title: GC cells-1_H

description:
Gene expression after 24hr under hypoxia
7901_N.normalized

source_name: Gastric cancer cell line-1, hypoxia,24h

value: Gastric cancer cell line-1


title: C20

status: Public on Dec 31 2025

type: genomic

city: Taiyuan

first: Yue

last: Sui

state: --- Select One ---

address: No.85 of South Jiefang Road, Yingze District, Taiyuan, Shanxi, China

country: China

institute: First Hospital of Shanxi Medical University

hyb_protocol: Using the EZ DNA Methylation Kit (D5001, Zymo) for bisulfite transformation of genomic DNA, the methylated cytosine remains unchanged, while the unmethylated cytosine is converted to uracil. The detection process of the Illumina Infinium MethylationEPIC v2.0 BeadChip mainly includes the following steps:   (1) Isothermal displacement amplification of DNA transformed by bisulfite using random primers and polymerase;   (2) Fragmentation of amplified products;   (3) The fragmented products were hybridized with the Illumina Infinium MethylationEPIC v2.0 BeadChip, and the target region sequences were captured by the specific probe on the BeadChip, and then used as templates for single base extension and fluorescence labeling;   (4) The probe fluorescence labeling data is captured by scanning with Iscan platform.

scan_protocol: BeadArray Reader and standard  Illumina scanner setting

data_processing: Packages in R version 4.4.0

label: other

molecule: genomic DNA

organism: Homo sapiens

source_name: DNA from normal control

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA from the fresh-frozen tissue samples were extracted by the DNA extraction kit (DP304-02, Tiangen).

tag: tissue

value: rectal mucosa

tag: disease state

value: normal control


title: Volunteer BA01046_Timepoint D01

type: RNA

city: Barcelona

first: Gemma

last: Moncunill

state: Barcelona

address: Rosselló 153

department: Malaria

country: Spain

institute: ISGlobal

description: Gene expression data from Volunteer BA01046_Timepoint D01

hyb_protocol: Affymetrix WT Terminal Labeling and Hybridization

scan_protocol: Affymetrix GeneTitan® system was used

data_processing: Sample processing was performed at an Affymetrix Service Provider and Core Facility, “KFB - Center of Excellence for Fluorescent Bioanalytics”

label: Biotin

molecule: total RNA

source_name: Sample Volunteer BA01046_Timepoint D01

label_protocol: Purified ss cDNA was fragmented using a combination of uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) followed by a terminal labeling with biotin.

extract_protocol: QIAamp RNA Blood Mini Kit

treatment_protocol: Homogenized cell lysates from a middle step were stored at -80°C

tag: group

tag: phase

value: B

tag: route

value: IV

tag: Sex

value: Female

tag: age


title: GC cells-2_H

city: Shanghai

first: Pengshan

last: Zhang

state: Shanghai

address: No. 650, Xinsongjiang Road

institute: Shanghai General Hospital

description:
Gene expression after 24hr under hypoxia
823_N.normalized

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Human Gene Expression for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 13.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

source_name: Gastric cancer cell line-2, hypoxia,24h

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions.

extract_protocol: TRIzol reagent (Life Technologies, USA) according to the manufacturer’s protocol

treatment_protocol: Two different gastric cancer cell lines were cultured in a hypoxia chamber with 1% O2, 94% N2 and normoxia at 37°C for 24h, then RNA-seq were performed to examine the circRNA expression profiles.

tag: cell line

value: Gastric cancer cell line-2

tag: treatment


title: C13


title: C14


title: C12


title: Volunteer BA01036_Timepoint D07

description: Gene expression data from Volunteer BA01036_Timepoint D07

source_name: Sample Volunteer BA01036_Timepoint D07

value: Male


title: C11


title: C10


title: GC cells-1_N

description:
Gene expression after 24hr under normoxia
7901_H.normalized

source_name: Gastric cancer cell line-1, normoxia,24h


title: C9


title: C8


title: C7


title: C6


title: Volunteer BA01013_Timepoint M0

description: Gene expression data from Volunteer BA01013_Timepoint M0

source_name: Sample Volunteer BA01013_Timepoint M0

value: A

value: IM


title: Volunteer BA01036_Timepoint D-1

description: Gene expression data from Volunteer BA01036_Timepoint D-1

source_name: Sample Volunteer BA01036_Timepoint D-1


title: C5


title: C3


title: Volunteer BA01013_Timepoint D07

description: Gene expression data from Volunteer BA01013_Timepoint D07

source_name: Sample Volunteer BA01013_Timepoint D07


title: Volunteer BA01036_Timepoint D01

description: Gene expression data from Volunteer BA01036_Timepoint D01

source_name: Sample Volunteer BA01036_Timepoint D01


title: C2


title: C4


title: Volunteer BA01013_Timepoint D-1

description: Gene expression data from Volunteer BA01013_Timepoint D-1

source_name: Sample Volunteer BA01013_Timepoint D-1


title: Volunteer BA01046_Timepoint D-1

description: Gene expression data from Volunteer BA01046_Timepoint D-1

source_name: Sample Volunteer BA01046_Timepoint D-1


title: A23

source_name: DNA from patient with colorectal adenoma

value: colorectal adenoma


title: A24


title: A22


title: A21


title: C1


title: A20


title: Volunteer BA01009_Timepoint D01

description: Gene expression data from Volunteer BA01009_Timepoint D01

source_name: Sample Volunteer BA01009_Timepoint D01


title: Volunteer BA01009_Timepoint D07

description: Gene expression data from Volunteer BA01009_Timepoint D07

source_name: Sample Volunteer BA01009_Timepoint D07


title: Volunteer BA01006_Timepoint M0

description: Gene expression data from Volunteer BA01006_Timepoint M0

source_name: Sample Volunteer BA01006_Timepoint M0


title: INS-1 832/3 cells, urolithin B and IAPP treatment rep 1

type: SRA

city: Lisboa

first: Regina

last: Menezes

address: Campo Grande 376

country: Portugal

institute: Universidade Lusófona de Humanidades e Tecnologias

library_source: transcriptomic

data_processing:
assessment of the quality of the data using FastQC program
sequence trimming was performed with Seqtk tool and re-assessment of the quality using FastQC program
reads were mapped using Bowtie2
files were transformed to BAM and sorted using Samtools
quantification of the transcripts expression using Artemis
Assembly: rnor6
Supplementary files format and content: raw counts of sequencing reads for the features of interest in ODS format

organism: Rattus norvegicus

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

extract_protocol:
RNA was harvested using High Pure RNA Isolation Kit
RNA libraries for RNA-seq were prepared using QuantSeq 3prime mRNA FWD (Standard) following manufacturer's protocols.

treatment_protocol: cells were either left untreated (control), treated with urolithin B (50 uM, 12h), challenged with IAPP (2 uM, 24h) or treated with urolithin B (50 uM, 12h) and then challenged with IAPP (2 uM,  24h)

