title: Methyl_seq_6B3

city: New Orleans

first: Mona

last: Elgazzaz

state: LA

address: 533 Bolivar Street

department: Cardiovascular Center

institute: LSUHSC

data_processing:
Paired-end fastq reads were aligned to mm9 using Bismark(v0.22.3).
Methylation counts were extracted, clustered, and tested for differentially methylated regions using DMRfinder(v0.3).
Assembly: mm9
Supplementary files format and content: Tab-delimited text file with methylation counts for each sample.

source_name: RD-RD Female

extract_protocol:
At 3 month age, mice were euthanized and hypothalamus was flash frozen on dry ice for DNA extraction.
Extracted DNA was used to perform whole epigenome methylation sequencing. Methyl-Seq library preparation was performed using the SureSelectXT Methyl-Seq Target Enrichment System for Illumina Multiplexed Sequencing (Agilent Technologies, USA) as described by the manufacturer’s protocol. Briefly, 3 ìg of DNA was sheared to fragments of 100-200 bp using a Covaris M220 instrument followed by end repair and adapter ligation. DNA fragments were then subjected to hybridization to the SureSelectXT Methyl-Seq Mouse Capture Library for 16 h (Agilent Technologies, USA). Hybridized products were purified by capture with streptavidin beads and then subjected to bisulfite conversion using the Zymo EZ-DNA Methylation-Gold kit (Zymo Resesarch, USA). Libraries were enriched by PCR amplification. Unique indexes were then ligated to the amplified libraries by PCR amplification. The quality of the libraries was determined after end repair, adapter ligation, and indexing by Agilent’s Bioanalyzer 2100 using a high sensitivity DNA kit, to verify that the library peak size fell within the range recommended by the manufacturer’s protocol. Quantification of the final libraries was performed using the Qubit dsDNA high sensitivity assay (ThermoFisher Scientific, USA). Sequencing was performed on Illumina’s NextSeq 500 instrument with pair-end 100 bp reads.

treatment_protocol: For Dams, C57BL/6J mice were maintained on either 52% fat high sucrose diet TD.04059.PWD hypercaloric diet (HCD) or regular chow diet (RD) for 1 month prior to mating and were kept on this diet for the duration of pregnancy and lactation. For offspring, mice were placed on either HCD or RD at weaning time and maintained until they reached 3 months old.

value: Hypothalamus

value: female

value: RD (no treatment)


title: PeDa01_dsDNA_rep2

status: Public on Jan 31 2024

type: SRA

city: Ipswich

first: Zhiyi

last: Sun

state: MASSACHUSETTS

address: 240 County Road

department: Research

country: USA

institute: New England Biolabs

library_source: genomic

data_processing:
basecalls were performed using Illumina RTA software and fastq files were generated from the BCL files using Picard’s basecallstofastq.
Reads were trimmed for adaptor sequence and low quality bases at the 3' end using the trim_galore program.
The trimmed read sequences were C to T converted and were then mapped to the a composite reference including E.coli and all the control sequences using the Bismark program with the default Bowtie2 settings.
The first 5 bp at the 5’ end of R2 reads were removed to reduce end-repair errors and aligned read pairs that shared the same alignment ends were regarded as PCR duplicates and were discarded.
The numbers of Ts (converted not methylated) and Cs (unconverted modified) of each covered cytosine position were then calculated from the remaining good quality alignments using Bismark methylation extractor.
Assembly: E. coli C2566, human hg38
Supplementary files format and content: tab-delimited text/bed files include genomic coordinates, number of Cs and number of Ts and sequence contexts of covered cytosines.
Library strategy: SEM-seq

molecule: genomic DNA

organism: Escherichia coli

source_name: E. coli C2566, phage lambda, plasmid pRSSM1.PleII, phage XP12, and phage T4147

extract_protocol:
E. coli C2566 genomic DNA was purified using Monarch Genomic DNA Purification Kit (NEB Ipswich, MA), GM12878 genomic DNA was obtained from Coriell Cell Repositories (Camden, NJ).
Input DNA was sheared to 300 bp using the Covaris S2 instrument. Sheared material was transferred to a PCR strip tube to begin library construction. NEBNext DNA Ultra II Reagents (NEB, Ipswich, MA) were used according to the manufacturer’s instructions for end repair, A-tailing, and adaptor ligation. The custom made Pyrollo-dC adaptor (NEB Organic Synthesis Division, Ipswich MA), where all dCs are replaced with Pyrollo-dC, was used. The ligated samples were purified using NEBNext Sample Purification Beads  according to the manufacturer’s instructions. For ssDNA libraries, prior to deamination the DNA was denatured by heating at 90oC for 10 minutes followed by cooling for 2 minutes on ice. The DNA was then deaminated using 1 µL of PURExpress (NEB, Ipswich, MA) synthesized deaminase protein following manufacturer's recommendations for 1 hour at 37oC. Then 1 µL of Thermolabile Proteinase K (NEB, Ipswich, MA) was added and incubated for 30 min at 37oC followed by 10 min at 60oC. Then the library was amplified using NEBNext Q5U Master Mix (NEB, Ipswich, MA, USA). Paired-end sequencing of 150 cycles (2 x 75 bp) was performed for all the sequencing runs.
DNA sequencing of deaminated double-stranded and single-stranded DNA

tag: cell type


title: PeDa01_dsDNA_rep1

value: E. coli C2566, phage lambda, plasmid pRSSM1.PleII, phage XP12, and phage T4147


title: Genomic DNA from ependymoma 675

type: genomic

city: Hamburg

first: Michael

last: Bockmayr

address: Martinistr. 52

department: Pediatric Hematology and Oncology

country: Germany

institute: University Medical Center Hamburg-Eppendorf

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip or the Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol.

scan_protocol: Arrays were imaged using the iScan System and the standard recommended Illumina scanner setting.

data_processing:
Statistical analysis was performed using the minfi package version 1.46.0 with the statistical programming language R version 4.3.0.
Average beta-values after combining arrays and normalization using the Noob method.

label: Cy5 and Cy3

organism: Homo sapiens

source_name: ependymoma 675

label_protocol: Standard Illumina protocol

extract_protocol: DNA was isolated using the ReliaPrep™ FFPE gDNA Miniprep System (Promega) according to manufacturer’s instructions. About 100-500 ng DNA was used for bisulfite conversion by the EZ DNA Methylation Kit (Zymo Research). The DNA Clean & Concentrator-5 (Zymo Research) and the Infinium HD FFPE DNA Restore Kit (Illumina) were employed to clean and restore the converted DNA.

tag: Sex

value: F

tag: age

tag: localization

value: posterior fossa

tag: resection

value: GTR

tag: patho diagnosis

value: Ependymoma III

tag: OS status

tag: os [months]

tag: pfs status

tag: pfs [months]

tag: classification result v12

tag: classification score


title: Genomic DNA from ependymoma 674

source_name: ependymoma 674

value: M

value: supratentorial

value: STR


title: VB194 L BF

type: protein

city: North Grafton

first: Jillian

middle: M

last: Richmond

state: Massachusetts

address: 200 Westboro Road

department: Comparative Pathobiology

institute: Tufts Cummings School of Veterinary Medicine

hyb_protocol: Hybridization and RT-PCR was performed per Olink Proteomics manufacturer's protocol

scan_protocol: Plates were read fee-for-service at Olink Proteomics in Watertown, MA

data_processing: Data were analyzed with Olink NPX manager software 2.1.0.224

label: antibody-linked oligonucleotide tag

molecule: protein

source_name: blister biopsy

label_protocol: Sample labeling was performed per Olink Proteomics manufacturer's protocol

extract_protocol: Blister biopsies and/or EDTA anticoagulated blood samples were centrifuged at 330xg for 10 minutes. Interstitial skin fluid and/or plasma was frozen in 1mL aliquots and stored at -70C until analysis.

tag: disease status

value: UV

tag: location

value: lesional


title: Methyl_seq_6B2

organism: Mus musculus

tag: tissue

tag: strain

tag: genotype

value: WT

tag: treatment


title: Cd4_PeDa01_extN21_ssDNA_rep2

tag: cell type


title: Genomic DNA from ependymoma 672

source_name: ependymoma 672

tag: Sex

tag: age


title: VB127 NL BF

value: CLE/Vitiligo

value: nonlesional


title: Methyl_seq_6B1


title: CL190 NL 031020 BF

value: CLE


title: Cd4_PeDa01_extN21_ssDNA_rep1


title: Genomic DNA from ependymoma 671

source_name: ependymoma 671

tag: localization

tag: resection


title: A1-OVA_n4

city: Montreal

first: Moutih

last: Rafei

address: Montreal

country: Canada

institute: Universite de Montreal

description: STAR aligner 2.7 and FeatureCounts 2.0

library_source: transcriptomic

data_processing:
Basecalls performed using Illumina RTA 2.4.11.
Samples demultiplexed using bcl2fastq 2.20 allowing 1 mismatch in the index.
Sequenced reads were aligned and mapped with STAR 2.7 to the reference genome Gencode version 35
Expression values were also computed using FeatureCounts version 2.0 based on the same assembly (GTF GRCm38)
Assembly: Mus_musculus.GRCm38 (ENSEMBL 102 mouse Mouse(Mus musculus)
Supplementary files format and content: Raw Readcounts: Tab-delimited file where 1st column is the Ensembl gene identifier, counts for forward stranded RNA,

molecule: polyA RNA

source_name: Bone marrow

growth_protocol: Mesenchymal stromal cells were maintained in AMEM supplemented with 10% fetal bovine serum (FBS) and 50 U/mL Penicillin-Streptomycin in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) + RNeasy mini kit (Qiagen, #74106)
cDNA libraries were prepared from total RNA using a PolyA selection and the KAPA RNA Hyperprep Kit and were further amplified for sequencing; ssRNA-seq

treatment_protocol: Treatment was added post confluency of 80%. A1 condition consisted of 50uM of A1 diluted in AMEM supplemented with 10% fetal bovine serum (FBS) and 50 U/mL Penicillin-Streptomycin. A1+OVA condition consisted of 50uM of A1, plus 1 mg/mL of Albumin from chicken egg white, diluted in AMEM supplemented with 10% fetal bovine serum (FBS) and 50 U/mL Penicillin-Streptomycin/ml insulin (Sigma). Cell were treated and incubated for 6h in humidified atmosphere with 5% CO2 at 37C.

value: Bone marrow

tag: cell line

value: Primary cell

value: Mesenchymal stromal cell

value: 50 uM of A1 + 1 mg/mL of ovalbumin


title: CB 049 020620 BF

value: Healthy

value: healthy


title: Genomic DNA from ependymoma 677

source_name: ependymoma 677

value: F

value: posterior fossa

tag: patho diagnosis

tag: OS status

tag: os [months]


title: Cd4_PeDa01_extN21_dsDNA_rep2

value: E. coli C2566, phage lambda, plasmid pRSSM1.PleII, phage XP12, and phage T4147


title: Genomic DNA from ependymoma 670

source_name: ependymoma 670

value: Ependymoma II

tag: pfs status

tag: pfs [months]

tag: classification result v12


title: Methyl_seq_6A2

source_name: RD-RD Male

value: Hypothalamus

value: male

value: RD (no treatment)


title: Genomic DNA from ependymoma 669

source_name: ependymoma 669

value: supratentorial

value: GTR

value: Ependymoma III

tag: classification score


title: CL179 NL BF_1

tag: disease status

value: CLE

tag: location

value: nonlesional


title: DM145 L 011419 BF

value: DM

value: lesional


title: Methyl_seq_6A1

tag: tissue

tag: strain

tag: genotype

value: WT


title: CB 036 BF

value: Healthy


title: Cd4_PeDa01_extN21_dsDNA_rep1

tag: cell type


title: Genomic DNA from ependymoma 668

source_name: ependymoma 668

tag: Sex

value: M

tag: age

value: STR


title: VB127 VL BF

value: Vitiligo


title: Genomic DNA from ependymoma 667

source_name: ependymoma 667

value: F

tag: localization

value: posterior fossa

tag: resection


title: Methyl_seq_5B3

source_name: RD-HCD Female

value: Hypothalamus

value: female

tag: treatment

value: Perinatal RD and postnatal HCD


title: xp12da_ssDNA_rep1

value: E. coli C2566, phage lambda, plasmid pRSSM1.PleII, phage XP12, and phage T4147


title: VB175 NL BF

value: Morphea


title: Methyl_seq_5B2


title: xp12da_dsDNA_rep2


title: Methyl_seq_6A3

value: male

value: RD (no treatment)


title: DM145 NL 011419 BF

value: nonlesional


title: Methyl_seq_5B1


title: Genomic DNA from ependymoma 663

source_name: ependymoma 663

value: supratentorial

value: GTR

tag: patho diagnosis

value: Ependymoma III

tag: OS status


title: CL067 L1 BF

value: CLE

value: lesional


title: xp12da_dsDNA_rep1


title: Genomic DNA from ependymoma 655

source_name: ependymoma 655

tag: os [months]

tag: pfs status


title: Methyl_seq_5A3

source_name: RD-HCD Male

value: WT


title: gp317_ssDNA_rep2

source_name: E. coli C2566, phage lambda, plasmid pRSSM1.PleII, phage XP12, and phage T4147


