen

value: healthy control

value: PBMC

value: no antigen


title: Mig3DBD_Gcn4AD_lib_HOdMig3_G05_1


title: subject HC3 PBMC, stimulated with candida


title: RMS9_M5_2D_P1 [methylation]

value: Primary

value: Foot

value: fresh


title: subject HC3 PBMC, stimulated with influenza


title: Mig3DBD_Gcn4AD_lib_HOdMig3_B04_1

value: cultured yeast cells

value: HO

value: TRUE


title: RMS1_O_P13 [methylation]

value: Relapse

value: Parameningeal


title: Mig3DBD_Gcn4AD_lib_HOdMig3_A10_1


title: Mig3DBD_Gcn4AD_lib_HOdMig3_TEF_4


title: subject HC3 PBMC, stimulated with autologous LCL

value: LCL


title: subject HC3 PBMC, ex vivo


title: Mig3DBD_Gcn4AD_lib_HOdMig3_H09_1

value: synthetic


title: Mig3DBD_Gcn4AD_lib_HOdMig3_TEF_5


title: Mig3DBD_Gal4AD_lib_HOdMig3_G11_1


title: subject HC3 PBMC, stimulated with EBV

value: EBV


title: subject HC2 PBMC, stimulated with no antigen


title: Mig3DBD_Gal4AD_lib_HOdMig3_B06_1


title: subject HC3 PBMC, stimulated with VZV

value: VZV


title: subject HC2 PBMC, stimulated with candida

value: candida


title: Mig3DBD_Gal4AD_lib_HOdMig3_H04_1


title: Mig3DBD_Gal4AD_lib_HOdMig3_C10_1


title: subject HC2 PBMC, stimulated with influenza

value: influenza


title: Mig3DBD_Gcn4AD_lib_HOdMig3_G06_1


title: Mig3DBD_Gcn4AD_lib_HOdMig3_F12_1


title: subject HC2 PBMC, stimulated with VZV

value: healthy control


title: subject HC2 PBMC, stimulated with autologous LCL

value: PBMC


title: subject HC2 PBMC, stimulated with EBV


title: Mig3DBD_Gal4AD_lib_HOdMig3_F04_1


title: subject HC2 PBMC, ex vivo


title: Mig3DBD_Gcn4AD_lib_HOdMig3_H08_1


title: Mig3DBD_Gcn4AD_lib_HOdMig3_F04_1


title: subject HC1 PBMC, stimulated with candida


title: RMS1_O_P17 [methylation]

value: Rhabdomyosarcoma

value: M

value: Embryonal


title: subject HC1 PBMC, stimulated with influenza


title: BY_61

value: Control


title: subject HC1 PBMC, stimulated with VZV


title: BY_62

value: cultured yeast cells


title: Mig3DBD_Gal4AD_lib_HOdMig3_B10_1

value: HO


title: subject HC1 PBMC, stimulated with EBV


title: Mig3DBD_Gal4AD_lib_HOdMig3_TEF_5

value: TRUE


title: Mig3DBD_Gal4AD_lib_HOdMig3_E07_1


title: Mig3DBD_Gal4AD_lib_HOdMig3_G07_1


title: subject MS8 PBMC, stimulated with no antigen

source_name: multiple sclerosis

value: multiple sclerosis

value: no antigen


title: subject HC1 PBMC, stimulated with autologous LCL

value: LCL


title: Mig3DBD_Gal4AD_lib_HOdMig3_E02_1

value: synthetic


title: subject MS8 PBMC, stimulated with candida


title: subject HC1 PBMC, ex vivo


title: Mig3DBD_Gcn4AD_lib_HOdMig3_G02_1


title: Mig3DBD_Gcn4AD_lib_HOdMig3_D11_1


title: subject MS8 PBMC, stimulated with EBV

value: EBV


title: Mig3DBD_Gcn4AD_lib_HOdMig3_A09_1


title: subject MS8 PBMC, stimulated with autologous LCL


title: Mig3DBD_Gcn4AD_lib_HOdMig3_D06_1


title: subject MS8 PBMC, ex vivo


title: subject MS8 PBMC, stimulated with VZV

value: VZV


title: subject MS8 PBMC, stimulated with influenza


title: BY_63


title: subject MS8 CSF cells, ex vivo

value: cerebrospinal fluid


title: subject MS7 PBMC, stimulated with no antigen


title: BY_65


title: BY_64


title: subject MS7 PBMC, stimulated with candida

value: candida


title: Mig3DBD_Gal4AD_lib_HOdMig3_C11_1


title: Mig3DBD_Gal4AD_lib_HOdMig3_H11_1


title: subject MS7 PBMC, stimulated with influenza

value: influenza


title: Mig3DBD_Gcn4AD_lib_HOdMig3_E11_1


title: Mig3DBD_Gal4AD_lib_HOdMig3_A10_1


title: subject MS7 PBMC, stimulated with EBV

value: PBMC


title: Mig3DBD_Gal4AD_lib_HOdMig3_H09_1


title: subject MS7 PBMC, stimulated with VZV


title: Mig3DBD_Gal4AD_lib_HOdMig3_D05_1


title: subject MS7 PBMC, stimulated with autologous LCL


title: BY_66


title: Yap1DBD_Gcn4AD_lib_HOdYap1_G11_1


title: subject MS7 CSF cells, ex vivo


title: subject MS6 PBMC, stimulated with no antigen


title: subject MS6 PBMC, stimulated with candida


title: subject MS7 PBMC, ex vivo


title: Yap1DBD_Gcn4AD_lib_HOdYap1_A02_1


title: subject MS6 PBMC, stimulated with influenza


title: Yap1DBD_Gcn4AD_lib_HOdYap1_C04_1


title: subject MS6 PBMC, stimulated with VZV


title: Yap1DBD_Gcn4AD_lib_HOdYap1_TEF_1


title: subject MS6 PBMC, stimulated with EBV


title: Yap1DBD_Gcn4AD_lib_HOdYap1_TEF_2


title: Yap1DBD_Gcn4AD_lib_HOdYap1_TEF_3


title: Yap1DBD_Gcn4AD_lib_HOdYap1_G07_1


title: subject MS6 PBMC, ex vivo


title: subject MS6 CSF cells, ex vivo


title: Yap1DBD_Gal4AD_lib_HOdYap1_G08_1


title: subject MS5 PBMC, stimulated with influenza, biol rep 2


title: Yap1DBD_Gal4AD_lib_HOdYap1_C08_1


title: subject MS5 PBMC, stimulated with candida


title: subject MS5 PBMC, stimulated with no antigen


title: Yap1DBD_Gal4AD_lib_HOdYap1_D05_1


title: Yap1DBD_Gal4AD_lib_HOdYap1_H11_1


title: Yap1DBD_Gcn4AD_lib_HOdYap1_D07_1


title: subject MS5 PBMC, stimulated with VZV


title: Mig3DBD_Gcn4AD_lib_HOdMig3_TEF_3


title: subject MS5 PBMC, stimulated with influenza, biol rep 1


title: Yap1DBD_Gcn4AD_lib_HOdYap1_A03_1


title: subject MS6 PBMC, stimulated with autologous LCL


title: Yap1DBD_Gcn4AD_lib_HOdYap1_H06_1


title: Yap1DBD_Gcn4AD_lib_HOdYap1_F01_1


title: subject MS5 PBMC, stimulated with EBV


title: Yap1DBD_Gal4AD_lib_HOdYap1_TEF_1


title: subject MS5 PBMC, stimulated with autologous LCL


title: Yap1DBD_Gal4AD_lib_HOdYap1_TEF_2


title: subject MS5 PBMC, ex vivo


title: Yap1DBD_Gcn4AD_lib_HOdYap1_C11_1


title: subject MS5 CSF cells, ex vivo


title: subject MS4 PBMC, stimulated with candida


title: subject MS4 PBMC, stimulated with influenza


title: Yap1DBD_Gal4AD_lib_HOdYap1_E11_1


title: Yap1DBD_Gal4AD_lib_HOdYap1_TEF_3


title: Yap1DBD_Gal4AD_lib_HOdYap1_C07_1


title: subject MS4 PBMC, ex vivo


title: subject MS4 PBMC, stimulated with VZV


title: Yap1DBD_Gal4AD_lib_HOdYap1_B02_1


title: Yap1DBD_Gal4AD_lib_HOdYap1_C01_1


title: subject MS4 PBMC, stimulated with EBV


title: Yap1DBD_Gcn4AD_lib_HOdYap1_D10_1


title: subject MS4 CSF cells, ex vivo


title: Yap1DBD_Gal4AD_lib_HOdYap1_A09_1


title: Mig3DBD_Gal4AD_lib_HOdMig3_E03_1


title: subject MS3 PBMC, stimulated with candida


title: Yap1DBD_Gcn4AD_lib_HOdYap1_F03_1


title: subject MS3 PBMC, stimulated with influenza


title: subject MS3 PBMC, stimulated with VZV


title: Yap1DBD_Gcn4AD_lib_HOdYap1_A09_1


title: Yap1DBD_Gcn4AD_lib_HOdYap1_F12_1


title: subject MS3 PBMC, stimulated with autologous LCL


title: BY_67


title: Yap1DBD_Gcn4AD_lib_HOdYap1_C07_1


title: BY_68


title: Yap1DBD_Gal4AD_lib_HOdYap1_B05_1


title: subject MS3 PBMC, ex vivo


title: subject MS3 CSF cells, ex vivo


title: subject MS2 PBMC, stimulated with candida


title: subject MS2 PBMC, stimulated with influenza


title: Yap1DBD_Gal4AD_lib_HOdYap1_A07_1


title: Yap1DBD_Gal4AD_lib_HOdYap1_D04_1


title: subject MS2 PBMC, stimulated with VZV


title: Yap1DBD_Gal4AD_lib_HOdYap1_E04_1


title: Yap1DBD_Gcn4AD_lib_HOdYap1_E12_1


title: subject MS2 PBMC, stimulated with EBV


title: subject MS2 PBMC, stimulated with autologous LCL


title: Yap1DBD_Gcn4AD_lib_HOdYap1_G02_1


title: Yap1DBD_Gcn4AD_lib_HOdYap1_C05_1


title: subject MS2 CSF cells, ex vivo


title: Yap1DBD_Gcn4AD_lib_HOdYap1_C10_1


title: subject MS3 PBMC, stimulated with EBV


title: Yap1DBD_Gcn4AD_lib_HOdYap1_B08_1


title: Yap1DBD_Gcn4AD_lib_HOdYap1_TEF_4


title: subject MS1 PBMC, stimulated with EBV


title: subject MS1 PBMC, stimulated with autologous LCL


title: Yap1DBD_Gal4AD_lib_HOdYap1_A06_1


title: subject MS1 PBMC, ex vivo


title: Yap1DBD_Gcn4AD_lib_HOdYap1_TEF_5


title: Yap1DBD_Gal4AD_lib_HOdYap1_C02_1


title: subject MS1 CSF cells, ex vivo


title: Mig3DBD_Gcn4AD_lib_HOdMig3_C05_1


title: constant34

city: Nagoya

first: Takashi

last: Yoshimura

address: Furo-cho, Chikusa-ku

country: Japan

institute: Nagoya University

data_processing:
Clean reads were mapped on the Oryzias latipes reference assembly using bowtie2 (version 2.2.5)
The fragments per kilobase of exon per million fragments mapped (FPKM) was calculated using RSEM (version 1.2.12).
Assembly: Oryzias latipes reference assembly
Supplementary files format and content: Excel file include FPKM for each sample.