tag: cell type

value: rat insulinoma cell line

tag: genotype

value: WT

value: 12h of urolitin B and 24h of IAPP


title: INS-1 832/3 cells, urolithin B and IAPP treatment rep 3


title: INS-1 832/3 cells, urolithin B and IAPP treatment rep 2


title: Volunteer BA01009_Timepoint D-1

description: Gene expression data from Volunteer BA01009_Timepoint D-1

source_name: Sample Volunteer BA01009_Timepoint D-1


title: A18


title: Volunteer BA01006_Timepoint D07

description: Gene expression data from Volunteer BA01006_Timepoint D07

source_name: Sample Volunteer BA01006_Timepoint D07


title: Volunteer BA01002_Timepoint M0

description: Gene expression data from Volunteer BA01002_Timepoint M0

source_name: Sample Volunteer BA01002_Timepoint M0


title: Volunteer BA01006_Timepoint D-1

description: Gene expression data from Volunteer BA01006_Timepoint D-1

source_name: Sample Volunteer BA01006_Timepoint D-1


title: Volunteer BA01009_Timepoint M0

description: Gene expression data from Volunteer BA01009_Timepoint M0

source_name: Sample Volunteer BA01009_Timepoint M0


title: INS-1 832/3 cells, IAPP treatment rep 3

value: 24h of IAPP


title: A16


title: Volunteer BA01013_Timepoint D01

description: Gene expression data from Volunteer BA01013_Timepoint D01

source_name: Sample Volunteer BA01013_Timepoint D01


title: A17


title: A19


title: Volunteer BA01002_Timepoint D07

description: Gene expression data from Volunteer BA01002_Timepoint D07

source_name: Sample Volunteer BA01002_Timepoint D07


title: Volunteer BA01002_Timepoint D01

description: Gene expression data from Volunteer BA01002_Timepoint D01

source_name: Sample Volunteer BA01002_Timepoint D01


title: INS-1 832/3 cells, IAPP treatment rep 2


title: A15


title: INS-1 832/3 cells, urolithin B treatment rep 3

value: 12h of urolitin B


title: A14


title: Volunteer BA01006_Timepoint D01

description: Gene expression data from Volunteer BA01006_Timepoint D01

source_name: Sample Volunteer BA01006_Timepoint D01


title: Volunteer BA01002_Timepoint D-1

description: Gene expression data from Volunteer BA01002_Timepoint D-1

source_name: Sample Volunteer BA01002_Timepoint D-1


title: A13


title: A12


title: INS-1 832/3 cells, control rep 3

value: no treatment


title: A10


title: INS-1 832/3 cells, urolithin B treatment rep 1


title: INS-1 832/3 cells, control rep 2


title: INS-1 832/3 cells, urolithin B treatment rep 2


title: A11


title: A9


title: INS-1 832/3 cells, IAPP treatment rep 1


title: INS-1 832/3 cells, control rep 1


title: A7


title: A8


title: L4_mut-16_small-RNA-20C_rep_2

city: Arlington

first: Alicia

middle: Kathryn

last: Rogers

state: Texas

address: 1225 W Mitchell Street

department: Department of Biology

country: USA

institute: University of Texas at Arlington

description: size selected RNA from total RNA

data_processing:
Libraries were sequenced on the Illumina NextSeq500 (SE 75-bp reads) platform.
Sequences were parsed from adapters using Cutadapt(Martin, 2011) and mapped to the C. elegans genome, WS258, using HISAT2 (Kim, Langmead, & Salzberg, 2015) and the transcriptome using Salmon(Patro, Duggal, Love, Irizarry, & Kingsford, 2017). Data analysis was done using R, Excel, and custom Python scripts.
Assembly: WS258
Supplementary files format and content: tab-delimited text files including total reads mapping to each gene

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: Synchronized L1s of wild-type and mut-16(pk710) worms were plated on enriched peptone plates and cultured at 20°C and 25°C until they reached the L4 developmental stage.

extract_protocol:
10,000 animals per sample were harvested as L4s8,000 animals per sample were harvested as L4s (~56hrs at 20°C and ~39hrs at 25°C) for RNA extraction. Worms were washed off plates using water and then settled on ice to form a pellet. Water was aspirated off and worm pellets were resuspended in 1mL TRIzol reagent (Life Technologies) and freeze-thawed on dry ice followed by vortexing. Worm carcasses were pelleted using centrifugation and the supernatant containing RNA was collected. 0.2 volume chloroform was add to supernatant, vortexed, centrifuged, and then the aqueous phase was transferred to a new tube. Samples were precipitated using isopropanol and rehydrated in 50μL nuclease-free H2O.
Small RNA library preparation. Small RNAs (18- to 30- nt) were size selected on denaturing 15% polyacrylamide gels (Criterion 3450091) from total RNA samples. Libraries were prepared as previously described(Montgomery et al., 2012). Library quality was assessed (Agilent BioAnalyzer Chip) and concentration was determined using the Qubit 1X dsDNA HS Assay kit. Libraries were sequenced on the Illumina NextSeq500 (SE 75-bp reads) platform. Two biological replicates were generated for wild-type (N2) and mut-16 mutants cultured at 20°C and 25°C.

value: whole animal

tag: developmental stage

tag: strain

tag: temperature


title: A4

value: rectal mucosa


title: A2


title: L4_mut-16_small-RNA-20C_rep_1

description: size selected RNA from total RNA


title: A5


title: L4_WT_small-RNA-25C_rep_1

description: size selected RNA from total RNA

value: N2- wild type


title: A6


title: L4_WT_small-RNA-25C_rep_2

description: size selected RNA from total RNA


title: L4_mut-16_small-RNA-25C_rep_2

description: size selected RNA from total RNA


title: L4_mut-16_small-RNA-25C_rep_1

description: size selected RNA from total RNA


title: A3


title: L4_WT_small-RNA-20C_rep_2

description: size selected RNA from total RNA


title: A1


title: Non_Load_Ti1

city: Beijing

first: Yunshu

last: Wu

address: No.22 Zhongguancun South Avenue

institute: Peking University School and Hospital of Stomatology

description: Library name: Sample10

data_processing:
Illumina Casava 1.8 software used for basecalling
Raw data (raw reads) of fastp format were firstly processed through in-house perl scripts..In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: ensembl_108_rattus_norvegicus_mratbn7_2_toplevel
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

molecule: polyA RNA

source_name: bone

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: bone

value: non-loaded cpTi peri-implant bone tissue


title: Non_Load_Ti2

description: Library name: Sample11


title: Non_Load_Ti3

description: Library name: Sample12


title: FFPE tissue of glioblastoma, case 44

city: Rome

first: Evelina

last: Miele

address: Piazza di Sant'Onofrio 4

department: Oncoematologia

country: Italy

institute: Ospedale Pediatrico Bambino Gesù

description:
208250190150_R08C01
44

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to either Illumina Infinium MethylationGPL21145 v1 or Illumina Infinium MethylationGPL33022 v2 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using Illumina iScan

data_processing: RStudio (R package ChAMP v2.26.0)

label: Cy5 and Cy3

source_name: FFPE tissue of glioblastoma

extract_protocol: We extracted DNA from unstained sections of paraffin blocks containing at least 50% tumour cells, using MagPurix FFPE DNA Extraction Kit (Zzinexts).

