title: human_miRNA+lncRNA+mRNA_glioma_without_epilepsy_rep15 [LNC_MRNA_TN15]

description:
RNA expression of human brain tissue in glioma without epilepsy patient
Agilent Human miRNA Microarray, Release 19.0, 8x60K; Agilent LncRNA+mRNA Human Gene Expression Microarray V3.0

source_name: Brain tissue, glioma without epilepsy, replicate 15

extract_protocol: Total RNA was extracted with Invitrogen’s TRIzol Reagent, purified with NucleoSpin RNA clean-up, and quantified with a NanoDrop. Gel electrophoresis was used to check the RNA’s purity and integrity. MirVana miRNA Isolation Kit was used to purify total microRNA.

treatment_protocol: All of the glioma tissue was taken from the cerebral cortex. Tissues were obtained and kept at –80°C until microarray analysis.

value: frontal lobe


title: human_miRNA+lncRNA+mRNA_glioma_without_epilepsy_rep14 [LNC_MRNA_TN14]

status: Public on Jun 07 2022

type: RNA

city: ChangSha

first: ZhaoQian

last: Liu

state: China

address: xiangya road 110

country: China

institute: Xiangya Hospital, Central South University

hyb_protocol: The labeled product is purified by the Nucleospin® Extract II kit in an elution volume of about 30 µL. 100µL of hybridization solution was added to the hybridization cover fence. The hybridization box is installed on the rotor of the hybridization furnace, Meanwhile, after adding appropriate amount of ultrapure water in the tray, hybridize at 45°C overnight.

scan_protocol: Agilent G2565CA Microarray Scanner was used to scan the slides.

data_processing: Agilent Feature Extraction Software v10.7 was used to analyze the scanned pictures of the microarray.

molecule: total RNA

organism: Homo sapiens

source_name: Brain tissue, glioma without epilepsy, replicate 14

label_protocol: The volume of cDNA product obtained after reverse transcription and purification was concentrated to 14µL, mixed with 4µL Random Primer, briefly centrifuged and placed on a PCR instrument, denatured at 95°C for 3 minutes and ice bath for 5 minutes. Add the reagents (5 µL 5×Klenow Buffer; 1 µL Cy3-dCTP; 1.2 µL Klenow Fragmen) in sequence and mix well by blowing 2-3 times with a pipette. After a short centrifugation, place on a PCR instrument and react for 1.5 h at 37°C and 5 min at 70°C. Hold at 4°C. After the fluorescent dye labeling reaction, cDNA was purified using the Nucleospin® Extract II (MN, Cat. No. 740609.250) kit, and the purified fluorescently labeled products were quantified for fluorescence admixture and nucleic acid using a UV spectrophotometer.

tag: tissue

value: Parietal lobe

tag: gender

value: Female

tag: age


title: human_miRNA+lncRNA+mRNA_glioma_without_epilepsy_rep16 [LNC_MRNA_TN16]

source_name: Brain tissue, glioma without epilepsy, replicate 16


title: human_miRNA+lncRNA+mRNA_glioma_without_epilepsy_rep12 [LNC_MRNA_TN12]

source_name: Brain tissue, glioma without epilepsy, replicate 12

value: Male


title: human_miRNA+lncRNA+mRNA_glioma_without_epilepsy_rep10 [LNC_MRNA_TN10]

source_name: Brain tissue, glioma without epilepsy, replicate 10

value: temporal lobe


title: human_miRNA+lncRNA+mRNA_glioma_without_epilepsy_rep13 [LNC_MRNA_TN13]

source_name: Brain tissue, glioma without epilepsy, replicate 13


title: human_miRNA+lncRNA+mRNA_glioma_without_epilepsy_rep11 [LNC_MRNA_TN11]

source_name: Brain tissue, glioma without epilepsy, replicate 11


title: Thalamus,MOCK,31dpi,2

type: SRA

city: New York

first: Justin

middle: J

last: Frere

state: NY

address: Alexandria Center for Life Sciences, West Tower, 430 E 29th St.

department: Microbiology

country: USA

institute: NYU Langone Health

library_source: transcriptomic

data_processing:
Base calling and sample deconvolution performed via Illumina BaseSpace
Reads aligned to MesAur1.0 genome assembly using Ensembl GTF file and quantified using Salmon as made available in Illumina BaseSpace "RNA-Seq Alignment" application
Assembly: Mesocricetus Auratus MesAur1.0
Supplementary files format and content: .quant.genes.sf Salmon files (show raw and normalized read counts by gene)

organism: Mesocricetus auratus

source_name: Thalamus

extract_protocol:
Trizol Phenol Chloroform
Poly A tail enrichment and preparation using True Strand RNA-seq Prep

value: Thalamus

tag: genotype

value: WT

tag: infection

value: Mock (PBS-treated)

tag: time

value: 31 dpi


title: Thalamus,MOCK,31dpi,4


title: Striatum,SARSCOV2,3dpi,2

source_name: Striatum

value: Striatum

value: SARS-CoV-2 (1000 PFU)

value: 3 dpi


title: human_miRNA+lncRNA+mRNA_glioma_without_epilepsy_rep9 [LNC_MRNA_TN9]

source_name: Brain tissue, glioma without epilepsy, replicate 9


title: Striatum,SARSCOV2,3dpi,1


title: human_miRNA+lncRNA+mRNA_glioma_without_epilepsy_rep8 [LNC_MRNA_TN8]

source_name: Brain tissue, glioma without epilepsy, replicate 8


title: Thalamus,IAV,31dpi,3

value: Influenza (100,000 PFU)


title: human_miRNA+lncRNA+mRNA_glioma_without_epilepsy_rep4 [LNC_MRNA_TN4]

source_name: Brain tissue, glioma without epilepsy, replicate 4


title: Striatum,SARSCOV2,31dpi,4


title: human_miRNA+lncRNA+mRNA_glioma_without_epilepsy_rep5 [LNC_MRNA_TN5]

source_name: Brain tissue, glioma without epilepsy, replicate 5


title: human_miRNA+lncRNA+mRNA_glioma_without_epilepsy_rep3 [LNC_MRNA_TN3]

source_name: Brain tissue, glioma without epilepsy, replicate 3


title: human_miRNA+lncRNA+mRNA_glioma_without_epilepsy_rep2 [LNC_MRNA_TN2]

source_name: Brain tissue, glioma without epilepsy, replicate 2


title: Striatum,SARSCOV2,31dpi,3


title: Striatum,SARSCOV2,31dpi,1


title: Striatum,MOCK,3dpi,2


title: Striatum,MOCK,3dpi,1


title: Striatum,MOCK,3dpi,3


title: Striatum,MOCK,31dpi,3


title: human_miRNA+lncRNA+mRNA_glioma_without_epilepsy_rep6 [LNC_MRNA_TN6]

source_name: Brain tissue, glioma without epilepsy, replicate 6

value: Occipital Lobe


title: Striatum,MOCK,31dpi,4


title: human_miRNA+lncRNA+mRNA_glioma-related_epilepsy_rep9 [LNC_MRNA_TE9]

description:
RNA expression of human brain tissue in glioma-related epilepsy patient
Agilent Human miRNA Microarray, Release 19.0, 8x60K; Agilent LncRNA+mRNA Human Gene Expression Microarray V3.0

source_name: Brain tissue, glioma-related epilepsy, replicate 9


title: Striatum,MOCK,31dpi,2


title: human_miRNA+lncRNA+mRNA_glioma_without_epilepsy_rep7 [LNC_MRNA_TN7]

source_name: Brain tissue, glioma without epilepsy, replicate 7


title: human_miRNA+lncRNA+mRNA_glioma-related_epilepsy_rep8 [LNC_MRNA_TE8]

source_name: Brain tissue, glioma-related epilepsy, replicate 8


title: human_miRNA+lncRNA+mRNA_glioma-related_epilepsy_rep7 [LNC_MRNA_TE7]

source_name: Brain tissue, glioma-related epilepsy, replicate 7


title: human_miRNA+lncRNA+mRNA_glioma-related_epilepsy_rep5 [LNC_MRNA_TE5]

source_name: Brain tissue, glioma-related epilepsy, replicate 5


title: Striatum,SARSCOV2,31dpi,2


title: Striatum,MOCK,31dpi,1


title: human_miRNA+lncRNA+mRNA_glioma-related_epilepsy_rep6 [LNC_MRNA_TE6]

source_name: Brain tissue, glioma-related epilepsy, replicate 6


title: human_miRNA+lncRNA+mRNA_glioma-related_epilepsy_rep4 [LNC_MRNA_TE4]

source_name: Brain tissue, glioma-related epilepsy, replicate 4


title: human_miRNA+lncRNA+mRNA_glioma_without_epilepsy_rep16 [miRNA_TN16]

source_name: Brain tissue, glioma without epilepsy, replicate 16


title: human_miRNA+lncRNA+mRNA_glioma-related_epilepsy_rep3 [LNC_MRNA_TE3]

source_name: Brain tissue, glioma-related epilepsy, replicate 3


title: human_miRNA+lncRNA+mRNA_glioma-related_epilepsy_rep2 [LNC_MRNA_TE2]

source_name: Brain tissue, glioma-related epilepsy, replicate 2


title: Striatum,IAV,3dpi,3

source_name: Striatum


title: human_miRNA+lncRNA+mRNA_glioma_without_epilepsy_rep1 [LNC_MRNA_TN1]

source_name: Brain tissue, glioma without epilepsy, replicate 1


title: human_miRNA+lncRNA+mRNA_glioma_without_epilepsy_rep15 [miRNA_TN15]

source_name: Brain tissue, glioma without epilepsy, replicate 15


title: Striatum,MOCK,31dpi,5


title: Striatum,IAV,3dpi,1


title: human_miRNA+lncRNA+mRNA_glioma-related_epilepsy_rep1 [LNC_MRNA_TE1]

source_name: Brain tissue, glioma-related epilepsy, replicate 1


title: Striatum,IAV,3dpi,2


title: human_miRNA+lncRNA+mRNA_glioma_without_epilepsy_rep14 [miRNA_TN14]

source_name: Brain tissue, glioma without epilepsy, replicate 14


title: human_miRNA+lncRNA+mRNA_glioma_without_epilepsy_rep13 [miRNA_TN13]

source_name: Brain tissue, glioma without epilepsy, replicate 13


title: Striatum,IAV,31dpi,4


title: human_miRNA+lncRNA+mRNA_glioma_without_epilepsy_rep11 [miRNA_TN11]

source_name: Brain tissue, glioma without epilepsy, replicate 11


title: human_miRNA+lncRNA+mRNA_glioma_without_epilepsy_rep12 [miRNA_TN12]

source_name: Brain tissue, glioma without epilepsy, replicate 12


title: human_miRNA+lncRNA+mRNA_glioma_without_epilepsy_rep9 [miRNA_TN9]

source_name: Brain tissue, glioma without epilepsy, replicate 9


title: Striatum,IAV,31dpi,2


title: human_miRNA+lncRNA+mRNA_glioma_without_epilepsy_rep8 [miRNA_TN8]

source_name: Brain tissue, glioma without epilepsy, replicate 8


title: Striatum,IAV,31dpi,1


title: human_miRNA+lncRNA+mRNA_glioma_without_epilepsy_rep7 [miRNA_TN7]

source_name: Brain tissue, glioma without epilepsy, replicate 7


title: Olfactory Bulb,SARSCOV2,3dpi,2

source_name: Olfactory Bulb

value: Olfactory Bulb


title: Striatum,IAV,31dpi,3


title: human_miRNA+lncRNA+mRNA_glioma_without_epilepsy_rep10 [miRNA_TN10]

source_name: Brain tissue, glioma without epilepsy, replicate 10


title: Striatum,IAV,31dpi,5


title: human_miRNA+lncRNA+mRNA_glioma_without_epilepsy_rep3 [miRNA_TN3]

source_name: Brain tissue, glioma without epilepsy, replicate 3


title: human_miRNA+lncRNA+mRNA_glioma_without_epilepsy_rep5 [miRNA_TN5]

source_name: Brain tissue, glioma without epilepsy, replicate 5


title: Olfactory Bulb,SARSCOV2,3dpi,3


title: Olfactory Bulb,SARSCOV2,31dpi,2


title: Olfactory Bulb,SARSCOV2,31dpi,3


title: Olfactory Bulb,SARSCOV2,3dpi,1


title: human_miRNA+lncRNA+mRNA_glioma_without_epilepsy_rep6 [miRNA_TN6]

source_name: Brain tissue, glioma without epilepsy, replicate 6


title: Olfactory Bulb,MOCK,3dpi,1


title: human_miRNA+lncRNA+mRNA_glioma_without_epilepsy_rep4 [miRNA_TN4]

source_name: Brain tissue, glioma without epilepsy, replicate 4


title: human_miRNA+lncRNA+mRNA_glioma-related_epilepsy_rep9 [miRNA_TE9]

source_name: Brain tissue, glioma-related epilepsy, replicate 9


title: Olfactory Bulb,MOCK,3dpi,3


title: Olfactory Bulb,MOCK,3dpi,2


title: Olfactory Bulb,SARSCOV2,31dpi,1


title: Olfactory Bulb,MOCK,31dpi,3


title: human_miRNA+lncRNA+mRNA_glioma_without_epilepsy_rep2 [miRNA_TN2]

source_name: Brain tissue, glioma without epilepsy, replicate 2


title: Olfactory Bulb,MOCK,31dpi,2


title: human_miRNA+lncRNA+mRNA_glioma-related_epilepsy_rep8 [miRNA_TE8]

source_name: Brain tissue, glioma-related epilepsy, replicate 8


title: Olfactory Bulb,IAV,3dpi,1


title: Olfactory Bulb,MOCK,31dpi,1


title: Olfactory Bulb,IAV,3dpi,3


title: human_miRNA+lncRNA+mRNA_glioma-related_epilepsy_rep7 [miRNA_TE7]