organism: Oryzias latipes

source_name: Ventral part of telenchephalon, hypothalamus and pituitary

growth_protocol: Medaka were kept under kept under constant photoperiodic conditions

extract_protocol:
Total RNA of brain (ventral part of telenchephalon, hypothalamus and pituitary) were isolated with elimination of DNA contamination using DNase.
mRNA was first purified from the total RNA using poly-T oligo-attached magnetic beads and then fragmented, after which cDNA synthesis was performed. Then the synthesized cDNA was used for the preparation of PE100 strand specific sequencing libraries.
Strand-specific RNA-seq

treatment_protocol: Brain (ventral part of telenchephalon, hypothalamus and pituitary) were collected every month.

value: 150 days after transition to LW conditions


title: constant33

value: Ventral part of telenchephalon, hypothalamus and pituitary


title: subject MS2 PBMC, ex vivo


title: Yap1DBD_Gal4AD_lib_HOdYap1_F03_1


title: constant32


title: Yap1DBD_Gal4AD_lib_HOdYap1_G11_1


title: subject MS1 PBMC, stimulated with candida


title: constant31

value: 120 days after transition to LW conditions


title: constant30


title: Yap1DBD_Gcn4AD_lib_HOdYap1_B12_1


title: Yap1DBD_Gcn4AD_lib_HOdYap1_C09_1


title: subject MS1 PBMC, stimulated with influenza


title: Yap1DBD_Gcn4AD_lib_HOdYap1_C06_1


title: constant29


title: subject MS1 PBMC, stimulated with VZV


title: constant27

value: 90 days after transition to LW conditions


title: Yap1DBD_Gcn4AD_lib_HOdYap1_D01_1

value: cultured yeast cells


title: Yap1DBD_Gal4AD_lib_HOdYap1_TEF_5

value: HO


title: Yap1DBD_Gal4AD_lib_HOdYap1_B09_1

value: TRUE


title: Yap1DBD_Gal4AD_lib_HOdYap1_B04_1


title: constant19

value: 60 days after transition to LW conditions


title: constant23


title: Yap1DBD_Gcn4AD_lib_HOdYap1_F07_1


title: constant18

value: 30 days after transition to LW conditions


title: Yap1DBD_Gal4AD_lib_HOdYap1_E03_1


title: Yap1DBD_Gal4AD_lib_HOdYap1_F05_1


title: Yap1DBD_Gal4AD_lib_HOdYap1_D07_1


title: constant14


title: Yap1DBD_Gal4AD_lib_HOdYap1_G01_1


title: Yap1DBD_Gal4AD_lib_HOdYap1_B01_1


title: constant28


title: constant9

value: 7 days after transition to LW conditions


title: Yap1DBD_Gcn4AD_lib_HOdYap1_F08_1

value: synthetic


title: Yap1DBD_Gal4AD_lib_HOdYap1_TEF_4


title: Yap1DBD_Gcn4AD_lib_HOdYap1_D02_1


title: constant4

value: 0 days after transition to LW conditions


title: Yap1DBD_Gcn4AD_lib_HOdYap1_H03_1


title: Yap1DBD_Gcn4AD_lib_HOdYap1_A08_1


title: constant8


title: constant3


title: Yap1DBD_Gcn4AD_lib_HOdYap1_A07_1


title: constant2


title: BY_69

value: Control


title: 50_150929_1

growth_protocol: Medaka were kept under outdoor natural conditions in the National Institute for Basic Biology, Okazaki, Japan (35.0°N, 137.2°E)

treatment_protocol: Samples were collected every month at around 8 pm (Japan Standard Time) for two years, from October 2015 to October 2017.

value: September, 2015


title: 48_170919_2

value: September, 2017


title: 49_150929_1


title: constant15


title: BY_70


title: 47_170919_1


title: Yap1DBD_Gal4AD_lib_HOdYap1_E02_1


title: constant11


title: Yap1DBD_Gal4AD_lib_HOdYap1_D10_1


title: Yap1DBD_Gal4AD_lib_HOdYap1_G06_1


title: 45_170824_1

value: August, 2017


title: constant25


title: Yap1DBD_Gal4AD_lib_HOdYap1_E07_1


title: 46_170824_2


title: Yap1DBD_Gcn4AD_lib_HOdYap1_G03_1


title: Yap1DBD_Gcn4AD_lib_HOdYap1_B02_1


title: 43_170720_1


title: Yap1DBD_Gcn4AD_lib_HOdYap1_C08_1


title: 42_170622_2


title: Yap1DBD_Gal4AD_lib_HOdYap1_G02_1


title: Yap1DBD_Gcn4AD_lib_HOdYap1_D12_1


title: 39_170522_1


title: 41_170622_1


title: Yap1DBD_Gal4AD_lib_HOdYap1_G09_1


title: 38_170420_2

value: April, 2017


title: 40_170522_2


title: Yap1DBD_Gal4AD_lib_HOdYap1_E08_1


title: 37_170420_1


title: 35_170316_1

value: March, 2017


title: Yap1DBD_Gal4AD_lib_HOdYap1_H09_1


title: Yap1DBD_Gcn4AD_lib_HOdYap1_B07_1


title: 34_170214_2

value: Ventral part of telenchephalon, hypothalamus and pituitary

value: February, 2017


title: Yap1DBD_Gal4AD_lib_HOdYap1_D01_1


title: 33_170214_1


title: 44_170720_2


title: Yap1DBD_Gcn4AD_lib_HOdYap1_C01_1


title: 36_170316_2


title: Yap1DBD_Gal4AD_lib_HOdYap1_H06_1


title: Yap1DBD_Gcn4AD_lib_HOdYap1_H07_1


title: 30_161219_2

value: December, 2016


title: BY_71

value: cultured yeast cells


title: Yap1DBD_Gcn4AD_lib_HOdYap1_G04_1

value: HO


title: 31_170120_1

value: January, 2017


title: Yap1DBD_Gal4AD_lib_HOdYap1_G07_1

value: TRUE


title: 28_161121_2

value: November, 2016


title: 29_161219_1


title: 27_161121_1


title: Yap1DBD_Gal4AD_lib_HOdYap1_E06_1


title: mtC_b0603_2DRec [scRNA-seq]

city: New York

first: Rohit

last: Chandwani

state: NY

address: 413 East 69th St, BRB 1360G

department: Surgery

institute: Weill Cornell Medicine

library_source: transcriptomic single cell

data_processing:
The 10× Libraries were sequenced on the Illumina NovaSeq6000 sequencer with pair-end reads (28bp for read 1 and 91bp for read2).
The sequencing data were processed by the 10× cellranger pipeline (v6.0.2) in two steps. In the first step, cellranger mkfastq demultiplexed samples and generated fastq files; and in the second step, cellranger count aligned fastq files to the reference genome and extracted gene expression UMI counts matrix.
In order to measure both mouse and marker gene expression, we built a custom reference genome by integrating the tdTomato-WPRE marker gene into the 10× pre-built mouse reference (refdata-gex-mm10-2020-A) using cellranger mkref.
Assembly: mm10
Supplementary files format and content: For each sample, there is a filtered feature matrix file in h5 format from cell ranger.
Supplementary files format and content: Processed data includes two SingleCellExperiment R object with log-normalized counts, metadata,and dimensionality reduction. sce_allSamples_allCells.rds contains all cell types, and sce_acinarDuctalOnly.rds contains just the acinar and ductal compartments. Samples were processed with DecontX, and only cells with at least 200 genes detected and less than 10% mitochondrial were retained.   Samples were integrated with fastMNN from the batchelor package, and scater was used to create UMAP embedding and generate log-normalized counts.

molecule: polyA RNA

source_name: Pancreas

extract_protocol:
Single cell suspensions were prepared from pancreata and stained with DAPI. ~300k DAPI(-) cells were sorted and collected via FACS. ~300k DAPI(-) tdTomato(+) cells were sorted and collected via FACS. ~300k DAPI(-) & ~300k DAPI(-) tdTomato(+) were combined into a single tube for scRNA-seq.
10X Genomics Chromium was employed to add barcoded primer gel beads to each single cell. The captured polyA mRNA from single cells was reversely transcribed, barcoded and amplified following the standard 10X Genomics Chromium Single-cell 3' Library RNA-Seq Assays protocol. Libraries were sequenced on Illumina NovaSeq6000 at the Epigenomics Core Facility at Weill Cornell Medicine.

value: Pancreas

value: all pancreas-derived cells

value: WT

value: Pancreatitis

tag: time point

value: 2 days recovery


title: 26_161026_2

value: October, 2016


title: BY_72

source_name: cultured yeast cells

value: Control


title: mtS_b0602_2DRec [scRNA-seq]

value: Inflammation-naïve


title: 23_160928_1

value: September, 2016


title: mtC_b0599_2DRec [scRNA-seq]


title: 32_170120_2

value: Ventral part of telenchephalon, hypothalamus and pituitary


title: mtC_2547_12WRec [scRNA-seq]

value: 12 weeks recovery


title: mtS_b0600_2DRec [scRNA-seq]


title: 25_161026_1


title: 21_160825_1

value: August, 2016


title: 20_160720_2


title: 19_160720_1


title: mktS_2544_12WRec_2DRas [scRNA-seq]

value: 12 weeks recovery, 2days Ras


title: 18_160623_2


title: mtS_2546_12WRec [scRNA-seq]


title: 2519_mtC_12WRec [scATAC-seq]

library_source: genomic single cell

data_processing:
The 10× Libraries were sequenced on the Illumina NovaSeq6000 sequencer with pair-end reads (PE51).
The sequencing data were processed with cellranger-arc pipeline (v2.0.0) mkfastq module to demultiplexed samples and generated fastq files. The cellranger-atac (v2.0.0) count module was used to aligned fastq files to the reference genome (refdata-cellranger-arc-mm10-2020-A-2.0.0) and extracted UMI counts matrix.
The resulting output from cellranger-ARC was further analyzed in R using the ArchR v1.0.2 package. Cells were filtered based on sequencing depth and signal-to-noise ratio: cells with fewer than 10ˆ3.4 unique fragments and a TSS enrichment ratio outside the range of 10 to 35 were discarded. Doublet enrichment was computed using ArchR's addDoubletScores function (default parameters), followed by doublet filtering with the filterDoublets function (filterRatio=1). Iterative latent semantic indexing (LSI) dimensionality reduction was performed with ArchR's addIterativeLSI function, and a UMAP embedding was computed with ArchR's addUMAP function.
Assembly: mm10
Supplementary files format and content: fragments.tsv files are BED-like tabular files produced from cellranger-ARC, where each line represents a unique ATAC-seq fragment captured by the assay.
Supplementary files format and content: the archR_projectDir.tar.gz file contains the ArchR project directory of post-filtered data, complete with arrow files, UMAP coordinates, and metadata

extract_protocol:
Single cell suspensions were prepared from pancreata and stained with DAPI. ~300k DAPI(-) cells were sorted and collected via FACS. ~300k DAPI(-) tdTomato(+) cells were sorted and collected via FACS. ~300k DAPI(-) & ~300k DAPI(-) tdTomato(+) were combined into a single tube for scATAC-seq.
Libraries were prepared for single cell Multiome ATAC + Gene Expression. Only single-cell ATAC-seq passed quality control. Therefore, single-cell ATAC libraries were prepared for sequencing using Chromium Next GEM Chip J Single Cell, Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle, Dual Index Kit TT Set A, and Single Index Kit N Set A.