tag: score os

value: favorable

tag: score pfs

tag: mgmt promoter status

value: methylated

tag: dna methylation class

value: MC Glioblastoma IDH-wildtype RTK2 subtype

value: FFPE tissue of glioblastoma


title: FFPE tissue of glioblastoma, case 41

description:
208197680055_R07C01
41

value: Methylated

tag: tissue


title: FFPE tissue of glioblastoma, case 43

description:
208197680095_R05C01
43

value: unmethylated

value: MC Glioblastoma IDH-wildtype mesenchymal subtype


title: L4_WT_small-RNA-20C_rep_1

description: size selected RNA from total RNA


title: FFPE tissue of glioblastoma, case 40

description:
207953350049_R05C01
40

value: unfavorable

value: MC Glioblastoma IDH-wildtype RTK1 subtype


title: Non_Load_Nb1

description: Library name: Sample7

value: WT

value: non-loaded Nb3 peri-implant bone tissue


title: FFPE tissue of glioblastoma, case 39

description:
207953350049_R04C01
39


title: FFPE tissue of glioblastoma, case 37

description:
207953350049_R03C01
37


title: Non_Load_Nb2

description: Library name: Sample8


title: Load_Ti3

description: Library name: Sample6

value: loaded cpTi peri-implant bone tissue


title: FFPE tissue of glioblastoma, case 36

description:
207953350049_R02C01
36


title: Non_Load_Nb3

description: Library name: Sample9


title: Load_Ti2

description: Library name: Sample5


title: Load_Nb3

description: Library name: Sample3

value: loaded Nb3 peri-implant bone tissue


title: Load_Ti1

description: Library name: Sample4


title: Load_Nb2

description: Library name: Sample2


title: FFPE tissue of glioblastoma, case 32

description:
207953350049_R01C01
32

value: UNmethylated


title: FFPE tissue of glioblastoma, case 26

description:
207953350059_R05C01
26


title: FFPE tissue of glioblastoma, case 24

description:
208197680076_R01C01
24


title: FFPE tissue of glioblastoma, case 20

description:
207953350059_R03C01
20


title: Load_Nb1

description: Library name: Sample1


title: rat liver Cyp7b1 KO_plasmid_004

city: Zaragoza

first: Luis

middle: Vicente

last: Herrera-Marcos

state: Zaragoza

address: C/Miguel servet nº177

department: Bioquimica y biologia molecular y celular

institute: Universidad de Zaragoza. Facultad de Veterinaria

description: RES group

data_processing:
Libraries were sequenced on the Genome Analyzer IIx (Illumina) at the CNIC Genomic Unit following the standard RNA sequencing protocol with the TruSeq SBS Kit v5. The number of reads obtained per sample was in the range of 25 to 41 million. Sequencing reads were pre-processed by means of a pipeline that used fastq.gzC to asses read quality, and Cutadapt software tool to trim sequencing reads, eliminate Illumina adaptors, and discard reads that were shorter than 30 bp. The resulting reads were mapped against the rat transcriptome and quantified using RSEM v1.17. Data were then processed with a differential expression analysis pipeline that used Bioconductor package EdgeR for normalization and differential expression testing.
Assembly: Ensembl Rnor 6.0, release 82
Supplementary files format and content: DEG_AllContrasts.xlsx
Supplementary files format and content: Excel file with 3 sheets
Supplementary files format and content: Differential Expressed Genes after normalization of diferent comparations (KO vs WT;RES vs KO; RES vs WT)

source_name: Liver

extract_protocol:
chloroform-phenol RNA extraction
TruSeq RNA Sample Preparation v2 Kit (Illumina, San Diego, CA)

value: Liver

value: Cypb1 KO

value: genetic modification + plasmid overexpresion


title: rat liver Cyp7b1 KO_plasmid_003

description: RES group


title: FFPE tissue of glioblastoma, case 12

description:
207953350059_R01C01
12

value: favorable


title: FFPE tissue of glioblastoma, case 9

description:
207953350059_R04C01
9

value: methylated

value: MC Glioblastoma IDH-wildtype subtype posterior fossa (novel)


title: rat liver Cyp7b1 KO_008

description: KO group

value: genetic modification


title: rat liver Cyp7b1 KO_plasmid_002

description: RES group


title: rat liver Cyp7b1 KO_007

description: KO group


title: rat liver Cyp7b1 KO_plasmid_001

description: RES group


title: FFPE tissue of glioblastoma, case 34

description:
208197680055_R06C01
34

value: FFPE tissue of glioblastoma


title: rat liver Cyp7b1 KO_006

description: KO group


title: rat liver Wild Type_003

description: WT group

value: Wild Type

value: control


title: rat liver Wild Type_004

description: WT group


title: rat liver Cyp7b1 KO_005

description: KO group


title: β5i_IH_B

city: Greifswald

first: Sophie

last: Wolfgramm

address: Ferdinand-Sauerbruch Straße

department: Medical Biochemistry and Molecular Biology

country: Germany

institute: University Medicine Greifswald

hyb_protocol: Total RNA (100ng) were used for hybridization with the human nCounter AutoImmune Profiling Panel CodeSets for 16 hours at 65°C.

scan_protocol: Cartridges are streptavidin-coated, which enables immobilization of the hybridized samples. The counting was performed by nCounterTM Analyzer.

data_processing: RNA counts wihtin the RCC files were normalized using the geometric mean and housekeeping genes, according to the manufacturer's instructions, including a threshold of 20 counts using the nSolver4.0 software.

label: biotin

source_name: stimulated T cells

label_protocol: The supplier provided gene-specific biotin-tagged molecular barcodes (CodeSet) for labeling

growth_protocol: PBMCs were co-cultured with irridated feeder cells in 96-well plates using RPMI1640 medium, supplemented with 10% human serum and 1% Penicillin/Streptomycin

extract_protocol: Total RNA isolation from T cells were extracted with the kit from Analytic Jena, following the supplier's instructions

treatment_protocol: Stimulation of PBMCs included 1µg/µL PHA-L (Sigma) and 150 U/mL IL-2 (Miltenyi Biotech) for T cell expansion based on the method from Fonteneau et al. 2001

value: stimulated T cells

value: PRAAS PSMB8 inherited

tag: phenotype


title: FFPE tissue of glioblastoma, case 29

description:
208197680076_R02C01
29

value: unfavorable

value: MC Glioblastoma IDH-wildtype RTK1 subtype


title: β5i_IH_A


title: HD_E

value: clinical healthy


title: FFPE tissue of glioblastoma, case 16

description:
207953350059_R02C01
16

value: unmethylated

value: MC Glioblastoma IDH-wildtype mesenchymal subtype


title: rat liver Wild Type_001

description: WT group

value: Liver


title: HD_D


title: rat liver Wild Type_002

description: WT group


title: Pt_C

value: PRAAS PSMB8 DN


title: rat liver Cyp7b1 KO_003

description: KO group

value: Cypb1 KO


title: Pt_A


title: C16

source_name: DNA from normal control

value: rectal mucosa

tag: disease state

value: normal control


title: Pt_B


title: HD_C


title: HD_B


title: rat liver Cyp7b1 KO_004

description: KO group


title: Rstyl-48h-Subm-Rep-3

city: Groningen

first: Hans

last: van Veen

address: Nijenborgh 7

department: GELIFES

country: Netherlands

institute: University of Groningen

description: Library name: Rstyl-48h-Subm-Rep-3

data_processing:
RNA sequencing was checked by FastQC (v0.12.0; Andrews 2010) and aligned against the R. islandica transcriptome (Assembly Version v1, Annotation Version v1.1; Brassicales Map Alignment Project, DOE-JGI, https://bmap.jgi.doe.gov/) for both species using kallisto.
Assembly: R. islandica  (Assembly Version v1, Annotation Version v1.1; Brassicales Map Alignment Project, DOE-JGI, https://bmap.jgi.doe.gov/)
Supplementary files format and content: counts_Risl.txt - read counts of mapping to R.islandica transcriptome
Supplementary files format and content: counts_Rsty.txt - read counts of mapping to R.islandica transcriptome

organism: Rorippa pyrenaica

source_name: young leaves

extract_protocol:
ISOLATE II RNA Plant Kit (Meridian Bioscience Inc., USA)
by Genewiz GmbH (Germany)

value: young leaves

value: submergence


title: rat liver Cyp7b1 KO_001

description: KO group

value: genetic modification


title: Rstyl-48h-Subm-Rep-1

description: Library name: Rstyl-48h-Subm-Rep-1


title: Rstyl-48h-Subm-Rep-2

description: Library name: Rstyl-48h-Subm-Rep-2


title: organoid microglia, HC-1, biol rep2

city: Utrecht

first: Roland Jeroen

last: Pasterkamp

state: Utrecht

address: Universiteitsweg 100

department: Translational Neuroscience

institute: UMC Utrecht

description: Library name: X104700-001-003

data_processing:
Raw sequence reads were trimmed of low-quality bases and adapter sequences with cutadapt v2.10. Presumed adapter sequences were removed from the read when the bases matched a sequence in the adapter sequence set (TruSeq adapters). Trimmed reads were mapped the human GRCh38.p13 using a short read aligner based on Burrows—Wheeler Transform (STAR2 v2.5.4) with default settings. The mapped counts for each gene were determined and summarised in a count table using HTSeq v0.11.0, which served as input for downstream RNA-Seq differential expression analysis.
Assembly: GRCh38.p13
Supplementary files format and content: Tab-separated values files

source_name: Cerebral organoids

growth_protocol: iPSC derived cerebral organoids were generated as previously described (Ormel et al., 2018 & Geest et al., 2024). Organoids were grown for 64 days.