source_name: Brain tissue, glioma-related epilepsy, replicate 7


title: human_miRNA+lncRNA+mRNA_glioma-related_epilepsy_rep6 [miRNA_TE6]

source_name: Brain tissue, glioma-related epilepsy, replicate 6


title: Olfactory Bulb,IAV,3dpi,2


title: human_miRNA+lncRNA+mRNA_glioma-related_epilepsy_rep3 [miRNA_TE3]

source_name: Brain tissue, glioma-related epilepsy, replicate 3


title: human_miRNA+lncRNA+mRNA_glioma-related_epilepsy_rep2 [miRNA_TE2]

source_name: Brain tissue, glioma-related epilepsy, replicate 2


title: human_miRNA+lncRNA+mRNA_glioma_without_epilepsy_rep1 [miRNA_TN1]

source_name: Brain tissue, glioma without epilepsy, replicate 1


title: Olfactory Bulb,IAV,31dpi,2


title: Olfactory Bulb,IAV,31dpi,3


title: human_miRNA+lncRNA+mRNA_glioma-related_epilepsy_rep1 [miRNA_TE1]

source_name: Brain tissue, glioma-related epilepsy, replicate 1


title: KPCK124

city: Zurich

first: Patrik

last: Simmler

address: Otto-Stern-Weg 7

country: Switzerland

institute: ETH Zurich

data_processing:
The fastq data for the read pairs from the Illumina sequencer have been processed in abioinformatic workflow. First, the remains of the adapters and sub-standard quality reads have been trimmed with trimmomatic (v0.35).
For the pairs in which both reads have passed the trimming, they have been mapped to the mm10 mouse genome using STAR (v2.7.0a) and indexed BAM files obtained with samtools (v1.9).
The reads have been counted using featureCounts from subread package (v1.5.0) with the options for pairs of reads to be counted as RNA fragments. The count vectors for all the samples have been combined into a count table. The table has been processed in the secondary (statistical) analysis with R scripts using edgeR (v3.24.3), in particular binomial generalized log-linear model with contrast tests. It resulted in lists of genes ranked for differential expression by p-value and used Benjamini-Hochberg adjusted p-value as the estimate of the false discovery rate.
Supplementary files format and content: mm10

organism: Mus musculus

source_name: FACS-sorted murine PDAC cells

extract_protocol:
Murine tumors were excised and digested for 2–3 hours in collagenase (4mg/ml) at 37°C. After addition of fetal calf serum (FCS) to stop the digestion, cells were strained trough a 100 μm and a 70 μm cell strainer. Then, cells were washed twice in PBS + 2% FCS + 2 mM EDTA and incubated with mouse FcBlock (BD Biosciences), Epcam-APC (CD326 Monoclonal Antibody (G8.8), APC, eBioscience™, Thermo Fisher) and CD45-BV785 (Clone 30-F11, Biologened) antibodies for 30 minutes at 4°C. After washing, Epcam-positive-CD45-negative cells were sorted into lysis buffer with a BD FACSAriaIII Cell Sorter (BD Biosciences). Finally, RNA was extracted using NucleoSpin RNA XS kit (Macherey Nagel) according to the manufacturer’s instructions.
The quantity and quality of the isolated RNA was determined with a Qubit® (1.0) Fluorometer (Life Technologies, California, USA) and a Tapestion (Agilent, Waldbronn, Germany). The SMARTer Stranded Total RNA-Seq Kit - Pico Input Mammalian (Clontech Laboratories, Inc., A Takara Bio Company,California, USA) was used in the succeeding steps. Briefly, total RNA samples (0.25–10 ng) were reverse-transcribed using random priming into double-stranded cDNA in the presence of a template switch oligo (TSO). When the reverse transcriptase reaches the 5’ end of the RNA fragment, the enzyme’s terminal transferase activity adds non-templated nucleotides to the 3’ end of the cDNA.  The TSO pairs with the added non-templated nucleotide, enabling the reverse transcriptase to continue replicating to the end of the oligonucleotide. This results in a cDNA fragment that contains sequences derived from the random priming oligo and the TSO. PCR amplification using primers binding to these sequences can now be performed. The PCR adds full-length Illumina adapters, including the index for multiplexing.  Ribosomal cDNA is cleaved by ZapR in the presence of the mammalian-specific R-Probes. Remaining fragments are enriched with a second round of PCR amplification using primers designed to match Illumina adapters.The quality and quantity of the enriched libraries were validated using Qubit® (1.0) Fluorometer and the Tapestation (Agilent, Waldbronn, Germany). The product is a smear with an average fragment size of approximately 360 bp. The libraries were normalized to 10nM in Tris-Cl 10 mM, pH8.5 with 0.1% Tween 20.

tag: strain

tag: disease state

value: Pancreatic ductal adenocarcinoma (PDAC)

tag: disease model

value: KPC model (KrasG12D, Trp53-/-)

value: Sf3b1 K700E (heterozygous SNP)

tag: cell type

value: PDAC cells


title: human_miRNA+lncRNA+mRNA_glioma-related_epilepsy_rep5 [miRNA_TE5]

source_name: Brain tissue, glioma-related epilepsy, replicate 5

value: frontal lobe


title: KPCK131


title: KPCK80


title: KPCK54


title: Olfactory Bulb,IAV,31dpi,1

source_name: Olfactory Bulb


title: mPFC,SARSCOV2,3dpi,3

source_name: mPFC

value: mPFC


title: mPFC,SARSCOV2,3dpi,2


title: mPFC,SARSCOV2,3dpi,1


title: mPFC,SARSCOV2,31dpi,3


title: KPC81

value: Sf3b1 wildtype


title: mPFC,SARSCOV2,31dpi,2


title: human_miRNA+lncRNA+mRNA_glioma-related_epilepsy_rep4 [miRNA_TE4]

source_name: Brain tissue, glioma-related epilepsy, replicate 4

value: temporal lobe

value: Male


title: EpiLC_Neat1KO_H3K4me3_r2

first: Jianlong

last: Wang

state: New York

department: Department of Medicine

institute: Columbia University Irving Medical Center

library_source: genomic

data_processing:
FastQC (v0.10.1) was used to check the sequencing quality. Reads were pre-processed by Trim Galore (v.0.6.3) and Cutadapt programs.
Reads were aligned to the mouse genome mm9 using the bowtie2 (v2.3.5) program, with parameters -X 1000 --no-mixed --no-discordant.
The mapped reads were sorted and converted to a binary bam file using samtools (v1.10)
ChIP-seq peaks were determined by the MACS program (v.2.2.7), using input as the control data, and with parameters --broad -q 0.01.
Assembly: mm9
Supplementary files format and content: Bed file of MACS called peaks.

molecule: genomic DNA

source_name: mESC 46C derived EpiLC

growth_protocol: Feeder-free mouse embryonic stem cells (ESCs) were cultured on 0.1% gelatin-coated plates under standard conditions: DMEM supplemented with 15% fetal calf serum (FBS), 1000 units/mL recombinant leukemia inhibitory factor (LIF), 0.1 mM 2-mercaptoethanol, 2 mM L-glutamine, 0.1 mM MEM non-essential amino acids (NEAA), 1% nucleoside mix (100X stock, Sigma), and 1% penicillin-streptomycin. For in vitro ESC-to-EpiLC differentiation, ESCs were seeded on fibronectin-coated (10 μg/mL/cm2) plates and in ES medium. In the next day, medium was switch to formative (FA) culture condition using serum-free N2B27 medium (DMEM/F12 and Neurobasal medium mixed at a ratio of 1:1, 1x B27 supplement, 1x N2 supplement, 2 mM L-glutamine, 0.1 mM 2-mercaptoethanol, and 50 U/mL Penicillin/Streptomycin) supplemented with Fgf2 (12 ng/mL) and Activin A (20 ng/mL).

extract_protocol:
ChIP was performed as previously described (Lee et al., 2006).
ChIP libraries were prepared using the NEBNext Ultra II DNA library prep kit and index primers sets (NEB, #7645S, #E7335S) followed the standard protocol. Sequencing was performed by Novogene with the Illumina HiSeq 4000 Sequencer. Data with 150 bp paired-end reads were obtained.

treatment_protocol: Control DMSO or dTAG-13 (500 nM, Tocris, 6605) was used to induce TET1 protein degradation in Tet1-degron KI ESCs during ESC-to-EpiLC differentation

value: Epiblast-like stem cells

tag: cell line

value: mESC 46C derived EpiLC

tag: antibody

value: H3K4me3, EpiCypher, 13-0041


title: EpiLC_46C_H3K4me3_r2

description:
EpiLC_46C_H3K4me3_r2
46C_FA_K4me3.bed

value: WT


title: mPFC,SARSCOV2,31dpi,1

value: SARS-CoV-2 (1000 PFU)

value: 31 dpi


title: mPFC,MOCK,3dpi,3

value: Mock (PBS-treated)

value: 3 dpi


title: ESC_Neat1KO_H3K4me3_r2

source_name: mESC 46C

value: Embryonic stem cells

value: mESC 46C


title: mPFC,MOCK,3dpi,2


title: mPFC,MOCK,3dpi,1


title: EpiLC_CCE_H3K4me3_r2

description:
EpiLC_CCE_H3K4me3_r2
CCE_FA_K4me3.bed

source_name: mESC CCE derived EpiLC

value: mESC CCE derived EpiLC


title: ESC_46C_H3K4me3_r2

description:
ESC_46C_H3K4me3_r2
46C_ESC_K4me3.bed


title: ESC_Pspc1KO_H3K4me3_r2

source_name: mESC CCE

value: mESC CCE


title: mPFC,MOCK,31dpi,5


title: KPC110

value: Pancreatic ductal adenocarcinoma (PDAC)

value: KPC model (KrasG12D, Trp53-/-)

value: PDAC cells


title: EpiLC_Pspc1KO_H3K4me3_r2


title: KPC101

value: Sf3b1 wildtype


title: mPFC,MOCK,31dpi,2

value: mPFC


title: mPFC,MOCK,31dpi,3


title: mPFC,MOCK,31dpi,4


title: ESC_Neat1KO_H3K4me3_r1


title: ESC_CCE_H3K4me3_r2

description:
ESC_CCE_H3K4me3_r2
CCE_ESC_K4me3.bed


title: EpiLC_Neat1KO_H3K4me3_r1

value: Epiblast-like stem cells


title: mPFC,IAV,3dpi,2

value: Influenza (100,000 PFU)


title: ESC_46C_H3K4me3_r1

description:
ESC_46C_H3K4me3_r1
46C_ESC_K4me3.bed

value: H3K4me3, EpiCypher, 13-0041


title: mPFC,IAV,3dpi,1

value: WT


title: EpiLC_CCE_H3K4me3_r1

description:
EpiLC_CCE_H3K4me3_r1
CCE_FA_K4me3.bed


title: EpiLC_Pspc1KO_H3K4me3_r1


title: ESC_Pspc1KO_H3K4me3_r1


title: mPFC,IAV,31dpi,4


title: ESC_CCE_H3K4me3_r1

description:
ESC_CCE_H3K4me3_r1
CCE_ESC_K4me3.bed


title: mPFC,IAV,31dpi,2


title: EpiLC_Tet1D_dTAG_H3K27me3_r2

value: Tet1-degron KI

value: H3K27me3, Cell Signaling, 9733S


title: EpiLC_Tet1D_Ctrl_H3K27me3_r2


title: mPFC,IAV,31dpi,1

value: 31 dpi


title: Lungs,SARSCOV2,3dpi,3

source_name: Lungs

value: Lungs

value: SARS-CoV-2 (1000 PFU)

value: 3 dpi


title: ESC_Tet1D_dTAG_H3K27me3_r2

value: Embryonic stem cells


title: Lungs,SARSCOV2,3dpi,2


title: ESC_Tet1D_Ctrl_H3K27me3_r2

value: mESC CCE


title: EpiLC_46C_H3K4me3_r1

description:
EpiLC_46C_H3K4me3_r1
46C_FA_K4me3.bed

value: mESC 46C derived EpiLC


title: Lungs,SARSCOV2,3dpi,1


title: Lungs,SARSCOV2,31dpi,2


title: EpiLC_Neat1KO_H3K27me3_r2


title: EpiLC_Pspc1KO_H3K27me3_r2

value: mESC CCE derived EpiLC


title: Lungs,SARSCOV2,31dpi,1


title: mPFC,MOCK,31dpi,1

value: Mock (PBS-treated)


title: Lungs,SARSCOV2,31dpi,3


title: ESC_Neat1KO_H3K27me3_r2

value: mESC 46C


title: EpiLC_46C_H3K27me3_r2

description:
EpiLC_46C_H3K27me3_r2
46C_FA_K27me3.bed


title: ESC_46C_H3K27me3_r2

description:
ESC_46C_H3K27me3_r2
46C_ESC_K27me3.bed


title: EpiLC_CCE_H3K27me3_r2

description:
EpiLC_CCE_H3K27me3_r2
CCE_FA_K27me3.bed


title: mPFC,IAV,31dpi,3

value: mPFC


title: Lungs,MOCK,3dpi,1


title: ESC_CCE_H3K27me3_r2

description:
ESC_CCE_H3K27me3_r2
CCE_ESC_K27me3.bed


title: Lungs,MOCK,31dpi,2


title: Lungs,MOCK,31dpi,1


title: Lungs,SARSCOV2,3dpi,4


title: ESC_Pspc1KO_H3K27me3_r2


title: ESC_Tet1D_dTAG_H3K27me3_r1


title: Lungs,IAV,3dpi,2


title: ESC_46C_H3K27me3_r1

description:
ESC_46C_H3K27me3_r1
46C_ESC_K27me3.bed


title: ESC_Tet1D_Ctrl_H3K27me3_r1


title: Lungs,IAV,3dpi,1


title: ESC_CCE_H3K27me3_r1

description:
ESC_CCE_H3K27me3_r1
CCE_ESC_K27me3.bed


title: Lungs,IAV,31dpi,3


title: Lungs,IAV,31dpi,1


title: Kidney,SARSCOV2,3dpi,4

source_name: Kidney

value: Kidney


title: Lungs,MOCK,3dpi,2


title: EpiLC_Tet1D_dTAG_H3K27me3_r1

value: Epiblast-like stem cells


title: ESC_Pspc1KO_H3K27me3_r1


title: EpiLC_Tet1D_Ctrl_H3K27me3_r1


title: Kidney,SARSCOV2,3dpi,3


title: Kidney,SARSCOV2,3dpi,1


title: EpiLC_46C_H3K27me3_r1

description:
EpiLC_46C_H3K27me3_r1
46C_FA_K27me3.bed


title: Lungs,IAV,31dpi,2

value: Influenza (100,000 PFU)