value: all pancreas-derived


title: Yap1DBD_Gal4AD_lib_HOdYap1_A02_1

value: cultured yeast cells

value: HO

value: synthetic


title: 17_160623_1


title: mktC_2524_12WRec_2DRas [scRNA-seq]

value: Pancreas


title: 15_160524_1


title: 16_160524_2


title: 2515_mtS_12WRec [scATAC-seq]

value: Inlammation-naïve


title: 2518_mktS_12WRec_2DRas [scATAC-seq]


title: 14_160426_2

value: April, 2016


title: 24_160928_2


title: 13_160426_1


title: 12_160323_2

value: March, 2016


title: 11_160323_1


title: 22_160825_2


title: heart tissue, WT genotype, HFHS diet, Carnosine treatment rep 2

city: Iowa City

first: Ethan

middle: J.

last: Anderson

state: Iowa

address: 180 South Grand Ave, CPB 548

department: Pharmaceutical Sciences and Experimental Therapeutics

institute: University of Iowa - College of Pharmacy

description:
library name: 22
transcript_tpms_all_samples.tsv column 24

data_processing:
Reads were aligned using Kallisto version 0.43.1, to Ensemble transcriptome release 98 (119215 transcript targets), run using default settings, with specific input parameters of 100 bootstraps and 16 threads.
Differential gene expression was quantified using Sleuth version 0.30.0, aggregating abundance on Ensemble genes, with a two-step Likelihood Ratio Test and Wald Test
Gene ontology analyses were performed by inputting the indicated gene sets into the using ToppFun web-server tool, ToppGene Suiteand using default settings. Results were exported and up to the top 50 enriched terms in each “Category” were tabulated in Supplement Tables
Assembly: ftp://ftp.ensembl.org/pub/release-98/fasta/mus_musculus/cdna/Mus_musculus.GRCm38.cdna.all.fa.gz
Supplementary files format and content: TSV; transcript abundance table,  "Transcript Per Million"  TPM sample matrix per transcript with ensembl transcript annotation.

source_name: heart

extract_protocol:
Total RNA was extracted from left ventricular tissues (~10 mg), using the RNeasy Fibrous Tissue Kit (QIAGEN, Germantown, Maryland)
Illumina TruSeq® Stranded mRNA Library Prep kits (Illumina) were used to prepare sequencing libraries from mRNA, followed by reverse transcription to cDNA, fragment purification and ligation to indexed (barcoded) adaptors. Indexed libraries were pooled for multiplex sequencing and run on an SP flow cell on the Illumina NovaSeq 6000 sequencer for 300 cycles with 150-base paired-end reads.

value: heart

value: wt

value: hfhs/carn


title: heart tissue, WT genotype, HFHS diet, Carnosine treatment rep 3

description:
library name: 23
transcript_tpms_all_samples.tsv column 25


title: heart tissue, WT genotype, HFHS diet, Carnosine treatment rep 1

description:
library name: 21
transcript_tpms_all_samples.tsv column 23


title: 9_160222_1

value: February, 2016


title: heart tissue, GPX genotype, HFHS diet, rep 4

description:
library name: 19
transcript_tpms_all_samples.tsv column 21

value: gpx

value: hfhs


title: 8_160125_2

value: Ventral part of telenchephalon, hypothalamus and pituitary

value: January, 2016


title: heart tissue, GPX genotype, HFHS diet, rep 5

description:
library name: 20
transcript_tpms_all_samples.tsv column 22


title: heart tissue, GPX genotype, HFHS diet, rep 3

description:
library name: 18
transcript_tpms_all_samples.tsv column 20


title: 7_160125_1


title: 10_160222_2


title: 2520_mktC_12WRec_2DRas [scATAC-seq]

value: Pancreatitis


title: 5_151225_1

value: December, 2015


title: heart tissue, WT genotype, HFHS diet, rep 5

description:
library name: 15
transcript_tpms_all_samples.tsv column 17


title: heart tissue, WT genotype, HFHS diet, rep 4

description:
library name: 14
transcript_tpms_all_samples.tsv column 16


title: heart tissue, WT genotype, HFHS diet, Carnosine treatment rep 5

description:
library name: 25
transcript_tpms_all_samples.tsv column 27


title: Wi12

treatment_protocol: Samples were collected every 4 h for a 24-h period at the spring equinox, summer solstice, autumn equinox, and winter solstice.

value: Winter solstice 22:00


title: heart tissue, WT genotype, HFHS diet, rep 2

description:
library name: 12
transcript_tpms_all_samples.tsv column 14


title: 6_151225_2


title: heart tissue, GPX genotype, HFHS diet, rep 2

description:
library name: 17
transcript_tpms_all_samples.tsv column 19


title: 1_151021_1

value: October, 2015


title: heart tissue, WT genotype, HFHS diet, rep 1

description:
library name: 11
transcript_tpms_all_samples.tsv column 13


title: 4_151116_2

value: November, 2015


title: heart tissue, WT genotype, HFHS diet, rep 3

description:
library name: 13
transcript_tpms_all_samples.tsv column 15


title: Wi11


title: heart tissue, GPX genotype, untreated, rep 5

description:
library name: 10
transcript_tpms_all_samples.tsv column 12

value: ctl


title: Wi10

value: Winter solstice 18:00


title: heart tissue, GPX genotype, untreated, rep 4

description:
library name: 9
transcript_tpms_all_samples.tsv column 11


title: Wi9


title: heart tissue, GPX genotype, HFHS diet, rep 1

description:
library name: 16
transcript_tpms_all_samples.tsv column 18


title: heart tissue, GPX genotype, untreated, rep 2

description:
library name: 7
transcript_tpms_all_samples.tsv column 9


title: Wi7

value: Winter solstice 14:00


title: 3_151116_1


title: Wi6

value: Winter solstice 10:00


title: Wi8


title: heart tissue, GPX genotype, untreated, rep 1

description:
library name: 6
transcript_tpms_all_samples.tsv column 8

value: heart


title: Wi5


title: 2_151021_2


title: heart tissue, GPX genotype, untreated, rep 3

description:
library name: 8
transcript_tpms_all_samples.tsv column 10


title: heart tissue, WT genotype, untreated, rep 4

description:
library name: 4
transcript_tpms_all_samples.tsv column 6

value: wt


title: Wi4

value: Winter solstice 6:00


title: Wi3


title: heart tissue, WT genotype, untreated, rep 3

description:
library name: 3
transcript_tpms_all_samples.tsv column 5


title: heart tissue, WT genotype, untreated, rep 5

description:
library name: 5
transcript_tpms_all_samples.tsv column 7


title: heart tissue, WT genotype, untreated, rep 2

description:
library name: 2
transcript_tpms_all_samples.tsv column 4


title: Wi2

value: Winter solstice 2:00


title: Wi1


title: Au12

value: Autumn equinox 22:00


title: heart tissue, WT genotype, untreated, rep 1

description:
library name: 1
transcript_tpms_all_samples.tsv column 3


title: Au11


title: Au10

value: Autumn equinox 18:00


title: LB1 pA-DamID, R4-5 isolation in iLAD, clone 83, replicate 2, dam only

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

library_source: genomic

data_processing:
The full protocol is described in the corresponding manuscript.
The constant sequence of the DamID adapter was removed using cutadapt 1.11 and custom scripts.
Remaining sequences were mapped to the mouse genome (mm10) using bwa mem 0.7.17.
Reads overlapping GATC fragments were counted in 25 kb bins and normalized to 1 million reads, after which a log2-ratio was calculated of LaminB1 over the Dam control using custom R scripts.
Finally, samples were z-scale normalized to account for different in dynamic range between replicates and experiments.
Assembly: mm10
Supplementary files format and content: BigWig files of log2-normalized LaminB1 or H3K9me3 pA-DamID scores for 25 kb genomic bins.

source_name: F1 hybrid 129/Sv:CAST/EiJ

growth_protocol: F121/9 (CAST/EiJ x S129/Sv) female mouse embryonic stem cells (mESCs) F1 hybrid cell line and derived clones were cultured in 2i+LIF condition, according to the 4D Nucleome guidelines (https://data.4dnucleome.org/biosources/4DNSRMG5APUM/). Briefly, cells were cultured in serum-free DMEM/F12 (Gibco) and Neurobasal (Gibco) medium (1:1), supplemented with N-2 (Gibco), B-27 (Gibco), 0.05% BSA (Gibco), 10 × 4 U leukemia inhibitory factor (LIF; Millipore), 1 μM MEK inhibitor PD0325901 (Mirdametinib, MedChemExpress), 3 μM GSK-3β inhibitor CHIR99021 (Laduviglusib, MedChemExpress), 1.5 × 10−4 M 1-thioglycerol (Sigma-Aldrich), and 1% penicillin-streptomycin (Gibco, 15070063) on 0.1% gelatin-coated plates. Cells were passaged every 2 days. Cells were seeded and incubated overnight before harvesting. Mycoplasma contamination was ruled out by regular testings (#LT07-318; Lonza).

extract_protocol:
One million cells were collected by centrifugation (500 g, 3 min) and washed sequentially in PBS and digitonin wash buffer (DigWash) (20 mM HEPES-KOH pH 7.5, 150 mM NaCl, 0.5 mM spermidine, 0.02% digitonin, cOmplete Protease Inhibitor Cocktail). Cells were rotated for 2 h at 4 °C in 200 μL DigWash with 1:100 LaminB1 antibody (Abcam, ab16048, rabbit) or 1:100 H3K9me3 antibody (Diagenone, C15410193, Rabbit), followed by a wash step with DigWash. This was repeated with a 1:200 pA-Dam solution (~60 NEB Dam units), followed by 2 wash steps. Dam activity was induced by an incubation for 30 min at 37 °C in 100 μL DigWash supplemented with 80 μM SAM. For every condition, another 1 million cells were processed in only DigWash and during Dam activation incubated with 4 units of Dam enzyme (NEB, M0222L). This Dam only control sample serves to account for DNA accessibility and amplification biases.
Genomic DNA was isolated (Bioline, bio-52067) and ~ 500 ng were digested with DpnI (10 U, NEB, R0176L) in CutSmart Buffer 1X (8h 37°C, 20 min 80°C) in a total volume of 10 µL. A-tailing was performed by addition of 5 µL of the A-tailing mix (0.5 µL of Cutsmart buffer 10X, 0.25 µL Klenow 50 U/µL (NEB, M0212M), 0.05 µL dATP 100 mM, 4.2 µL H2O) and incubation 30 min at 37°C followed by 20 min at 75°C. Adapters were ligated by adding 15 µL of the ligation mix (3 µL T4 Ligase Buffer 10X, 0.5 µL T4 ligase (5 U/µL , Roche, 10799009001), 0.25 µl of x-Gene Stubby Adapter 50 mM (IDT), 11.25 µl H2O) and incubating samples 16h at 16°C and 10 min at 65°C. Finally, the Methyl Indexed PCR was performed by mixing 4 µL of ligated DNA with x-Gen Dual combinatorial Indexes (IDT) (125 nM final concentration) and MyTaq RedMix (Bioline, BIO-25048) in a final volume of 40 µL. The following PCR program was used: 1 X (1 min 94°C), 14 X (30 sec 94°C, 30 sec 58°C, 30 sec 72°C), 1X (2 min 72°C).