title: Genomic DNA from ependymoma 652

source_name: ependymoma 652

value: M

value: Ependymoma II

tag: pfs [months]

tag: classification result v12


title: CB 035 BF

tag: disease status

value: Healthy

value: healthy


title: CL067 NL BF

tag: location


title: Methyl_seq_5A2

tag: tissue

value: Hypothalamus


title: xp12da_ssDNA_rep2


title: gp317_ssDNA_rep1


title: Methyl_seq_5A1

tag: strain

value: Perinatal RD and postnatal HCD


title: DM 178 L 101719 BF

value: DM


title: Methyl_seq_4B3

source_name: HCD-RD Female

value: female

tag: genotype

value: Perinatal HCD and postnatal RD


title: gp317_dsDNA_rep2

tag: cell type

value: E. coli C2566, phage lambda, plasmid pRSSM1.PleII, phage XP12, and phage T4147


title: CL179 L BF_1

source_name: blister biopsy


title: Genomic DNA from ependymoma 647

source_name: ependymoma 647

tag: Sex

value: posterior fossa

value: STR

tag: classification score


title: Genomic DNA from ependymoma 650

source_name: ependymoma 650

value: F

tag: age

tag: localization

value: GTR


title: Genomic DNA from ependymoma 639

source_name: ependymoma 639

tag: resection

value: Ependymoma III


title: DM158 L BF

value: lesional


title: AbcDa01_ssDNA_rep1


title: AbcDa01_ssDNA_rep2


title: Genomic DNA from ependymoma 636

source_name: ependymoma 636

value: supratentorial

tag: patho diagnosis


title: Methyl_seq_4B1

value: WT

tag: treatment


title: Methyl_seq_4A3

source_name: HCD-RD Male

value: male


title: VB127 LL BF

value: CLE


title: AbcDa01_dsDNA_rep2


title: Genomic DNA from ependymoma 633

source_name: ependymoma 633

tag: OS status

tag: os [months]


title: DM 178 L 031020 BF


title: Genomic DNA from ependymoma 632

source_name: ependymoma 632

tag: pfs status

tag: pfs [months]


title: CL067 L2 BF

tag: disease status


title: Methyl_seq_4A1


title: Genomic DNA from ependymoma 631

source_name: ependymoma 631

tag: classification result v12


title: Methyl_seq_3B3

source_name: HCD-HCD Female

tag: tissue

value: Perinatal and postnatal HCD


title: RhDa01_ssDNA_rep1


title: gp317_dsDNA_rep1


title: Genomic DNA from ependymoma 630

source_name: ependymoma 630

value: M


title: Methyl_seq_3B2

value: Hypothalamus

tag: strain


title: AbcDa01_dsDNA_rep1


title: VB194 NL BF

value: UV

tag: location

value: nonlesional


title: VB175 L BF

value: Morphea


title: Methyl_seq_3B1

value: female

tag: genotype


title: Methyl_seq_4B2

tag: Sex

value: Perinatal HCD and postnatal RD


title: RhDa01_dsDNA_rep2

tag: cell type

value: E. coli C2566, phage lambda, plasmid pRSSM1.PleII, phage XP12, and phage T4147


title: DM 154 NL BF

value: DM


title: Genomic DNA from ependymoma 623

source_name: ependymoma 623

tag: age

value: posterior fossa

value: GTR

value: Ependymoma II

tag: classification score


title: Methyl_seq_4A2


title: CL143 L BF

value: lesional


title: Methyl_seq_3A2

source_name: HCD-HCD Male

value: WT


title: Methyl_seq_3A3

value: male


title: MGYPDa05_ssDNA_rep2


title: CONTROL_SAMPLE_US_CS_AS_2 2

source_name: Olink control

value: Control


title: MGYPDa05_ssDNA_rep1

source_name: E. coli C2566, phage lambda, plasmid pRSSM1.PleII, phage XP12, and phage T4147


title: CL179 NL BF_2

value: CLE


title: Genomic DNA from ependymoma 621

source_name: ependymoma 621

value: F

tag: localization

tag: resection

value: Ependymoma III


title: RhDa01_dsDNA_rep1


title: RhDa01_ssDNA_rep2


title: Genomic DNA from ependymoma 473

source_name: ependymoma 473

tag: patho diagnosis

value: high grade glioma


title: Methyl_seq_3A1

value: Hypothalamus

tag: treatment

value: Perinatal and postnatal HCD


title: CL143 NL Hem BF

source_name: blister biopsy

value: nonlesional hemorrhagic


title: Genomic DNA from ependymoma 451

source_name: ependymoma 451

value: M

value: supratentorial

tag: OS status

tag: os [months]


title: mDIV4-media-2

city: Richardson

first: Theodore

middle: J

last: Price

state: TX

address: 800 W Campbell Rd.

institute: University of Texas at Dallas

data_processing:
Sequence reads were mapped to gencode vM16 (mouse) and v27 (human) using STAR 2.6.1c
Assembly: GRCm38.p5(mouse)/GRCh38.p10(human)
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

molecule: total RNA

source_name: Neuronal cultures, 24 hours in control media

extract_protocol:
RNA was extracted using Rneasy mini plus kit (Qiagen) following manufacturer's instructions.
RNA libraries for RNA-seq were prepared using TruSeq Stranded Total RNA (Illumina) following manufacturer's instructions

value: Dorsal Root Ganglia

value: Neuron (Primary Cell)

value: 24 hours in control media


title: Genomic DNA from ependymoma 627

source_name: ependymoma 627

value: posterior fossa

value: GTR

tag: pfs status

tag: pfs [months]


title: mDIV4-media-3


title: VB067 NL BF

tag: disease status

value: nonlesional


title: Genomic DNA from ependymoma 435

source_name: ependymoma 435

value: Ependymoma II

tag: classification result v12


title: MGYPDa05_dsDNA_rep1

value: E. coli C2566, phage lambda, plasmid pRSSM1.PleII, phage XP12, and phage T4147


title: DM 193 L 081720 BF

value: DM

value: lesional


title: Genomic DNA from ependymoma 441

source_name: ependymoma 441

value: Anaplastic ependymoma III


title: mDIV4-media-1

tag: tissue


title: DM 158 NL BF

tag: location


title: C_terminus_MGYPDa829_onto_StsDa01_ssDNA_rep2


title: C_terminus_MGYPDa829_onto_StsDa01_ssDNA_rep1


title: Genomic DNA from ependymoma 415

source_name: ependymoma 415

value: spinal


title: C_terminus_MGYPDa829_onto_StsDa01_dsDNA_rep2


title: mDIV4-24hrec-2

source_name: Neuronal cultures, 30mM KCl treated for 24 hours + 24 hours recovery in control media

value: KCl for 24 hours + 24 hours recovery in control media


title: mDIV4-24hrec-1


title: Genomic DNA from ependymoma 404

source_name: ependymoma 404

value: F

value: STR


title: MGYPDa05_dsDNA_rep2


title: CONTROL_SAMPLE_US_CS_AS_2 1

value: Control


title: CL179 L BF_2

value: CLE


title: BaDa01_ssDNA_rep2


title: Genomic DNA from ependymoma 399

source_name: ependymoma 399

value: M

value: Anaplastic Ependymoma


title: C_terminus_MGYPDa829_onto_StsDa01_dsDNA_rep1


title: DM 154 L BF


title: BaDa01_ssDNA_rep1


title: Genomic DNA from ependymoma 398

source_name: ependymoma 398

value: Ependymoma


title: CL143 NL BF


title: mDIV4-24hKCl-2

source_name: Neuronal cultures, 30mM KCl treated for 24 hours

value: Dorsal Root Ganglia

value: Neuron (Primary Cell)

value: KCl for 24 hours


title: BaDa01_dsDNA_rep2


title: mDIV4-24hKCl-1


title: mDIV4-24hrec-3


title: RVL of 24 weeks SHR rat rep5

status: Public on Jan 30 2024

city: Albuquerque

first: Rajanikanth

last: Vadigepalli

state: PA

address: 1 University of New Mexico

institute: University of New Mexico

description:
RNA-seq from tissue punches of brainstem regions
RVLM_All_Raw_Counts.txt
S-24-F-5-RVL

data_processing:
GENEWIZ software used for quality control and basecalling.
RSEM was used to calculate Expected count
Assembly: rno9
Supplementary files format and content: Matrix table with Expected gene counts for every gene and every sample

organism: Rattus norvegicus

source_name: RVLM of brainsstem

extract_protocol:
Brainstems were removed and frozen in OCT blocks which were then sectioned at 200um. A tissue punch was used to extract the appropriate regions. The collected tissue was then lysed and RNA-extracted using the Direct-Zol kit from Zymo to obtain total RNA. Total RNA was sent to GENEWIZ for library preparation and RNA-sequencing.
Library construction performed by GENEWIZ.

value: RVLM of brainsstem

tag: strain

value: SHR

value: 24 weeks

tag: region

value: RVLM


title: RVL of 24 weeks SHR rat rep6

description:
RNA-seq from tissue punches of brainstem regions
RVLM_All_Raw_Counts.txt
S-24-F-6-RVL


title: RVL of 24 weeks SHR rat rep4

description:
RNA-seq from tissue punches of brainstem regions
RVLM_All_Raw_Counts.txt
S-24-F-4-RVL


title: RVL of 24 weeks SHR rat rep3

description:
RNA-seq from tissue punches of brainstem regions
RVLM_All_Raw_Counts.txt
S-24-F-3-RVL


title: RVL of 24 weeks SHR rat rep1

description:
RNA-seq from tissue punches of brainstem regions
RVLM_All_Raw_Counts.txt
S-24-F-1-RVL


title: Genomic DNA from ependymoma 407

source_name: ependymoma 407

tag: Sex

value: supratentorial

value: Ependymoma II


title: CL 190 L 031020 BF

value: lesional


title: BaDa01_dsDNA_rep1

source_name: E. coli C2566, phage lambda, plasmid pRSSM1.PleII, phage XP12, and phage T4147

tag: cell type


title: RVL of 16 weeks SHR rat rep6

description:
RNA-seq from tissue punches of brainstem regions
RVLM_All_Raw_Counts.txt
S-16-F-6-RVL

tag: age

value: 16 weeks


title: RVL of 16 weeks SHR rat rep5

description:
RNA-seq from tissue punches of brainstem regions
RVLM_All_Raw_Counts.txt
S-16-F-5-RVL


title: DM178 NL 031020 BF

value: DM

value: nonlesional


title: RVL of 16 weeks SHR rat rep2

description:
RNA-seq from tissue punches of brainstem regions
RVLM_All_Raw_Counts.txt
S-16-F-2-RVL


title: RVL of 16 weeks SHR rat rep4

description:
RNA-seq from tissue punches of brainstem regions
RVLM_All_Raw_Counts.txt
S-16-F-4-RVL


title: mDIV4-24hKCl-3


title: RVL of 16 weeks SHR rat rep3

description:
RNA-seq from tissue punches of brainstem regions
RVLM_All_Raw_Counts.txt
S-16-F-3-RVL


title: RVL of 16 weeks SHR rat rep1

description:
RNA-seq from tissue punches of brainstem regions
RVLM_All_Raw_Counts.txt
S-16-F-1-RVL


title: RVL of 12 weeks SHR rat rep4

description:
RNA-seq from tissue punches of brainstem regions
RVLM_All_Raw_Counts.txt
S-12-F-4-RVL

value: 12 weeks


title: RVL of 12 weeks SHR rat rep3

description:
RNA-seq from tissue punches of brainstem regions
RVLM_All_Raw_Counts.txt
S-12-F-3-RVL


title: RVL of 12 weeks SHR rat rep5

description:
RNA-seq from tissue punches of brainstem regions
RVLM_All_Raw_Counts.txt
S-12-F-5-RVL


title: RVL of 12 weeks SHR rat rep1

description:
RNA-seq from tissue punches of brainstem regions
RVLM_All_Raw_Counts.txt
S-12-F-1-RVL


title: RVL of 12 weeks SHR rat rep2

description:
RNA-seq from tissue punches of brainstem regions
RVLM_All_Raw_Counts.txt
S-12-F-2-RVL


title: RVL of 10 weeks SHR rat rep4

description:
RNA-seq from tissue punches of brainstem regions
RVLM_All_Raw_Counts.txt
S-10-F-4-RVL

value: 10 weeks


title: RVL of 10 weeks SHR rat rep2

description:
RNA-seq from tissue punches of brainstem regions
RVLM_All_Raw_Counts.txt
S-10-F-2-RVL


title: RVL of 24 weeks SHR rat rep2

description:
RNA-seq from tissue punches of brainstem regions
RVLM_All_Raw_Counts.txt
S-24-F-2-RVL


title: RVL of 10 weeks SHR rat rep3

description:
RNA-seq from tissue punches of brainstem regions
RVLM_All_Raw_Counts.txt
S-10-F-3-RVL


title: RVL of 10 weeks SHR rat rep1

description:
RNA-seq from tissue punches of brainstem regions
RVLM_All_Raw_Counts.txt
S-10-F-1-RVL


title: RVL of 8 weeks SHR rat rep4

description:
RNA-seq from tissue punches of brainstem regions
RVLM_All_Raw_Counts.txt
S-8-F-4-RVL