title: Kidney,SARSCOV2,3dpi,2

value: WT


title: Lungs,MOCK,3dpi,3


title: EpiLC_Neat1KO_H3K27me3_r1


title: Kidney,SARSCOV2,31dpi,2


title: EpiLC_Pspc1KO_H3K27me3_r1


title: EpiLC_Neat1KO_H3_input


title: Lungs,IAV,3dpi,3


title: Kidney,SARSCOV2,31dpi,1


title: ESC_Neat1KO_H3K27me3_r1


title: EpiLC_CCE_H3K27me3_r1

description:
EpiLC_CCE_H3K27me3_r1
CCE_FA_K27me3.bed


title: Kidney,MOCK,3dpi,3


title: EpiLC_46C_H3_input


title: Kidney,MOCK,3dpi,2


title: ESC_Neat1KO_H3_input


title: ESC_46C_H3_input


title: Kidney,MOCK,3dpi,1


title: Kidney,MOCK,31dpi,3


title: EpiLC_Pspc1KO_H3_input


title: Kidney,MOCK,31dpi,2


title: EpiLC_CCE_H3_input


title: Kidney,MOCK,31dpi,1


title: Kidney,IAV,3dpi,3


title: Kidney,IAV,3dpi,2


title: Kidney,IAV,31dpi,2


title: EpiLC_Neat1KO_odd

data_processing:
FastQC (v0.10.1) was used to check the sequencing quality. Reads were pre-processed by Trim Galore (v.0.6.3) and Cutadapt programs.
Reads were aligned to the mouse genome mm9 using the bowtie2 (v2.3.5) program, with parameters -X 1000 --no-mixed --no-discordant.
The mapped reads were sorted and converted to a binary bam file using samtools (v1.10)
ChIP-seq peaks were determined by the MACS program (v.2.2.7), using the knockout cells as the control data, and with the default parameters.
Assembly: mm9
Supplementary files format and content: Bed file of MACS called peaks.
Library strategy: ChIRP-Seq

source_name: Epiblast-like stem cells

extract_protocol:
ChIRP assay was performed as previously described (Chu et al., 2011).
ChIRP libraries were prepared using the NEBNext Ultra II DNA library prep kit and index primers sets (NEB, #7645S, #E7335S) followed the standard protocol. Sequencing was performed by Novogene with the Illumina HiSeq 4000 Sequencer. Data with 150 bp paired-end reads were obtained.

tag: probes

value: Neat1 odd probes


title: ESC_CCE_H3_input


title: EpiLC_Neat1KO_even

value: Neat1 even probes


title: Kidney,IAV,3dpi,1


title: EpiLC_Neat1KO_input


title: Kidney,IAV,31dpi,1

value: 31 dpi


title: Heart,SARSCOV2,3dpi,4

source_name: Heart

value: Heart


title: ESC_Neat1KO_odd

source_name: Embryonic stem cells


title: Heart,SARSCOV2,3dpi,3

value: SARS-CoV-2 (1000 PFU)


title: EpiLC_CCE_input


title: EpiLC_CCE_odd


title: EpiLC_CCE_even


title: Heart,SARSCOV2,3dpi,1

value: 3 dpi


title: Heart,SARSCOV2,31dpi,3


title: ESC_Neat1KO_even


title: Heart,SARSCOV2,3dpi,2


title: Heart,MOCK,3dpi,3


title: ESC_Neat1KO_input


title: Heart,SARSCOV2,31dpi,1


title: ESC_Pspc1KO_H3_input

value: Embryonic stem cells


title: Heart,SARSCOV2,31dpi,2


title: ESC_CCE_input


title: Heart,MOCK,3dpi,1


title: IgG

city: Illkirch

first: Tao

last: YE

address: 1 rue Laurent Fries

country: France

institute: IGBMC (CNRS/INSERM/UDS)

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Sequence reads were mapped to reference genome mm10 using Bowtie 1.0.0 with the following parameters -m 1 --strata --best -y -S -l 40 -p 2.
Reads overlapping with ENCODE mm10 blacklisted region V2 were removed using Bedtools
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files were generated using Homer software makeUCSCfile script with default parameters and scaled to 1e7 reads.

source_name: DMOG-treated Myc-CaP cells

growth_protocol: Myc-CaP cells were grown to 70-80% confluency in DMEM medium (4.5 g/L glucose, 10% FCS, 1% penicillin/streptomycin)

extract_protocol:
DMOG-treated Myc-CaP cells were incubated in 1% paraformaldehyde for 8 min and quenched with 0.125 M glycine buffer for 5 min at room temperature. Cross-linked cells were resuspended in 500 µL of 10 mM HEPES, 60 mM KCl, 1 mM EDTA, 0.075% (v/v) NP40, 1 mM DTT, and 1 mM PMSF (pH 7.6) and incubated on ice for 5 min. After centrifugation at 400 g for 5 min, nuclear pellets were resuspended in ChIP lysis buffer (50 mM Tris-HCl pH 8, 0.1% SDS, 10 mM EDTA) and sonicated in 300–400 bp DNA fragments (Covaris). 50 µg of chromatin were immunoprecipitated in ChIP buffer (50 mM Tris-HCl pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100) using 5 µg of HIF1A antibody (CST 36169) or a rabbit IgG as negative control. 30 µL of Dynabeads Protein G (ThermoFisher Scientific) were added to the immunocomplexes for 2 h at 4°C. DNA was recovered by reverse crosslinking overnight at 65°C, and extracted using phenol/chloroform/isoamyl alcohol.
ChIP samples were purified using Agencourt AMPure XP beads (Beckman Coulter) and quantified with the Qubit (Invitrogen). ChIP-seq libraries were prepared from 0 TO 10 ng of double-stranded purified DNA using the MicroPlex Library Preparation kit v2 (C05010014, Diagenode s.a., Seraing, Belgium), according to manufacturer's instructions. In the first step, the DNA was repaired and yielded molecules with blunt ends. In the next step, stem-loop adaptors with blocked 5 prime ends were ligated to the 5 prime end of the genomic DNA, leaving a nick at the 3 prime end. The adaptors cannot ligate to each other and do not have single-strand tails, avoiding non-specific background. In the final step, the 3 prime ends of the genomic DNA were extended to complete library synthesis and Illumina compatible indexes were added through a PCR amplification (7 + --- cycles). Amplified libraries were purified and size-selected using Agencourt AMPure XP beads (Beckman Coulter) to remove unincorporated primers and other reagents.

treatment_protocol: Myc-CaP cells were treated for 6 hours with DMOG (HIF1A stabilizer) at a final concentration of 1.0 mM.

value: FVB; Hi-Myc transgenic

value: Prostate carcinoma

value: IgG


title: Heart,MOCK,31dpi,1

value: Mock (PBS-treated)


title: Input DNA.

value: Input DNA


title: Heart,MOCK,31dpi,2


title: Heart,MOCK,31dpi,3


title: Heart,IAV,3dpi,2


title: IP_HIF1A


title: Heart,IAV,3dpi,3


title: ESC_CCE_even

value: mESC 46C


title: Heart,IAV,3dpi,1


title: ChIP-seq_EpiLC_Tet1D-dTAG-Suz12_r2

data_processing:
FastQC (v0.10.1) was used to check the sequencing quality. Reads were pre-processed by Trim Galore (v.0.6.3) and Cutadapt programs.
Reads were aligned to the mouse genome mm9 using the bowtie2 (v2.3.5) program, with parameters -X 1000 --no-mixed --no-discordant.
The mapped reads were sorted and converted to a binary bam file using samtools (v1.10)
ChIP-seq peaks were determined by the MACS program (v.2.2.7), using input as the control data, and all other parameters followed the default settings.
Genome_build: mm9
Supplementary_files_format_and_content: Bed file of MACS called peaks.

value: mESC CCE derived EpiLC

value: Tet1-degron KI

value: Suz12, Active Motif, 39357


title: Cerebellum,SARSCOV2,3dpi,3

source_name: Cerebellum

value: Cerebellum

value: WT


title: Heart,IAV,31dpi,1

value: Influenza (100,000 PFU)


title: ESC_CCE_odd

value: Neat1 odd probes


title: ChIP-seq_EpiLC_Tet1D-dTAG-Suz12_r1


title: ChIP-seq_EpiLC_Tet1D-Ctrl-Suz12_r2


title: Cerebellum,SARSCOV2,3dpi,2


title: ChIP-seq_EpiLC_Tet1D-Ctrl-Suz12_r1


title: ChIP-seq_EpiLC_Neat1KO_Suz12_r2

description:
EpiLC_Neat1KO_Suz12_r2
EpiLC_Neat1KO_Suz12.bed

value: mESC 46C derived EpiLC


title: ChIP-seq_EpiLC_Neat1KO_Suz12_r1

description:
EpiLC_Neat1KO_Suz12_r1
EpiLC_Neat1KO_Suz12.bed


title: Cerebellum,SARSCOV2,3dpi,1

value: SARS-CoV-2 (1000 PFU)


title: Cerebellum,SARSCOV2,31dpi,4

value: 31 dpi


title: Cerebellum,SARSCOV2,31dpi,3


title: Heart,MOCK,3dpi,2

value: Heart

value: 3 dpi


title: ChIP-seq_EpiLC_Neat1KO_input


title: Cerebellum,SARSCOV2,31dpi,2


title: Cerebellum,SARSCOV2,31dpi,5


title: ChIP-seq_EpiLC_46C_WT_Suz12_r2


title: ChIP-seq_EpiLC_46C_WT_Suz12_r1


title: ChIP-seq_EpiLC_46C_WT_input


title: ChIP-seq_EpiLC_Pspc1KO_Suz12_r1


title: Heart,IAV,31dpi,2


title: Cerebellum,MOCK,3dpi,3


title: ChIP-seq_EpiLC_Pspc1KO_Suz12_r2


title: Cerebellum,MOCK,3dpi,2


title: Cerebellum,SARSCOV2,31dpi,1


title: Cerebellum,MOCK,3dpi,1


title: ChIP-seq_EpiLC_Pspc1KO_input


title: ChIP-seq_EpiLC_CCE_WT_Suz12_r1


title: Cerebellum,MOCK,31dpi,5


title: Cerebellum,MOCK,31dpi,1


title: Cerebellum,MOCK,31dpi,3


title: ChIP-seq_ESC_CCE_WT_Pspc1

description:
ESC_CCE_WT_Pspc1
Pspc1_ESC_2324.bed

value: mESC CCE

value: Pspc1, Santa Cruz, sc-84577


title: Cerebellum,MOCK,31dpi,4

value: Mock (PBS-treated)


title: ChIP-seq_ESC_CCE_WT_input


title: ChIP-seq_EpiLC_CCE_WT_Suz12_r2


title: ChIP-seq_ESC_Pspc1KO_Pspc1


title: Cerebellum,IAV,3dpi,3


title: Cerebellum,IAV,3dpi,1


title: ChIP-seq_ESC_CCE_WT_Suz12

description:
ESC_CCE_WT_Suz12
Suz12_ESC_6539.bed


title: Cerebellum,MOCK,31dpi,2


title: FA_Neat1KO_D4_rep2

data_processing:
FastQC (v0.10.1) was used to check the sequencing quality. Reads were pre-processed by Trim Galore (v.0.6.3) and Cutadapt programs.
Reads were aligned to the mouse genome mm9 using STAR (v2.7.6a) with the default settings.
Transcript assembly and differential expression analysis were performed using Cufflinks (v2.2.1). Assembling of novel transcripts was not allowed (-G), other parameters of Cufflinks followed the default setting.
Genome_build: mm9
Supplementary_files_format_and_content: tsv files - tab-delimited files containing FPKM values for RefSeq genes in each sample generated using Cufflinks.

extract_protocol:
Total RNAs were extracted using the RNeasy kit (#74136, Qiagen) according to the manufacturer’s instructions
100 ng total RNA was processed for RNA-seq library construction using the Ovation Mouse RNA-seq kit (NuGEN, #0348–32) following the manufacturer’s protocol. Sequencing was performed by Novogene with the Illumina HiSeq 4000 Sequencer. Data with 150 bp paired-end reads were obtained.