value: F1 hybrid 129/Sv:CAST/EiJ

value: mESC

value: recombined + CRISPR/Cas9 edited

tag: antibody


title: LB1 pA-DamID, R4-5 isolation in iLAD, clone 70, replicate 2, dam only


title: LB1 pA-DamID, R4-5 isolation in iLAD, clone 83, replicate 2, dam-LB1


title: Au8

value: Ventral part of telenchephalon, hypothalamus and pituitary

value: Autumn equinox 14:00


title: Au9


title: LB1 pA-DamID, R4-5 isolation in iLAD, clone 70, replicate 2, dam-LB1


title: LB1 pA-DamID, R4-5 isolation in iLAD, parental, replicate 2, dam-LB1

value: recombined


title: LB1 pA-DamID, R4-5 isolation in iLAD, clone 83, replicate 1, dam-LB1


title: Au6

value: Autumn equinox 10:00


title: Au5


title: LB1 pA-DamID, R4-5 isolation in iLAD, parental, replicate 2, dam only


title: Au3

value: Autumn equinox 6:00


title: LB1 pA-DamID, R4-5 isolation in iLAD, clone 70, replicate 1, dam-LB1


title: Au2

value: Autumn equinox 2:00


title: Au7


title: LB1 pA-DamID, R4-5 isolation in iLAD, clone 83, replicate 1, dam only


title: LB1 pA-DamID, R4-5 isolation in iLAD, parental, replicate 1, dam only


title: Au4


title: Su12

value: Summer solstice 22:00


title: LB1 pA-DamID, R4-5 isolation in iLAD, clone 70, replicate 1, dam only


title: Su11


title: LB1 pA-DamID, R4-5 isolation close to LAD, clone 127, replicate 2, dam-LB1


title: LB1 pA-DamID, R4-5 isolation in iLAD, parental, replicate 1, dam-LB1


title: LB1 pA-DamID, R4-5 isolation close to LAD, clone 84, replicate 2, dam-LB1


title: Au1


title: Su8

value: Summer solstice 14:00


title: Su10

value: Summer solstice 18:00


title: LB1 pA-DamID, R2-3 isolation close to LAD, clone 58, replicate 2, dam only


title: Su7


title: Su6

value: Summer solstice 10:00


title: LB1 pA-DamID, R4-5 isolation close to LAD, clone 84, replicate 2, dam only


title: LB1 pA-DamID, R2-3 isolation close to LAD, clone 58, replicate 2, dam-LB1


title: LB1 pA-DamID, R2-3 isolation in iLAD, clone 81, replicate 2, dam-LB1


title: LB1 pA-DamID, R2-3 isolation, parental, replicate 2, dam-LB1


title: LB1 pA-DamID, R2-3 isolation, parental, replicate 2, dam only


title: Su9


title: Su2

value: Summer solstice 2:00


title: LB1 pA-DamID, R4-5 isolation close to LAD, parental, replicate 2, dam only


title: LB1 pA-DamID, R4-5 isolation close to LAD, parental, replicate 2, dam-LB1


title: Su3

value: Summer solstice 6:00


title: Sp12

value: Spring equinox 22:00


title: Sp11


title: LB1 pA-DamID, R2-3 isolation close to LAD, clone 58, replicate 1, dam-LB1


title: LB1 pA-DamID, R4-5 isolation close to LAD, clone 127, replicate 1, dam-LB1


title: LB1 pA-DamID, R2-3 isolation in iLAD, clone 81, replicate 2, dam only


title: Su1


title: LB1 pA-DamID, R2-3 isolation close to LAD, clone 58, replicate 1, dam only


title: LB1 pA-DamID, R4-5 isolation close to LAD, clone 127, replicate 1, dam only


title: Sp9

value: Spring equinox 18:00


title: Sp7

value: Spring equinox 14:00


title: LB1 pA-DamID, R4-5 isolation close to LAD, clone 84, replicate 1, dam-LB1

value: F1 hybrid 129/Sv:CAST/EiJ

value: mESC


title: Sp8

value: Ventral part of telenchephalon, hypothalamus and pituitary


title: LB1 pA-DamID, R4-5 isolation close to LAD, clone 84, replicate 1, dam only

value: recombined + CRISPR/Cas9 edited


title: LB1 pA-DamID, R2-3 isolation in iLAD, clone 81, replicate 1, dam-LB1


title: Sp5

value: Spring equinox 10:00


title: Sp6


title: Sp10


title: LB1 pA-DamID, R2-3 isolation in iLAD, clone 81, replicate 1, dam only


title: LB1 pA-DamID, R2-3 isolation, parental, replicate 1, dam-LB1

value: recombined


title: Su5


title: Sp4

value: Spring equinox 6:00


title: LB1 pA-DamID, R4-5 isolation close to LAD, parental, replicate 1, dam-LB1


title: Sp3


title: Su4


title: Sp2

value: Spring equinox 2:00


title: LB1 pA-DamID, R2-3 isolation, parental, replicate 1, dam only


title: LB1 pA-DamID, R4-5 isolation close to LAD, parental, replicate 1, dam only


title: Sp1


title: LB1 pA-DamID, R4-5 deletion, recombined, clone 92, replicate 2, dam-LB1

value: CRISPR/Cas9 edited


title: LB1 pA-DamID, R4-5 deletion, recombined, clone 165, replicate 2, dam-LB1


title: LB1 pA-DamID, R4-5 deletion, recombined, clone 165, replicate 2, dam only


title: LB1 pA-DamID, R4-5 deletion, recombined, clone 92, replicate 2, dam only


title: LB1 pA-DamID, R4-5 deletion, parental, replicate 2, dam-LB1

value: control


title: LB1 pA-DamID, R4-5 deletion, parental, replicate 2, dam only


title: LB1 pA-DamID, R4-5 deletion, recombined, clone 165, replicate 1, dam only


title: LB1 pA-DamID, R4-5 deletion, recombined, clone 92, replicate 1, dam-LB1


title: LB1 pA-DamID, R4-5 deletion, recombined, clone 165, replicate 1, dam-LB1


title: LB1 pA-DamID, R4-5 deletion, recombined, clone 92, replicate 1, dam only


title: LB1 pA-DamID, R4-5 deletion, parental, replicate 1, dam-LB1


title: LB1 pA-DamID, R4-5 deletion, parental, replicate 1, dam only


title: UO3, IP

city: Jinzhong

first: Qing

last: Liu

address: Taigu, Shanxi Province, PR China

country: China

institute: Shanxi Agricultural university

data_processing:
Cutadapt software (v1.9.3) was used to eliminate the reads containing adaptor contaminants and low quality bases.
HISAT2 software was applied to align clean reads of all libraries to the reference genome of E. tenella
MACS software was used to identify methylated sites on RNAs (peaks),and differentially methylated sites were identified by diffReps
The m5C-enriched motifs were identified with DREME.
Assembly: pEimTen1.1 GCA_905310635.1
Supplementary files format and content: The xlsx format sheet (named Gene Expression Profiling) showed gene_id,counts of all samples of the gene, normalized counts by edgeR, and annotation of the genes.
Supplementary files format and content: The xlsx format sheet (named Methylated_RNA_sites.mRNA) showed information about methylation sites,methylated RNA,enrichment information,and annotations.

organism: Eimeria tenella

source_name: Unsporulated oocysts

extract_protocol:
Input: Total RNA was extracted from oocysts with TRIzol reagent (Invitrogen Carlsbad, CA, USA).IP:Total RNA was extracted from oocysts with TRIzol reagent (Invitrogen Carlsbad, CA, USA), and then subjected to immunoprecipitation (IP) by using the GenSeq® m5C-IP Kit (Cloudseq Biotech, Inc., Shanghai, China) following the manufacturer’s specifications.
RNA libraries for IP and input samples were constructed with the GenSeq® Low Input Whole RNA Library Prep Kit (Cloudseq Biotech, Inc., Shanghai, China) according to the manufacture’s instructions.
MeRIP-seq and RNA-seq

tag: strain

value: Unsporulated oocysts

tag: fraction

value: IP


title: SO3, Input

source_name: Sporulated oocysts

value: Sporulated oocysts

value: Input


title: UO2, Input


title: UO1, IP


title: UO1, Input


title: UO3, Input


title: SO3, IP


title: LB1 pA-DamID, i8, recombined, clone 62, replicate 2, dam-LB1

tag: genotype


title: UO2, IP


title: SO2, IP


title: SO1, IP


title: SO1, Input


title: LB1 pA-DamID, i8, recombined, clone 58, replicate 2, dam only


title: LB1 pA-DamID, i8, recombined, clone 62, replicate 2, dam only


title: LB1 pA-DamID, i8, parental, replicate 2, dam only


title: EVT, CREBBP_siRNA, rep5

first: Remco

last: Keijser

address: Meibergdreef 9

department: Reproductive Biology Laboratory

institute: Amsterdam UMC

data_processing:
Reads were quality-trimmed and adapters were removed using Trim Galore (v.0.6.6).
The processed reads were mapped to the human reference genome GRCh38 (Ensembl v105) using STAR aligner (v2.7.1a), and BAM files were indexed with Samtools (v1.11).
Using UMI-tools dedup (v1.1.2), aligned reads were deduplicated.
Fragment counts were obtained with FeatureCounts (v2.0.0). Reads were counted at the gene level and multi-mapped reads were discarded from counting.
All statistical calculations were performed in R programming language (v4.2.0). The EdgeR Bioconductor package (v3.38.1) was used to perform data normalization and differential expression analysis.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample
Supplementary files format and content: Tab-delimited text file includes FPKM calculated counts from TMM normalized data for each sample
Supplementary files format and content: Tab-delimited text file includes TMM normalised counts for each sample (log2-transformed with an offset value of 1.0)

source_name: Placenta

growth_protocol: TSCs were plated in a 5 µg/mL mouse collagen IV-coated culture plate at a density of 1x104 /cm2 in TSC medium (DMEM/F-12 + Glutamax supplemented with 0.1 mM 2-mercaptoethanol, 0.2% embryonicstem cell FBS, 0.5% Penicillin-Streptomycin, 0.3% BSA, 1% ITS-X, 1.5 µg/mL L-ascorbic acid, 50 ng/ mL human recombinant EGF, 2 µM CHIR99021, 0.5 µM A83-01, 1 µM SB431542, 0.8 mM Valproic Acid and 5 µM Y-27632) (see Table S2 for details of chemicals used in cell culture). Cells were cultured at 37 °C in 5% CO2 and medium was replaced every 2-3 days. When cells reached 70-80% confluence, they were dissociated with TrypLE for 15 min at 37 °C and passaged. TSCs at passages 10-30 were used for experiments. For EVT differentiation, TSCs were plated in a 1 µg/mL mouse collagen IV-coated culture plate at a density of 7,5x103 /cm2 in EVT medium A (DMEM/F12 + Glutamax supplemented with 0.1 mM 2-mercaptoethanol, 0.5% Penicillin-Streptomycin, 0.3% BSA, 1% ITS-X, 100 ng/mL human recombinant neuregulin-1/heregulin-beta 1, 7.5 µM A83-01, 2.5 µM Y-27632, 4% KnockOut Serum Replacement and 2% Matrigel growth factor reduced (GFR)) (day 1). At day 3 of differentiation, the medium was replaced by EVT medium B (medium A with 0.5% Matrigel GFR and without neuregulin-1/heregulin-beta 1). EVTs were harvested for analysis at day 4 of differentiation.

extract_protocol:
Cells were washed in PBS and lysed directly in the culture plate using RLT buffer (from RNeasy Mini Kit (QIAGEN, 74104)) with 1% 2-mercaptoethanol. Total RNA was extracted using the RNeasy Mini Kit (QIAGEN, 74104) according to the manufacturer’s protocol.
Total RNA libraries were prepared using the KAPA RNA HyperPrep Kit with RiboErase (Roche, 8098140702) ), after which 150 bp paired-end sequencing was performed on an Illumina NovaSeq 6000 system.