value: 8 weeks


title: RVL of 8 weeks SHR rat rep1

description:
RNA-seq from tissue punches of brainstem regions
RVLM_All_Raw_Counts.txt
S-8-F-1-RVL


title: RVL of 8 weeks SHR rat rep5

description:
RNA-seq from tissue punches of brainstem regions
RVLM_All_Raw_Counts.txt
S-8-F-5-RVL


title: RVL of 8 weeks SHR rat rep2

description:
RNA-seq from tissue punches of brainstem regions
RVLM_All_Raw_Counts.txt
S-8-F-2-RVL


title: RVL of 16 weeks WKY rat rep2

description:
RNA-seq from tissue punches of brainstem regions
RVLM_All_Raw_Counts.txt
W-16-F-2-RVL

value: WKY


title: RVL of 12 weeks SHR rat rep6

description:
RNA-seq from tissue punches of brainstem regions
RVLM_All_Raw_Counts.txt
S-12-F-6-RVL


title: RVL of 16 weeks WKY rat rep3

description:
RNA-seq from tissue punches of brainstem regions
RVLM_All_Raw_Counts.txt
W-16-F-3-RVL


title: RVL of 24 weeks WKY rat rep2

description:
RNA-seq from tissue punches of brainstem regions
RVLM_All_Raw_Counts.txt
W-24-F-2-RVL


title: RVL of 24 weeks WKY rat rep3

description:
RNA-seq from tissue punches of brainstem regions
RVLM_All_Raw_Counts.txt
W-24-F-3-RVL


title: RVL of 12 weeks WKY rat rep1

description:
RNA-seq from tissue punches of brainstem regions
RVLM_All_Raw_Counts.txt
W-12-F-1-RVL


title: RVL of 24 weeks WKY rat rep1

description:
RNA-seq from tissue punches of brainstem regions
RVLM_All_Raw_Counts.txt
W-24-F-1-RVL


title: RVL of 16 weeks WKY rat rep1

description:
RNA-seq from tissue punches of brainstem regions
RVLM_All_Raw_Counts.txt
W-16-F-1-RVL


title: RVL of 10 weeks WKY rat rep4

description:
RNA-seq from tissue punches of brainstem regions
RVLM_All_Raw_Counts.txt
W-10-F-4-RVL


title: RVL of 12 weeks WKY rat rep2

description:
RNA-seq from tissue punches of brainstem regions
RVLM_All_Raw_Counts.txt
W-12-F-2-RVL


title: RVL of 10 weeks WKY rat rep2

description:
RNA-seq from tissue punches of brainstem regions
RVLM_All_Raw_Counts.txt
W-10-F-2-RVL


title: RVL of 12 weeks WKY rat rep3

description:
RNA-seq from tissue punches of brainstem regions
RVLM_All_Raw_Counts.txt
W-12-F-3-RVL


title: RVL of 10 weeks SHR rat rep5

description:
RNA-seq from tissue punches of brainstem regions
RVLM_All_Raw_Counts.txt
S-10-F-5-RVL


title: RVL of 8 weeks WKY rat rep3

description:
RNA-seq from tissue punches of brainstem regions
RVLM_All_Raw_Counts.txt
W-8-F-4-RVL


title: RVL of 10 weeks WKY rat rep1

description:
RNA-seq from tissue punches of brainstem regions
RVLM_All_Raw_Counts.txt
W-10-F-1-RVL


title: RVL of 8 weeks WKY rat rep1

description:
RNA-seq from tissue punches of brainstem regions
RVLM_All_Raw_Counts.txt
W-8-F-2-RVL


title: RVL of 8 weeks WKY rat rep5

description:
RNA-seq from tissue punches of brainstem regions
RVLM_All_Raw_Counts.txt
W-8-F-6-RVL


title: CVL of 24 weeks SHR rat rep6

description:
RNA-seq from tissue punches of brainstem regions
CVLM_All_Raw_Counts.txt
S-24-F-6-CVL

source_name: CVLM of brainsstem

value: CVLM of brainsstem

value: CVLM


title: RVL of 8 weeks WKY rat rep4

description:
RNA-seq from tissue punches of brainstem regions
RVLM_All_Raw_Counts.txt
W-8-F-5-RVL


title: CVL of 24 weeks SHR rat rep4

description:
RNA-seq from tissue punches of brainstem regions
CVLM_All_Raw_Counts.txt
S-24-F-4-CVL


title: CVL of 24 weeks SHR rat rep3

description:
RNA-seq from tissue punches of brainstem regions
CVLM_All_Raw_Counts.txt
S-24-F-3-CVL


title: CVL of 24 weeks SHR rat rep2

description:
RNA-seq from tissue punches of brainstem regions
CVLM_All_Raw_Counts.txt
S-24-F-2-CVL


title: RVL of 8 weeks WKY rat rep2

description:
RNA-seq from tissue punches of brainstem regions
RVLM_All_Raw_Counts.txt
W-8-F-3-RVL


title: CVL of 16 weeks SHR rat rep6

description:
RNA-seq from tissue punches of brainstem regions
CVLM_All_Raw_Counts.txt
S-16-F-6-CVL


title: CVL of 16 weeks SHR rat rep4

description:
RNA-seq from tissue punches of brainstem regions
CVLM_All_Raw_Counts.txt
S-16-F-4-CVL


title: CVL of 16 weeks SHR rat rep5

description:
RNA-seq from tissue punches of brainstem regions
CVLM_All_Raw_Counts.txt
S-16-F-5-CVL


title: CVL of 16 weeks SHR rat rep2

description:
RNA-seq from tissue punches of brainstem regions
CVLM_All_Raw_Counts.txt
S-16-F-2-CVL


title: CVL of 24 weeks SHR rat rep1

description:
RNA-seq from tissue punches of brainstem regions
CVLM_All_Raw_Counts.txt
S-24-F-1-CVL


title: CVL of 12 weeks SHR rat rep6

description:
RNA-seq from tissue punches of brainstem regions
CVLM_All_Raw_Counts.txt
S-12-F-6-CVL


title: CVL of 16 weeks SHR rat rep1

description:
RNA-seq from tissue punches of brainstem regions
CVLM_All_Raw_Counts.txt
S-16-F-1-CVL


title: CVL of 16 weeks SHR rat rep3

description:
RNA-seq from tissue punches of brainstem regions
CVLM_All_Raw_Counts.txt
S-16-F-3-CVL


title: RVL of 8 weeks SHR rat rep3

description:
RNA-seq from tissue punches of brainstem regions
RVLM_All_Raw_Counts.txt
S-8-F-3-RVL


title: CVL of 12 weeks SHR rat rep3

description:
RNA-seq from tissue punches of brainstem regions
CVLM_All_Raw_Counts.txt
S-12-F-3-CVL


title: CVL of 12 weeks SHR rat rep1

description:
RNA-seq from tissue punches of brainstem regions
CVLM_All_Raw_Counts.txt
S-12-F-1-CVL


title: CVL of 10 weeks SHR rat rep5

description:
RNA-seq from tissue punches of brainstem regions
CVLM_All_Raw_Counts.txt
S-10-F-5-CVL


title: CVL of 12 weeks SHR rat rep4

description:
RNA-seq from tissue punches of brainstem regions
CVLM_All_Raw_Counts.txt
S-12-F-4-CVL


title: CVL of 12 weeks SHR rat rep2

description:
RNA-seq from tissue punches of brainstem regions
CVLM_All_Raw_Counts.txt
S-12-F-2-CVL


title: CVL of 12 weeks SHR rat rep5

description:
RNA-seq from tissue punches of brainstem regions
CVLM_All_Raw_Counts.txt
S-12-F-5-CVL


title: CVL of 24 weeks SHR rat rep5

description:
RNA-seq from tissue punches of brainstem regions
CVLM_All_Raw_Counts.txt
S-24-F-5-CVL


title: Kidney, Hp-/-Hpx-/-, 7-months old, non-infected, replicate 4

city: Oeiras

first: Rui

last: Martins

address: Rua da Quinta Grande 6

department: Inflammation

country: Portugal

institute: Gulbenkian Institute for Molecular Medicine

data_processing:
Fastq reads were aligned against the mouse reference genome GRCm39using the annotation GENCODE M28 (STAR; v.2.7.9a)
Read summarization was performed using FeatureCounts (v2.0.0)m by assigning uniquely mapped reads to genomic features
Gene expression tables were imported into the R programming language and environment (v.3.6.3)
Analysis of differential gene expression was performed using the DESeq2 R package (Love et al., 2014) (v.1.31.7)
Gene expression was modeled by the following linear design~ genotype + treatment + age + genotype:treatment + genotype:age + treatment:age + genotype:treatment:age
Genes not expressed or presenting an average expression inferior to 5 counts across the 18 sampleswere removed resulting in 14,073 genes for downstream differential gene expression analysis
Assembly: GRCm39
Supplementary files format and content: Single table containing the normalized counts per feature (geneid) and sample

source_name: Kidney - Hp-/-Hpx-/-, 7-months old, non-infected

extract_protocol:
Total RNA was isolated from mouse organs using tripleXtractor reagent (GRiSP, #GB23.0100), chloroform, isopropanol, and ethanol, according to manufacturer’s instructions.
Full-length cDNAs and sequencing libraries were generated following the SMART-Seq2 protocol, as previously described (Picelli et al, 2014). Quality control (Agilent Technologies) and "tagmentation" - PCR-mediated adaptor addition and amplification of the adapted libraries was performed following the Nextera library preparation protocol (llumina Tagment DNA Enzyme and Buffer, Illumina #20034211; KAPA HiFi HotStart ReadyMix, Roche #07958935001; Nextera XT Index Kit v2 Set A, Illumina #15052163; Nextera XT Index Kit v2 Set D, Illumina #15052166), essentially as previously described (Baym et al, 2015).  Libraries were sequenced (NextSeq2000 sequencing; Illumina) using 100 SE P2 and sequence information was extracted in FastQ format, using Illumina DRAGEN FASTQ Generation v3.8.4, producing around 25-65 million reads per sample.

treatment_protocol: 9 week-old or 7-month old Hp+/+Hpx+/+ and Hp-/-Hpx-/- C57BL/6 mice were infected or not with Pcc AS (1x10^5 parasites, intraperitoneal). Kidney samples were collected at day 7 post-infection.

tag: genotype

value: Uninfected

value: 7 months

tag: time

value: Day 7 post-infection


title: Kidney, Hp-/-Hpx-/-, 7-months old, non-infected, replicate 5

value: Kidney - Hp-/-Hpx-/-, 7-months old, non-infected


title: CVL of 10 weeks SHR rat rep4

description:
RNA-seq from tissue punches of brainstem regions
CVLM_All_Raw_Counts.txt
S-10-F-4-CVL

value: SHR


title: Kidney, Hp-/-Hpx-/-, 7-months old, Pcc-infected, replicate 4

source_name: Kidney - Hp-/-Hpx-/-, 7-months old, Pcc-infected, day7 post-infection

value: Pcc-infected


title: Kidney, Hp-/-Hpx-/-, 7-months old, Pcc-infected, replicate 5

value: Kidney - Hp-/-Hpx-/-, 7-months old, Pcc-infected, day7 post-infection


title: Kidney, Hp-/-Hpx-/-, 7-months old, Pcc-infected, replicate 3


title: Kidney, Hp-/-Hpx-/-, 7-months old, non-infected, replicate 3


title: Kidney, Hp+/+Hpx+/+, 7-months old, Pcc-infected, replicate 4

source_name: Kidney - Hp+/+Hpx+/+, 7-months old, Pcc-infected, day7 post-infection


title: CVL of 10 weeks SHR rat rep3

description:
RNA-seq from tissue punches of brainstem regions
CVLM_All_Raw_Counts.txt
S-10-F-3-CVL


title: CVL of 10 weeks SHR rat rep2

description:
RNA-seq from tissue punches of brainstem regions
CVLM_All_Raw_Counts.txt
S-10-F-2-CVL


title: Kidney, Hp+/+Hpx+/+, 7-months old, Pcc-infected, replicate 3

value: Kidney - Hp+/+Hpx+/+, 7-months old, Pcc-infected, day7 post-infection


title: CVL of 10 weeks SHR rat rep1

description:
RNA-seq from tissue punches of brainstem regions
CVLM_All_Raw_Counts.txt
S-10-F-1-CVL


title: Kidney, Hp+/+Hpx+/+, 7-months old, non-infected, replicate 4

source_name: Kidney - Hp+/+Hpx+/+, 7-months old, non-infected


title: CVL of 8 weeks SHR rat rep5

description:
RNA-seq from tissue punches of brainstem regions
CVLM_All_Raw_Counts.txt
S-8-F-5-CVL


title: Kidney, Hp+/+Hpx+/+, 7-months old, non-infected, replicate 1

value: Kidney - Hp+/+Hpx+/+, 7-months old, non-infected


title: Kidney, Hp-/-Hpx-/-, 9-weeks old, Pcc-infected, replicate 4

source_name: Kidney - Hp-/-Hpx-/-, 9-weeks old, Pcc-infected, day7 post-infection

value: 9 weeks


title: Kidney, Hp-/-Hpx-/-, 9-weeks old, non-infected, replicate 4

source_name: Kidney - Hp-/-Hpx-/-, 9-weeks old, non-infected


title: CVL of 8 weeks SHR rat rep4

description:
RNA-seq from tissue punches of brainstem regions
CVLM_All_Raw_Counts.txt
S-8-F-4-CVL