title: FA_46C_WT_D4_rep2


title: Cerebellum,IAV,3dpi,2


title: Cerebellum,IAV,31dpi,3


title: Cerebellum,IAV,31dpi,4


title: FA_46C_WT_D4_rep1


title: FA_Neat1KO_D4_rep1


title: FA_Neat1KO_D2_rep2


title: FA_46C_WT_D2_rep2


title: ChIP-seq_EpiLC_CCE_WT_input


title: FA_Neat1KO_D2_rep1


title: Cerebellum,IAV,31dpi,2


title: FA_46C_WT_D2_rep1


title: Cerebellum,IAV,31dpi,1


title: Haustorial region_rep4

city: BLACKSBURG

first: James

middle: H

last: Westwood

state: VA

address: 401 Latham Hall (0390)

department: School of Plant and Environmental Sciences

institute: Virginia Tech

data_processing:
FASTP v.1.0.0 was used to detect and trim adaptors, and filter out sequences shorter than 50nt, with low quality or low complexity.
Clean reads were mapped with STAR 2.5.2b against the genome of C. campestris (Vogel et al., 2018).
Gene counts were obtained using STAR 2.5.2b
Genome_build: C. campestris (Vogel et al., 2018), PRJEB19879
Supplementary_files_format_and_content: Each is a .txt file cointaining a matrix with the C. campestris genes ID and the counts for each gene in the corresponding sample

molecule: polyA RNA

organism: Cuscuta campestris

source_name: Haustorial region

growth_protocol: 3cm vegetative shoot tip from Cuscuta campestris, previously grown on Beta vulgaris, were cut, surface-sterilized, and attached to artificial hosts in the artificial host system (AHS) with liquid MMS media plus 1-naphthaleneacetic acid (NAA) (3 mg l-1) and 6-benzylaminopurine (BA) (1 mg l-1). Plants were expossed to far-red enriched light for 2.5 days, then they were  kept under full spectrum light for 12.5 days. Parasites did not contact the liquid media directly, except via the contact between the haustoria and the artificial host.

extract_protocol:
Samples were collected 15 days post inoculation. Plants with healthy holdfasts and new developed shoots were detached from the artificial host. For haustorial samples, regions harboring visibly healthy holdfasts (identified by formation of new shoots) were separated from any shoot or lateral meristem. For non-haustorial stem samples, new healthy and turgid shoots were collected after removing 5 mm of the stem connecting to the haustorial region to avoid tissue contamination. All tissues were immediately frozen in liquid nitrogen. Samples from 3-4 plants were pooled in each replicate and four replicates were used for each type of tissue. For RNA extraction, frozen tissue was ground using glass beads in a bead beater and RNeasy Plant Mini Kit (Qiagen). After kit extraction, RNA was precipitated using 3M NaOAc and Ethanol 100%, and resuspended in RNAse-free water.
mRNA library was prepared using Poly-A enrichment

value: Haustorial region


title: Shoot_rep4

source_name: Shoot

value: Vegetative shoot


title: Shoot_rep3


title: ESC_Neat1KO_rep2

value: mESC 46C


title: Haustorial region_rep3


title: Shoot_rep1


title: Cerebellum,IAV,31dpi,5


title: ESC_Neat1KO_rep1


title: Haustorial region_rep2


title: FA_Pspc1KO_D4_rep2

value: mESC CCE derived EpiLC


title: FA_Pspc1KO_D4_rep1


title: ESC_46C_WT_rep2


title: ESC_46C_WT_rep1


title: Haustorial region_rep1


title: Shoot_rep2


title: FA_CCE_WT_D4_rep2


title: FA_Pspc1KO_D2_rep2


title: FA_Pspc1KO_D2_rep1


title: 2769

city: Münster

first: Marisol

last: Herrera-Rivero

state: NRW

address: Albert-Schweitzer-Campus 1

country: Germany

institute: University of Münster

description: batch 2

data_processing:
Data was automatically demultiplexed using the Illumina bcl2fastq2 Conversion Software v2.20
FastQ files underwent two rounds of quality control, pre-trimming and post-alignment, using FastQC v0.11.7
Removal of Illumina adapters and low-quality sequences was performed with Trimmomatic v0.38. Reads of length<15 bases, as well as leading and/or trailing bases with quality< 3 or no base call, and bases with average quality<15 in a 4-base sliding window were removed
Alignment was performed with HISAT2 v2.1.0 [29] using the mouse genome assembly mm10 (Mus musculus, GRCm38)
Mapped reads (primary alignments) were sorted by read name using SAMtools v1.8 and read counts were calculated with HTSeq v0.11.2
Assembly: mm10
Supplementary files format and content: Raw counts

source_name: liver

extract_protocol:
Total RNA was isolated using the Direct-zol RNA Microprep Kit (Zymo Research)
followed by a DNase digestion step.
Library preparation was carried out upon mRNA enrichment with the NEBNext Poly(A) mRNA Magnetic Isolation Module, using the NEBNext Ultra II RNA Directional Library Prep Kit for Illumina (New England BioLabs). Single read sequencing took place on a NextSeq 500 System (Illumina), using the corresponding NextSeq 500 High Output Kit v2.5, with a read length of 75 base pairs. The integrity of the RNA and quality of the library were assessed using a TapeStation 4200 (Agilent).

treatment_protocol: In phase 1, two groups of adolescent animals (postnatal day-PND- 28-70 ± 1) were exposed to low (L) food availability, while another two groups were exposed to high (H) food availability for a period of six weeks. In phase 2, animals were considered to have reached early adulthood (PND 71 ± 2) and were kept either in the same (match) or the opposite (mismatch) situation of food availability for another six weeks.

value: liver

tag: treatment

value: HH


title: 2753

description: batch 2

value: HL


title: 2760

description: batch 2

value: LL


title: ESC_Pspc1KO_rep2


title: 2748

description: batch 2

value: LH


title: FA_CCE_WT_D2_rep2

value: WT


title: FA_CCE_WT_D2_rep1


title: ESC_Pspc1KO_rep1


title: FA_CCE_WT_D4_rep1


title: ESC_CCE_WT_rep1


title: ESC_CCE_WT_rep2


title: 2653

description: batch 1


title: 2656

description: batch 1


title: 2742

description: batch 2


title: 2654

description: batch 1


title: 2639

description: batch 1


title: 2646

description: batch 1


title: Synovium,TMJOA,rep5

city: shanghai

first: Chuyao

address: The Ninth People's Hospital, No. 639, Zhizaoju Road, Huangpu District, Shanghai

institute: shanghai ninth people hospital

description:
LKK-11-18
LncRNA Expression Profiling.xlsx
mRNA Expression Profiling.xlsx

data_processing:
Paired-end reads were harvested from Illumina HiSeq 4000 sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3). The high quality trimmed reads were used to analyse LncRNAs and mRNAs.
LncRNA & mRNA: The high quality reads were aligned to the human reference genome (UCSC hg19) with hisat2 software. Then, guided by the Ensembl gtf gene annotation file, cuffdiff software (part of cufflinks) was used to get the FPKM as the expression profiles of LncRNA and mRNA, and fold change and p-value were calculated based on FPKM, differentially expressed LncRNA and mRNA were identified. LncRNA target genes were predicted by the locations to nearby genes. And GO and Pathway analysis were performed on these target genes. GO and Pathway enrichment analysis were also performed based on the differentially expressed mRNAs.
Assembly: hg19
Supplementary files format and content: excel format

source_name: human temporomandibular joint

extract_protocol:
Total RNA was used for removing the rRNAs using Ribo-Zero rRNA Removal Kits (Illumina, USA) following the manufacturer's instructions.
RNA libraries were constructed by using rRNA-depleted RNAs with TruSeq Stranded Total RNA Library Prep Kit (Illumina, USA) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using  the BioAnalyzer 2100 system (Agilent Technologies, USA).
RNA-seq : 10 pM libraries were denatured as single-stranded DNA molecules, captured on Illumina flow cells, amplified in situ as clusters and finally sequenced for 150 cycles on Illumina HiSeq Sequencer according to the manufacturer’s instructions.

value: human temporomandibular joint


title: 2747

description: batch 2


title: Synovium,reducible anterior disc displacement,rep5

description:
XXF-12-14
LncRNA Expression Profiling.xlsx
mRNA Expression Profiling.xlsx


title: Synovium,TMJOA,rep4

description:
CWH-11-18
LncRNA Expression Profiling.xlsx
mRNA Expression Profiling.xlsx


title: Synovium,TMJOA,rep3

description:
OQY-12-14
LncRNA Expression Profiling.xlsx
mRNA Expression Profiling.xlsx


title: 2745

description: batch 2


title: PolyA-seq_HBG-175.ABE8e.L1-RTm_2

city: Boston

first: Roberto

last: Chiarle

state: Massachusetts

address: 300 Longwood Avenue

department: Department of Pathology

institute: Children’s Hospital Boston and Harvard Medical School

data_processing:
Sequences in library were similarly processed as previously described(Mara Compagno et al., Nature 2017). Briefly, reads for each experimental condition were demultiplexed by designed barcodes plus followed portion of primer if barcode length less than 8 bp.  For non-PolyA-seq, reads were further filtered by the presence of primer plus additional 10 downstream bases to enhance specificity, then the barcode, primer and L1 ORFeus portion of the remained sequences were masked for alignment analysis. For PolyA-seq, reads were further filtered by the presence of primer (7 Poly(A) was imposed to primer directly) plus additional 8 Poly(A), then the barcode and primer portion of the remained sequences were masked for alignment analysis. Next, the processed sequences were aligned to human genome (GRCh38/hg38) using BLAT, and finally aligned sequences were further cleaned by removing PCR repeats (reads with same junction position in alignment to the reference genome and a start position in the read less than 3 bp apart), invalid alignments (including alignment scores < 30, reads with multiple alignments having a score difference < 4 and alignments having 10-nucleotide gaps) and ligation artifacts (for example, random ligation with HaeIII restriction sites). L1 insertion junction position was determined based on the genomic position of the 5’ end of the aligned read.
Genome_build: hg38
Supplementary_files_format_and_content: bed file for L1 insertion junction

growth_protocol: Cells were cultured at 37 °C with 5% CO2

extract_protocol:
standard isopropanol extraction, wash in ethanol 70% and resuspension in TE buffer
See Supplemental Experimental procedures from this paper
PolyA-seq

treatment_protocol: no treatment

tag: crispr tech

tag: target

value: HBG 175

tag: seq type

value: PolyA L1 insertion

tag: condition


title: PolyA-seq_HBG-175.ABE8e.L1-RTm_1


title: PolyA-seq_HBG-198.ABE8e.L1-ORFeus_2

value: HBG 198


title: PolyA-seq_HBG-175.ABE8e.L1-ORFeus_2


title: PolyA-seq_HBG-198.ABE8e.L1-RTm_2


title: 2629

description: batch 1

tag: tissue


title: 2766

description: batch 2


title: Synovium,TMJOA,rep2

description:
ZXR-12-07
LncRNA Expression Profiling.xlsx
mRNA Expression Profiling.xlsx


title: Synovium,reducible anterior disc displacement,rep4

description:
HYX-11-23
LncRNA Expression Profiling.xlsx
mRNA Expression Profiling.xlsx


title: PolyA-seq_BCL11A.ABE8e.L1-RTm_2


title: PolyA-seq_HBG-198.ABE8e.L1-ORFeus_1


title: PolyA-seq_HBG-175.ABE8e.L1-ORFeus_1


title: PolyA-seq_HBG-198.ABE8e.L1-RTm_1


title: 2635

description: batch 1


title: 2626

description: batch 1


title: Synovium,reducible anterior disc displacement,rep3

description:
CLF-11-18
LncRNA Expression Profiling.xlsx
mRNA Expression Profiling.xlsx


title: PolyA-seq_BCL11A.ABE8e.L1-ORFeus_1


title: PolyA-seq_MYC.ABE8e.L1-RTm_2

value: MYC


title: Synovium,reducible anterior disc displacement,rep2

description:
SYL-12-07
LncRNA Expression Profiling.xlsx
mRNA Expression Profiling.xlsx


title: WT_HSPCs_3

city: Milwaukee

first: Sridhar

last: Rao

state: WI

address: 8727 Watertown Plank Road

department: Blood Research Institute

institute: BloodCenter of Wisconsin

data_processing:
Illumina NextSeq 500 system used for base calling
RNA seq data were aligned to the mm9 genome using STAR
DESEQ2  was used to obtain a list of differentially expressed genes between genotypes of interest.
Genome_build: MM9
Supplementary_files_format_and_content: Excel spreadsheet and log2FC

growth_protocol: HSPCs were isolated from mice 4-6 weeks post treatment using red cell lysis and lineage depletion.

extract_protocol:
Total RNA was isolated from 1x10^6 cells using Trizol (ThermoFisher Scientific, 15596018) and the manufacturer’s recommended protocol.
Libraries were prepped in exact accordance with the NEBNext Ultra II RNA library prep kit for Illumina (NEB, E7770) in combination with the NEBNext Poly(A) mRNA magnetic isolation module (NEB, E7490), the NEBNext multiplex oligos for Illumina set 1 and set 2 (NEB, E7335 and E7500), and Ampure XP magnetic beads (Beckman Coulter, A6388).

treatment_protocol: 4-6 week old mice were injected intraperitoneally with 300 mL of 1 mg/mL PIpC every other day for a total of 7 doses.