treatment_protocol: TSCs were transfected with 80 nM CREBBP, EP300, or nontargeting siRNA using 7.5 µl X-tremeGENE HP DNA Transfection Reagent (Roche, 6366236001) according to manufacturer’s instructions. One day later, transfected TSCs were dissociated and EVT differentiation was initiated.

value: Placenta

value: Trophoblast

value: CREBBP knockdown

tag: treatment

value: EVT Differentiation

tag: batch

value: male


title: LB1 pA-DamID, i8, recombined, clone 62, replicate 1, dam-LB1

value: F1 hybrid 129/Sv:CAST/EiJ

value: mESC


title: EVT, non_targeting_control_siRNA, rep5

value: Non Targeting knockdown

tag: Sex


title: EVT, EP300_siRNA, rep5

value: EP300 knockdown


title: EVT, non_targeting_control_siRNA, rep4


title: EVT, EP300_siRNA, rep4


title: LB1 pA-DamID, i8, parental, replicate 2, dam-LB1


title: LB1 pA-DamID, i8, recombined, clone 58, replicate 1, dam-LB1

value: recombined


title: SO2, Input


title: EVT, EP300_siRNA, rep3


title: EVT, CREBBP_siRNA, rep3


title: EVT, non_targeting_control_siRNA, rep3


title: EVT, CREBBP_siRNA, rep2


title: EVT, EP300_siRNA, rep2


title: LB1 pA-DamID, i8, recombined, clone 58, replicate 2, dam-LB1


title: LB1 pA-DamID, i8, parental, replicate 1, dam-LB1


title: EVT, CREBBP_siRNA, rep1


title: H3K9me3 pA-DamID, i12, recombined, clone 10, replicate 2, dam-H3K9me3


title: LB1 pA-DamID, i8, parental, replicate 1, dam only


title: H3K9me3 pA-DamID, i10, parental, replicate 2, dam-H3K9me3


title: EVT, non_targeting_control_siRNA, rep2


title: LB1 pA-DamID, i8, recombined, clone 58, replicate 1, dam only


title: H3K9me3 pA-DamID, i10, parental, replicate 1, dam-H3K9me3


title: EVT, EP300_siRNA, rep1


title: H3K9me3 pA-DamID, i10, recombined, clone 18, replicate 1, dam-H3K9me3


title: EVT, non_targeting_control_siRNA, rep1


title: H3K9me3 pA-DamID, i12, recombined, clone 10, replicate 1, dam-H3K9me3


title: 293T_total_ActD_2h

city: Hefei,

first: Xu

state: Anhui Province

address: School of Basic Medical Sciences University of Science and Technology of China 443 Huangshan Road

data_processing:
For ng-circRNA identification, the clean reads not aligned to rDNA sequences filtered by bowtie2 were mapped to the reference genome by bwa-mem. circRNA candidates were predicted by CIRI2 (v 2.0.6).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include count values for each Sample

extract_protocol:
Total cells were lysed in TRizol reagent (Life Technologies). RNA were extracted by using TRizol reagent according to the manufacturer’s instructions.
For total RNA sequencing, rRNA is removed from the total RNA sample using TruSeq Stranded Total RNA Library Prep Gold (Illumina, 20020599), and sequencing libraries were generated using NEB Next Ultra Directional RNA Library Prep Kit for Illumina (NEB, E7420) following the manufacturer’s recommendations. The libraries were subjected to 150 nt paired-end sequencing with an Illumina Nova seq 6000 system. Each library generated a depth of ~10 G read pairs.

value: WT

tag: library type

value: RNA-seq


title: 293T_total_ActD_6h

institute: University of Science and Technology of China


title: H3K9me3 pA-DamID, i10, parental, replicate 2, dam only

tag: cell type

value: control


title: H3K9me3 pA-DamID, i12, parental, replicate 1, dam-H3K9me3


title: H3K9me3 pA-DamID, i12, recombined, clone 10, replicate 2, dam only


title: H3K9me3 pA-DamID, i12, parental, replicate 2, dam-H3K9me3


title: H3K9me3 pA-DamID, i12, parental, replicate 2, dam only


title: AP2XI-2-mAID-6HA_+IAA

city: Lanzhou

first: JinLei

last: Wang

address: yanchangbao

institute: LVRI

description: Parasite of PruAP2XI-2-mAID-6HA strain grown in HFF with IAA

data_processing:
Raw reads in fastq format were processed using fastp (v0.20.0) and clean reads were obtained by removing reads containing adapter, reads containing ploy-N and low-quality reads from the raw data.
Clean reads were aligned to the ME49 genome using BWA (v0.7.12)
Only uniquely mapped (MAPQ ≥ 13) and de-duplicated reads were used for further analysis.
The peak calling was performed with MACS2 (v2.1.0) and ChIPseeker was used to retrieve the nearest genes around the peak and annotate the genomic region of the peak.
Visualization of peak distribution along genomic regions of genes of interest was performed with IGV.
Assembly: Toxoplasma gondii ME49
Supplementary files format and content: bw
Library strategy: CUT&TAG

organism: Toxoplasma gondii

growth_protocol: Parasites were maintained at 37 ℃ in confluent monolayers of human foreskin fibroblast (HFF) cells

extract_protocol:
Briefly, ~ 107 intracellular tachyzoites were collected and the parasite nuclei were isolated by resuspension of the washed parasite pellet in NE Buffer. The nuclei were then processed according to the manufacturer’s protocol and libraries were constructed using ‘TD903 Hyperactive Universal CUT&Tag Assay Kit for Illumina’ and ‘TD202 TruePrep Index Kit V2 for Illumina’ from Vazyme Biotech (#TD202, China)
Libraries were sequenced on Illumina Novaseq platform at Novogene Science and Technology Co., Ltd (Beijing, China) and 150 bp paired-end reads were generated.

value: Pru

value: Parasites in HFF

value: Type 2

value: Parasites in HFF with IAA


title: AP2XII-1-mAID-6HA_-IAA

description: Parasite of PruAP2XII-1-mAID-6HA strain grown in HFF without IAA

value: Parasites in HFF without IAA


title: MORC-2Ty-AP2XI-2-mAID-6HA_-IAA

description: Parasite of PruAP2XI-2-mAID-6HA-MORC-2Ty grown in HFF without IAA


title: AP2XII-1-mAID-6HA_+IAA

description: Parasite of PruAP2XII-1-mAID-6HA strain grown in HFF with IAA


title: MORC-2Ty-AP2XI-2-mAID-6HA_+IAA

description: Parasite of PruAP2XI-2-mAID-6HA-MORC-2Ty grown in HFF with IAA


title: Intraocular RB 2, scRNAseq

city: Shanghai

first: wei

last: hu

address: No. 650 Songjiang Road

institute: Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine

description: 10x Genomics

data_processing:
Raw scRNA-seq reads were first processed by the Cell Ranger (version 6.0.2) software44 by default settings.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files

source_name: Retinoblastoma

extract_protocol:
Fresh human RB tissue samples were immediately washed three times in ice-cold PBS after collection. Dissociation into single cells was achieved by incubation in 0.25% trypsin-0.01% EDTA (Invitrogen) at 37 °C for 5 min, gentle pipetting and flicking, and trypsin was then blocked with addition of FBS (Gibco). Dissociated cells were filtered with 70 μm cell strainer (Corning) and centrifuged at 1000 rpm for 5 min, and followed by resuspension in 200 to 500 ul ice-cold PBS. Cell counting and viability rate were determined with Countess II automated cell counter (Invitrogen) after 0.4% trypan blue staining, and the sample quality was only considered ideal for further single-cell assessment when the cell viability was higher than 90% and clustering rate was less than 1%. Samples were processed within 3 h from surgical removal to loading on the Chromium (10x Genomics) instrument.
GEMs (Gel Bead-In-EMulsions) are formed by combining the prepared single-cell suspension with gel beads containing barcode information and a mixture of enzymes, which are then encapsulated by oil droplets located in microfluidic "single-cross" junctions. Valid GEMs include beads (pre-made 10x primers in beads), single cells, and Master Mix. Then, cell lysis and reverse transcription reactions were performed within the GEMs. In valid GEMs, 10x Barcode would be ligated with the cDNA product. Next, GEMs and oil droplets were broken. PCR amplification was performed using the cDNA as a template. After the amplification was completed, the quality inspection of the amplified products (the size of the amplified fragments and the yield of the amplified products) was performed. After the amplification products were qualified, the sequencing library was constructed. First, the cDNA was chemically broken into fragments of about 200~300bp; cDNA was fragmented, end-repaired and A-added; cDNA fragments were screened; the P7 adapter was connected and the sample index was introduced by PCR amplification; and finally fragment screening is performed to obtain cDNA library.

value: Retinoblastoma


title: RNA-seq, i10, recombined, clone 18, replicate 2

data_processing:
Reads were mapped to the 129S1 and CAST genomes separately, using STAR aligner.
Only reads with MAPQ > 10 were kept, using SAMtools.
Reads coming from each allele were then split using a custom R script. Briefly, the alignment score (AS tag in BAM file) of a given read to the 129S1 genome is compared to its alignment score to the CAST genome. If it is higher for 129S1 genome (resp. CAST), the read is assigned to 129S1 genome (resp. CAST). If alignment scores are equal and greater than zero, the read is tagged as ambiguous. If both alignment scores are zero, the read is tagged as unmapped. Split allele-specific and ambiguous/unmapped bam files are produced as output.
To generate allele-specific gene counts, gene annotations from GENCODE (Release M23 – mm10) were first lifted over to 129S1 and CAST genomes using Liftoff (https://github.com/agshumate/Liftoff). Then, read coordinates from the allele-specific filtered bam files were overlapped with the corresponding lifted-over gene coordinates, using the “summarizeOverlaps” function from the GenomicAlignments Bioconductor package.
Assembly: GCA_001624185.1 (129S1 allele), GCA_001624445.1 (CAST allele) and mm10
Supplementary files format and content: tab-delimited text file including the raw read count mapped to the CAST and the 129S1 genomes, for each sample

extract_protocol:
One million cells were harvested, washed once in cold PBS, resuspended in 600 µL of RTL buffer (RNeasy Mini kit, 74104, Qiagen) and stored at -80°C until subsequent RNA isolation. RNA was isolated using the RNeasy Mini kit (74104, Qiagen).
Libraries were prepared using the TruSeq® Stranded mRNA Library Prep (20020594, Illumina) and TruSeq RNA Single Indexes Set A (Illumina) kits, according to the manufacturer's protocol. Libraries were sequenced for single-end 75-bp reads on a NextSeq platform. Approximately 25 million reads were sequenced for every condition.