title: CVL of 8 weeks SHR rat rep2

description:
RNA-seq from tissue punches of brainstem regions
CVLM_All_Raw_Counts.txt
S-8-F-2-CVL


title: Kidney, Hp-/-Hpx-/-, 9-weeks old, non-infected, replicate 3

value: Kidney - Hp-/-Hpx-/-, 9-weeks old, non-infected


title: Kidney, Hp-/-Hpx-/-, 9-weeks old, Pcc-infected, replicate 5

value: Kidney - Hp-/-Hpx-/-, 9-weeks old, Pcc-infected, day7 post-infection


title: CVL of 8 weeks SHR rat rep3

description:
RNA-seq from tissue punches of brainstem regions
CVLM_All_Raw_Counts.txt
S-8-F-3-CVL


title: Kidney, Hp+/+Hpx+/+, 9-weeks old, Pcc-infected, replicate 2

source_name: Kidney - Hp+/+Hpx+/+, 9-weeks old, Pcc-infected, day7 post-infection


title: Kidney, Hp+/+Hpx+/+, 9-weeks old, non-infected, replicate 2

source_name: Kidney - Hp+/+Hpx+/+, 9-weeks old, non-infected


title: Kidney, Hp+/+Hpx+/+, 9-weeks old, Pcc-infected, replicate 1

value: Kidney - Hp+/+Hpx+/+, 9-weeks old, Pcc-infected, day7 post-infection


title: CVL of 24 weeks WKY rat rep3

description:
RNA-seq from tissue punches of brainstem regions
CVLM_All_Raw_Counts.txt
W-24-F-3-CVL

value: 24 weeks


title: Kidney, Hp+/+Hpx+/+, 9-weeks old, non-infected, replicate 1

value: Kidney - Hp+/+Hpx+/+, 9-weeks old, non-infected


title: RVL of 10 weeks WKY rat rep3

description:
RNA-seq from tissue punches of brainstem regions
RVLM_All_Raw_Counts.txt
W-10-F-3-RVL

value: RVLM of brainsstem

value: WKY

value: 10 weeks

value: RVLM


title: FHFR119

city: Illkirch

first: Manuel

last: Mendoza

address: 1 rue Laurent Fries

country: France

institute: INSTITUTE OF GENETICS AND MOLECULAR AND CELLULAR BIOLOGY

description: Nuclear

data_processing:
Image analysis and base calling were performed using RTA 2.7.7 and BclConvert 3.8.4.
Alignment : Reads were mapped onto mm10 assembly of Mus musculus genome using STAR v.2.5.3a
Quantification : Gene expression was quantified using HTSeq v.0.6.1p1 (union mode) and Ensembl release 102 annotations.
Assembly: mm10
Supplementary files format and content: Tabulated text file containing raw read counts in each sample.

source_name: TIP60-AID transgenic mESC line

growth_protocol: The auxin-inducible TIP60KI/KI mouse Embryonic Stem Cell (ESC) line was grown on 0.1% gelatinized (Sigma-Aldrich, Cat# G1890) tissue-culture plates in 2i medium, DMEM (4.5g/L glucose) with GlutaMAX-I supplemented with ES-tested 15% fetal calf serum (FCS, ThermoFisher Scientific, Cat# 10270-106), 2 mM L-glutamine (ThermoFisher Scientific, Cat# 25030-024), 0.1% β-mercaptoethanol (ThermoFisher Scientific, Cat# 31350-010), 100 UI/ml penicillin, 100 μg/ml streptomycin (ThermoFisher Scientific, Cat# 15140-122), 0.1 mM non-essential amino acids (ThermoFisher Scientific, Cat# 11140-035), 1500 U/ml leukemia inhibitory factor (produced in-house) and 2i, 3 μM CHIR99021 (Axon Medchem, Cat# 1386) and 1 μM PD0325901 (Axon Medchem, Cat# 1408) were added freshly to the medium.

extract_protocol:
P2955
RNA extraction was performed using TRI Reagent® (Molecular Research Center Inc., Cat# TR 188), following the manufacturer's instructions. DNase I treatment was performed to prevent genomic DNA contamination using the TURBO DNA-free™ Kit (ThermoFisher Scientific, Cat# AM1907) manufacturer's instructions.
P2955 : Total RNA-Seq libraries were generated from 600 ng of total RNA using Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus kit and IDT for Illumina RNA UD Indexes, Ligation (Illumina, San Diego, USA), according to manufacturer's instructions. DNA library were amplified using 12 cycles of PCR. Surplus PCR primers were further removed by two successive purifications using SPRIselect beads (Beckman-Coulter, Villepinte, France).  The final libraries were checked for quality and quantified using Bioanalyzer 2100 system (Agilent technologies, Les Ulis, France).

treatment_protocol: KI cells were treated with Auxin for 24 hours

tag: cell line

value: TIP60-AID transgenic mESC line

value: stem cell

value: Auxin


title: FHFR117

description: Total

tag: treatment


title: FHFR121

description: Total


title: FHFR120

description: Total


title: CVL of 8 weeks SHR rat rep1

description:
RNA-seq from tissue punches of brainstem regions
CVLM_All_Raw_Counts.txt
S-8-F-1-CVL

value: CVLM of brainsstem

value: SHR

value: 8 weeks

value: CVLM


title: CVL of 24 weeks WKY rat rep2

description:
RNA-seq from tissue punches of brainstem regions
CVLM_All_Raw_Counts.txt
W-24-F-2-CVL


title: CVL of 16 weeks WKY rat rep1

description:
RNA-seq from tissue punches of brainstem regions
CVLM_All_Raw_Counts.txt
W-16-F-1-CVL

value: 16 weeks


title: CVL of 12 weeks WKY rat rep3

description:
RNA-seq from tissue punches of brainstem regions
CVLM_All_Raw_Counts.txt
W-12-F-3-CVL

value: 12 weeks


title: CVL of 16 weeks WKY rat rep2

description:
RNA-seq from tissue punches of brainstem regions
CVLM_All_Raw_Counts.txt
W-16-F-2-CVL


title: CVL of 10 weeks WKY rat rep3

description:
RNA-seq from tissue punches of brainstem regions
CVLM_All_Raw_Counts.txt
W-10-F-3-CVL


title: CVL of 24 weeks WKY rat rep1

description:
RNA-seq from tissue punches of brainstem regions
CVLM_All_Raw_Counts.txt
W-24-F-1-CVL


title: CVL of 12 weeks WKY rat rep2

description:
RNA-seq from tissue punches of brainstem regions
CVLM_All_Raw_Counts.txt
W-12-F-2-CVL


title: CVL of 8 weeks WKY rat rep5

description:
RNA-seq from tissue punches of brainstem regions
CVLM_All_Raw_Counts.txt
W-8-F-6-CVL


title: FHFR116

description: Total

value: DMSO


title: FHFR106

description: Nuclear


title: FHFR115

description: Cytoplasmic


title: FHFR107

description: Total


title: FHFR114

description: Cytoplasmic


title: CVL of 10 weeks WKY rat rep2

description:
RNA-seq from tissue punches of brainstem regions
CVLM_All_Raw_Counts.txt
W-10-F-2-CVL


title: CVL of 8 weeks WKY rat rep4

description:
RNA-seq from tissue punches of brainstem regions
CVLM_All_Raw_Counts.txt
W-8-F-5-CVL


title: CVL of 16 weeks WKY rat rep3

description:
RNA-seq from tissue punches of brainstem regions
CVLM_All_Raw_Counts.txt
W-16-F-3-CVL


title: CVL of 12 weeks WKY rat rep1

description:
RNA-seq from tissue punches of brainstem regions
CVLM_All_Raw_Counts.txt
W-12-F-1-CVL


title: CVL of 8 weeks WKY rat rep3

description:
RNA-seq from tissue punches of brainstem regions
CVLM_All_Raw_Counts.txt
W-8-F-4-CVL


title: FHFR105

description: Nuclear


title: FHFR113

description: Total


title: FHFR104

description: Cytoplasmic


title: FHFR118

description: Nuclear


title: CVL of 8 weeks WKY rat rep2

description:
RNA-seq from tissue punches of brainstem regions
CVLM_All_Raw_Counts.txt
W-8-F-3-CVL


title: CVL of 8 weeks WKY rat rep1

description:
RNA-seq from tissue punches of brainstem regions
CVLM_All_Raw_Counts.txt
W-8-F-2-CVL


title: CVL of 10 weeks WKY rat rep4

description:
RNA-seq from tissue punches of brainstem regions
CVLM_All_Raw_Counts.txt
W-10-F-4-CVL


title: FHFR102

description: Total


title: NTS of 24 week SHR rat rep6

description:
RNA-seq from tissue punches of brainstem regions
NTS_All_Raw_Counts.txt
S-24-F-6-NTS

source_name: NTS of brainstem

value: NTS of brainstem

value: NTS


title: CVL of 10 weeks WKY rat rep1

description:
RNA-seq from tissue punches of brainstem regions
CVLM_All_Raw_Counts.txt
W-10-F-1-CVL


title: FHFR101

description: Nuclear


title: FHFR100

description: Nuclear


title: NTS of 24 week SHR rat rep4

description:
RNA-seq from tissue punches of brainstem regions
NTS_All_Raw_Counts.txt
S-24-F-4-NTS

value: 24 weeks


title: NTS of 24 week SHR rat rep5

description:
RNA-seq from tissue punches of brainstem regions
NTS_All_Raw_Counts.txt
S-24-F-5-NTS


title: NTS of 24 week SHR rat rep3

description:
RNA-seq from tissue punches of brainstem regions
NTS_All_Raw_Counts.txt
S-24-F-3-NTS


title: FHFR99

description: Cytoplasmic


title: FHFR98

description: Cytoplasmic


title: NTS of 16 week SHR rat rep5

description:
RNA-seq from tissue punches of brainstem regions
NTS_All_Raw_Counts.txt
S-16-F-5-NTS


title: NTS of 16 week SHR rat rep4

description:
RNA-seq from tissue punches of brainstem regions
NTS_All_Raw_Counts.txt
S-16-F-4-NTS


title: AZD-treated tumor, Input 2

city: New York

first: Athanassios

last: Dovas

state: NY

address: 1130St Nicholas Avenue

institute: Columbia University

data_processing:
NextSeq 500 sequencer with a 75-cycle high-output kit (Illumina)
The RNA-Seq data were aligned to the mm10 genome and RefSeq transcriptome annotation using the STAR aligner
Normalized data were generated using DEseq2 package in R
Assembly: mm10
Supplementary files format and content: tab delimited txt file contains raw counts for each sample
Library strategy: RiboTag

source_name: brain

extract_protocol:
RNA was extracted using Rneasy Mini kit (Qiagen)
Libraries were generated using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina from New England Biolabs (E7420S) according to the manufacturer’s protocol.

value: brain

value: AZD8055-treated tumor

tag: fraction

value: Input


title: AZD-treated tumor, IP 2

value: IP


title: AZD-treated tumor, Input 3


title: NTS of 16 week SHR rat rep6

description:
RNA-seq from tissue punches of brainstem regions
NTS_All_Raw_Counts.txt
S-16-F-6-NTS


title: AZD-treated tumor, Input 1


title: NTS of 24 week SHR rat rep1

description:
RNA-seq from tissue punches of brainstem regions
NTS_All_Raw_Counts.txt
S-24-F-1-NTS


title: Tumor, IP 3

value: tumor


title: NTS of 16 week SHR rat rep3

description:
RNA-seq from tissue punches of brainstem regions
NTS_All_Raw_Counts.txt
S-16-F-3-NTS


title: NTS of 16 week SHR rat rep2

description:
RNA-seq from tissue punches of brainstem regions
NTS_All_Raw_Counts.txt
S-16-F-2-NTS


title: AZD-treated tumor, IP 1


title: FHFR103

description: Cytoplasmic

value: TIP60-AID transgenic mESC line

value: stem cell


title: NTS of 16 week SHR rat rep1

description:
RNA-seq from tissue punches of brainstem regions
NTS_All_Raw_Counts.txt
S-16-F-1-NTS


title: Tumor, IP 2


title: Tumor, IP 1


title: NTS of 12 week SHR rat rep5

description:
RNA-seq from tissue punches of brainstem regions
NTS_All_Raw_Counts.txt
S-12-F-5-NTS


title: NTS of 12 week SHR rat rep6

description:
RNA-seq from tissue punches of brainstem regions
NTS_All_Raw_Counts.txt
S-12-F-6-NTS


title: Tumor, Input 3


title: Tumor, Input 2


title: NTS of 24 week SHR rat rep2

description:
RNA-seq from tissue punches of brainstem regions
NTS_All_Raw_Counts.txt
S-24-F-2-NTS


title: AZD-treated tumor, IP 3


title: NTS of 12 week SHR rat rep3

description:
RNA-seq from tissue punches of brainstem regions
NTS_All_Raw_Counts.txt
S-12-F-3-NTS


title: Control, IP 3

value: control


title: Tumor, Input 1


title: Control, IP 2


title: NTS of 12 week SHR rat rep2

description:
RNA-seq from tissue punches of brainstem regions
NTS_All_Raw_Counts.txt
S-12-F-2-NTS