tag: strain background

tag: genotype/variation

value: hematopoietic stem and progenitor cells (HSPCs)


title: PolyA-seq_MYC.ABE8e.L1-RTm_1


title: WT_HSPCs_2


title: Synovium,TMJOA,rep1

description:
SQ-12-14-Y
LncRNA Expression Profiling.xlsx
mRNA Expression Profiling.xlsx


title: WT_HSPCs_1


title: PolyA-seq_MYC.ABE8e.L1-ORFeus_2


title: PolyA-seq_MYC.AncBE4Max.L1-RTm_2


title: Synovium,reducible anterior disc displacement,rep1

description:
FJY-11-21
LncRNA Expression Profiling.xlsx
mRNA Expression Profiling.xlsx


title: PolyA-seq_BCL11A.ABE8e.L1-RTm_1


title: Smc3_HSPCs_3


title: PolyA-seq_MYC.AncBE4Max.L1-RTm_1


title: PolyA-seq_MYC.ABE8e.L1-ORFeus_1


title: PolyA-seq_MYC.AncBE4Max.L1-ORFeus_2


title: PolyA-seq_BCL11A.ABE8e.L1-ORFeus_2


title: Normal_patient1

city: Changsha

first: Kuijie

state: Hunan

address: 139 Renmin Middle Road

department: Department of General Surgery

institute: The Second Xiangya Hospital

data_processing:
CASAVA
Clean reads were generated by removing raw reads with an adapter or any N (N means that the base information cannot be determined), as well as low-quality bases (Reads with bases that have Qphred <= 20 accounting for more than 50% of the entire read length).
Q20, Q30 and GC ratio were calculated as the evaluating indicator of clean reads.
Reads were aligned against reference genome using HISAT2 v2.0.5.
Assembly: GRCh38
Supplementary files format and content: clean reads matrix

source_name: tumor-adjacent normal colon

extract_protocol:
Each sample's total RNA was extracted using TRIzol Reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions.
The cDNA library is constructed by enriching mRNA with polyA tail from total RNA by Oli-go (dT) magnetic beads, and then randomly fragmenting the obtained mRNA with diva-lent cations in Fragmentation Buffer. The first strand of cDNA was then synthesized in the M-MuL V reverse transcriptase system using random oligonucleotides as primers and frag-mented mRNA as templates. The second strand of cDNA was synthesized under the DNA polymerase I system using dNTPs from RNaseH-degraded RNA strand. The purified dou-ble-stranded cDNA was end-repaired, A-tailed, and connected to a sequencing adapter. AMPure XP beads were used to screen cDNAs of about 370-420 bp, followed by PCR am-plification and AMPure XP beads were again used to purify the PCR products. At last, we obtained a library.

value: tumor-adjacent normal colon

tag: patient diagnosis

value: colorectal cancer

tag: patient number


title: Smc3_HSPCs_2


title: PolyA-seq_MYC.PE3b.5GtoC.L1-RTm_2

value: MYC 5GtoC


title: Smc3_HSPCs_1


title: CRC_patient2

source_name: colorectal cancer


title: PolyA-seq_MYC.PE3b.5GtoC.L1-RTm_1


title: PolyA-seq_MYC.PE3b.5GtoC.L1-ORFeus_2


title: PolyA-seq_MYC.PE3b.5GtoC.L1-ORFeus_1


title: CRC_patient1


title: PolyA-seq_MYC.PE3.5GtoC.L1-RTm_1


title: Npm1_HSPCs_3


title: PolyA-seq_MYC.PE3.5GtoC.L1-ORFeus_2


title: PolyA-seq_MYC.PE3.5GtoC.L1-RTm_2


title: Npm1_HSPCs_1


title: Npm1_HSPCs_2


title: PolyA-seq_MYC.AncBE4Max.L1-ORFeus_1


title: PolyA-seq_MYC.PE3.d2-4A.L1-RTm_2

value: MYC d2-4A


title: anti_FoxM1_chip_2_ACGAGAAC-ACAGTTCG_L003_R1_001.fastq.gz

city: Chicago

first: Vaibhav

last: Chand

state: IL

address: 900S Ashland Ave

department: Biochemistry and Molecular Genetics

institute: University of Illinois at Chicago

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the GRCH38 genome assembly using BWA
Data were filtered using the SAM tools and bed graph were generated
peaks were called using MACS2 version 2.2.7.1 with the following setting: ChIP threshold (0.2), Enrichment Fold (2.5).
Genome_build: GRCH38
Supplementary_files_format_and_content: BigWig files were generated using WigToBigWig

growth_protocol: Human HCC Huh7 cells were obtained from American Type Culture Collection. All experiments were performed within 8 to 10 passages. Cells were maintained in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% fetal bovine serum (HyClone Laboratories Inc.), with 100 units of penicillin/streptomycin used to culture cells at 37ºC with 5% CO2.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
The ChIPseq libraries were prepared with the Hyper Library Construction Kit from Kapa Biosystems with two modifications: adaptors were diluted 1:20 and adaptored DNA were amplified for 10 cycles.

treatment_protocol: No treatment

value: HCC Cell line

value: No treatment

value: Anti-FOXM1 Antibody (G-5):sc-376471


title: anti_FoxM1_chip_3_CGACCTAA-CTAACCTG_L003_R1_001.fastq.gz


title: PolyA-seq_MYC.PE3.5GtoC.L1-ORFeus_1


title: Normal_patient2


title: Input_GTACACCT-GAGACCAA_L003_R1_001.fastq.gz


title: PolyA-seq_MYC.PE3.d2-4A.L1-RTm_1


title: Double_HSPCs_2

value: Double


title: PolyA-seq_MYC.PE3.d2-4A.L1-ORFeus_2


title: Double_HSPCs_3


title: PolyA-seq_MYC.PE3.d2-4A.L1-ORFeus_1


title: PolyA-seq_RAG1.L1-RTm_2

value: canonical CRISPR


title: Double_HSPCs_1


title: PolyA-seq_RAG1.L1-RTm_1


title: PolyA-seq_RAG1.L1-ENm_2


title: PolyA-seq_RAG1.L1-ORFeus_3


title: U2OS siRELB Rep 3

first: Brian

last: Budke

address: 920 E 58th St

department: Radiation and Cellular Oncology

institute: University of Chicago

data_processing:
Read filtering using Trimmomatic v0.38 with the parameters ILLUMINACLIP:Trimmomatic-0.38/adapters/TruSeq3-SE.fa:2:30:10 SLIDINGWINDOW:4:20 LEADING:3 TRAILING:3 MINLEN:36
Align reads to human genome GRCh38.p13 using STAR 2.7.1a with the parameter --outSAMtype BAM SortedByCoordinate
Count features in BAM files using Subread 1.6.4 with the parameteres -t exon -g gene_id -s 0
Genome_build: Genome Reference Consortium Human Build 38 patch release 13
Supplementary_files_format_and_content: Tab-delimited text files containing the number of reads for each Sample

source_name: Cultured U2OS osteosarcoma cells

growth_protocol: Cells were grown in 6-well plates in DMEM high glucose medium with 1 mM sodium pyruvate and 10% fetal bovine serum at 37 C, 5% CO2

extract_protocol:
Total RNA was extracted using an RNeasy Mini Kit (Qiagen)
Oligo-dT selected mRNA libraries were prepared at the Functional Genomics Facility core at the University of Chicago

treatment_protocol: Cells were transfected with the indicated siRNA or non-silencing siRNA ("NS") at 75 nM final concentration using Lipofectamine RNAiMAX (Life Technologies) according to manufacturer instructions and incubated for 48 hours prior to RNA extraction.

tag: sirna

value: RELB

tag: replicate


title: U2OS siRELB Rep 2


title: U2OS siNFKB2 Rep 3


title: gr_wt_rep3 [RNA-Seq]

city: Copenhagen

first: Bo

last: Porse

address: Ole Maaløes Vej 5, 4

department: Finsen Laboratory and BRIC

country: Denmark

institute: University of Copenhagen

data_processing:
Reads were mapped to mouse genome assembly (mm9) using STAR, and gene expression levels were quantified using featureCounts (GTF.featureType=exon, countMultiMappingReads=Y, fraction=T) on Gencode gene annotation (release M1).
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph files were generated using bedtools. Signal is normalized to TPM. bedGraph files were converted to bigWig format using bedGraphToBigWig tool.

source_name: gr

growth_protocol: All cell types were FACS sorted from freshly harvested murine bone marrow

extract_protocol:
Total RNA was purified from sorted BM populations using the RNeasy Micro Kit (QIAGEN) as described by the manufacturer. RNA was subjected to double-stranded cDNA synthesis using the Ovation RNA-Seq System V2 (NuGEN),
cDNA libraries were prepared form sheared cDNA fragments (150-550 bp) using the Ovation Ultralow System V2 (NuGEN).
The indexed cDNA libraries were pooled in equimolar ratios and subjected to 75-cycles of sequencing at Exiqon (Exiqon now at Quiagen, Aarhus, DK) on a Illumina NextSeq 500 System (Illumina, San Diego, CA, USA.

tag: cell type - immunophenptype of sorted bm population

tag: mouse strain


title: PolyA-seq_RAG1.L1-ORFeus_1

tag: cell line


title: gr_wt_rep1 [RNA-Seq]


title: PolyA-seq_MYC.L1-RTm_2


title: gr_wt_rep2 [RNA-Seq]


title: U2OS siRELB Rep 1


title: PolyA-seq_RAG1.L1-ORFeus_2


title: PolyA-seq_MYC.L1-ENm_1


title: U2OS siNS Rep 3

value: NS


title: PolyA-seq_MYC.L1-ORFeus_2


title: PolyA-seq_MYC.L1-RTm_1


title: U2OS siNFKB2 Rep 1


title: PolyA-seq_MYC.GFP control_1

value: GFP control


title: PolyA-seq_RAG1.GFP control_1


title: bc_wt_rep2 [RNA-Seq]

source_name: bc


title: bc_wt_rep3 [RNA-Seq]


title: U2OS siNFKB2 Rep 2


title: PolyA-seq_RAG1.L1-ENm_1


title: PolyA-seq_MYC.L1-ORFeus_1


title: U2OS siNS Rep 1


title: bc_wt_rep1 [RNA-Seq]


title: PolyA-seq_MYC.GFP control_2


title: mm_ko_rep3 [RNA-Seq]


title: PolyA-seq_MYC.L1-ENm_2


title: mm_ko_rep1 [RNA-Seq]


title: U2OS siNS Rep 2


title: mm_wt_rep3 [RNA-Seq]

source_name: mm


title: mm_ko_rep2 [RNA-Seq]


title: mm_wt_rep2 [RNA-Seq]


title: my2_wt_rep3 [RNA-Seq]


title: mm_wt_rep1 [RNA-Seq]


title: Patient 8 LP

city: Aarhus

first: Kirsten

last: Rønholt

address: Palle Juul-Jensens Boulevard

department: Department of Dermatology

institute: Aarhus University Hospital

hyb_protocol: Samples were hybridized overnight to the GeneChip and scanned using an Affymetrix GCS 3000 7G scanner.

scan_protocol: GeneChips were scanned using an Affymetrix GCS 3000 7G scanner.

data_processing: The data were processed using rma with background correction, quantile normalization and log2 transformation. Only the PM probes were used.

label: biotin

source_name: Lesional psoriasis skin

label_protocol: A total of 100 ng RNA was labeled with the Ambion WT Expression Kit (Ambion, CA, USA) according to the manufacturer’s instructions.

extract_protocol: The RNA purification procedure was performed according to the manufacturer's protocol, using the SV Total RNA Isolation System (Promega, Madison, USA).

treatment_protocol:
Nine adult patients with psoriasis vulgaris were included. Excisional biopsies (2.5 cm x 1 cm) from non-involved (NP) and involved tissue (LP) were obtained using a local anesthetic containing 1% Lidocaine. Subcutis was removed and biopsies were snap frozen in liquid nitrogen and used for RNA isolation.
24 hours before RNA purification, 1 ml of −80 °C RNAlater-ICE (Ambion, Carlsbad, CA, USA) was applied to the cryotubes containing the excision biopsies. After 20 minutes, the samples were transferred from −80 to −20 °C and left overnight.

value: skin

value: Lesional psoriasis skin


title: Dermal_FB_NS5

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

institute: Lille University

description: effects of purified IgG from SSc patients

hyb_protocol: Agilent-026655 Whole Mouse Genome Microarray 4x44K v2 were scanned on an Agilent G2505B scanner.

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version V.10.7.3.1).

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and LOWESS normalization.

label_protocol: manufacturer's instructions

growth_protocol: Primary dermal normal human FB (ATCC® Number: PCS-201-012 ™) were used at the 5th culture passage. FB were initially cultured with Dulbecco's Modified Eagle medium combined with antibiotics at 1% concentration (penicillin and streptomycin) and 10% fetal calf serum (FCS). To avoid interference due to the presence of FCS, cells were FCS deprived for 24 hours after seeding.

extract_protocol: Total RNA extracted using manufacturer's instructions

treatment_protocol: FB were cultured 24 hours in the presence of purified IgG at a concentration of 100µg/mL (healthy subject, dcSSc ATA+ and dcSSc ATA-)

value: Human dermal fibroblast

value: non stimulated


title: Patient 9 LP


title: Patient 8 NP

source_name: Non-lesional psoriasis skin

value: Non-lesional psoriasis skin


title: Patient 7 LP


title: my2_wt_rep2 [RNA-Seq]


title: Patient 5 NP


title: Dermal_FB_NS4


title: Patient 6 NP


title: my2_wt_rep1 [RNA-Seq]


title: Dermal_FB_NS1


title: Patient 9 NP


title: Patient 4 LP


title: Dermal_FB_NS3


title: Patient 6 LP


title: Patient 5 LP


title: Patient 3 LP


title: Patient 7 NP


title: Dermal_FB_NS2


title: Patient 3 NP


title: my1+2_ko_rep3 [RNA-Seq]


title: Patient 2 NP


title: Patient 2 LP


title: my1+2_ko_rep2 [RNA-Seq]


title: Patient 1 LP


title: input_my12_ko_Rep1

data_processing:
Reads were mapped to mouse genome assembly (mm9) using bowtie2
IDR along with MACS2 was used to identify reproducible set of CEBPE enriched region between the two replicates.
We used uniquely mapped and PCR duplicates (exact copies) collapsed as one read that are extended to their fragment length by determining the read extension size using MACS2 (predicted parameter). Raw read counts were normalized to TPM using deeptools (bamCoverage).
Genome_build: mm9
Supplementary_files_format_and_content: bigWig

source_name: MY1+2 (Cebpe KO)

growth_protocol: Cells were sorted from freshly harvested murine bone marrow

extract_protocol:
500,000 sorted MY1+2s (pooled MY1s+MY2s), MMs from Cebpe WT mice were used for CEBPE ChIP-seq experiments. 1,000,000 pooled MYs and MMs purified from Cebpe KO mice were used as negative control. Chromatin bound by antibodies was captured with Protein-A sepharose beads, washed, de-crosslinked and precipitated.
The precipitated DNA was then mixed with 2 ng E. Coli DNA and amplified using NEB Next ChIP-seq sample prep kit (New England Biolabs) as described by the manufacturer.
The indexed cDNA libraries were pooled in equimolar ratios and subjected to sequencing on an Illumina Hiseq2000.