extract_protocol:
Total RNA was isolated using QIAzol Lysis reagent (Qiagen) and miRNeasy mini kit (Qiagen) with DNA digestion on-column, according to the manufacturer's instructions. RNA concentration and integrity (RIN) was verified in an Agilent 2100 bioanalyzer and only samples with RIN ≥ 9.0 were used for RNA sequencing.
Sample preparation was performed according to "NEBNext Ultra II Directional RNA Library Prep Kit for Illumina" (NEB #E7760S/L). Briefly, mRNA was isolated from total RNA using the oligo-dT magnetic beads. After fragmentation of the mRNA, a cDNA synthesis was performed. This was used for ligation with the sequencing adapters and PCR amplification of the resulting product. The quality and yield after sample preparation was measured with the Fragment Analyzer. The size of the resulting products was consistent with the expected size distribution (a broad peak between 300-500 bp). Samples were sequenced using the Illumina NovaSeq 6000, following a data quality metrics check for possible sample and barcode contamination, using third-party (FastQC v0.11.9) and in-house (FastQA v3.1.25) quality control tools.

value: Cerebral organoids

value: Organoid derived Microglia

value: Healthy control

value: Untreated


title: organoid microglia, HC-2, biol rep1

description: Library name: X104700-001-002


title: FFPE tissue of glioblastoma, case 7

description:
208250190150_R07C01
7

value: favorable

value: FFPE tissue of glioblastoma


title: rat liver Cyp7b1 KO_002

description: KO group


title: HD_A

value: stimulated T cells

value: clinical healthy


title: organoid microglia, HC-1, biol rep1

description: Library name: X104700-001-001


title: Rstyl-48h-Ctrl-Rep-3

description: Library name: Rstyl-48h-Ctrl-Rep-3

value: control


title: IgG CUT&Tag

city: Hangzhou

first: Tianyuan

last: Gu

state: Zhejiang

address: 3 Qingchun East Road, Shangcheng District, Hangzhou City, Zhejiang Province, China

department: Department of Orthopedic Surgery

institute: Zhejiang University School of Medicine Sir Run Run Shaw Hospital

library_source: genomic

data_processing:
library strategy:CUT&Tag
The CUT & Tag libraries were constructed using HyperactiveTM In-Situ ChIP Library Prep Kit (TD901, Vazyme, China) and sequenced on an Illumina NovaSeq platform, and 150-bp paired-end reads were generated. Fastp v 0.20.0 was used to remove the adapter and low-quality reads.
Paired-end reads were aligned to hg38 using Bowtie2 version 2.3.4.3 with options: --end-to-end –sensitive. Duplicated reads were removed using Picard v2.18.17 with this parameter: REMOVE_DUPLICATES = true.
Peak calling used SEACR v1.3 with a threshold: of 0.01. Scatterplots, correlation plots, and heatmaps were displayed using deepTools v2.27.1. Annotation of peaks was performed using an R package ChIPseeker v1.12.1. MEME-ChIP v 5.0.5 was used to search for the binding site.
Peaks with M-value > 0.2 and P-value < 0.05 are defined as specific peaks.
Assembly: mm9
Supplementary files format and content: peaks

source_name: Nucleus pulposus cells

growth_protocol: To isolate NPCs, the nucleus pulposus was cut into small pieces and treated with 10ml DMEM media (Gibco-Thermo Fisher Scientific, Waltham, MA, USA) with 0.1% collagenase type II (Biosharp, Hefei, China) for 4 to 6 hours at 37℃. Liberated cells were filtered through a 40 µm cell strainer, and the filtrate was centrifuged for 5 minutes at 1,200 rpm. The supernatant was aspirated, and the cell pellets were washed with sterile phosphate-buffered saline (PBS), then cultured in Dulbecco’s modified Eagle’s medium (DMEM) with 10% fetal bovine serum (FBS) (Thermo Fisher Scientific, Waltham, MA, USA) at 37°C in 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
The CUT & Tag libraries were constructed using HyperactiveTM In-Situ ChIP Library Prep Kit (TD901, Vazyme, China) and sequenced on an Illumina NovaSeq platform, and 150-bp paired-end reads were generated. Fastp v 0.20.0 was used to remove the adapter and low-quality reads.

value: Nucleus pulposus cells

value: incubate the Goat anti-Rabbit IgG secondary antibody (1:5000, Fudebio, Hangzhou, China)


title: CDK9 CUT&Tag

value: incubate the anti-CDK9 antibody


title: Rstyl-48h-Ctrl-Rep-2

description: Library name: Rstyl-48h-Ctrl-Rep-2


title: Rstyl-48h-Ctrl-Rep-1

description: Library name: Rstyl-48h-Ctrl-Rep-1


title: Rstyl-24h-Subm-Rep-3

description: Library name: Rstyl-24h-Subm-Rep-3


title: 812-12 HuLM RNA-seq_HuLM_VEH_rep4_I-BET 762 RNA

city: San Antonio

first: Azad

last: Khosh

state: TX

address: 7703 Floyd Curl Dr

institute: UTHSCSA

data_processing:
The quality of reads controlled using FastQC, version 0.73 then reads were processed  using Trimmomatic, and parameters were chosen to trim the reads  according to FastQC results. The reads were mapped to the human reference genome,  version hg38 using Hisat2, version 2.2.1. Next, raw reads were mapped to the  human reference transcriptome using featurecounts, version 2.0.3 and annotation  file of Gencode, version V41. Gene counts pre-processed and normalized using  the DESeq2 package in R, version 1.36.0. quality of samples examined using  comparative boxplot and PCA and outlier samples excluded from the analysis.  Differentially expressed genes identify using DESeq2.
Assembly: HG38
Supplementary files format and content: csv format

source_name: HuLM

extract_protocol:
We performed whole transcriptome analysis to determine the mechanism  underlying the inhibitory effect of BET protein inhibition on the uterine fibroid cells. The HuLM cells  were treated with BET protein inhibitors JQ1 and I-BET 762 at a concentration of 5 µM  for 48 h. RNA was isolated using Trizol. RNA quality and quantity were assessed using  the Agilent bio-analyzer.
Strand-specific RNA-Seq libraries were prepared using a  TruSeq total RNA-Seq library protocol (Illumina provided). Library quality and quantity  were assessed using the Agilent bio-analyzer, and libraries were sequenced using an  Illumina NovaSEQ6000 (illumine provided reagents and protocols).

value: HuLM

value: human uterine fibroid cell line

value: I-BET 762


title: 812-11 HuLM RNA-seq_HuLM_VEH_rep3_I-BET 762 RNA


title: Rstyl-24h-Subm-Rep-2

description: Library name: Rstyl-24h-Subm-Rep-2

value: young leaves

value: submergence


title: 812-10 HuLM RNA-seq_HuLM_VEH_rep2_I-BET 762 RNA


title: Rstyl-24h-Subm-Rep-1

description: Library name: Rstyl-24h-Subm-Rep-1


title: Rstyl-24h-Ctrl-Rep-3

description: Library name: Rstyl-24h-Ctrl-Rep-3


title: 812-8 HuLM RNA-seq_HuLM_VEH_rep4_JQ1 RNA


title: 812-7 HuLM RNA-seq_HuLM_VEH_rep3_JQ1 RNA


title: Rstyl-24h-Ctrl-Rep-1

description: Library name: Rstyl-24h-Ctrl-Rep-1


title: 812-4 HuLM RNA-seq_HuLM_VEH_rep4_DMSO RNA

value: DMSO


title: Ri-48h-Subm-Rep1

description: Library name: Ri-48h-Subm-Rep1

organism: Rorippa islandica


title: 812-5 HuLM RNA-seq_HuLM_VEH_rep1_JQ1 RNA


title: Ri-48h-Subm-Rep2

description: Library name: Ri-48h-Subm-Rep2


title: 812-3 HuLM RNA-seq_HuLM_VEH_rep3_DMSO RNA


title: 812-6 HuLM RNA-seq_HuLM_VEH_rep2_JQ1 RNA


title: 812-2 HuLM RNA-seq_HuLM_VEH_rep2_DMSO RNA


title: Ri-48h-Ctrl-Rep2

description: Library name: Ri-48h-Ctrl-Rep2


title: Ri-48h-Ctrl-Rep3

description: Library name: Ri-48h-Ctrl-Rep3


title: NSG-Huh7-T cell treat-soat1-ko-3

first: guangchuan

last: Wang

address: 320 Yue Yang Road

institute: Chinese Academy of Sciences

data_processing:
HISAT2
Assembly: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file include RPKM values for each sample