value: SHR


title: NTS of 10 week SHR rat rep5

description:
RNA-seq from tissue punches of brainstem regions
NTS_All_Raw_Counts.txt
S-10-F-5-NTS

value: 10 weeks


title: NTS of 12 week SHR rat rep1

description:
RNA-seq from tissue punches of brainstem regions
NTS_All_Raw_Counts.txt
S-12-F-1-NTS


title: NTS of 10 week SHR rat rep4

description:
RNA-seq from tissue punches of brainstem regions
NTS_All_Raw_Counts.txt
S-10-F-4-NTS


title: Control, Input 2


title: NTS of 10 week SHR rat rep2

description:
RNA-seq from tissue punches of brainstem regions
NTS_All_Raw_Counts.txt
S-10-F-2-NTS


title: Control, Input 1


title: NTS of 10 week SHR rat rep3

description:
RNA-seq from tissue punches of brainstem regions
NTS_All_Raw_Counts.txt
S-10-F-3-NTS


title: NTS of 10 week SHR rat rep1

description:
RNA-seq from tissue punches of brainstem regions
NTS_All_Raw_Counts.txt
S-10-F-1-NTS


title: NTS of 8 week SHR rat rep4

description:
RNA-seq from tissue punches of brainstem regions
NTS_All_Raw_Counts.txt
S-8-F-4-NTS

value: 8 weeks


title: NTS of 8 week SHR rat rep2

description:
RNA-seq from tissue punches of brainstem regions
NTS_All_Raw_Counts.txt
S-8-F-2-NTS


title: NTS of 8 week SHR rat rep3

description:
RNA-seq from tissue punches of brainstem regions
NTS_All_Raw_Counts.txt
S-8-F-3-NTS


title: Control, Input 3


title: NTS of 8 week SHR rat rep1

description:
RNA-seq from tissue punches of brainstem regions
NTS_All_Raw_Counts.txt
S-8-F-1-NTS


title: NTS of 12 week SHR rat rep4

description:
RNA-seq from tissue punches of brainstem regions
NTS_All_Raw_Counts.txt
S-12-F-4-NTS


title: NTS of 8 week SHR rat rep5

description:
RNA-seq from tissue punches of brainstem regions
NTS_All_Raw_Counts.txt
S-8-F-5-NTS


title: OVX-EPC-2_H3K9me3

city: Philadelphia

first: Charan

middle: Thej

last: Gurrala

state: Pennsylvania

address: 3500 N Broad St, MERB 983

department: Aging + Cardiovascular Discovery Center

institute: Temple University

data_processing:
The paired-end 38 bp sequencing reads (PE38) generated by Illumina sequencing (using NextSeq 500) are mapped to the genome using the BWA algorithm with default settings (“bwa mem”). Alignment information for each read is stored in the BAM format. Only reads that pass Illumina’s purity filter, align with no more than 2 mismatches, and map uniquely to the genome are used in the subsequent analysis. In addition, duplicate reads (“PCR duplicates”) are removed.
Genomic regions with high levels of transposition/tagging events are determined using the MACS2 peak calling algorithm (Zhang et al., Genome Biology 2008, 9:R137). Since both reads (tags) from paired-end sequencing represent transposition events, both reads are used for peak-calling but treated a single, independent reads. Note that we use the generic term “Interval” to describe the genomic regions identified by MACS2. Intervals are defined by the chromosome number and a start and end coordinate.
To identify the density of transposition events along the genome, the genome is divided into 32 bp bins and the number of fragments in each bin is determined. For this purpose, reads are extended to 200 bp, which is close to the average length of the sequenced library inserts. In silico extension also helps to smooth the data. This information (“signal map”; histogram of fragment densities) is stored in a bigWig file, which can be visualized in genome browsers (see Section VI.). BigWig files are also the basis of the peak metrics in the Active Motif analysis program described below.
In the default analysis, the tag number of all samples is reduced (by random sampling) to the number of tags present in the smallest sample. When samples are not directly comparable or in cases of projects with outlier samples, this strategy is either forgone or can potentially be customized to fit the experimental design.
To compare peak metrics between 2 or more samples, overlapping Intervals (orange bars in diagram on next page) are grouped into “Merged Regions” (green bars), which are defined by the start coordinate of the most upstream Interval and the end coordinate of the most downstream Interval (= union of overlapping Intervals; “merged peaks”). In locations where only one sample has an Interval, this Interval defines the Merged Region. The use of Merged Regions is necessary because the locations and lengths of Intervals are rarely exactly the same when comparing different samples. Furthermore, with this approach fragment density values can be obtained even for samples for which no peak was called.
Assembly: mm10
Supplementary files format and content: Excel workbook peak,  log2FoldChange
Library strategy: CUT&Tag

source_name: Bone marrow

growth_protocol: Cultured in EGM-2 medium

extract_protocol:
Cells were washed with DPBS, counted, and 1×106 cells per vial were frozen in a freeze mix (90%FBS+10% Dimethyl sulfoxide-DMSO) and set aside in duplicates for CUT&TagTM sequencing. Approximately 2×105 nuclei were used for performing CUT&Tag-ITTM sequencing using a standard assay kit (Active Motif, USA cat no. 53160) for the H3K9me3 mark using a CHIP grade antibody (Cat no. 391691, Active Motif, USA). Further downstream steps were performed according to the protocol provided in the kit (Active Motif, 53160).
DNA libraries were prepared using unique i7 and i5 index primers for each sample, size selected with SPRI beads (Cat No. 53160, Active Motif), quality checked with fragment analyzer, a capillary electrophoresis instrument for NGS library quality check and sequenced by the UMass Deep Sequencing Core with 25 bp paired-end Illumina Miseq system.

value: Bone marrow

value: freshly isolated

value: Female

value: Ovariectomized Endothelial Progenitor Cells

tag: chip antibody

value: H3K9me3 (39765 Active Motif)

value: Sca-1/CD31 + magnetic sorting


title: NTS of 24 week WKY rat rep3

description:
RNA-seq from tissue punches of brainstem regions
NTS_All_Raw_Counts.txt
W-24-F-3-NTS

value: NTS of brainstem

value: WKY

value: 24 1eeks

value: NTS


title: Male-EPC-1_H3K9me3

value: Male

value: Endothelial Progenitor Cells


title: Male-EPC-2_H3K9me3


title: OVX-EPC-1_H3K9me3


title: Female-EPC-1_H3K9me3


title: NTS of 24 week WKY rat rep2

description:
RNA-seq from tissue punches of brainstem regions
NTS_All_Raw_Counts.txt
W-24-F-2-NTS


title: Female-EPC-2_H3K9me3


title: NTS of 24 week WKY rat rep1

description:
RNA-seq from tissue punches of brainstem regions
NTS_All_Raw_Counts.txt
W-24-F-1-NTS


title: NTS of 16 week WKY rat rep3

description:
RNA-seq from tissue punches of brainstem regions
NTS_All_Raw_Counts.txt
W-16-F-3-NTS

value: 16 1eeks


title: GFP_MCHERRY_scRNAseq

city: Dallas

first: Simeng

last: Wang

address: 5323 Harry Hines Blvd

institute: UT Southwestern Medical Center

library_source: transcriptomic single cell

data_processing:
Raw data was demultiplexed using cellranger (version 6.1.2) and barcode-aware wrapper supported by 10X Genomics’ pipeline. New custom mice gene reference genomes were created by adding both GFP and mCherry into existing mouse gene reference genomes “refdata-gex-mm10-2020-A”. Transcriptomes were aligned to the new custom mice gene referrence.
Addition of GFP and mCherry marker genes to the available mouse gene reference was achieved via 10x Genomics instructions.
Assembly: mm10_cg_genome
Supplementary files format and content: Tab-separeated values files and matrix files

source_name: Liver

growth_protocol: Mice were housed at room temperature (23˚C) and maintained on a 12 hr light/dark cycle and provided ad libitum access to rodent chow (Harlan, Teklad Global 18% Protein Rodent Diet 2018; 18% kcal from fat, 3.1 kcal/g).

extract_protocol:
Hepatocytes and NPCs were isolated using Liberase-based perfusion. After OptiPrep density gradient solution-treated centrifugation, whole liver tissue is fully digested. We further treated, washed and collected the single cell suspension.
10X Genomics Chromium Single Cell 3’ Library and Gel Beads Kit (version 3) according to manufacturer’s protocol. Libraries were sequenced on an Illumina NextSeq 500 with high output of 400 million reads.

treatment_protocol: An 8-week-old C57BL/6J male mouse was injected retro-orbitally with an AAV-DJ virus that was engineered to express GFP and AAV-8 engineered to express mCherry. The mouse was fed a chow diet ad lib and sacrificed in 3 weeks after virus injection. Hepatocytes and non-parenchymal liver cells (NPCs) were isolated for the sc-RNA seq.

value: Liver


title: Control, IP 1

value: brain

value: control

value: IP


title: Human Milk 50 - Duplicate

type: RNA

city: Lebanon

first: Caitlin

middle: G

last: Howe

state: NH

address: 1 Medical Center Dr

department: Epidemiology

institute: Geisel School of Medicine at Dartmouth

description:
miRNAs were isolated from extracellular vesicles and particles extracted from the supernatant portion of the milk samples
SAMPLE 58

hyb_protocol: NanoString recommended protocols were followed as described in the nCounter miRNA Expression Assay User's Manual

data_processing: We provide the RCC files here with the raw read counts including for sample-specific positive and negative controls. Counts from duplicate samples were averaged. We use the first sample number for duplicates in the matrix tab.

label: biotin

source_name: Milk, supernatant fraction

extract_protocol: EVP miRNAs were extracted from 500 ul of the supernatant fraction of human milk using the Norgen Urine Exosome RNA Isolation Kit (Norgen Biotek, Thorold, ON, Canada) according to the manufacturer's protocol. Eluted miRNAs were then further purified using Amicon Ultra Centrifugal Filters and concentrated using a speed vacuum concentrator

tag: gender

tag: life stage

value: Postpartum

tag: days postpartum at sample collection

tag: molecule subtype

value: miRNA


title: NTS of 16 week WKY rat rep2

description:
RNA-seq from tissue punches of brainstem regions
NTS_All_Raw_Counts.txt
W-16-F-2-NTS

tag: tissue


title: Human Milk 8 - Duplicate

description:
miRNAs were isolated from extracellular vesicles and particles extracted from the supernatant portion of the milk samples
SAMPLE 56

scan_protocol: NanoString recommended protocols were followed as described in the nCounter miRNA Expression Assay User's Manual

value: Female


title: Human Milk 22 - Duplicate

description:
miRNAs were isolated from extracellular vesicles and particles extracted from the supernatant portion of the milk samples
SAMPLE 57

label_protocol: NanoString recommended protocols were followed as described in the nCounter miRNA Expression Assay User's Manual


title: NTS of 12 week WKY rat rep2

description:
RNA-seq from tissue punches of brainstem regions
NTS_All_Raw_Counts.txt
W-12-F-2-NTS

value: 12 1eeks


title: NTS of 12 week WKY rat rep1

description:
RNA-seq from tissue punches of brainstem regions
NTS_All_Raw_Counts.txt
W-12-F-1-NTS


title: Human Milk 54

description:
miRNAs were isolated from extracellular vesicles and particles extracted from the supernatant portion of the milk samples
SAMPLE 54


title: NTS of 10 week WKY rat rep3

description:
RNA-seq from tissue punches of brainstem regions
NTS_All_Raw_Counts.txt
W-10-F-3-NTS

value: 10 1eeks


title: Human Milk 45 - Duplicate

description:
miRNAs were isolated from extracellular vesicles and particles extracted from the supernatant portion of the milk samples
SAMPLE 55


title: NTS of 10 week WKY rat rep2

description:
RNA-seq from tissue punches of brainstem regions
NTS_All_Raw_Counts.txt
W-10-F-2-NTS


title: Human Milk 53

description:
miRNAs were isolated from extracellular vesicles and particles extracted from the supernatant portion of the milk samples
SAMPLE 53


title: NTS of 10 week WKY rat rep1

description:
RNA-seq from tissue punches of brainstem regions
NTS_All_Raw_Counts.txt
W-10-F-1-NTS


title: NTS of 8 week WKY rat rep5

description:
RNA-seq from tissue punches of brainstem regions
NTS_All_Raw_Counts.txt
W-8-F-6-NTS

value: 8 weeks


title: NTS of 8 week WKY rat rep4

description:
RNA-seq from tissue punches of brainstem regions
NTS_All_Raw_Counts.txt
W-8-F-5-NTS

value: NTS of brainstem


title: NTS of 8 week WKY rat rep3

description:
RNA-seq from tissue punches of brainstem regions
NTS_All_Raw_Counts.txt
W-8-F-4-NTS

value: WKY


title: Human Milk 51

description:
miRNAs were isolated from extracellular vesicles and particles extracted from the supernatant portion of the milk samples
SAMPLE 51


title: Human Milk 50

description:
miRNAs were isolated from extracellular vesicles and particles extracted from the supernatant portion of the milk samples
SAMPLE 50


title: Human Milk 49

description:
miRNAs were isolated from extracellular vesicles and particles extracted from the supernatant portion of the milk samples
SAMPLE 49