value: bone marrow

tag: cell type

tag: strain

tag: genotype

value: Cebpe KO

tag: chip antibody

value: irrelevant IgG control (sc-2027, Santa Cruz Biotechnologies)


title: input_mm_ko_Rep1

source_name: MM (Cebpe KO)


title: input_mm_wt_Rep1

source_name: MM (Cebpe WT)

value: Cebpe WT


title: my1+2_ko_rep1 [RNA-Seq]


title: my1_wt_rep3 [RNA-Seq]


title: h3k27ac_mm_wt_Rep2

value: H3K27ac (ab4729, Abcam, Cambridge, UK)


title: h3k27ac_mm_ko_Rep2


title: h3k27ac_mm_ko_Rep1


title: Patient 4 NP


title: Patient 1 NP


title: Dermal_FB_SSC_IgG_ATA-4

tag: treatment

value: IgG from dcSSc ATA-negative patient


title: Dermal_FB_SSC_IgG_ATA-5


title: Dermal_FB_SSC_IgG_ATA-3


title: Dermal_FB_SSC_IgG_ATA-2


title: h3k27ac_my12_wt_Rep2

source_name: MY1+2 (Cebpe WT)


title: h3k27ac_my12_ko_Rep1


title: h3k27ac_my12_ko_Rep2


title: my1_wt_rep2 [RNA-Seq]


title: input_my12_wt_Rep1


title: h3k27ac_my12_wt_Rep1


title: Dermal_FB_SSC_IgG_ATA+5

value: IgG from dcSSc ATA-positive patient


title: Dermal_FB_SSC_IgG_ATA-1


title: Dermal_FB_SSC_IgG_ATA+3


title: Dermal_FB_SSC_IgG_ATA+4


title: h3k27ac_mm_wt_Rep1


title: cebpa_mm_ko_Rep2

value: CEBPA (clone 14AA, Santa Cruz Biotechnology, discontinued)


title: mo2_wt_rep2 [RNA-Seq]


title: cebpa_mm_ko_Rep1


title: mo2_wt_rep3 [RNA-Seq]


title: cebpa_mm_wt_Rep1


title: cebpa_mm_wt_Rep2


title: Dermal_FB_SSC_IgG_ATA+2


title: cebpa_my12_ko_Rep2


title: cebpa_my12_ko_Rep1


title: my1_wt_rep1 [RNA-Seq]


title: mo1_wt_rep1 [RNA-Seq]


title: mo2_wt_rep1 [RNA-Seq]


title: mo1_wt_rep2 [RNA-Seq]


title: m34 WT sh-GLS2 liver

city: Tarrytown

first: Xiping

last: Cheng

address: 777 Old Saw Mill River Road

institute: Regeneron Pharmaceuticals

data_processing:
Raw BCL sequence data were converted to FASTQ files using Illumina Casava v1.8.2. Reads were decoded based on their barcodes, and FastQC was used to evaluate read quality. Reads were mapped to the mouse transcriptome (NCBI GRCm38) using Array Studio (QIAGEN OmicSoft) allowing up to two mismatches. Reads mapped to the exons of a gene were summed at the gene level.
Genome_build: NCBI GRCm38
Supplementary_files_format_and_content: gene count and TPM csv files

extract_protocol:
Total RNA was purified from all samples using MagMAX-96 for Microarrays Total RNA Isolation Kit (Ambion by Life Technologies) according to manufacturer’s specifications. Genomic DNA was removed using MagMAX TURBO DNase Buffer and TURBO DNase from the MagMAX kit listed above.
Strand-specific RNA-seq libraries were prepared using KAPA Stranded mRNA-Seq Library Preparation Kit (Kapa Biosystems). Twelve-cycle PCR was performed to amplify libraries.

value: WT

value: liver

tag: Sex

value: male

tag: age

value: 5 months


title: m39 OTC sh-GLS2 liver

value: OTC

tag: tissue


title: cebpa_my12_wt_Rep2


title: Dermal_FB_SSC_IgG_ATA+1


title: pmo2_wt_rep2 [RNA-Seq]


title: m79 WT sh-GLS2 liver


title: pmo2_wt_rep3 [RNA-Seq]


title: Dermal_FB_HC_IgG3

value: IgG from healthy control


title: RNA-seq of lung tissue from MCT4 Rat

city: Guangzhou

first: Ruidi

last: Tang

state: Guangdong

address: 151 Yanjiang Road, Guangzhou, Guangdong, China

institute: State  Key  Laboratory  of  Respiratory  Diseases

description: MCT model

data_processing:
Fastq files demultiplexing done by bcl2fastq2 Conversion Software v2.20.0.422
Quality control for adapter contamination and trimming was performed with fastp v0.20.1
Cleaned fastq files were aligned to the rn6 genome assembly using hisat2 v2.2.1 allowing for multiple hits
Samtools v1.11 converted the SAM files generated by the alignment into BAM files and sorted them
Counts of reads in genes was determined by featureCounts of the subread v2.0.1 with Ensembl Rattus_norvegicus.Rnor_6.0.102.gtf
DESeq2 v1.28.1 was used to compare raw gene counts between groups and genes with a false discovery rate (FDR) adjusted p<0.05 and |log2FoldChange| >1 were identified as differentially expressed genes (DEGs).
Genome_build: rn6
Supplementary_files_format_and_content: tab-delimited text files include rlog normalized values for each sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Rattus norvegicus

source_name: lung tissue

extract_protocol:
Total RNA was isolated from lung tissue of MCT-PH rats with or without DMB treatment using QIAzol Lysis Reagent (20874, QIAGEN Sciences, Maryland, USA). To enrich for mRNA and noncoding RNAs (ncRNAs), ribosomal RNA (rRNA) was removed from total RNA using rRNA Depletion Kit v2 (E7400L, NEBNext, MA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Sprague Dawley Rat

value: lung

value: monocrotaline


title: m28 WT control liver

value: control


title: m10 WT control liver


title: m04 OTC sh-GLS2 liver


title: pmo1_wt_rep2 [RNA-Seq]


title: pmo2_wt_rep1 [RNA-Seq]


title: Dermal_FB_HC_IgG4

value: Human dermal fibroblast


title: Dermal_FB_HC_IgG5


title: m21 OTC sh-GLS2 liver


title: m43 OTC control liver


title: Dermal_FB_HC_IgG2


title: cebpa_my12_wt_Rep1

value: bone marrow


title: m33 OTC sh-GLUD1 liver


title: RNA-seq of lung tissue from MCT3 Rat

description: MCT model


title: RNA-seq of lung tissue from MCT1 Rat

description: MCT model


title: Dermal_FB_HC_IgG1


title: m38 OTC control liver


title: RNA-seq of lung tissue from MCT2 Rat

description: MCT model


title: pmo1_wt_rep1 [RNA-Seq]


title: m44 OTC sh-GLUD1 liver


title: m25 OTC control liver


title: RNA-seq of lung tissue from DMB4 Rat

description: Intervention in the MCT model


title: pm_ko_rep3 [RNA-Seq]


title: m11 WT control liver


title: m20 WT control liver


title: m17 WT sh-GLUD1 liver


title: m15 WT sh-GLUD1 liver


title: m37 WT sh-GLUD1 liver


title: RNA-seq of lung tissue from DMB2 Rat

description: Intervention in the MCT model


title: pm_ko_rep2 [RNA-Seq]


title: pm_ko_rep1 [RNA-Seq]


title: m42 OTC sh-GLUD1 liver


title: m32 WT sh-GLUD1 liver


title: RNA-seq of lung tissue from DMB3 Rat

description: Intervention in the MCT model


title: m03 OTC control liver


title: m02 WT control liver


title: m41 WT control liver


title: pm_wt_rep1 [RNA-Seq]

source_name: pm


title: m14 WT sh-GLS2 liver


title: RNA-seq of lung tissue from DMB1 Rat

description: Intervention in the MCT model


title: mp_wt_rep2 [RNA-Seq]

source_name: mp


title: m08 WT sh-GLS2 liver

source_name: liver


title: m07 WT control liver


title: Tp53_HET2

city: Rehovot

first: Tsviya

last: Olender

address: 234 Herzl St.

department: Molecular Genetics

country: Israel

institute: The Weizmann Institute

description: MARS-Seq

data_processing:
Bulk RNAseq:
fastq reads were trimmed from the adapter with cutadapt, and aligned to the genome with STAR_2.5.2b. Read count was also performed with STAR
MARSseq:
fastq reads were trimmed from the adapter with cutadapt, and aligned to the genome with STAR_2.5.2b. Umi reduction was performed with custom home script followed by read count with htseq-count
scRNAseq:
Alignment, quantitation and aggregation of sample count matrices were performed using the 10x Genomics Cell Ranger pipeline as the manufacturer’s protocol (GENEWIZ JAPAN Corp.).
Genome_build: mm10
Supplementary_files_format_and_content: MEX format file with the scRNAseq feature cellular barcodes
Supplementary_files_format_and_content: tsv file with the scRNAseq feature list
Supplementary_files_format_and_content: tsv file with the scRNAseq cellular barcodes
Supplementary_files_format_and_content: Matrix table with the raw gene counts for the bulk RNAseq and for the MARSseq experiments

source_name: Hnrnpu +/+ Tp53 loxP/+

growth_protocol: For scRNA seq, cortices of E13 embryos were dissected in oxygenated dissection media (cold L15 supplemented with Glucose (0.6%)). After meninges removal, the cortices were mechanically dissociated and immediately plate in low adherence plates in NeuroBasal media containing B27 (x1) GlutaMAX (x1) Gentamicin (25ug/ml), EGF (20ng/ml), bFGF (20ng/ml) and Heparin (2ug/ml).

extract_protocol:
For the Bulk MARS-Seq and total RNAseq experiments E13 embryos were removed and their cortices dissected in cold PBS and immediately flash frozen in liquid nitrogen and kept in -80C until RNA extraction. RNA was harvested using RNeasy Mini kit, Quiagen
The 10x Genomics© Chromium system was used to capture 5000 single cells. The sequencing library was generated using the 10x Genomics© Single Cell 3′ Solution kit and subjected to Illumina NextSeq 500.
Bulk MARS-Seq library preparation was done according to MARS-seq protocol (Jaitin et al. 2014 Science.343:776-9, Keren-Shaul et al. 2019 Nature Protocols) and sequenced using NextSeq 500 High Output Kit v2.0  75 Cycles (Illumina).
For the Bulk RNA-Seq libraries we applied ribosomal RNA-depletion using Illumina's RiboZero, followed by library preparation with Illumina's TruSeq Stranded Total RNA library preparation kit.
libraries were sequenced using NextSeq 500/550 High Output Kit v2.0  75 Cycles (Illumina)

treatment_protocol: After two days in culture, Neurospheres were dissociated with Accutase, washed with OptiMEM and mixed with a DNA solution (4ug of each pX330 CRISPR/CAS9 plasmid, 1ug of pCAG::GFP). Dissociated cells (1-2x106) were electroporated in 2mm cuvettes, in Nepa21 Electroporator (poring parameters: 2x150V, 3ms long pulses, with a 50ms interval and 10% decay rate. Transfer: 5x20 volts pulses, 50ms long, with 50ms intervals and 40% decay rate. Cells were collected 24 hours post electroporation, dissociated using Accutase and passed through a 40 micron strainer.

value: E13 embryo dissected cortices

value: mixed

value: embryonic mouse cortex

value: Emx1 Cre/+, Hnrnpu +/+ Tp53 loxP/+


title: Tp53_HET3

description: MARS-Seq


title: m01 WT sh-GLS2 liver


title: mp_wt_rep1 [RNA-Seq]


title: Tp53_HET1

description: MARS-Seq


title: mp_wt_rep3 [RNA-Seq]


title: m30 WT sh-GLS2 liver


title: gp_ko_rep3 [RNA-Seq]


title: gp_ko_rep1 [RNA-Seq]


title: pm_wt_rep2 [RNA-Seq]


title: m13 WT control liver


title: m18 WT sh-GLS2 liver


title: m23 OTC sh-GLUD1 liver


title: B_12_3

city: Kunming

first: wenjie

last: wang

address: Kunming

institute: Yunnan University

data_processing:
The data from high-throughput sequencing were analyzed using the OmicShare tools, a free online platform for data analysis (www.majorbio.com).
Assembly: https://www.ncbi.nlm.nih.gov/assembly/GCF_000225545.1
Supplementary files format and content: Expression analysis table include TPM values for each sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Orbilia oligospora

source_name: Fungal hyphae

growth_protocol: The wild-type and ΔAosnf1 mutant strains were cultured on potato dextrose agar (PDA) medium at 28°C for 5 days.

extract_protocol:
The mycelium was divided and induced with about 600 nematodes for 0 and 12 h, respectively.
The libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Mycelium was collected and washed three times with 0.1 Mphosphate buffer saline (PBS) (pH 6.8-7.2).