title: H3K9me3 pA-DamID, i10, parental, replicate 1, dam only


title: 293T_total_ActD_0h


title: H3K9me3 pA-DamID, i10, recombined, clone 18, replicate 2, dam only


title: Extraocular RB 2, scRNAseq

description: 10x Genomics


title: H3K9me3 pA-DamID, i12, recombined, clone 10, replicate 1, dam only


title: RNA-seq, i10, parental, replicate 2


title: Extraocular RB 1, scRNAseq

description: 10x Genomics


title: RNA-seq, i10, recombined, clone 18, replicate 1


title: LB1 pA-DamID, R4-5 isolation close to LAD, clone 127, replicate 2, dam only

value: recombined + CRISPR/Cas9 edited


title: RNA-seq, i10, parental, replicate 1


title: RNA-seq, i12, recombined, clone 10, replicate 1


title: smallRNA-seq for Frac 4

data_processing:
For mecciRNA identification, the clean data were filtered by bowtie2 (v 1.2.1) to remove reads mapped to rDNA. The left reads were mapped to the reference genome by bwa-men (v 0.7.17). The discontinuously mapped reads were extracted and mapped again to mitochondrial genome by bowtie (v 1.2.1). mecciRNA candidates were predicted by pepline mentioned in our article.
For ng-circRNA identification, the clean reads not aligned to rDNA sequences filtered by bowtie2 were mapped to the reference genome by bwa-mem. circRNA candidates were predicted by CIRI2 (v 2.0.6).
For smallRNA-seq analysis, the raw data were trimmed by cutadapt (v 1.15) to remove adaptor sequences to get clean data. The clean data were mapped to the mitochondrial genome with bowtie, and the forward or reverse mapping reads were extracted by samtools (v 1.10). The distribution of peaks was generated with an integrative genomics viewer (IGV) (v 2.11.0).
Assembly: hg38, mm10, ce11
Supplementary files format and content: comma-separated value files include count values for each Sample
Supplementary files format and content: tab-delimited text files include count values for each Sample
Supplementary files format and content: bigwig

extract_protocol:
The isolated mitochondria, total cells were lysed in TRizol reagent (Life Technologies). RNA from  mitochondia, whole cell, mitochondrial fractions and RNA-IP were extracted by using TRizol reagent according to the manufacturer’s instructions.
For small RNA seq, the small RNA bands in fractions 2–4 and the input were excised from the gel and RNAs were purified. Small RNA libraries were constructed with NEBNext Multiplex Small RNA Library Prep Set for Illumina following the manufacturer’s protocol. For total RNA and mitochondrial RNA sequencing, rRNA is removed from the total RNA sample using TruSeq Stranded Total RNA Library Prep Gold (Illumina, 20020599), and sequencing libraries were generated using NEB Next Ultra Directional RNA Library Prep Kit for Illumina (NEB, E7420) following the manufacturer’s recommendations. The libraries were subjected to 150 nt paired-end sequencing with an Illumina Nova seq 6000 system. Each library generated a depth of ~10 G read pairs.
For TRAP1 RIP and ATP5B RIP, sequencing libraries were generated using NEB Next Ultra Directional RNA Library Prep Kit for Illumina (NEB, E7420) following the manufacturer’s recommendations.
For other RIP-seq, NEB Next Ultra RNA Library Prep Kit (NEB) was used for library construction of immunoprecipitated RNA. The libraries were subjected to 150 nt paired-end sequencing with an Illumina Nova seq 6000 system. Each library generated a depth of ~10 G read pairs.

value: small RNA-seq


title: RNA-seq, i12, recombined, clone 10, replicate 2


title: H3K9me3 pA-DamID, i12, parental, replicate 1, dam only


title: H3K9me3 pA-DamID, i10, recombined, clone 18, replicate 1, dam only


title: smallRNA-seq for Frac 3


title: AP2XI-2-mAID-6HA_-IAA

description: Parasite of PruAP2XI-2-mAID-6HA strain grown in HFF without IAA


title: smallRNA-seq for input


title: Intraocular RB 1, scRNAseq

description: 10x Genomics


title: H3K9me3 pA-DamID, d1, parental, replicate 2, dam-H3K9me3


title: RNA-seq, i12, parental, replicate 1


title: RNA-seq, i7, recombined, clone 12, replicate 2


title: LB1 pA-DamID, i8, recombined, clone 62, replicate 1, dam only


title: RNA-seq, i7, recombined, clone 7, replicate 2


title: H3K9me3 pA-DamID, d3, recombined, clone 21, replicate 2, dam-H3K9me3


title: RNA-seq, i7, recombined, clone 12, replicate 1


title: 293T_HET_total


title: RNA-seq, i7, parental, replicate 2


title: RNA-seq, i7, recombined, clone 7, replicate 1


title: RNA-seq, d6, recombined, clone 16, replicate 2


title: 293T_WT_total


title: 293T_HET_mito


title: RNA-seq, d6, recombined, clone 16, replicate 1


title: 293T_WT_mito


title: H3K9me3 pA-DamID, d1, recombined, clone 28, replicate 2, dam-H3K9me3


title: smallRNA-seq for Frac 2


title: IgG for 293Tmito_ATP5B_RIP

value: RIP-seq


title: RNA-seq, d3, recombined, clone 21, replicate 2

value: F1 hybrid 129/Sv:CAST/EiJ


title: RNA-seq, d3, recombined, clone 21, replicate 1

value: mESC


title: RNA-seq, d6, parental, replicate 2


title: RNA-seq, d3, recombined, clone 12, replicate 1


title: H3K9me3 pA-DamID, d1, recombined, clone 28, replicate 2, dam only


title: H3K9me3 pA-DamID, d6, parental, replicate 2, dam-H3K9me3


title: RNA-seq, i12, parental, replicate 2


title: H3K9me3 pA-DamID, d1, parental, replicate 2, dam only


title: RNA-seq, d3, recombined, clone 12, replicate 2


title: H3K9me3 pA-DamID, d3, parental, replicate 2, dam-H3K9me3


title: 293Tmito_ATP5B_RIP


title: RNA-seq, i7, parental, replicate 1


title: RNA-seq, d6, parental, replicate 1


title: RNA-seq, d3, parental, replicate 2


title: RNA-seq, d3, parental, replicate 1


title: IgG for 293Tmito_TRAP1_RIP


title: H3K9me3 pA-DamID, d3, recombined, clone 21, replicate 2, dam only


title: H3K9me3 pA-DamID, d3, parental, replicate 2, dam only


title: 293Tmito_TRAP1_RIP


title: B6E14-5-2_ATAC

city: HOUSTON

first: Zhongming

last: Zhao

state: Texas

address: 7000 Fannin St

department: School of Biomedical Informatics

institute: UTHealth

description:
chromatin accessibility
10x Genomics

data_processing:
The 10x Genomics Cell Ranger ARC (v2.0.0) pipeline was used to process the multiome data. Raw sequencing data were first converted to fastq format using ‘cellranger-arc mkfastq’. The raw files of RNA-seq and ATAC-seq libraries from the same sample were aligned to the UCSC mouse genome (mm10) and quantified using ‘cellranger-arc count’. Samples were aggregated using ‘cellranger-arc aggr’ to normalize the sequencing depth.
Assembly: mm10
Supplementary files format and content: h5 file: contains both RNA-seq counts and ATAC-seq counts; tsv.gz: frangments file for ATAC-seq; tsv.gz.tbi: frangments file index for ATAC-seq

source_name: E14.5, replicate 2, single-cell multiome

extract_protocol:
Single-cell suspensions were prepared from pooled paired secondary palatal shelves of three embryos at E12.5, two embryos at E13.5, and one embryo at E14.0 and E14.5. The micro-dissected palatal shelves were treated with 0.25% trypsin and 0.05% EDTA (150 μL) for 5 min at 37 °C with gentle agitation (300 rpm). The dissociated cell mixtures were then suspended with 300 μL Dulbecco’s Modified Eagle’s Medium (DMEM, Millipore Sigma) supplemented with heat-inactivated 10% fetal bovine serum (FBS).The cells were centrifuged at 500 g for 5 min at 4 °C and the cell pellets were resuspended and incubated with chilled 300 μL of 0.1x Lysis Buffer [10 mM Tris-HCl (pH7.4), 10 mM NaCl, 3 mM MgCl2, 1% BSA, 1mM DTT, 1U/μL RNase inhibitor, 0.01% Tween20, 0.01% Nonidet P40 Substitute, and 0.001 % Digitonin] for 3 min on ice, followed by stopped with chilled 300 μL Wash Buffer [10 mM Tris-HCl (pH7.4), 10 mM NaCl, 3 mM MgCl2, 1% BSA, 1mM DTT, 1U/μL RNAase inhibitor, and 0.1% Tween20]. The cells were then collected by centrifuge at 500 g for 5 min at 4 °C, rinsed with 200 uL Wash Buffer twice, and resuspended in Diluted Nuclei Buffer [1x Nuclei Buffer, 1 mM DTT, and 1U/μL RNase inhibitor]. Isolated single-cell nuclei were filtered using a cell strainer (40 μm pore size) and inspected under a microscope to ensure they were successfully dissociated into single cell level for subsequent sequencing.
The single cell libraries were constructed by following the 10x Genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression protocol (CG000338). Briefly, nuclei suspensions were incubated with a transposase, which fragmented the DNA in open regions of the chromatin and added the adapter sequences to the ends of the DNA fragments. The transposed nuclei were loaded onto Chromium Next GEM Chip J (PN-1000234, 10xGenomics, Pleasanton, CA) with partitioning oil and barcoded single-cell gel beads, followed by PCR amplification. The ATAC library and the gene expression library were then prepared separately. The quality of the libraries was examined using Agilent High Sensitive DNA Kit (#5067-4626) by Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, USA). The library concentrations were determined by qPCR using Collibri Library Quantification kit (#A38524500, Thermo Fisher Scientific) on a QuantStudio3 (ThermoFisher Scientific). We then pooled the libraries evenly and performed the paired-end sequencing on an Illumina NextSeq 550 System (Illumina, Inc., USA) using High Output Kit v2.5 (#20024907, Illumina, Inc., USA).
Multiome (snRNA-seq and snATAC-seq)

value: Palatal shelves

tag: developmental stage


title: IgG for 293Ttotal_SUPV3L1_RIP


title: H3K9me3 pA-DamID, d6, recombined, clone 16, replicate 2, dam-H3K9me3


title: B6E14-5-2_RNA

description:
nuclear RNA
10x Genomics


title: H3K9me3 pA-DamID, d6, recombined, clone 16, replicate 2, dam only


title: B6E14-5-1_ATAC

description:
chromatin accessibility
10x Genomics

source_name: E14.5, replicate 1, single-cell multiome


title: IgG for 293Tmito_SUPV3L1_RIP


title: B6E14-0-2_ATAC

description:
chromatin accessibility
10x Genomics

source_name: E14.0, replicate 2, single-cell multiome


title: B6E14-5-1_RNA

description:
nuclear RNA
10x Genomics


title: B6E14-0-2_RNA

description:
nuclear RNA
10x Genomics


title: HeLa_mito_ActD_0h


title: B6E14-0-1_ATAC

description:
chromatin accessibility
10x Genomics

source_name: E14.0, replicate 1, single-cell multiome


title: H3K9me3 pA-DamID, d1, recombined, clone 28, replicate 1, dam-H3K9me3


title: H3K9me3 pA-DamID, d6, parental, replicate 2, dam only


title: HeLa_total_ActD_2h


title: H3K9me3 pA-DamID, d1, parental, replicate 1, dam-H3K9me3


title: B6E13-5-2_ATAC

description:
chromatin accessibility
10x Genomics

source_name: E13.5, replicate 2, single-cell multiome


title: HeLa_mito_ActD_2h


title: B6E13-5-3_RNA

description:
nuclear RNA
10x Genomics

source_name: E13.5, replicate 3, single-cell multiome


title: B6E13-5-3_ATAC

description:
chromatin accessibility
10x Genomics


title: B6E13-5-2_RNA

description:
nuclear RNA
10x Genomics


title: B6E13-5-1_RNA

description:
nuclear RNA
10x Genomics

source_name: E13.5, replicate 1, single-cell multiome


title: B6E13-5-1_ATAC

description:
chromatin accessibility
10x Genomics


title: H3K9me3 pA-DamID, d3, recombined, clone 21, replicate 1, dam-H3K9me3


title: 293T_mito_ActD_6h


title: B6E12-5-1_ATAC

description:
chromatin accessibility
10x Genomics

source_name: E12.5, replicate 1, single-cell multiome

value: embryonic day (E) 12.5


title: B6E12-5-2_RNA

description:
nuclear RNA
10x Genomics

source_name: E12.5, replicate 2, single-cell multiome


title: B6E12-5-2_ATAC

description:
chromatin accessibility
10x Genomics


title: H3K9me3 pA-DamID, d6, recombined, clone 16, replicate 1, dam-H3K9me3

value: recombined


title: HeLa_total_ActD_0h

value: WT


title: 293T_mito_ActD_2h

value: RNA-seq


title: Postransplant lymphoproliferative disorder (PTLD) 43

description: Hybridized to Affymetrix OncoScan FFPE Assay

data_processing:
Nexus biodiscovery software
Gains and losses were evaluated with visual inspection by 2 different observers using Nexus Biodiscovery software (Biodiscovery, Hawthorne CA, USA). The CNAs with a minimum size of 100kb were considered real. Loss of heterozigosity regions where considered when size was >5Mb.