source_name: tumor

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

value: tumor

value: Liver cancer cell

value: Soat1 knockdown

value: Tail vein injection of T cells


title: 812-1 HuLM RNA-seq_HuLM_VEH_rep1_DMSO RNA


title: Ri-24h-Subm-Rep3

description: Library name: Ri-24h-Subm-Rep3


title: Ri-48h-Subm-Rep3

description: Library name: Ri-48h-Subm-Rep3


title: NSG-Huh7-T cell treat-soat1-ko-2


title: Ri-24h-Subm-Rep2

description: Library name: Ri-24h-Subm-Rep2


title: Ri-24h-Subm-Rep1

description: Library name: Ri-24h-Subm-Rep1


title: NSG-Huh7-T cell treat-vector-3

value: WT


title: Ri-24h-Ctrl-Rep3

description: Library name: Ri-24h-Ctrl-Rep3


title: NSG-Huh7-T cell treat-soat1-ko-1


title: 812-9 HuLM RNA-seq_HuLM_VEH_rep1_I-BET 762 RNA


title: NSG-Huh7-T cell treat-vector-2


title: Rstyl-24h-Ctrl-Rep-2

description: Library name: Rstyl-24h-Ctrl-Rep-2


title: NSG-Huh7-T cell treat-vector-1


title: Ri-24h-Ctrl-Rep1

description: Library name: Ri-24h-Ctrl-Rep1


title: Ri-24h-Ctrl-Rep2

description: Library name: Ri-24h-Ctrl-Rep2


title: NSG-Huh7-soat1-ko-3

value: Tail vein injection of PBS


title: BY-2_10d_3

city: Praha 6

first: Karel

last: Muller

address: Rozvojová 263

department: Lab. of hormonal regulations in plants

country: Czech Republic

institute: Institute of Experimenal Botany of the Czech Academy of Sciences

description: Library name: KM1928

data_processing:
reads were quality filterred by rcorrector and Trimmomatic, rRNA contamination was removed using SortMeRNA
transcript quantification and normalization done by Salmon v1.3.0 with parameters--seqBias, --gcBias, --PosBias, --numBootstraps 30
Assembly: Nicotiana tabacum v1 Edwards 2017
Supplementary files format and content: sf files generated by Salmon software, include TPM values

organism: Nicotiana tabacum

source_name: suspension cell culture

growth_protocol: Tobacco cell line BY-2 (Nicotiana tabacum L. cv. Bright Yellow 2) was maintained in liquid Murashige and Skoog (MS) medium (3% sucrose (w/v), 4.3 g/l MS salts, 100 mg/l myo-inositol, 1mg/l thiamin, 0.2 mg/l 2,4-dichlorophenoxyacetic acid (2,4-D), and 200 mg/l KH2PO4; pH 5.8), in the dark, at 27°C, under continuous shaking (150 rpm; orbital diameter 30 mm) and sub-cultured every 7 days.

extract_protocol:
protocol from Plant Total RNA Mini Kit, Favorgen
KAPA HyperPrep kit (Roche)

treatment_protocol: no treatment

tag: cultivar

value: Bright Yellow 2

value: suspension cell culture

tag: life cycle_stage

value: late stationary


title: NSG-Huh7-soat1-ko-2


title: NSG-Huh7-soat1-ko-1


title: BY-2_7d_2

description: Library name: KM1926

value: stationary


title: BY-2_1d_4

description: Library name: KM1924

value: early exponential


title: BY-2_7d_1

description: Library name: KM1925


title: Ri-48h-Ctrl-Rep1

description: Library name: Ri-48h-Ctrl-Rep1

value: control


title: NSG-Huh7-vector-2


title: BY-2_1d_2

description: Library name: KM1922


title: BY-2_1d_3

description: Library name: KM1923


title: NSG-Huh7-vector-1


title: Huh7-soat1-ko-3

source_name: cell

value: cell

value: Normal culture


title: BY-2_1d_1

description: Library name: KM1921


title: Huh7-soat1-ko-2


title: Huh7-soat1-ko-1


title: BY-2_10d_2

description: Library name: KM1920


title: BY-2_10d_1

description: Library name: KM1918


title: Huh7-vector-3


title: Tobacco leaf tissue - MuGDH64_rep3

city: Guiyang

first: kai

last: pi

state: Guizhou

department: Key Laboratory for Tobacco Quality Research Guizhou Province

institute: Guizhou University

description: Library name: S702_3

data_processing:
Perform sequence alignment analysis using TopHat2 software. When the reference genome annotation is complete and there is no contamination in the relevant experiments, the mapping rate is generally higher than 65% (Total Mapped Reads). On the basis of the existing reference genome, the mapped reads were assembled and spliced using the software Cufflinks, compared with known transcripts to obtain transcripts without annotation information, and potential new transcripts were functionally annotated.
Assembly: 2017 K326：https://solgenomics.net/organism/Nicotiana_tabacum/genome
Supplementary files format and content: CSV format, including calculated（TPM） expression level data for all transcripts.

source_name: leaf

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent (Plant RNA Purification Reagent for plant tissue) according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara). Then RNA quality was determined by 2100 Bioanalyser (Agilent) andquantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample(OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >1μg) was used to construct sequencing library.
RNA-seq transcriptome librariy was prepared following TruSeqTM RNA sample preparation Kit from Illumina (San Diego, CA) using 1μg of total RNA. After quantified by TBS380, paired-end RNA-seq sequencing library was sequenced with the Illumina NovaSeq Xsequencer (2 × 150bp read length)

value: leaf


title: Huh7-vector-2


title: Tobacco leaf tissue - MuGDH64_rep2

description: Library name: S702_2


title: Huh7-vector-1


title: Tobacco leaf tissue - MuGDH64_rep1

description: Library name: S702_1


title: MCF7_sias-B_RNAseq

city: Pittsburgh

first: Da

last: Yang

address: 308 Salk Pavilion

institute: University of Pittsburgh

data_processing:
Reads were aligned using STAR.
Gene expression quantification and differential expression analysis were done by cuffdiff.
Assembly: hg38
Supplementary files format and content: RNAseq_fpkm_cdk_sirna, comma-separated values file include gene expression analysis result

source_name: Mammary gland/Breast

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit (Qiagen). 10 µg total RNA was treated with RNase-free DNase I (Promega) for 30 min at 37 °C and RNA cleanup was performed using the RNA Clean & Concentrator-5 columns (Zymo). 1 µg of total RNA was used for the construction of sequencing libraries.
Poly-A RNA-Seq; RNA libraries for RNA-seq were prepared using KAPA RNA Hyper RiboErase HMR (96 rxn) following manufacturer's protocols.

value: Mammary gland/Breast

value: Human epithelial cell

value: TENM3-AS1 knockdown


title: MCF7_siLINC01117-B_RNAseq

value: LINC01117 knockdown


title: MCF7_siLINC01117-A_RNAseq


title: Tobacco leaf tissue - GDH64_rep3

description: Library name: S701_3


title: NSG-Huh7-vector-3

value: tumor

value: Liver cancer cell


title: 9001 root,dark flooding recovery phase,24h,rep3

city: 安阳

first: 新彦

last: 刘

address: 文峰区黄河大道38号

institute: 中国农业科学院棉花研究所

description:
Library name: Sample 24
DW9001_24_G3

data_processing:
CLC Genomics Workbench y 11.0.1
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Gossypium

source_name: root

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seg were prepared using SMARTER mRNA-Seg Library PrepKit following manufacturer's protocols.