value: Fungal hyphae

value: Fungal hyphae cells

value: Aosnf1 knockdown

tag: time

tag: condition


title: B_12_1


title: gp_ko_rep2 [RNA-Seq]


title: B_12_2


title: gp_wt_rep2 [RNA-Seq]

source_name: gp


title: Tp53_KO1

description: MARS-Seq

source_name: Tp53 KO

value: Emx1 Cre/+, Hnrnpu +/+ Tp53 loxP/loxP


title: gp_wt_rep3 [RNA-Seq]


title: Tp53_HET4

description: MARS-Seq


title: m40 WT sh-GLUD1 liver

value: WT

value: liver

value: male

value: 5 months


title: B_0_2

value: 0 h


title: m35 OTC control liver

value: OTC


title: Tp53_KO4

description: MARS-Seq


title: Tp53_KO3

description: MARS-Seq


title: HET_Tp53 HET3

description: MARS-Seq

source_name: Hnrnpu HET, Tp53 HET

value: Emx1 Cre/+, Hnrnpu fl/+ Tp53 loxP/+


title: gp_wt_rep1 [RNA-Seq]


title: m19 WT control liver

value: control


title: Tp53_KO2

description: MARS-Seq


title: m31 OTC sh-GLS2 liver


title: A_12_2


title: HET_Tp53KO4

description: MARS-Seq

source_name: Hnrnpu HET, Tp53KO

value: Emx1 Cre/+, Hnrnpu fl/+ Tp53 loxP/loxP


title: B_0_3


title: A_12_3


title: A_0_3


title: m36 WT sh-GLS2 liver


title: HET_Tp53KO2

description: MARS-Seq

value: E13 embryo dissected cortices


title: HET_Tp53 HET1

description: MARS-Seq

value: mixed


title: HET_Tp53 HET2

description: MARS-Seq

value: embryonic mouse cortex


title: m24 OTC sh-GLS2 liver


title: HET_Tp53KO3

description: MARS-Seq


title: m56 WT sh-GLUD1 liver


title: B_0_1


title: A_12_1


title: A_0_2


title: m78 WT sh-GLS2 liver


title: Mutant4

description: MARS-Seq

source_name: Hnrnpu mutant, Tp53 HET

value: Emx1 Cre/+, Hnrnpu fl/fl Tp53 loxP/+


title: m57 WT sh-GLUD1 liver


title: Jejunum - NX_10µM -pig19-07

city: Toulouse

first: Philippe

last: Pinton

address: 180 Chemin de Tournefeuille

department: TOXALIM

institute: INRAE

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 10x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturer's instructions (Agilent Technologies, Santa Clara, CA). On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Porcinet 60K_DEC2011 microarray (8X60K, Design 037880) enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min) and Wash buffer 2 (Agilent Technologies, 37°C, 1 min).

scan_protocol: Slides were scanned immediately after washing on a Agilent G2505C Microarray Scanner with Agilent Scan Control A.8.5.1 software

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent Technologies, Santa Clara, CA) using default parameters (protocol GE1_1010_Sep10 and Grid: 037880_D_F_20120213). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);} We selected the spots with a minimal weight of 1 for 20 out of 24 microarrays or with a minimal weight of 4 per group from at least one experimental group. At this step, 38942 spots out of 61625 were selected. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore R library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 38941 rows each corresponding to a unique ProbeName (provided as data Matrix).

organism: Sus scrofa

source_name: Jejunum

label_protocol: For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng of total RNA using the One-Color Quick Amp Labeling kit (Agilent Technologies, Santa Clara, CA) according to the manufacturer's instructions, followed by Agencourt RNAClean XP (Agencourt Bioscience Corporation, Beverly, Massachusetts) purification. Dye incorporation and cRNA yield were checked using Dropsense™ 96 UV/VIS droplet reader (Trinean, Belgium).

growth_protocol: Jejunal explants were obtained from 6-week-old crossbred castrated male piglet (n=6)

extract_protocol: RNA was prepared using ExtractAll reagent (Eurobio, Courtaboeuf, France) following the manufacturer's recommendations, after tissue homogenization using Precellys Evolution tissue homogenizer (Bertin Technologies, Montigny‐le‐Bretonneux, France).

treatment_protocol: The explants were incubated 30 minutes in control medium before being treated for 4 hours at 39 °C with 10 μM of DON, NX or 3ANX in complete medium.

value: NX

tag: animal

tag: dose


title: Jejunum - DON_10µM -pig19-06

value: DON


title: A_0_1

value: Fungal hyphae

value: Fungal hyphae cells


title: m65 OTC sh-GLUD1 liver


title: m67 OTC control liver


title: Jejunum - 3aNX_10µM -pig19-03


title: m72 OTC control liver


title: Intestinal_stem_cell_ATAC_Rep_1 (intestinal crypt cell dedifferentiation)

first: Ramesh

last: Shivdasani

state: MA

address: 450 Brookline Ave. Dana 720D

department: Medical Oncology

institute: Dana Farber Cancer Institute

data_processing:
Alignment: bowtie2
Peak calling: MACS, version 2.0
Bigwig: DeepTools BamCoverage 1X normalization with 10bp windows smoothed over 30bp
Genome_build: mm10
Supplementary_files_format_and_content: bigwig file for visualizing aligned sequence tags

source_name: Intestinal stem cells

extract_protocol:
Whole nuclei were used for chromatin transposition using Nextera Tn5 Transposase (Illumina).
DNA libraries were prepared using NEBNext High-Fidelity 2X PCR Master Mix (New England Biolabs) and 150bp paired end sequencing was performed on the HiSeq-X (Illumina).

value: Flow sorted GFP+ Lgr5+ stem cells

value: Lgr5-IRES-GFP mice


title: Intestinal_stem_cell_ATAC_Rep_2 (intestinal crypt cell dedifferentiation)


title: m77 WT control liver

value: WT

value: liver

value: male


city: Showa-ku, Nagoya

first: Shingo

last: Narita

state: Aichi

address: 65 Tsurumai-cho

department: Cardiology

country: Japan

institute: Nagoya University Graduate School of Medicine

description:
10x Genomics
9,000 cells of ADRCs 3 weeks after transduction with 6 factors, scRNAseq / 1,000 cells of culture ADRCs from C57BL/6 wild type as negative control

library_source: transcriptomic single cell

data_processing:
Sequencing results were demultiplexed and converted into the FASTQ format using the Illumina package bcl2fastq. Alignment, barcode processing, and UMI counting were performed using 10x Cell Ranger (version 6.1.2) with a 10mm-based default reference. Downstream work was predominantly performed using the R package Seurat (version 4.0.6)
Cells with less than 200 features, less than 2,000 or more than 75,000 transcripts, and more than 30% mitochondrial reads were excluded. Expression counts were normalized using Seurat’s NormalizeData function and variable features were selected by FindVariableFeatures (nFeatures = 2,000, selection.method=‘vst’). The data were scaled using Seurat’s ScaleData function. The main cell-type clusters were identified using Louvain clustering with a resolution parameter of 0.2, utilizing the top six principal components. Dimensionality reduction plots are based on the uniform manifold approximation and projection (UMAP) using Seurat’s RunUMAP function. Doublets were identified using DoubletFinder (version 2.0.3) and were subsequently removed.
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
ADRCs were isolated from the inguinal and axillary fat pads of mice after sufficient anesthesia. The adipose tissues were washed with phosphate buffered saline (PBS), chopped fully with scissors, and then treated with 5 ml of collagenase type 1 (FUJIFILM, Cat# 037-17603) solution; subsequently, 2 mg/ml Hank's balanced salt solution was added after passing through a 0.22 μm mesh filter. Enzyme treatment was performed with gentle rocking at 37 ℃ for 30 to 45 min. The digested tissues were filtered through a 100 μm mesh filter and centrifuged at 500 × g for 5 min. The supernatant was removed and the pellet was stirred with 10 ml Dulbecco’s modified Eagle medium (DMEM; Sigma Aldrich, Cat# D6046-500ML) supplemented with 10% fetal bovine serum (FBS), 100 U/ml penicillin, and 100 μg/ml streptomycin. The suspension was plated in 10 cm dishes (passage 0), and the medium was exchanged the day after isolating the ADRC. ADRCs were cultured under 5% CO2 at 37 ℃ conditions. The medium was changed every 2–3 days. After achieving the desired confluency of 80–90%, ADRCs were harvested by trypsinization for 5 min at 37 ℃  and pipetting to passage 1. After reaching approximately 80-90% confluency at passage 1, ADRCs were harvested and plated on 24 well plates at 30,000 cells/well. The next day, each viral solution was diluted with DMEM (with 10% FBS and 1% penicillin/streptomycin), and 10 μg/ml polybrene was added to the cells. The viral titer was confirmed using Lenti-XTM GoStixTM Plus (Cat #631280; Takara Bio), and the amount of each virus solution was adjusted to MOI=2. The mock cells were infected with a control lentivirus that did not contain the inserted target genes. The plates were incubated for 24 h. The medium was changed every 2–3 days.
Transduced ADRCs were counted in 9,000 cells using CountessTM II FL (Invitrogen). As a negative control, 1,000 ADRCs without lentiviral induction were mixed with the sample. The Chromium Next GEM Single Cell 3’ Reagent kit v3.1 (10X Genomics, Cat# PN-1000121) was used to label each cell and individual transcript with a unique molecular identifier (UMI), and cDNA libraries were generated according to the manufacturer’s instructions.

value: ADRCs

value: C57BL/6-Tg (Myh6-EGFP) MG3Tm; MG3

value: 12-24 weeks old


title: Mutant1

description: MARS-Seq


title: Mutant3

description: MARS-Seq


title: m71 OTC sh-GLUD1 liver

value: OTC

value: 5 months


title: Rescue2

description: MARS-Seq

source_name: Rescue

value: E13 embryo dissected cortices

value: mixed

value: Emx1 Cre/+, Hnrnpu fl/fl Tp53 loxP/loxP


title: Rescue3

description: MARS-Seq

value: embryonic mouse cortex


title: Jejunum - 3aNX_10µM -pig19-06


title: Jejunum - CTRL_0µM -pig19-08

value: CTRL


title: Jejunum - NX_10µM -pig19-06

value: NX


title: HET_Tp53KO1

description: MARS-Seq

value: Emx1 Cre/+, Hnrnpu fl/+ Tp53 loxP/loxP


title: Jejunum - CTRL_0µM -pig19-07


title: Jejunum - DON_10µM -pig19-07

value: DON


title: Jejunum - NX_10µM -pig19-08


title: Mutant2

description: MARS-Seq

value: Emx1 Cre/+, Hnrnpu fl/fl Tp53 loxP/+


title: m49 OTC sh-GLS2 liver


title: IMF-8d-3: Intramuscular  adipocytes-Differentiation day 8-rep3 [miRNA-seq]

city: Beijing

first: Pan

last: Zhang

address: No. 2, Yuanmingyuan West Road, Beijing

institute: China Agricultural University

data_processing:
The Illumina Novaseq6000 (Illumina, San Diego, CA, USA) platform is used for transcriptome sequencing
The clean reads were mapped to the pig reference genome (scrofa. Sscrofa11.1) with perfect matches using Bowtie software.
Annotated tRNA, rRNA, snoRNA, and snRNA sequences were filtered out, and conserved miRNAs were identified by the BLAST method against miRBase.
The miRDeep2 software was used to predict new miRNAs based on the characteristics of the miRNA precursor hairpin structure. Differential expression analysis of two groups was performed using the DESeq2 R package.
Differentially expressed miRNAs (DE-miRNAs) were screened with criterion of fold change > 1.5 and FDR < 0.05 using DESeq2.
Genome_build: ss11.1
Supplementary_files_format_and_content: TPM values for each Sample

source_name: Intramuscular  adipocytes

extract_protocol:
Total RNA was isolated at various stages of subcutaneous adipocytes and Intramuscular  adipocyte differentiation (0d, 2d, 4d, 8d) using the Trizol reagen. RNase-free DNase was added to total RNA to remove DNA contamination. The integrity of RNA was checked by 1.2% agarose gel electrophoresis and the quality of RNA and the amount of total RNA were determined by Nanodrop 2000
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Longissimus dorsi

value: six-day-old

tag: breed

value: Yorkshire


title: m73 OTC sh-GLS2 liver

value: liver

value: male


title: Rescue1

description: MARS-Seq


title: H2BK123R_Rad69MYC

city: Chuncheon

first: Junsoo

last: Oh

country: South Korea

institute: Kangwon National University

description: 9myc ChIP seq in Rad6-9myc  H2B K123R (DY20 background : Quad histone knockouts with URA3 plasmid carrying wt HTA-HTB and HHT-HHF genes)

data_processing:
The sequencing adapter removal and quality-based trimming on raw data was performed by Trimmomatic v. 0.36 with TruSeq adapter sequences.
Cleaned reads were mapped to reference genome using tophat2 v2.1.1 with default parameter
To visualize ChIP-Seq data, BAM files were converted to bigwig files.
Genome_build: Saccharomyces cerevisiae S288C genome assembly R64 (sacCer3)
Supplementary_files_format_and_content: bigwig

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae

growth_protocol: Cells were prepared from exponentially growing at OD600=1.0. Harvested cells were resuspended with 4ml of 1XTBS and evenly divided into 4 eppendorf tubes. Cell is harvested by Centrifuge 3000 rpm 5min and supernatant was removed. After one more wash step, samples were stored at -80℃.

extract_protocol:
Cells were resuspended with lysis buffer and homogenized with glass beads at cold room. Lysed cells were sonicated and centrifuged to obtain soluble chromatin fraction. Chromatin lysates were incubated with antibody against 9myc(Rad6) or HA(Swd2) and antibody-protein-chromatin complex was captured by Protein A/G agarose. After sequential washing steps and reverse crosslinking, remaining DNA is purified by phenol-chloroform extraction and washing.
ChIP-Seq DNA samples were quantified by Quant-iT PicoGreen dsDNA Assay kit and their quality were assessed Bioanalyzer 2100. ChIP-Seq library was constructed with TruSeq ChIP Sample Prep Kit (Illumina) according to manufacturer’s instructions.