source_name: LN

extract_protocol: DNA from formalin-fixed paraffin-embedded (FFPE)  was extracted using AllPrep DNA/RNA FFPE Qiagen extraction kit (Qiagen, Hilden, Germany)

tag: disease state

value: PTLD

tag: morphology

value: Monomorphic PTLD

tag: diagnosis

value: DLBCL

tag: gender

value: male

tag: tissue preparation

value: FFPE


title: B6E12-5-1_RNA

description:
nuclear RNA
10x Genomics

tag: tissue


title: B6E14-0-1_RNA

description:
nuclear RNA
10x Genomics


title: 293T_mito_ActD_0h

tag: cell line


title: Postransplant lymphoproliferative disorder (PTLD) 42

source_name: abdominal mass

value: BL


title: H3K9me3 pA-DamID, d1, recombined, clone 28, replicate 1, dam only

tag: antibody


title: H3K9me3 pA-DamID, d3, parental, replicate 1, dam-H3K9me3

value: control


title: Postransplant lymphoproliferative disorder (PTLD) 38

source_name: intestine


title: H3K9me3 pA-DamID, d1, parental, replicate 1, dam only

source_name: F1 hybrid 129/Sv:CAST/EiJ


title: Postransplant lymphoproliferative disorder (PTLD) 39

source_name: Tonsil

value: female


title: Postransplant lymphoproliferative disorder (PTLD) 37

source_name: scalp


title: Postransplant lymphoproliferative disorder (PTLD) 33

source_name: mesenterio


title: Postransplant lymphoproliferative disorder (PTLD) 36


title: Postransplant lymphoproliferative disorder (PTLD) 32

source_name: Axilar LN


title: H3K9me3 pA-DamID, d3, parental, replicate 1, dam only


title: Postransplant lymphoproliferative disorder (PTLD) 31

source_name: jejunum


title: RMS1_O_P14 [scRNAseq]

data_processing:
gene-barcode count matrices were generated from raw sequencing reads using Cell Ranger (v.3.1.0, 10x Genomics) mkfastq and count.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
FNRMS-derived organoids were dissociated using TrypLE Express Enzyme (ThermoFisher Scientific, cat. no. 12605010) preheated to 37 °C for 3 min. Cells were then filtered through a 30-µm strainer (Miltenyi Biotec, cat. no. 130 098 458), centrifuged at 500 × g for 5 min, resuspended in complete culture medium and sorted using a FACSAria (BD Biosciences). Cells were centrifuged again at 500 × g for 8 min and resuspended in PBS (Gibco, cat. no. 14190-094) with 0.04% BSA (Sigma-Aldrich, cat. no. A7030) for a final cell concentration of 1 000 cells/µL.
Approximately 20 µL of isolated cells were loaded on a 10X Genomic chip and run on the Chromium Controller system (10X Genomics) to target 10 000 cells per sample. Gene expression data were generated with the Chromium Single Cell 5’ v3.1 assay (10X Genomics) and sequenced on the NovaSeq 6000 platform (S1 flow cell, Illumina).

value: RMS1 organoid

value: Rhabdomyosarcoma

tag: age in_years

value: M

tag: histological subtype

value: Embryonal

value: Relapse

tag: sample location

value: Parameningeal

tag: primary tumor_location

tag: fresh/cryopreserved

value: fresh

tag: medium

tag: passage number

tag: culture type


title: H3K9me3 pA-DamID, d6, parental, replicate 1, dam-H3K9me3

value: F1 hybrid 129/Sv:CAST/EiJ

tag: cell type

value: mESC

tag: genotype


title: DMEM_2D_P5 [RNAseq]

data_processing:
Trimming of adapter sequences was done with Cutadapt (v.3.4) using -a CTGTCTCTTATACACATCT and -A CTGTCTCTTATACACATCT parameters.
Reads were mapped using STAR (v.2.7.9) to the human reference genome assembly GRCh38.p13 with --seedSearchStartLmax 38 --outFilterMatchNminOverLread 0.66 --outReadsUnmapped Fastx --outSAMmultNmax -1 --outMultimapperOrder Random --outFilterScoreMinOverLread 0.66 --quantMode TranscriptomeSAM --outSAMstrandField intronMotif --twopassMode Basic --limitSjdbInsertNsj 1324910 parameters.
Gene expression data was generated with HTseq-count (v.0.13.5) using --order pos --stranded reverse parameters.
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

extract_protocol:
RNA from both RMS tissues and matched in vitro models cultured in 2D or 3D conditions with DMEM, M3 and M5 media were extracted using the Allprep DNA/RNA/miRNA universal kit (Qiagen, cat. no. 80224) and Arcturus® PicoPure® RNA Isolation Kit (ThermoFisher Scientific, cat. no. KIT0204) only for small tumor pieces, following manufacturer’s instructions.
For RNA‑seq library construction, 100 to 1 000 ng of total RNAs were used. Libraries were prepared with Illumina Stranded mRNA Prep (Illumina, cat. no. 20040534) following recommendations.
ssRNA-seq (stranded RNA-seq)

value: RMS2 cell line

tag: Sex

tag: disease state

value: Relapse/metastatic

value: Lung

value: Ischioanal

value: DMEM


title: DMEM_2D_P3 [RNAseq]


title: Postransplant lymphoproliferative disorder (PTLD) 29

source_name: transmural ileum

value: PTLD

tag: morphology

value: Monomorphic PTLD

tag: diagnosis

value: BL

tag: gender

value: male

value: FFPE


title: RMS2_O_P3 [RNAseq]

tag: tissue

tag: cell line

value: RMS2 organoid

value: Rhabdomyosarcoma

value: M


title: Postransplant lymphoproliferative disorder (PTLD) 30

source_name: hepatic

value: DLBCL

tag: tissue preparation


title: Postransplant lymphoproliferative disorder (PTLD) 28

source_name: intestinal


title: H3K9me3 pA-DamID, d6, parental, replicate 1, dam only

value: control

tag: antibody


title: RMS2_O_P14* [RNAseq]

tag: age in_years

tag: histological subtype

value: Embryonal

tag: sample location

value: cryopreserved


title: Postransplant lymphoproliferative disorder (PTLD) 26

source_name: Mesenteric LN


title: H3K9me3 pA-DamID, i7, recombined, clone 12, replicate 2, dam-H3K9me3

value: F1 hybrid 129/Sv:CAST/EiJ

value: mESC

value: recombined


title: Postransplant lymphoproliferative disorder (PTLD) 22

value: female


title: H3K9me3 pA-DamID, d3, recombined, clone 21, replicate 1, dam only


title: RMS2_O_P13* [RNAseq]

value: Relapse/metastatic

value: Lung

tag: primary tumor_location

value: Ischioanal

tag: fresh/cryopreserved

tag: medium


title: H3K9me3 pA-DamID, i7, recombined, clone 7, replicate 2, dam-H3K9me3

tag: cell type


title: Postransplant lymphoproliferative disorder (PTLD) 21

source_name: Mesenteric LN, intestinal

value: PTLD

value: Monomorphic PTLD


title: Postransplant lymphoproliferative disorder (PTLD) 25

value: male

value: FFPE


title: RMS2_O_P2 [RNAseq]

value: RMS2 organoid

value: Rhabdomyosarcoma

value: fresh

tag: passage number

tag: culture type


title: RMS1_O_P13 [scRNAseq]

value: RMS1 organoid

tag: Sex

value: M

tag: disease state

value: Relapse

value: Parameningeal


title: Postransplant lymphoproliferative disorder (PTLD) 20

source_name: LN, intestinal

tag: morphology

tag: diagnosis

value: DLBCL


title: Postransplant lymphoproliferative disorder (PTLD) 19

source_name: Intestinal

tag: gender


title: H3K9me3 pA-DamID, i7, parental, replicate 2, dam-H3K9me3

tag: cell line

value: F1 hybrid 129/Sv:CAST/EiJ

value: mESC

tag: genotype

value: control


title: H3K9me3 pA-DamID, d6, recombined, clone 16, replicate 1, dam only

value: recombined

tag: antibody


title: Postransplant lymphoproliferative disorder (PTLD) 14

tag: tissue preparation


title: RMS2_O_P29* [RNAseq]

tag: tissue

tag: age in_years

tag: histological subtype

value: Embryonal

value: Relapse/metastatic

value: Lung

value: Ischioanal

value: cryopreserved


title: RMS2_O_P28* [RNAseq]

value: RMS2 organoid

tag: sample location

tag: primary tumor_location

tag: fresh/cryopreserved


title: Postransplant lymphoproliferative disorder (PTLD) 13

source_name: Cervical LN

value: PTLD

value: Monomorphic PTLD

value: male

value: FFPE


title: Postransplant lymphoproliferative disorder (PTLD) 11

source_name: Inguinal L LN

value: BL


title: Postransplant lymphoproliferative disorder (PTLD) 7

source_name: Lung

value: female


title: RMS2_O_P17 [RNAseq]

tag: cell type

value: Rhabdomyosarcoma

value: M

value: fresh

tag: medium

tag: passage number


title: Postransplant lymphoproliferative disorder (PTLD) 12

source_name: LN

tag: disease state

value: DLBCL


title: Postransplant lymphoproliferative disorder (PTLD) 2

source_name: Duodenal mucosa

tag: morphology


title: H3K9me3 pA-DamID, i7, parental, replicate 2, dam only

source_name: F1 hybrid 129/Sv:CAST/EiJ

value: F1 hybrid 129/Sv:CAST/EiJ

value: mESC

value: control


title: RMS2_O_P15 [RNAseq]

tag: Sex

value: Embryonal

value: Relapse/metastatic

value: Lung

tag: culture type


title: H3K9me3 pA-DamID, i7, recombined, clone 12, replicate 1, dam-H3K9me3

tag: cell line

value: recombined


title: H3K9me3 pA-DamID, i10, recombined, clone 18, replicate 2, dam-H3K9me3

tag: genotype


title: FLAG; TetR-SET; Sir2Sp-HP1; Sir3-SET; hfl1D; ChIP-seq (A, B, C)

city: BOSTON

first: Andy

last: Yuan

state: MA

address: 240 Longwood Avenue

department: Cell Biology

institute: Harvard Medical School

data_processing:
ChIP-seq reads were mapped to the S288C reference genome R64.3.1 using Bowtie with default settings
Data was normalized to counts per million using the bamCoverage module of deepTools 3.5.2
Data was visualized in IGV 2.16.0.