value: root

value: root cell line

value: root cells

value: dark flooding recovery phase


title: MCF7_sias-A_RNAseq


title: 9001 root,dark flooding recovery phase,0h,rep3

institute: 中国农业科学院棉花研究所

description:
Library name: Sample 21
DW9001_0_G3


title: MCF7_si226706-A_RNAseq

value: ENSG00000226706 knockdown


title: MCF7_si226706-C_RNAseq


title: MCF7_sicon-2_RNAseq

value: siRNA control


title: U87-MG_L-Phe(-)_2

city: Kyoto

first: Rie

last: Saba

state: Kyoto

address: Kajii-cho 465, Kawaramachi-dori, Kamigyo-ku

department: Dapartment of Radiology

country: Japan

institute: Kyoto Prefectural University of Medicine

data_processing:
java-11
Sequencing reads were trimmed for adaptor sequence using Trimmomatic-0.39
Trimmed sequence reads were qualified using FastQC
Trimmed sequence reads were mappled to hg38 reference genome using STAR-2.7.10b
Read count extraction and normalization were performed using RSEM-1.3.3
Assembly: hg38
Supplementary files format and content: tab-deliminated text files include raw, TPM, and FPKM counts for each sample
Supplementary files format and content: tab-deliminated csv file include TPM counts for each sample

growth_protocol: U87-MG cells were maintained in EMEM supplemented with 10% of fetal bovine serum (FBS) and antibiotics in CO2 incubator of 5% CO2 at 37C.

extract_protocol:
Total RNA was purified with Rneasy mini Kit (Qiagen).
RNA libraries for RNA-seq were prepared using TruSeq Library Prep Kit following manufatcturer's protocols.

treatment_protocol: Harvested 5x10^5 cells per well in 6 well plate in normal medium, and cultivated for 24 hours, then changed the medium to normal (Sample 1 and 2) and L-Phe-deprived medium (Sample 3 and 4), respectively. After 24 hours of further cultivation, cells were collected by trypsinization and washed in PBS for three times.

value: glioblastoma-like

value: L-phenylalanine-deprivation for 24 hours


title: MCF7_sicon-1_RNAseq


title: 9001 root,dark flooding recovery phase,0h,rep1

institute: 中国农业科学院棉花研究所

description:
Library name: Sample 19
DW9001_0_G1


title: U87-MG_L-Phe(-)_1


title: U87-MG_L-Phe(+)_2

value: no treatment


title: U87-MG_L-Phe(+)_1


title: 9001 root,dark flooding recovery phase,24h,rep1

institute: 中国农业科学院棉花研究所

description:
Library name: Sample 22
DW9001_24_G1


title: SAS_4_L-Phe(-)_2

source_name: tongue

growth_protocol: SAS cells were maintained in DMEM/F12 supplemented with 10% of fetal bovine serum (FBS) and antibiotics in CO2 incubator of 5% CO2 at 37C.

treatment_protocol: Harvested 5x10^5 cells per well in 6 well plate in normal medium, and cultivated for 24 hours, then changed the medium to normal (Sample 1 and 2) and L-Phe-deprived medium (Sample 3 and 4), respectively. After 24 hours of further cultivation, cells were collected by trypsinization.

value: tongue

value: SAS

value: squamous carcinoma


title: Tobacco leaf tissue - GDH64_rep2

description: Library name: S701_2

value: leaf


title: 4847 root,dark flooding recovery phase,0h,rep2

institute: 中国农业科学院棉花研究所

description:
Library name: Sample 14
DW4847_0_G2


title: SAS_3_L-Phe(-)_1


title: Tobacco leaf tissue - GDH64_rep1

description: Library name: S701_1


title: 4847 root,dark flooding recovery phase,24h,rep3

institute: 中国农业科学院棉花研究所

description:
Library name: Sample 18
DW4847_24_G3


title: SAS_2_L-Phe(+)_2


title: 4847 root,dark flooding recovery phase,0h,rep1

institute: 中国农业科学院棉花研究所

description:
Library name: Sample 13
DW4847_0_G1


title: HaCaT_L-Phe(-)_2

source_name: skin

growth_protocol: HaCaT cells were maintained in DMEM supplemented with 10% of fetal bovine serum (FBS) and antibiotics in CO2 incubator of 5% CO2 at 37C.

value: skin

value: HaCaT

value: keratynocyte


title: 9001 root,dark recovery phase,24h,rep2

institute: 中国农业科学院棉花研究所

description:
Library name: Sample 11
DN9001_24_G2

value: dark recovery phase


title: 9001 root,dark flooding recovery phase,24h,rep2

institute: 中国农业科学院棉花研究所

description:
Library name: Sample 23
DW9001_24_G2

value: root


title: 9001 root,dark flooding recovery phase,0h,rep2

institute: 中国农业科学院棉花研究所

description:
Library name: Sample 20
DW9001_0_G2

value: root cell line


title: HaCaT_L-Phe(-)_1


title: HaCaT_L-Phe(+)_1


title: 9001 root,dark recovery phase,0h,rep3

institute: 中国农业科学院棉花研究所

description:
Library name: Sample 9
DN9001_0_G3

value: root cells


title: 9001 root,dark recovery phase,0h,rep2

institute: 中国农业科学院棉花研究所

description:
Library name: Sample 8
DN9001_0_G2


title: 9001 root,dark recovery phase,24h,rep1

institute: 中国农业科学院棉花研究所

description:
Library name: Sample 10
DN9001_24_G1


title: HaCaT_L-Phe(+)_2


title: 4847 root,dark flooding recovery phase,24h,rep2

institute: 中国农业科学院棉花研究所

description:
Library name: Sample 17
DW4847_24_G2

value: dark flooding recovery phase


title: 4847 root,dark recovery phase,24h,rep3

institute: 中国农业科学院棉花研究所

description:
Library name: Sample 6
DN4847_24_G3


title: 4847 root,dark flooding recovery phase,24h,rep1

institute: 中国农业科学院棉花研究所

description:
Library name: Sample 16
DW4847_24_G1


title: 4847 root,dark flooding recovery phase,0h,rep3

institute: 中国农业科学院棉花研究所

description:
Library name: Sample 15
DW4847_0_G3


title: A375_L-Phe(-)_1

growth_protocol: A375 cells were maintained in DMEM supplemented with 10% of fetal bovine serum (FBS) and antibiotics in CO2 incubator of 5% CO2 at 37C.