title: Human Milk 52

description:
miRNAs were isolated from extracellular vesicles and particles extracted from the supernatant portion of the milk samples
SAMPLE 52


title: NTS of 8 week WKY rat rep2

description:
RNA-seq from tissue punches of brainstem regions
NTS_All_Raw_Counts.txt
W-8-F-3-NTS


title: Human Milk 46

description:
miRNAs were isolated from extracellular vesicles and particles extracted from the supernatant portion of the milk samples
SAMPLE 46


title: NTS of 16 week WKY rat rep1

description:
RNA-seq from tissue punches of brainstem regions
NTS_All_Raw_Counts.txt
W-16-F-1-NTS


title: NTS of 12 week WKY rat rep3

description:
RNA-seq from tissue punches of brainstem regions
NTS_All_Raw_Counts.txt
W-12-F-3-NTS


title: Human Milk 48

description:
miRNAs were isolated from extracellular vesicles and particles extracted from the supernatant portion of the milk samples
SAMPLE 48


title: Human Milk 45

description:
miRNAs were isolated from extracellular vesicles and particles extracted from the supernatant portion of the milk samples
SAMPLE 45


title: NTS of 10 week WKY rat rep4

description:
RNA-seq from tissue punches of brainstem regions
NTS_All_Raw_Counts.txt
W-10-F-4-NTS


title: Human Milk 42

description:
miRNAs were isolated from extracellular vesicles and particles extracted from the supernatant portion of the milk samples
SAMPLE 42


title: Human Milk 43

description:
miRNAs were isolated from extracellular vesicles and particles extracted from the supernatant portion of the milk samples
SAMPLE 43


title: Human Milk 44

description:
miRNAs were isolated from extracellular vesicles and particles extracted from the supernatant portion of the milk samples
SAMPLE 44


title: Human Milk 41

description:
miRNAs were isolated from extracellular vesicles and particles extracted from the supernatant portion of the milk samples
SAMPLE 41


title: NTS of 8 week WKY rat rep1

description:
RNA-seq from tissue punches of brainstem regions
NTS_All_Raw_Counts.txt
W-8-F-2-NTS


title: Scc1-FLAG, IP [2017_034B_234-X_IP]

city: Bunkyo-ku

first: Naoko

last: Yokota

state: Tokyo

address: 1-1-1 yayoi

department: Department of Cell and Molecular Biology

country: Japan

institute: The University of Tokyo

data_processing:
Sequenced single-end 65-bp reads were mapped to the yeast genome using Bowtie2 version 2.4.1 with default parameters.
BigWig files (100-bp bin) were generated by DROMPAplus version 1.8.2 with "--nofilter" option. The read distribution is normalized based on the total read number of nonredundant mapped reads.
Assembly: Saccharomyces Genome Database (SGD), identical with sacCer3
Supplementary files format and content: bigwig

organism: Saccharomyces cerevisiae

growth_protocol: Cells were cultured in YEP medium (1 % yeast extract, 2 % peptone, 40 μg ml-1 adenine) supplemented with 2 % glucose, or 2 % galactose, as stated, and at 30°C if not stated otherwise.

extract_protocol:
Chromatin immunoprecipitation was performed as detailed in Jeppsson et al., 2022. Briefly, S. cerevisiae cells were crosslinked with 1 % formaldehyde for 30 minutes at room temperature, followed by incubation at 4°C overnight. Chromatin was then sheared to a size of 300-500 bp by sonication (Bandelin Sonopuls HD 2070.2) and IP reactions, with anti-FLAG antibody (Merck, F1804) conjugated to Dynabeads Protein A (Invitrogen, 10002D), were allowed to proceed overnight at 4°C. After completing the immunoprecipitation and reversing crosslinks, the DNA was purified.
For ChIP-seq, DNA from ChIP and input fractions were prepared for sequencing using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645).

treatment_protocol: For synchronization in G1-phase, 3 μg ml-1 α-factor mating pheromone (Merck, custom peptide WHWLQLKPGQPMY) was added every hour (a total of three additions) to cells growing logarithmically. For G2/M cell cycle arrest, benomyl (Merck, 381586) was added to the YEPD media for a final concentration 80 µg ml-1. A complete G2/M-arrest of logarithmically growing cells was achieved after 90 minutes at 30°C, or 120 minutes at 23°C. For G2/M-arrest following synchronization in G1-phase, cells were released into benomyl-containing YEPD for 60 minutes. For depletion of Scc2, Wpl1, Top1, Smc6, Nse4, Nse5 and Top2 in Figures 1A, 1D, 4A, S10C, auxin (3-indoleacetic acid, 1 mM final concentration, Merck, I2886) and doxycycline (5 μg ml-1 final concentration, Merck, D9891) were added to simultaneously degrade the proteins and inhibit their transcription, respectively. For degradation of Smc5 and Smc6 in Figure S9C, auxin (3-indoleacetic acid, Merck, I2886) was added at a final concentration of 1 mM. For transcription inhibition, thiolutin (Abcam, ab143556) was added to cell cultures for the final concentration of 20 µg ml-1 for 30 minutes.

tag: target protein

tag: antibody

value: anti-FLAG (Merck, F1804)

value: G2/M-arrest following an S-phase at 35°C


title: Human Milk 39

description:
miRNAs were isolated from extracellular vesicles and particles extracted from the supernatant portion of the milk samples
SAMPLE 39


title: Human Milk 40

description:
miRNAs were isolated from extracellular vesicles and particles extracted from the supernatant portion of the milk samples
SAMPLE 40


title: Scc1-FLAG top2-4, IP [2017_034B_383-X_IP]

tag: strain


title: Smc6-FLAG, Input [2017_035A_173-X_Input]

value: Input


title: Smc6-FLAG, IP [2017_035A_173-X_IP]


title: Smc6-FLAG top2-4, IP [2017_036B_1367-X_IP]


title: Human Milk 47

description:
miRNAs were isolated from extracellular vesicles and particles extracted from the supernatant portion of the milk samples
SAMPLE 47


title: Human Milk 38

description:
miRNAs were isolated from extracellular vesicles and particles extracted from the supernatant portion of the milk samples
SAMPLE 38


title: Smc6-FLAG Top1-AID top2-4, IP [2019_030B_3341-3_IP]

value: Auxin+doxycycline


title: Human Milk 37

description:
miRNAs were isolated from extracellular vesicles and particles extracted from the supernatant portion of the milk samples
SAMPLE 37


title: Smc6-FLAG top2-4, IP [2019_030B_3069-3_IP]


title: Smc6-FLAG, Input [2019_030B_3067-3_WCE]


title: Human Milk 36

description:
miRNAs were isolated from extracellular vesicles and particles extracted from the supernatant portion of the milk samples
SAMPLE 36


title: Smc6-FLAG Top1-AID, IP [2019_030B_3318-3_IP]


title: Smc6-FLAG, IP [2019_030B_3067-3_IP]


title: Rpo21-FLAG top2-4, 30 min DMSO, IP [2017_036B_1959-2_30-_IP]

value: 30 min DMSO


title: Human Milk 35

description:
miRNAs were isolated from extracellular vesicles and particles extracted from the supernatant portion of the milk samples
SAMPLE 35


title: Rpo21-FLAG top2-4, 30 min thiolutin, IP [2017_036B_1959-2_30+_IP]

value: 30 min thiolutin


title: Human Milk 32

description:
miRNAs were isolated from extracellular vesicles and particles extracted from the supernatant portion of the milk samples
SAMPLE 32


title: Human Milk 34

description:
miRNAs were isolated from extracellular vesicles and particles extracted from the supernatant portion of the milk samples
SAMPLE 34


title: Rpo21-FLAG top2-4, 15 min thiolutin, IP [2017_036B_1959-2_15+_IP]

value: 15 min thiolutin


title: Rpo21-FLAG top2-4, 3 min thiolutin, IP [2017_036B_1959-2_3+_IP]

value: 3 min thiolutin


title: Human Milk 31

description:
miRNAs were isolated from extracellular vesicles and particles extracted from the supernatant portion of the milk samples
SAMPLE 31


title: Human Milk 29

description:
miRNAs were isolated from extracellular vesicles and particles extracted from the supernatant portion of the milk samples
SAMPLE 29


title: Human Milk 30

description:
miRNAs were isolated from extracellular vesicles and particles extracted from the supernatant portion of the milk samples
SAMPLE 30


title: Human Milk 28

description:
miRNAs were isolated from extracellular vesicles and particles extracted from the supernatant portion of the milk samples
SAMPLE 28


title: Rpo21-FLAG top2-4, 0 min thiolutin, IP [2017_036B_1959-2_0_IP]

value: 0 min thiolutin


title: Rpo21-FLAG, 30 min DMSO, IP [2017_036B_1958-2_30-_IP]


title: Rpo21-FLAG, 15 min thiolutin, IP [2017_034B_1958-2_15+_IP]


title: Scc1-FLAG top2-4, 30 min DMSO, IP [2017_032B_383-2_30-_IP]


title: Human Milk 33

description:
miRNAs were isolated from extracellular vesicles and particles extracted from the supernatant portion of the milk samples
SAMPLE 33

value: Postpartum


title: Rpo21-FLAG, 0 min thiolutin, IP [2017_035A_1958-2_0_IP]


title: Human Milk 26

description:
miRNAs were isolated from extracellular vesicles and particles extracted from the supernatant portion of the milk samples
SAMPLE 26

value: miRNA


title: Scc1-FLAG top2-4, 15 min thiolutin, IP [2017_032B_383-2_15+_IP]


title: Human Milk 27

description:
miRNAs were isolated from extracellular vesicles and particles extracted from the supernatant portion of the milk samples
SAMPLE 27

value: Female


title: Human Milk 23

description:
miRNAs were isolated from extracellular vesicles and particles extracted from the supernatant portion of the milk samples
SAMPLE 23


title: Human Milk 22

description:
miRNAs were isolated from extracellular vesicles and particles extracted from the supernatant portion of the milk samples
SAMPLE 22


title: Human Milk 24

description:
miRNAs were isolated from extracellular vesicles and particles extracted from the supernatant portion of the milk samples
SAMPLE 24


title: Scc1-FLAG top2-4, 3 min thiolutin, IP [2017_032B_383-2_3+_IP]


title: Human Milk 25

description:
miRNAs were isolated from extracellular vesicles and particles extracted from the supernatant portion of the milk samples
SAMPLE 25


title: Scc1-FLAG, 30 min thiolutin, IP [2017_034B_234-2_30+_IP]


title: Scc1-FLAG, 30 min DMSO, IP [2017_032B_234-2_30-_IP]


title: Rpo21-FLAG, 30 min thiolutin, IP [2017_035A_1958-2_30+_IP]


title: Scc1-FLAG, 15 min thiolutin, IP [2017_034B_234-2_15+_IP]


title: Human Milk 17

description:
miRNAs were isolated from extracellular vesicles and particles extracted from the supernatant portion of the milk samples
SAMPLE 17


title: Scc1-FLAG top2-4, 30 min thiolutin, IP [2017_032B_383-2_30+_IP]


title: Human Milk 20

description:
miRNAs were isolated from extracellular vesicles and particles extracted from the supernatant portion of the milk samples
SAMPLE 20


title: Human Milk 16

description:
miRNAs were isolated from extracellular vesicles and particles extracted from the supernatant portion of the milk samples
SAMPLE 16


title: Human Milk 21

description:
miRNAs were isolated from extracellular vesicles and particles extracted from the supernatant portion of the milk samples
SAMPLE 21


title: Human Milk 14

description:
miRNAs were isolated from extracellular vesicles and particles extracted from the supernatant portion of the milk samples
SAMPLE 14


title: Human Milk 15

description:
miRNAs were isolated from extracellular vesicles and particles extracted from the supernatant portion of the milk samples
SAMPLE 15


title: Scc1-FLAG, 0 min thiolutin, IP [2017_032B_234-2_0_IP]


title: Smc6-FLAG top2-4, 30 min DMSO, IP [2017_032B_1367-2_30-_IP]


title: Scc1-FLAG top2-4, 0 min thiolutin, IP [2017_032B_383-2_0_IP]


title: Human Milk 12

description:
miRNAs were isolated from extracellular vesicles and particles extracted from the supernatant portion of the milk samples
SAMPLE 12


title: Human Milk 11

description:
miRNAs were isolated from extracellular vesicles and particles extracted from the supernatant portion of the milk samples
SAMPLE 11


title: Human Milk 18

description:
miRNAs were isolated from extracellular vesicles and particles extracted from the supernatant portion of the milk samples
SAMPLE 18


title: Human Milk 10

description:
miRNAs were isolated from extracellular vesicles and particles extracted from the supernatant portion of the milk samples
SAMPLE 10


title: Smc6-FLAG top2-4, 30 min thiolutin, input [2017_032B_1367-2_30+_Input]


title: Smc6-FLAG top2-4, 15 min thiolutin, IP [2017_032B_1367-2_15+_IP]


title: Smc6-FLAG top2-4, 30 min thiolutin, IP [2017_032B_1367-2_30+_IP]


title: Human Milk 8

description:
miRNAs were isolated from extracellular vesicles and particles extracted from the supernatant portion of the milk samples
SAMPLE 8


title: Human Milk 7

description:
miRNAs were isolated from extracellular vesicles and particles extracted from the supernatant portion of the milk samples
SAMPLE 7