treatment_protocol: Before wash the cells with 1XTBS, cells were treated with 1% formaldehyde for 5mins and quenched with 2.5M Glycine for 20mins

value: Quad histone knockouts with URA3 plasmid carrying wt HTA-HTB and HHT-HHF genes, H2BK123R Rad6::9MYC::TRP


title: Jejunum - DON_10µM -pig19-03


title: Rad6S120A9MYC

description: 9myc ChIP seq in Rad6-S120A-9myc (FY23 background)

value: MATa ura3-52 leu2delta1 trp1delta63 Rad6(S120A)::9MYC::TRP


title: H2BWT_Rad69MYC

description: 9myc ChIP seq in Rad6-9myc H2B WT (DY20 background : Quad histone knockouts with URA3 plasmid carrying wt HTA-HTB and HHT-HHF genes)

value: Quad histone knockouts with URA3 plasmid carrying wt HTA-HTB and HHT-HHF genes, Rad6::9MYC::TRP


title: Swd2-3HA_wt_a-HA

description: HA ChIP seq in Swd2-3HA WT

value: MATa ura3-52 his3delta200 ade2-101(ochre) lys2-80(1m) trp-1delta1 leu2-delta1 TEladh4:L:URA3(VIIL Telomere) Swd2::3HA::HIS

value: HA


title: m74 OTC sh-GLS2 liver

value: OTC

value: 5 months


title: IMF-8d-1: Intramuscular  adipocytes-Differentiation day 8-rep1 [miRNA-seq]


title: m50 OTC sh-GLS2 liver


title: IMF-4d-3: Intramuscular  adipocytes-Differentiation day 4-rep3 [miRNA-seq]


title: Rad6C88A9MYC

description: 9myc ChIP seq in Rad6-C88A-9myc (FY23 background)

value: MATa ura3-52 leu2delta1 trp1delta63 Rad6(C88A)::9MYC::TRP


title: IMF-8d-2: Intramuscular  adipocytes-Differentiation day 8-rep2 [miRNA-seq]


title: RAD69MYC

description: 9myc ChIP seq in Rad6-9myc (FY23 background)

value: MATa ura3-52 leu2delta1 trp1delta63 Rad6::9MYC::TRP


title: notagWT_9MYC

description: 9myc ChIP seq in FY23

value: MATa ura3-52 leu2delta1 trp1delta63


title: m69 WT sh-GLUD1 liver

value: WT


title: Jejunum - 3aNX_10µM -pig19-08


title: Jejunum - CTRL_0µM -pig19-03

value: CTRL


title: m58 OTC sh-GLUD1 liver


title: Jejunum - CTRL_0µM -pig19-04


title: Jejunum - 3aNX_10µM -pig19-07


title: SKOV3_12h

city: Wuhan

first: Guannan

last: Li

state: Hubei

address: 1095 Jiefang Avenue

department: Department of Gynecological Oncology

institute: Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology

description: This sample is of SKOV3 cells treated with elaiophylin for 12h.

hyb_protocol: Hybridization was performed following the standard operating protocol by NimbleGen Systems Inc.. See www.nimblegen.com.

scan_protocol: Scanning was performed following the standard operating protocol by NimbleGen Systems Inc.. See www.nimblegen.com.

data_processing: The raw data was subjected to Robust Multi-Array Analysis, quantile normalization, and background correction as implemented in the NimbleScan software package (Roche NimbleGen, Inc.).

source_name: SKOV3 cells, elaiophylin, 12h

label_protocol: Labeling was performed following the standard operating protocol by NimbleGen Systems Inc.. See www.nimblegen.com.

growth_protocol: Human ovarian cancer cell line SKOV3 was cultured in McCoy's 5A medium with 10% FBS in a humidified atmosphere incubator with 5% CO2 at 37 °C.

extract_protocol: Cells were digested and washed with PBS, then dissoved in 1ml TRIzol and then stored in -80℃ for futher RNA isolation.

treatment_protocol: When the cell confluence reached 70%, the medium were replaced with new complete medium containing 0.5 μM elaiophylin.

value: ovarian cancer

value: elaiophylin, 12h


title: Jejunum - 3aNX_10µM -pig19-04


title: IMF-4d-1: Intramuscular  adipocytes-Differentiation day 4-rep1 [miRNA-seq]

value: Longissimus dorsi

value: six-day-old

value: Yorkshire


title: Jejunum - DON_10µM -pig19-05

value: DON


title: m46 OTC control liver

value: liver

value: control

value: male


title: IMF-4d-2: Intramuscular  adipocytes-Differentiation day 4-rep2 [miRNA-seq]


title: IMF-2d-3: Intramuscular  adipocytes-Differentiation day 2-rep3 [miRNA-seq]


title: Jejunum - NX_10µM -pig19-05

value: NX


title: m45 WT sh-GLS2 liver


title: m53 OTC sh-GLUD1 liver

value: OTC


title: m70 WT sh-GLUD1 liver

value: 5 months


title: WTVeh4

city: Edinburgh

first: Emily

last: Osterweil

state: Scotland

address: Hugh Robson Building, 15 George Square

department: Centre for Discovery Brain Sciences

country: United Kingdom

institute: University of Edinburgh

data_processing:
Filtering and QC were performed by the sequencing facility
RNA-seq reads were aligned to the GRCm39 genome assembly using STAR version 2.7.1a
GRCm39
Assembly: count files were generating using feature counts

source_name: Hippocampal slice

growth_protocol: acute hippocampal slices

extract_protocol:
TRAP
Smartseq v4 amplification followed by Nextera library preparation for Illumina sequencing

treatment_protocol: pre-incubation with vehicle or 200nM CX-5461,  stimulated with 50uM S-DHPG 5 minutes, and removed to fresh ACSF (+/- CX-5461) for an additional 25 min.

tag: sample type

value: IP

value: Vehicle


title: IMF-2d-2: Intramuscular  adipocytes-Differentiation day 2-rep2 [miRNA-seq]


title: WTVeh2


title: IMF-0d-3: Intramuscular  adipocytes-Differentiation day 0-rep3 [miRNA-seq]


title: SKOV3_0h

description: This sample is of SKOV3 cells treated with elaiophylin for 0h. It serves as control in this study.

source_name: SKOV3 cells, elaiophylin, 0h

value: elaiophylin, 0h


title: Jejunum - NX_10µM -pig19-04


title: SKOV3_6h

description: This sample is of SKOV3 cells treated with elaiophylin for 6h.

source_name: SKOV3 cells, elaiophylin, 6h

value: elaiophylin, 6h


title: Jejunum - NX_10µM -pig19-03


title: Jejunum - CTRL_0µM -pig19-06

value: CTRL


title: Jejunum - DON_10µM -pig19-04


title: IMF-2d-1: Intramuscular  adipocytes-Differentiation day 2-rep1 [miRNA-seq]


title: SKOV3_3h

description: This sample is of SKOV3 cells treated with elaiophylin for 3h.

source_name: SKOV3 cells, elaiophylin, 3h

value: ovarian cancer

value: elaiophylin, 3h


title: WTDHPG4

value: DHPG

value: WT


title: Jejunum - DON_10µM -pig19-08


title: WTVeh1


title: IMF-0d-2: Intramuscular  adipocytes-Differentiation day 0-rep2 [miRNA-seq]

value: Longissimus dorsi

value: six-day-old

value: Yorkshire


title: cebpe_pmn_Rep2

data_processing:
Reads were mapped to mouse genome assembly (mm9) using bowtie2
IDR along with MACS2 was used to identify reproducible set of CEBPE enriched region between the two replicates.
Genome_build: mm9
Supplementary_files_format_and_content: We used uniquely mapped and PCR duplicates (exact copies) collapsed as one read that are extended to their fragment length by determining the read extension size using MACS2 (predicted parameter). Raw read counts were normalized to TPM using deeptools (bamCoverage).

source_name: GR

extract_protocol:
500,000 sorted MY1+2s (pooled MY1s+MY2s), MMs, BCs, and GRs from Cebpe WT mice were used for CEBPE ChIP-seq experiments. 1,000,000 pooled MYs and MMs purified from Cebpe KO mice were used as negative control. Chromatin bound by antibodies was captured with Protein-A sepharose beads, washed, de-crosslinked and precipitated.
The precipitated DNA was then mixed with 2 ng E. Coli DNA and amplified using NEB Next ChIP-seq sample prep kit (New England Biolabs) as described by the manufacturer.
The indexed cDNA libraries were pooled in equimolar ratios and subjected to sequencing  on an Illumina Hiseq2000.

tag: chip-antibody

value: CEBPE, H-75, Santa Cruz


title: BF-8d-3: Subcutaneous adipocytes-Differentiation day 8-rep3 [miRNA-seq]

source_name: Subcutaneous adipocytes

value: Back subcutaneous fat


title: m60 OTC sh-GLS2 liver

source_name: liver

value: liver

value: male


title: cebpe_bc_Rep2

source_name: BC


title: WTDHPG2


title: WTDHPG1


title: BF-8d-2: Subcutaneous adipocytes-Differentiation day 8-rep2 [miRNA-seq]


title: cebpe_ko_control_Rep1

source_name: MY1+MY2+MM _ko_control


title: cebpe_bc_Rep1


title: cebpe_pmn_Rep1


title: IMF-0d-1: Intramuscular  adipocytes-Differentiation day 0-rep1 [miRNA-seq]


title: WTCXDHPG4

value: CX+DHPG


title: Jejunum - 3aNX_10µM -pig19-05


title: Jejunum - CTRL_0µM -pig19-05


title: WTCXDHPG2

value: IP


title: Renal cell carcinoma_C9K1

type: genomic

city: Nagoya

first: Shinya

last: Toyokuni

address: 65 Tsuruma-Cho, Showa-Ku

department: Pathology

institute: Nagoya University

hyb_protocol: The labeled DNA was hybridized with Agilent SurePrint G3 Mouse CGH 4x180k microarray at 67°C for 24 hours according to the manufacturer's protocol (Version 8.0).

scan_protocol: The slides were scanned in an Agilent DNA microarray scanner with SureScan High-Resolution Technology (G2565CA).

data_processing: The scanned images were analyzed with Agilent Feature Extraction Software 10.7 using default parameters (CGH_107_Sep09 protocol).

source_name: normal kidney cortex

label_protocol: The extracted genomic DNA was labeled using Aagilent Sure tag DNA labeling kit according to the manufacturer's protocol (Version 8.0).

extract_protocol: Genomic DNA was extracted using DNeasy Blood & Tissue Kit (QIAGEN).

treatment_protocol: Male wild-type and BRCA1+/- rats at 5 weeks of age were injected intraperitonealy with Fe-NTA by the dose of 5 mg iron/kg for the first three times then 7 for the last two times for the first week, and by 7 mg iron/kg for the first time then 5 for four times for the second week, and by 7 mg iron/kg for the first three time then 10 for two times for the third week. The treatment for next 8 weeks was by the dose of 10 mg iron/kg weight, three times per week. The rats were euthanized when they were dying.

value: Jcl:SD BRCA1+/-

value: Fe-NTA, 3 months


title: BF-4d-1: Subcutaneous adipocytes-Differentiation day 4-rep1 [miRNA-seq]


title: BF-4d-3: Subcutaneous adipocytes-Differentiation day 4-rep3 [miRNA-seq]


title: cebpe_lpmmy_Rep1


title: WTCXDHPG1


title: cebpe_mm_Rep2

source_name: MM


title: BF-2d-3: Subcutaneous adipocytes-Differentiation day 2-rep3 [miRNA-seq]


title: cebpe_mm_Rep1


title: BF-2d-2: Subcutaneous adipocytes-Differentiation day 2-rep2 [miRNA-seq]


title: BF-8d-1: Subcutaneous adipocytes-Differentiation day 8-rep1 [miRNA-seq]


title: WTCX1

value: CX


title: WTCX4


title: cebpe_lpmmy_Rep2


title: KOVeh4

value: Vehicle

value: Fmr1 KO


title: Renal cell carcinoma_C10K3


title: BF-4d-2: Subcutaneous adipocytes-Differentiation day 4-rep2 [miRNA-seq]


title: KOVeh2


title: WTCX2


title: BF-2d-1: Subcutaneous adipocytes-Differentiation day 2-rep1 [miRNA-seq]


title: KOVeh1


title: KODHPG2


title: KODHPG4


title: KODHPG1


title: KOCXDHPG4


title: IMF-8D-2: Intramuscular  adipocytes-Differentiation day 8-rep2 [mRNA-seq]

data_processing:
The Illumina Novaseq6000 (Illumina, San Diego, CA, USA) platform is used for transcriptome sequencing
Clean reads were mapped to the reference pig genome version scrofa.Sscrofa11.1by using HISAT2tool software for alignment.
We used StringTie (1.3.4d) software to calculate FPKM (Fragments per Kilobase Millon Mapped Reads) values to represent gene expression levels.
DESeq2 (V1.6.3) was used to analyze the differences between group
Genome_build: ss11.1
Supplementary_files_format_and_content: FPKM values for each Sample


title: BF-0d-3: Subcutaneous adipocytes-Differentiation day 0-rep3 [miRNA-seq]


title: BF-0d-2: Subcutaneous adipocytes-Differentiation day 0-rep2 [miRNA-seq]


title: IMF-8D-1: Intramuscular  adipocytes-Differentiation day 8-rep1 [mRNA-seq]


title: IMF-8D-3: Intramuscular  adipocytes-Differentiation day 8-rep3 [mRNA-seq]


title: BF-0d-1: Subcutaneous adipocytes-Differentiation day 0-rep1  [miRNA-seq]


title: IMF-4D-2: Intramuscular  adipocytes-Differentiation day 4-rep2 [mRNA-seq]


title: KOCX4