value: melanoma


title: 4847 root,dark recovery phase,24h,rep2

institute: 中国农业科学院棉花研究所

description:
Library name: Sample 5
DN4847_24_G2


title: A375_L-Phe(+)_1


title: 4847 root,dark recovery phase,0h,rep2

institute: 中国农业科学院棉花研究所

description:
Library name: Sample 2
DN4847_0_G2


title: SAS_1_L-Phe(+)_1


title: 9001 root,dark recovery phase,24h,rep3

institute: 中国农业科学院棉花研究所

description:
Library name: Sample 12
DN9001_24_G3


title: 4847 root,dark recovery phase,0h,rep3

institute: 中国农业科学院棉花研究所

description:
Library name: Sample 3
DN4847_0_G3


title: 1.65nM HCT116

first: Wen

last: Xiao

address: 320 Yueyang Road

department: Institute of Biochemistry and Cell Biology

institute: Shanghai Institutes for Biological Sciences, CAS

description: Testing the accuracy of the quantitative standard curve

data_processing:
Raw data (read1) were pre-processed using the FASTX Toolkit (v0.0.14). The first 70 bp of each read were retained, and low-quality sequences were filtered out (-q 20, -p 90). After quality filtering, adapter sequences were trimmed, requiring a minimum 10-nucleotide match at the 3' end. Reads without detected adapter or shorter than 32 bp were discarded. Only reads with "CGA" at positions 4-6 were retained, corresponding to the 5' random adapter. UMI extraction was performed with UMI_tools (v0.5.1) using the following parameters: extract --extract-method regex --bc-pattern="^(?P<umi_1>.{3})(?P<cell_1>.{3})(?P<umi_2>.{4})([A,T,C,G]{5,100})(?P<umi_3>.{4})$". Processed reads were aligned to the target genome using Bowtie (v1.2.1.1) with parameters --best -v 0. Duplicate reads were removed with UMI_tools using the following parameters: dedup --edit-distance-threshold 1 --soft-clip-threshold 0 --method adjacency. Unaligned reads were mapped to the spike-in reference sequences using Bowtie with parameters --best -v 1 --norc and de-duplicated in the same manner. Remaining unmapped reads were aligned to the isomiR reference library with the same parameters and de-duplicated. Molecules aligned to the genome were merged with isomiR molecules for downstream analysis. Molecules were annotated based on the following priority: mature miRNA > isomiR > tRNA > rRNA > snoRNA > snRNA > scRNA > scaRNA > YRNA > lncRNA > mRNA > piRNA > novel miRNA. Mature miRNA, isomiR, piRNA, and novel miRNA were annotated based on exact sequence and length matches, while other small RNA categories were aligned to known sequences using Bowtie with parameters -k=100 -v=0 -norc. Reads that aligned to the genome but lacked known annotations were classified as "others". The expression of molecules in each library was normalized using the standard curve generated from the external spike-ins.
Assembly: human:hg38;  mouse:mm10; crab-eating monkey:macFas5
Supplementary files format and content: tab-delimited text files include absolute quantification of miRNA expression for each Sample

extract_protocol:
1 ml of Trizol reagent (Invitrogen) was added to lyse the cells completely. Subsequently, 200 µl of trichloromethane was added and mixed thoroughly. The solution was then centrifuged at 12,000 rpm for 15 min at 4°C. The upper aqueous phase (450 µl) was transferred into a new 1.5 ml EP tube, followed by the addition of 900 µl of absolute ethanol. The solution was mixed by inversion, left to stand at -30°C for 30 min, and then centrifuged again at 12,000 rpm for 15 min at 4°C, until a distinct precipitate formed at the bottom of the tube. After removing the supernatant, the pellet was washed twice with 80% ethanol, air-dried for 2-3 min at room temperature, and dissolved in DEPC-treated water. RNA concentration was measured using a Nanodrop spectrophotometer, and the sample was diluted to a concentration of 100 ng/µl.
100 ng RNA with 0.05 µl of 20 nM EM or RM spike-in control oligos was ligated to a 0.55 µM 3' randomized adapter using 25 U/µl T4 RNA ligase 2 truncated KQ (NEB) in 0.83X T4 RNA ligase reaction buffer (NEB), supplemented with 20% PEG 8000 (NEB) at 25°C overnight. The ligated RNA was then annealed with 1.28 µM RTP. To remove the 3’ adapter-RTP byproduct, 3.33 U/µl 5’ deadenylase (NEB) and 0.2 U/µl lambda exonuclease (NEB) were added, followed by incubation at 30°C for 1 h and 37°C for 2 h, respectively. Subsequently, the product was ligated to a 5’ randomized adapter using 0.4 U/µl of T4 RNA ligase 1 (NEB) in 0.74X T4 RNA ligase reaction buffer, supplemented with 0.7 mM ATP and 17.3% PEG 8000 (NEB) at 25°C for 1 h. Reverse transcription was carried out using 5 U/µl of ProtoScriptII reverse transcriptase (NEB) in 1X ProtoScriptII RT reaction buffer (NEB), containing 0.5 mM dNTPs (Promega) and 10 mM DTT (NEB), at 50°C for 1 h. The resulting cDNA was then amplified using 0.02 U/µl of KOD-Plus-Neo (TOYOBO) in 1X PCR Buffer for KOD-Plus-Neo (TOYOBO), along with 0.5 µM primers, 1.5 mM MgSO4 (TOYOBO), and 0.2 mM dNTPs (TOYOBO). After PCR amplification, the cDNA was gel-purified on a 6% polyacrylamide gel to remove adapter dimers and sequenced using the Illumina NovaSeq platform.

tag: libtype

value: qMap-seq


title: 4847 root,dark recovery phase,24h,rep1

institute: 中国农业科学院棉花研究所

description:
Library name: Sample 4
DN4847_24_G1

tag: cell line


title: 4847 root,dark recovery phase,0h,rep1

institute: 中国农业科学院棉花研究所

description:
Library name: Sample 1
DN4847_0_G1

tag: treatment


title: 1.65nM A375


title: 1.65nM 293-rep2


title: purified LSEC, Sham, replicate 4

city: Gent

first: Steven

last: Timmermans

address: Technologiepark 71

country: Belgium

institute: VIB-UGent

description:
Library name: Sample 39
LSEC_Sham-4

data_processing:
Reads were quality checked with fastQC and preprocessed (adapter removal) with TRIMMOMATIC v0.34 (ILLUMINACLIP & MINLEN filters)
Reads were mapped to the mm39 reference genome with STAR (2.7.10b) and the gencode M30 and read counts were directly obtained using the "--quantMode GeneCounts" parameter for STAR
Assembly: mm39
Supplementary files format and content: tab delimited count matrix with the raw counts per sample

organism: Mus musculus

source_name: liver

growth_protocol: Male C57BL/6J mice were purchased from Janvier. All mice were housed in individually ventilated cages at standard housing conditions (22 °C, 14/10 h light/dark cycle) with food (chow diet consisting of 18% proteins, 4.5% fibers, 4.5% fat, 6.3% ashes, Provimi Kliba SA) and water ad libitum in a specific pathogen free facility.

extract_protocol:
Total RNA was isolated with Aurum Total RNA mini Kit (Bio-Rad) following the manufacturer’s instructions
Library preparation was done using the illumina truseq stranded library kit for sequencing with a Cloudbreak sequencing kit on the element AVITI according the the manufacturer's instructions

treatment_protocol: Mice were subjected to Sham or CLP and sampeling was performed 8 hours after the surgery