title: Human Milk 9

description:
miRNAs were isolated from extracellular vesicles and particles extracted from the supernatant portion of the milk samples
SAMPLE 9


title: Smc6-FLAG top2-4, 3 min thiolutin, input [2017_032B_1367-2_3+_Input]


title: Smc6-FLAG top2-4, 30 min DMSO, input [2017_032B_1367-2_30-_Input]


title: Smc6-FLAG top2-4, 3 min thiolutin, IP [2017_032B_1367-2_3+_IP]


title: Smc6-FLAG top2-4, 0 min thiolutin, input [2017_032B_1367-2_0+_Input]


title: Smc6-FLAG, 30 min DMSO, input [2017_032B_173-2_30-_Input]


title: Human Milk 13

description:
miRNAs were isolated from extracellular vesicles and particles extracted from the supernatant portion of the milk samples
SAMPLE 13


title: Smc6-FLAG, 30 min DMSO, IP [2017_032B_173-2_30-_IP]


title: Smc6-FLAG top2-4, 15 min thiolutin, input [2017_032B_1367-2_15+_Input]


title: Smc6-FLAG top2-4, 0 min thiolutin, IP [2017_032B_1367-2_0+_IP]


title: Human Milk 4

description:
miRNAs were isolated from extracellular vesicles and particles extracted from the supernatant portion of the milk samples
SAMPLE 4


title: Human Milk 5

description:
miRNAs were isolated from extracellular vesicles and particles extracted from the supernatant portion of the milk samples
SAMPLE 5


title: Human Milk 6

description:
miRNAs were isolated from extracellular vesicles and particles extracted from the supernatant portion of the milk samples
SAMPLE 6


title: Human Milk 1

description:
miRNAs were isolated from extracellular vesicles and particles extracted from the supernatant portion of the milk samples
SAMPLE 1


title: Human Milk 2

description:
miRNAs were isolated from extracellular vesicles and particles extracted from the supernatant portion of the milk samples
SAMPLE 2


title: Human Milk 3

description:
miRNAs were isolated from extracellular vesicles and particles extracted from the supernatant portion of the milk samples
SAMPLE 3


title: Smc6-FLAG, 30 min thiolutin, input [2017_032B_173-2_30+_Input]


title: SbGhd7 OE, Rep 2

city: Upton

first: Meng

last: Xie

address: 50 Bell Ave

institute: Brookhaven National Laboratory

data_processing:
Raw data with adapter sequences or low-quality sequences was filtered using SOAPnuke (v 2.1.7) with parameters: "-n 0.001 -l 20 -q 0.4 --adaMR 0.25 --ada_trim --minReadLen 150"
clean reads were aligned to the Sorghum bicolor genome v3.1.1 (Phytozome) using HISAT2 (v2.2.1)
Transcripts were then assembled using StringTie (v2.2.1).
DEGs were identified using DESeq2 (v2.11.40.7)
Assembly: Sorghum bicolor genome v3.1.1
Supplementary files format and content: tab-delimited tabular files include raw counts for each sample

organism: Sorghum bicolor

source_name: leaf

growth_protocol: 4-week-old sorghum plants

extract_protocol:
Total RNAs were isolated using the TRIzol Reagent (Invitrogen) and treated with DNase I (Invitrogen) to remove genomic DNA contamination
Libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB)

value: leaf

value: SbGhd7 OE


title: Smc6-FLAG, 15 min thiolutin, input [2017_032B_173-2_15+_Input]


title: Smc6-FLAG, 30 min thiolutin, IP [2017_032B_173-2_30+_IP]


title: empty vector, Rep 2

value: empty vector


title: SbGhd7 OE, Rep 1


title: empty vector, Rep 1


title: Smc6-FLAG, 15 min thiolutin, IP [2017_032B_173-2_15+_IP]


title: Smc6-FLAG, 3 min thiolutin, IP [2017_032B_173-2_3+_IP]


title: SbGhd7 OE, Rep 3


title: Smc6-FLAG, 3 min thiolutin, input [2017_032B_173-2_3+_Input]


title: Smc6-FLAG top2-4 Scc2-AID, IP [2019_030B_3543-2_IP]


title: Smc6-FLAG top2-4 Wpl1-AID, IP [2019_030B_3595-2_IP]


title: Smc6-FLAG, 0 min thiolutin, IP [2017_032B_173-2_0_IP]


title: Smc6-FLAG Wpl1-AID, IP [2019_030B_3594-2_IP]


title: Smc6-FLAG, 0 min thiolutin, input [2017_032B_173-2_0_Input]


title: Smc6-FLAG Scc2-AID, IP [2019_030B_3541-2_IP]


title: empty vector, Rep 3


title: Smc6-FLAG, Input [2019_030B_3067-2_WCE]


title: Smc6-FLAG Wpl1-AID, IP [2019_030B_3594-1_IP]


title: RelBKO_3_biol rep 3

city: Boston

first: Bidisha

last: Mitra

state: MA

address: 181 Longwood Avenue, 8th floor

department: Medicine

institute: Brigham and Women's Hospital

data_processing:
Adaptor-trimmed Illumina reads for each individual library were mapped back to the human GRCh37.83 transcriptome assembly using STAR v2.5.2b
featureCounts v1.5.1 was used to estimate the number of reads mapped to each contig. Only transcripts with at least 5 cumulative mapping counts were used in this analysis.
DESeq2 v1.14.1 was used to evaluate gene differential expression (DE)
Each DE analysis was composed of a pairwise comparison between experimental (induced) group and the control (uninduced) group. Differentially expressed genes were identified after a correction for false discovery rate (FDR 0.05).
Assembly: GRCh37.83
Supplementary files format and content: Raw files in fastq.gz format
Supplementary files format and content: Tab-delimited text files with normalized counts of genes also provided.

growth_protocol: Cells cultured in GIBCO RPMI 1640 medium (Life Technologies) with 10% fetal bovine serum (FBS) and penicillin-streptomycin in a humidified chamber at 37 degrees Celcius with 5% CO2.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (#74106, Qiagen) as per manufacturer's protocol. An in-column DNA digestion step was included to remove any residual genomic DNA contamination.
To construct RNA-seq libraries, 1ug total RNA was used for polyA mRNA-selection using NEBNext Poly(A) mRNA Magnetic Isolation Module (#E7490, New England Biolabs, Inc.  Ipswich, MA), followed by library construction via NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (#E7765, New England Biolabs, Inc., Ipswich, MA).

treatment_protocol: GM12878 LCL were transduced with lentivirus expressing sgRNAs for control, p50, p52, RelB, RelA and cRel. Transduced cells were subjected to to 3ug/ml puromycin(#A1113803, Thermo Fisher) selection for 5 days post transduction before confirming successful respective subunit knockout via immunoblot.

value: Lymphoblastoid

value: Wildtype LMP1


title: RelBKO_2_biol rep 2


title: Smc6-FLAG Scc2-AID, IP [2019_030B_3541-1_IP]

value: anti-FLAG (Merck, F1804)


title: Smc6-FLAG top2-4, IP [2019_030B_3069-2_IP]


title: Smc6-FLAG, Input [2019_030B_3067-1_WCE]


title: RelAKO_1_biol rep 1


title: RelBKO_1_biol rep 1


title: RelAKO_3_biol rep 3


title: HiC pGALScc1V137K, Scc1WT, cdc45 + oestradiol

city: Toulouse

first: christophe

last: chapard

address: 118 route de Narbonne

department: CBI - MCD

institute: CNRS

data_processing:
HiCstuff (www.github.com/koszullab/hicstuff) version 3.0.1; Chromosight (www.github.com/koszullab/chromosight) v1.3.1 36; Bowtie2 (version 2.3.4.1 available online at http://bowtie-bio.sourceforge.net/bowtie2/); Samtools (version 1.9 available online at http://www.htslib.org/download/); Bedtools (version 2.29.1 available online at https://bedtools.readthedocs.io/en/latest/content/installation.html); Cooler (version 0.8.7- 0.8.11 available online at https://cooler.readthedocs.io/en/latest/); bamCoverage (version 3.4.1 https://deeptools.readthedocs.io/en/develop/content/tools/bamCoverage.html)
Processing of the reads, computation of contact matrices, and generation of contact maps:  Reads were aligned and the contact data processed using Hicstuff, available on Github (https://github.com/koszullab/hicstuff). Briefly, pairs of reads were aligned iteratively and independently using Bowtie2 in its most sensitive mode against the S. cerevisiae W303 reference genome. Each uniquely mapped read was assigned to a restriction fragment. Quantification of pairwise contacts between restriction fragments was performed with default parameters: uncuts, loops and circularization events were filtered as described in (Cournac et al., 2012). PCR duplicates (defined as paired reads mapping at exactly the same position) were discarded. Contact maps from independent replicates were generated with the “view” function of Hicstuff, merged and normalized using the merge and balance functions of Cooler. Bins were set at 1, exp0.2 transformed, and rendered.
Computation of the contact probability as a function of genomic distance:  Computation of the contact probability as a function of genomic distance P(s) and its derivative have been determined using the “distance law” function of Hicstuff with default parameters, averaging the contact data of entire chromosome arms. P(s) from two independent replicates were determined and plotted.
For ChIP-seq analysis: Bowtie2 was used for two rounds of alignments, first on C.glabrata (CBS138) and then on S. cerevisiae allowing the generation of an alignment of IP and WCE that exclusively mapped on S. cerevisiae (an vice-versa for C.glabrata). The obtained SAM file was converted into a BAM file, sorted and indexed using Samtools. ChIP-seq profiles were then normalised by the number of million sequences and converted into BigWig using bamCoverage. Profiles were multiplied by the ORi factor (WCEglabrataIPcerevisiae / WCEcerevisiaeIPglabrata, in which WCE glabrata and IPglabrata correspond to the number of paired reads that mapped uniquely on C. glabrata genome and same for S. cerevisiae reads) using Integrated Genome Browser
Loop detection and scoring with Chromosight: Chromosight 1.3.1 36 was used to call loops de novo from contact maps binned at 1 kb and balanced with Cooler. Matrices were subsampled to contain the same total number of contacts.  De novo loop calling was computed using the “ detect ”  mode of Chromosight, with minimum loop length set at 2kb, percentage undetected set at 25 and pearson correlation threshold set at 0.315. Loop strength was quantified for each loop using the quantify mode of Chromosight and the mean loop score was calculated for each condition. Loop pile-up of averaged 17kb windows were generated with Chromosight. De novo loop calling and scoring were performed on independent HiC replicates, where indicated, which were subsampled independently for each experiment, using the number of contacts of the least covered map or subsampling to 20M reads. Loop score is shown as mean ± standard deviation.
Assembly: S.  cerevisiae W303: Telomere to telomere assembly, Gift from O’Donnell et al., BioRxiv 2022 ; C. glabrata: http://www.candidagenome.org/download/sequence/C_glabrata_CBS138/current/
Supplementary files format and content: bigWig
Supplementary files format and content: cool

organism: Saccharomyces cerevisiae W303

source_name: Unicellular eukaryote

growth_protocol: cells were grown overnight in YPD

extract_protocol:
Cell fixation with 3% formaldehyde (Sigma-Aldrich, Cat. F8775) was performed as described in Dauban et al. Quenching of formaldehyde with 300 mM glycine was performed at 4°C for 20 min. Hi-C experiments were performed with a Hi-C kit (Arima Genomics) with a double DpnII + HinfI restriction digestion following manufacturer instructions. Samples were sonicated using Covaris (DNA 300bp). For ChIP seq data: The cells were then resuspended in 300 mL of ChIP lysis buffer (50 mM HEPES KOH, pH 8.0; 140 mM NaCl; 1 mM EDTA; 1% (v/v) Triton X-100; 0.1% (w/v) sodium deoxycholate; 1 mM PMSF; 2X Complete protease inhibitor cocktail (Roche)) and transfer in tubes 2mL containing glass beads before mechanical cells lysis.
Preparation of the samples for paired-end sequencing on an Illumina NextSeq500 (2x35 bp) was performed using Invitrogen TM Collibri TM PS DNA Library Prep Kit for Illumina and following manufacturer instructions.

value: pGALScc1V137K, Scc1WT

value: Unicellular eukaryote

value: cdc45 + oestradiol


title: RelAKO_2_biol rep 2


title: lung_high-fat diet_LPS_rep2

city: Chongqing

first: Wenjing

last: Tang

country: China

institute: The First Affiliated Hospital of Chongqing Medical University

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies).

source_name: the upper and middle lobes of right lung, high-fat diet (60% kcal from fat), lipopolysaccharide, replicate 2

label_protocol: LncRNA and mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen).

growth_protocol: Six–week–old male C57BL/6 J mice weighing 15–18g were  housed in an environmentally controlled room. After a week of acclimatization, mice were fed either normal chow diet or a high–fat diet with 60% calories from fat  for 12 weeks. After 12 weeks, mice were randomly divided into three groups: control group, obese group and obese ALI group. After mice were anesthetized intraperitoneally with sodium pentobarbital. LPS intratracheally infused to develop an obesity–related ALI model. After 24 hours, all mice were euthanized , and the lung tissues were immediately collected.