organism: Saccharomyces cerevisiae

growth_protocol: 50-100 ml cultures of S. cerevisiae cells were grown in YPAD medium to an OD600 of 1 to 2.

extract_protocol:
Cells were fixed in the presence of 1% formaldehyde for 15 minutes at room temperature with gentle mixing on a moving platform.  For FLAG3X-Suv39x and Sir3-FLAG3X-SET immunoprecipitations, cells were fixed in the presence of 1.5 mM ethylene glycol bis(succinimidyl succinate) (EGS) for 30 minutes at room temperature and then fixed in the presence of 1% formaldehyde for 30 minutes at room temperature.  Crosslinking reactions were quenched in the presence of 125 mM glycine.  Crosslinked cells were pelleted, washed twice in cold tris-buffered saline (TBS), once in cold water, and stored at -80oC.  Samples were sonicated in a cold room using a tip sonicator (Sonics VCX 500; set at 30% amplitude) for a total of 80 seconds, with five-minute incubations on ice after every 20 seconds of sonication.  Samples were further sheared by sonication using a Q800R3 sonicator (Qsonica; set at 20% amplitude).  Samples were sonicated for a total of 15 minutes, with 15-second incubations without sonication following every 15 seconds of sonication.
Libraries were prepared by ligating Y-adapters encoding unique barcode sequences (Wong, Jin, and Moqtaderi, 2013) to immunoprecipitated DNA.  Libraries were amplified by PCR for 18 cycles.  Amplified DNA 150-500 bp in length was purified using a gel extraction kit (Omega Bio-tek) and SPRIselect beads (Beckman Coulter).

tag: antibody

value: anti-FLAG (Sigma M2)


title: RMS2_T2 [RNAseq]

source_name: RMS2 tissue

value: RMS2 tissue

value: Ischioanal


title: FLAG; TetR-SET; Sir2Sp-HP1; Sir3-SET; sir-; ChIP-seq (A, B, C)


title: FLAG; TetR-SET; Sir2Sp-HP1; Sir3-SET; ChIP-seq (A, B, C)


title: H3K9me3 pA-DamID, i7, recombined, clone 7, replicate 1, dam-H3K9me3


title: H3K9me3 pA-DamID, i7, recombined, clone 12, replicate 2, dam only


title: FLAG; TetR-SET; Suv39x: ChIP-seq (B)


title: Postransplant lymphoproliferative disorder (PTLD) 15

value: PTLD

value: Monomorphic PTLD

tag: diagnosis

tag: gender

tag: tissue preparation

value: FFPE


title: RMS2_T1 [RNAseq]

tag: tissue

value: Rhabdomyosarcoma

tag: age in_years

tag: histological subtype


title: FLAG; TetR-SET; Suv39x: ChIP-seq (A)


title: H3K9me3 pA-DamID, i7, recombined, clone 7, replicate 2, dam only


title: H3K9me3 pA-DamID, i7, recombined, clone 12, replicate 1, dam only


title: input DNA; AY4345 (A)


title: H3K9me3 pA-DamID, i7, parental, replicate 1, dam-H3K9me3


title: input DNA; AY4345 (B)


title: input DNA; AY4307 (B)


title: RMS1_O_P13* [RNAseq]

value: RMS1 organoid

value: M

value: Relapse

tag: sample location

value: Parameningeal

tag: primary tumor_location

tag: fresh/cryopreserved

value: cryopreserved


title: H3K9me3 pA-DamID, i7, recombined, clone 7, replicate 1, dam only

value: F1 hybrid 129/Sv:CAST/EiJ

tag: cell type

value: mESC


title: RMS1_O_P22* [RNAseq]

value: Embryonal

tag: disease state

tag: medium

tag: passage number


title: H3K9me3 pA-DamID, i7, parental, replicate 1, dam only

value: control


title: input DNA; AY2896 (B)


title: input DNA; AY4307 (A)


title: input DNA; AY2896 (A)


title: RMS1_O_P23* [RNAseq]

tag: Sex

tag: culture type


title: H3K9me2; TetR-SET; Sir2Sp-HP1; Sir3-SET; hfl1D; ChIP-seq (B)

tag: cell line

tag: genotype

value: anti-H3K9me2 (Abcam ab1220)


title: H3K9me2; TetR-SET; Sir2Sp-HP1; Sir3-SET; hfl1D; ChIP-seq (A)

tag: antibody


title: H3K9me2; TetR-SET; Sir2Sp-HP1; Sir3-SET; sir-; ChIP-seq (A, B, C)


title: RMS1_O_P12* [RNAseq]


title: H3K9me2; TetR-SET; Sir2Sp-HP1; Sir3-SET; ChIP-seq (A)


title: M3_2D_P12* [RNAseq]

value: RMS1 cell line


title: LB1 pA-DamID, i9, recombined, clone 14, replicate 2, dam-LB1

value: recombined


title: LB1 pA-DamID, i9, parental, replicate 2, dam-LB1


title: H3K9me2; TetR-SET; Sir2Sp-HP1; Suv39x; ChIP-seq (B)


title: M3_2D_P13* [RNAseq]


title: LB1 pA-DamID, i9, recombined, clone 12, replicate 2, dam-LB1


title: RMS1_O_P6 [RNAseq]

value: fresh


title: H3K9me2; TetR-SET; Suv39x; ChIP-seq (A)


title: LB1 pA-DamID, i7, recombined, clone 12, replicate 2, dam-LB1


title: H3K9me2; TetR-SET; ChIP-seq (A, B, C)


title: H3K9me2; TetR-SET; Sir2Sp-HP1; Suv39x; ChIP-seq (A)


title: RMS1_O_P8 [RNAseq]


title: LB1 pA-DamID, d11, recombined, clone 21, replicate 2, dam-LB1


title: H3K9me2; TetR-SET; Sir2Sp-HP1; Sir3-SET; ChIP-seq (B)


title: RMS1_O_P8* [RNAseq]


title: RMS1_O_P17 [RNAseq]


title: FLC sample 4, normal

city: Seattle

first: Taran

last: Gujral

state: WA

address: 1100 Fairview Ave N

institute: Fred Hutch Cancer Center

data_processing:
(1) For cell lines and tumors derived from human samples, sequencing data was aligned to human genome using STAR and raw counts were generated using Subread. (2) XenofilterR was applied to PDX tumor samples prior to above procedure to remove the mouse reads.
Assembly: GRCh38.p13
Supplementary files format and content: The processed files are in either csv or txt files and include the raw gene counts of expression data.

source_name: Normal liver

extract_protocol:
Total RNA is extracted from the samples via Rneasy kit from Qiagen.
Library construction followed standard Novogene workflow. Following cDNA synthesis, second-strand synthesis is initiated by adding second-strand synthesis buffer, deoxynucleotides, ribonuclease H, and DNA polymerase I. The process continues with terminal repair, A-ligation, and sequencing adaptor ligation. The double-stranded cDNA library is then completed through size selection and PCR enrichment.

value: Normal liver


title: LB1 pA-DamID, i7, recombined, clone 7, replicate 2, dam-LB1


title: FLC sample 3, tumor

source_name: Tumor

value: Tumor


title: LB1 pA-DamID, d11, recombined, clone 6, replicate 2, dam-LB1


title: FLC sample 3, normal


title: FLC sample 5, normal


title: FLC sample 4, tumor


title: RMS1_T2 [RNAseq]

source_name: RMS1 tissue

value: RMS1 tissue


title: FLC sample 2, normal


title: FLC sample 2, tumor


title: LB1 pA-DamID, d11, parental, replicate 2, dam-LB1


title: RMS1_T1 [RNAseq]

value: Rhabdomyosarcoma


title: LB1 pA-DamID, i9, recombined, clone 14, replicate 2, dam only


title: FLC sample 5, tumor


title: FLC sample 1, tumor


title: M2_3D_P6* [RNAseq]

value: RMS1 organoid


title: LB1 pA-DamID, i9, recombined, clone 12, replicate 2, dam only


title: RMS1_O_P15 [RNAseq]

value: M


title: FLC PDX Tumor, rep1

description:
FLC_2199
featureCounts_matrix.csv

source_name: PDX Tumor

value: PDX Tumor


title: LB1 pA-DamID, i7, parental, replicate 2, dam-LB1


title: FLC sample 1, normal


title: FLC PDX Tumor, rep2

description:
FLC_2200
featureCounts_matrix.csv


title: FLC PDX Tumor, rep3

description:
FLC_2203
featureCounts_matrix.csv


title: LB1 pA-DamID, i9, parental, replicate 2, dam only


title: FLC2, rep1

description:
FLC_2
featureCounts_matrix.csv

source_name: Tumor cell line

value: Tumor cell line


title: DMEM_2D_P14 [RNAseq]

value: RMS2 cell line

value: Relapse/metastatic

value: Lung

value: Ischioanal

value: DMEM


title: FLC1, rep2

description:
FLC_1B
featureCounts_matrix.csv


title: LB1 pA-DamID, i7, recombined, clone 12, replicate 2, dam only

value: F1 hybrid 129/Sv:CAST/EiJ

value: mESC


title: FLC2, rep2

description:
FLC_2B
featureCounts_matrix.csv


title: DMEM_2D_P15 [RNAseq]

value: Embryonal


title: FLC1, rep1

description:
FLC_1
featureCounts_matrix.csv


title: HeLa EGFP ChIP-Seq

city: Dresden

first: Maciej

last: Paszkowski-Rogacz

address: Tatzberg 47/49

department: UCC / Medical Faculty and University Hospital Carl Gustav Carus

country: Germany

institute: Technische Universität Dresden

data_processing:
Sequencing reads obtained from multiple sequencing runs were pooled and aligned to the human reference genome assembly GRCh38.p13 [PMID: 21750661] using bwa-mem2 aligner [DOI: 10.1109/IPDPS.2019.00041, https://doi.org/10.1109/IPDPS.2019.00041] and samtools [PMID: 19505943], followed by removal of PCR and optical duplicates by the Picard MarkDuplicates tool.
Assembly: hg38
Supplementary files format and content: Putative binding sites are provided in a narrowPeak format, as repored by Genrich (https://github.com/jsh58/Genrich).

source_name: Hela cells infected with a modified version of the tetracycline inducible LentiX vector carrying EGFP.

growth_protocol: Cells were grown in 10 cm dishes and the expression of D7ZF or EGFP (control) was induced for 24h with 100ng/mL doxycycline.

extract_protocol:
The cell lines were crosslinked with 1% formaldehyde for 10 min at room temperature and further processed following the manufacturer’s protocol for High Cell number using the kit TruChip Chromatin Shearing Kit, Covaris. Chromatin shearing was performed using Covaris M220 sonicator. 1% of the sheared chromatin was separated for qPCR validation (input sample) and the rest was used for immunoprecipitation. Sonicated chromatin was immunoprecipitated using a goat GFP-antibody (MPI-CBG antibody facility) and Protein G sepharose beads (Protein G Sepharose® 4 Fast Flow, GE Healthcare). Eluates were reverse crosslinked followed by RNA and protein digestion.
Sequencing libraries were prepared using NEBNext® Ultra™ DNA Library Prep Kit for Illumina® from 17-75 ng of ChIP DNA with 15 PCR amplification cycle and size selection using AMPure XP beads.

value: HeLa

tag: treatment

value: tetracycline inducible LentiX vector carying EGFP

tag: chip antibody

value: Anti-GFP antibody, MPI-CBG


title: LB1 pA-DamID, i7, recombined, clone 7, replicate 2, dam only

value: recombined


title: LB1 pA-DamID, i7, parental, replicate 2, dam only

value: control