extract_protocol: Total RNA was isolated from lung tissue of normal mice, obese mice and obese mice with acute lung injury using TRIzol reagent.RNA integrity was assessed by standard denaturing agarose gel electrophoresis.  The RNA samples were labeled, purified and amplified.  The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner

treatment_protocol: Lung tissue samples were collected from normal mice, obese mice and obese mice with acute lung injury, washed with sterile saline and dried, then placed in sterile EP tubes containing  TRIzol reagent and stored at -80°C.

value: Mus musculus

value: male

value: 20 weeks

tag: body weight


title: lung_normal diet_rep2

source_name: the upper and middle lobes of right lung, normal diet, sterile saline, replicate 2

value: normal diet, sterile saline


title: Smc6-FLAG, IP [2019_030B_3067-1_IP]

value: Auxin+doxycycline


title: lung_normal diet_rep3

source_name: the upper and middle lobes of right lung, normal diet, sterile saline, replicate 3


title: HiC pGALScc1V137K, Scc1WT, cdc45

tag: cell type


title: HiC pGALScc1V137K, Scc1-pk-aid, cdc45 + oestradiol

value: pGALScc1V137K, Scc1-pk-aid


title: lung_high-fat diet_rep3

source_name: the upper and middle lobes of right lung, high-fat diet (60% kcal from fat) , sterile saline, replicate 3

tag: age


title: lung_high-fat diet_rep2

source_name: the upper and middle lobes of right lung, high-fat diet (60% kcal from fat) , sterile saline, replicate 2


title: lung_high-fat diet_rep1

source_name: the upper and middle lobes of right lung, high-fat diet (60% kcal from fat) , sterile saline, replicate 1


title: p52KO_2_biol rep 2

tag: genotype


title: lung_high-fat diet_LPS_rep1

source_name: the upper and middle lobes of right lung, high-fat diet (60% kcal from fat), lipopolysaccharide, replicate 1


title: lung_high-fat diet_LPS_rep3

source_name: the upper and middle lobes of right lung, high-fat diet (60% kcal from fat), lipopolysaccharide, replicate 3


title: Smc6-FLAG, IP [2019_030B_3067-2_IP]


title: lung_normal diet_rep1

source_name: the upper and middle lobes of right lung, normal diet, sterile saline, replicate 1


title: p52KO_3_biol rep 3


title: Rpo21-FLAG, 3 min thiolutin, IP [2017_034B_1958-2_3+_IP]

value: 3 min thiolutin


title: p52KO_1_biol rep 1


title: HiC pGALScc1V137K, Scc1-pk-aid, cdc45


title: p50KO_3_biol rep 3


title: ChIP-seq Scc1-pk-aid, pGALScc1WT-HA, expressed inG2, WCE

value: Scc1-pk-aid, pGALScc1WT-HA, expressed in G2

value: WCE


title: p50KO_2_biol rep 2


title: ChIP-seq Scc1-pk-aid, pGALScc1V137K-HA, expressed inG2, WCE

value: Scc1-pk-aid, pGALScc1V137K-HA, expressed in G2


title: ChIP-seq Scc1-pk-aid, pGALScc1WT-HA, expressed inG2, IP anti-HA

value: IP anti-HA


title: p50KO_1_biol rep 1

value: Lymphoblastoid


title: cRelKO_3_biol rep 3

value: Wildtype LMP1


title: HiC pGALScc1V137K, Scc1WT, noco + oestradiol R2

value: noco + oestradiol R2


title: ChIP-seq Scc1-pk-aid, pGALScc1V137K-HA, expressed inG2, IP anti-HA


title: HiC pGALScc1V137K, Scc1WT, noco R2

value: pGALScc1V137K, Scc1WT

value: noco R2


title: cRelKO_2_biol rep 2


title: pxpr_control_2__biol rep 2


title: HiC pGALScc1V137K, Scc1WT, noco + oestradiol

value: Unicellular eukaryote

value: noco + oestradiol


title: HiC pGALScc1V137K, Scc1-pk-aid, noco R2


title: pxpr_control_3__biol rep 3


title: cRelKO_1_biol rep 1


title: HiC pGALScc1V137K, Scc1-pk-aid, noco + oestradiol R2


title: HiC pGALScc1V137K, Scc1WT, noco

value: noco


title: HiC pGALScc1V137K, Scc1-pk-aid, noco + oestradiol


title: RelBKO_plusDox_3_biol rep 3

data_processing:
Adaptor-trimmed Illumina reads for each individual library were mapped back to the human GRCh37.83 transcriptome assembly using STAR v2.5.2b
featureCounts v1.5.1 was used to estimate the number of reads mapped to each contig. Only transcripts with at least 5 cumulative mapping counts were used in this analysis.
DESeq2 v1.14.1 was used to evaluate gene differential expression (DE)
Each DE analysis was composed of a pairwise comparison between experimental (induced) group and the control (uninduced) group. Differentially expressed genes were identified after a correction for false discovery rate (FDR 0.05).
Assembly: GRCh37.83
Supplementary files format and content: Raw files in fastq.gz format
Supplementary files format and content: Tab-delimited text files with normalized counts of genes also provided

source_name: EBV negative Akata

growth_protocol: EBV-negative Akata cells cultured in GIBCO RPMI 1640 medium (Life Technologies) with 10% fetal bovine serum (FBS) and penicillin-streptomycin in a humidified chamber at 37 degrees Celcius with 5% CO2.

treatment_protocol: EBV-negative Akata cells were transduced with lentivirus expressing doxycycline-inducible vector bearing respective LMP1 (wildtype) transgene. Transduced cells were subjected to 3ug/ml puromycin(#A1113803, Thermo Fisher) selection for 5 days post transduction before confirming dox-induced LMP1 expression in respective stable cell lines. Stable cell line was then transduced with lentivirus expressing sgRNAs for control, p50, p52, RelB, cRel or RelA. Transduced cells were subjected to 25ug/ml hygromycin(#400052, Millipore) selection for 7 days post transduction followed by 50ug/ml of hygromycin selection for another 7 days before confirming successful respective subunit knockout via immunoblot. Stable cell lines then underwent 24 hours of untreated or treatment with Doxycycline (Sigma #D9891) treatment at 250ng/ml.

value: EBV negative Akata

value: Burkitt Lymphoma

value: Doxycycline


title: HiC WT noco + oestradiol

value: WT


title: HiC pGALScc1V137K, Scc1-pk-aid, noco

value: pGALScc1V137K, Scc1-pk-aid


title: pxpr_control_1__biol rep 1


title: HiC WT noco


title: ChIP-seq Scc1-pk-aid, pGALScc1WT-HA, expressed inG1, WCE


title: ChIP-seq Scc1-pk-aid, pGALScc1WT-HA, expressed inG1, IP anti-HA


title: RelAKO_plusDox_1_biol rep 1


title: p52KO_plusDox_3_biol rep 3


title: ChIP-seq Scc1-pk-aid, pGALScc1V137K-HA, expressed inG1, WCE


title: p52KO_plusDox_2_biol rep 2


title: RelAKO_plusDox_2_biol rep 2


title: ChIP-seq Scc1-pk-aid, pGALScc1V137K-HA, expressed inG1, IP anti-HA


title: HiC pGALScc1V137K, Scc1WT


title: p50KO_plusDox_3_biol rep 3


title: p50KO_plusDox_2_biol rep 2


title: p50KO_plusDox_1_biol rep 1


title: HiC Pds5-pk-aid


title: p52KO_plusDox_1_biol rep 1


title: RelBKO_plusDox_1_biol rep 1


title: HiC WT


title: cRelKO_plusDox_3_biol rep 3


title: cRelKO_plusDox_2_biol rep 2


title: cRelKO_plusDox_1_biol rep 1


title: smRNA IP_Col0_Rec1

city: Davis

first: Patricia

last: Baldrich Gonzalez

state: CA

address: 451 Health Sciences Dr., Davis, CA 95616

department: Genome Center

institute: University of California - Davis

library_source: other

data_processing:
we trimmed adapters and low-quality reads using Cutadapt v2.9 software (Martin, 2011) and retaining only reads between 18- and 34-nt long.
Reads were then mapped to the Arabidopsis genome version 10 (available at www.arabidopsis.org/download/) and its corresponding TAIR10 blastsets for all the features, using Bowtie2 (Langmead and Salzberg, 2012).
Assembly: Arabidopsis TAiR 10

molecule: other

organism: Arabidopsis thaliana

source_name: Seedlings

growth_protocol: Arabidopsis seeds were surface-sterilized using ethanol and plated on MS agar (MES-buffered MS salts medium [Duchefa, Murashige & Skoog medium inc. vitamins/MES- MO255)], 1% sucrose, and 0.8% agar, pH 5.7). The seeds were then stratified for 2 days at 4°C in the dark and then transferred in 16h light/8h dark (20,5/17°C,70% humidity) growth chamber, under fluorescent light (Osram Biolux 58W/965)

extract_protocol:
Total RNA was extracted using Tri-Reagent according to the manufacturer’s instructions. For AGO1-loaded sRNA samples, AGO1-IPs were performed as described above from 1g of 1-week-old Arabidopsis seedlings grown on MS-agar plates and following similar HS and recovery treatments. AGO1-loaded sRNAs were then extracted by adding Tri-Reagent directly on the magnetic beads and extraction of RNA was performed according to the manufacturer’s instructions. RNAs were precipitated O/N at -20°C in 2 volumes of isopropanol + 40 μg glycogen as described above.
Small RNA seq libraries were generated using RealSeq v2 kit (Barberán-Soler et al., 2018), following manufacturer’s instructions, with 100ng as initial input and 15 cycles PCR amplification.

treatment_protocol: 7-day old Col-0 seedling +/- 1hour treatment at 37°C (HS) and after an additional 2H period back at 22°C (Recovery)

value: Seedlings

value: Col 0

tag: developmental stage

value: Recovery

tag: ip antibody


title: smRNA IP_Col0_Rec3

tag: treatment


title: RelBKO_plusDox_2_biol rep 2

tag: cell line


title: 515plusDox_pxpr_control_3__biol rep 3


title: smRNA IP_Col0_Rec2


title: 515plusDox_pxpr_control_2__biol rep 2


title: RelAKO_plusDox_3_biol rep 3


title: 515_pxpr_control_no induction_3_biol rep 3

value: no Doxycycline


title: 515plusDox_pxpr_control_1__biol rep 1


title: smRNA IP_Col0_HS1

value: Heat shock


title: smRNA IP_Col0_C3

value: Control


title: smRNA IP_Col0_C2


title: smRNA IP_Col0_HS3


title: Scc1-FLAG, 3 min thiolutin, IP [2017_034B_234-2_3+_IP]

value: anti-FLAG (Merck, F1804)

value: 3 min thiolutin


title: smRNA IP_Col0_C1


title: 515_pxpr_control_no induction_1_biol rep 1

value: Wildtype LMP1


title: smRNA IP_Col0_HS2


title: 515_pxpr_control_no induction_2_biol rep 2


title: HiC pGALScc1V137K, Scc1-pk-aid

value: Unicellular eukaryote


title: Yuuki_3

city: Bethesda

first: Stefan

last: Ambs

state: MD

address: Building 37, Room 3050B

department: CCR

institute: NCI

description: Panc 10.05 control

data_processing:
mRNA-Seq samples were pooled and sequenced on NextSeq using Illumina Stranded mRNAseq ligation and paired-end sequencing. The samples have 32 to 60 million pass filter reads with more than 93% of bases above the quality score of Q30. Reads of the samples were trimmed for adapters and low-quality bases using Cutadapt before alignment with the reference genome (Human - hg38) and the annotated transcripts using STAR.
The gene expression quantification analysis was performed using STAR/RSEM tools. Differential expression analysis was done using DESeq2.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw count values for each Sample

source_name: Pancreatic cancer cell line

extract_protocol:
RNA isolation was done using TRIzol. Integrity of isolated RNA was evaluated with the Agilent 2100 Bioanalyzer (Agilent Technologies), and sequencing was performed on an Illumina NextSeq machine at the Sequencing Facility, Leidos Biomedical Research, Inc.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: condition

value: Panc 10.05_Ctrl_3

tag: cell lines

tag: outcome

value: Panc 10.05 control


title: Yuuki_2

description: Panc 10.05 control

value: Panc 10.05_Ctrl_2


title: Yuuki_7

description: Panc 10.05 ELAPOR1 transgene

value: Panc 10.05_ELAPOR1 overexpression_3

value: Panc 10.05 ELAPOR1 transgene


title: Yuuki_4

description: Panc 10.05 control

value: Panc 10.05_Ctrl_4


title: Yuuki_5

description: Panc 10.05 ELAPOR1 transgene

value: Panc 10.05_ELAPOR1 overexpression_1


title: smRNA Col0_Rec2

value: Seedlings


title: Yuuki_6

description: Panc 10.05 ELAPOR1 transgene

value: Panc 10.05_ELAPOR1 overexpression_2


title: smRNA Col0_HS2

value: Col 0


title: smRNA Col0_HS3


title: smRNA Col0_Rec1

value: Recovery


title: Human Milk 19

description:
miRNAs were isolated from extracellular vesicles and particles extracted from the supernatant portion of the milk samples
SAMPLE 19

tag: gender

value: Female

tag: life stage

value: Postpartum

tag: days postpartum at sample collection

value: miRNA