value: liver

tag: cell type

value: purified liver sinusoidal epithelial cells

value: WT

value: SHAM


title: 1.65nM 293-rep1

city: Shanghai


title: purified LSEC, Sham, replicate 3

description:
Library name: Sample 38
LSEC_Sham-3

tag: genotype


title: A375_L-Phe(-)_2

value: L-phenylalanine-deprivation for 24 hours


title: A375_L-Phe(+)_2

value: no treatment


title: purified LSEC, Sham, replicate 2

description:
Library name: Sample 37
LSEC_Sham-2


title: 9001 root,dark recovery phase,0h,rep1

institute: 中国农业科学院棉花研究所

description:
Library name: Sample 7
DN9001_0_G1


title: purified LSEC, CLP, replicate 3

description:
Library name: Sample 34
LSEC_CLP-3

value: CLP


title: spike ins conC

description: External validation of quantitative accuracy


title: C-rep2


title: C-rep1


title: purified LSEC, CLP, replicate 2

description:
Library name: Sample 33
LSEC_CLP-2


title: B-rep1


title: spike ins conB


title: 1.65nM K562


title: purified KC, Sham, replicate 4

description:
Library name: Sample 31
KC_Sham-4

value: purified kupffer cells


title: A-rep1


title: purified KC, Sham, replicate 3

description:
Library name: Sample 30
KC_Sham-3


title: purified KC, Sham, replicate 2

description:
Library name: Sample 29
KC_Sham-2


title: spike ins conA


title: Hela_100ng_100uM_2

description: Testing trends in library quality vs adapter concentration

value: Hela


title: Hela_100ng_100uM_1


title: purified LSEC, CLP, replicate 4

description:
Library name: Sample 35
LSEC_CLP-4


title: purified KC, CLP, replicate 4

description:
Library name: Sample 27
KC_CLP-4


title: purified LSEC, Sham, replicate 1

description:
Library name: Sample 36
LSEC_Sham-1


title: purified KC, CLP, replicate 2

description:
Library name: Sample 25
KC_CLP-2


title: Hela_100ng_33uM_2


title: purified HSC, Sham, replicate 2

description:
Library name: Sample 22
HSC_Sham-2

value: purified hepatic stellate cells


title: purified KC, CLP, replicate 3

description:
Library name: Sample 26
KC_CLP-3


title: purified KC, CLP, replicate 1

description:
Library name: Sample 24
KC_CLP-1


title: purified HSC, CLP, replicate 4

description:
Library name: Sample 20
HSC_CLP-4


title: Hela_100ng_33uM_1


title: Hela_100ng_10uM_1


title: 100pg-rep2

description: Testing method input


title: purified HSC, Sham, replicate 1

description:
Library name: Sample 21
HSC_Sham-1


title: 100pg-rep1

description: Testing method input


title: Hela_100ng_10uM_2


title: B-rep2


title: 10pg-rep2

description: Testing method input


title: 10pg-rep1

description: Testing method input


title: 1ng-rep2

description: Testing method input


title: purified HSC, CLP, replicate 3

description:
Library name: Sample 19
HSC_CLP-3


title: purified HSC, CLP, replicate 2

description:
Library name: Sample 18
HSC_CLP-2


title: purified LSEC, CLP, replicate 1

description:
Library name: Sample 32
LSEC_CLP-1


title: A-rep2


title: 1ng-rep1

description: Testing method input


title: purified HEP, Sham, replicate 4

description:
Library name: Sample 16
HEP_Sham-4

value: purified hepatocytes


title: 10ng-rep2

description: Testing method input


title: purified HSC, CLP, replicate 1

description:
Library name: Sample 17
HSC_CLP-1


title: 10ng-rep1

description: Testing method input


title: purified KC, Sham, replicate 1

description:
Library name: Sample 28
KC_Sham-1


title: purified HSC, Sham, replicate 3

description:
Library name: Sample 23
HSC_Sham-3


title: purified HEP, Sham, replicate 2

description:
Library name: Sample 14
HEP_Sham-2


title: purified HEP, CLP, replicate 2

description:
Library name: Sample 10
HEP_CLP-2


title: purified HEP, CLP, replicate 3

description:
Library name: Sample 11
HEP_CLP-3


title: purified HEP, Sham, replicate 3

description:
Library name: Sample 15
HEP_Sham-3


title: purified HEP, Sham, replicate 1

description:
Library name: Sample 13
HEP_Sham-1


title: 100uM AD-EM-100ng 293-rep2

description: Testing adapter concentration


title: 100ng-rep1

description: Testing method input


title: purified CD45, Sham, replicate 3

description:
Library name: Sample 7
CD45_Sham-3

value: purified CD45+ infiltrating cells


title: 33uM AD-EM-100ng 293-rep1

description: Testing adapter concentration/Comparison of CV of spike-ins in Truseq and qMap-seq library


title: 100uM AD-EM-100ng 293-rep1

description: Testing adapter concentration


title: purified CD45, Sham, replicate 1

description:
Library name: Sample 5
CD45_Sham-1


title: purified HEP, CLP, replicate 4

description:
Library name: Sample 12
HEP_CLP-4


title: 7.5uM AD-EM-100ng 293-rep2

description: Testing adapter concentration


title: 1ug-rep2

description: Testing method input


title: 1ug-rep1

description: Testing method input


title: 33uM AD-EM-100ng 293-rep2


title: 2.5uM AD-EM-100ng 293-rep2

description: Testing adapter concentration


title: 2.5uM AD-EM-100ng 293-rep1

description: Testing adapter concentration


title: purified CD45, Sham, replicate 4

description:
Library name: Sample 8
CD45_Sham-4


title: 22.5uM AD-EM-100ng 293-rep2

description: Testing adapter concentration


title: purified CD45, CLP, replicate 4

description:
Library name: Sample 4
CD45_CLP-4


title: 7.5uM AD-EM-100ng 293-rep1

description: Testing adapter concentration


title: 22.5uM AD-EM-100ng 293-rep1

description: Testing adapter concentration


title: purified CD45, CLP, replicate 1

description:
Library name: Sample 1
CD45_CLP-1


title: purified CD45, CLP, replicate 3

description:
Library name: Sample 3
CD45_CLP-3


title: purified CD45, CLP, replicate 2

description:
Library name: Sample 2
CD45_CLP-2


title: 0.83uM AD-EM-100ng 293-rep2

description: Testing adapter concentration


title: 100ng-rep2

description: Testing method input


title: purified HEP, CLP, replicate 1

description:
Library name: Sample 9
HEP_CLP-1


title: purified CD45, Sham, replicate 2

description:
Library name: Sample 6
CD45_Sham-2


title: qMap-100ng 293-EM-rep4

description: Comparison of CV of spike-ins in Truseq and qMap-seq library


title: qMap-100ng 293-EM-rep3


title: Photoreceptor nuclei, D50, ZT20, me2, rep3

city: West Lafayette

first: Sarah

last: McGovern

state: IN

address: Department of Biochemistry

department: Biochemistry

institute: Purdue University

data_processing:
For CUT&RUN and ATAC: Read trimming with trimmomatic
Alignment with Bowtie2, dovetail mates considered concordant for CUT&RUN
Indexing, generation of BAM files using Samtools
CPM-normalized bigWigs generated with deepTools
Assembly: BDGP6.46
Supplementary files format and content: bigWig files, CPM-normalized
Library strategy: CUT&RUN

organism: Drosophila melanogaster

source_name: Outer photoreceptors

growth_protocol: Drosophila were maintained in population cages in a 25°C incubator with a 12:12 hour light:dark cycle.

extract_protocol:
Photoreceptor nuclei were immunoenriched using the nuclei immunoenrichment protocol (dx.doi.org/10.17504/protocols.io.buiqnudw), followed by CUT&RUN (dx.doi.org/10.17504/protocols.io.zcpf2vn) or ATAC-seq. For CUT&RUN, 1 ug of anti-RNA PolII antibody (clone CTD4H8), or IgG (EpiCypher CUTANA IgG Negative Control Antibody) was used. MNase digestion was performed for 2 min for anti-RNA PolII and its corresponding IgG. For ATAC-seq, samples were incubated with Tn5 for 60 min. For histone marks, 0.5ug of anti-IgG (EpiCypher CUTANA IgG Negative Control Antibody), 0.5ug of H3K4me1 (abcam # 8895), 1ug of H3K4me2 (Thermo # 710796), or 1ug of H3K4me3 (EpiCypher # 13-0041) were used, together with 30min Mnase digestion.
Libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina and NEBNext Multiplex Oligos for Illumina (CUT&RUN) or ActiveMotif Nextera-Compatible Multiplex Primers. Modifications to the library preparation were made to preserve short DNA fragments (dx.doi.org/10.17504/protocols.io.bagaibse).

value: Outer photoreceptors

tag: cut&run antibody

tag: age

value: Adult, day 50

tag: time (zt)

tag: Sex

value: male


title: Photoreceptor nuclei, D50, ZT20, me1, rep3


title: Photoreceptor nuclei, D50, ZT20, me3, rep3


title: non4N-100ng 293-EM-rep1

value: Salt-seq


title: Photoreceptor nuclei, D50, ZT20, me3, rep2


title: Photoreceptor nuclei, D50, ZT20, me2, rep2


title: non4N-100ng 293-EM-rep2


title: Photoreceptor nuclei, D50, ZT20, IgG, rep3

value: IgG for H3K4me


title: Photoreceptor nuclei, D50, ZT20, me1, rep2


title: Photoreceptor nuclei, D50, ZT20, IgG, rep2


title: Photoreceptor nuclei, D50, ZT20, me2, rep1


title: Photoreceptor nuclei, D50, ZT20, me3, rep1


title: Photoreceptor nuclei, D50, ZT20, IgG, rep1


title: Photoreceptor nuclei, D50, ZT20, me1, rep1


title: Photoreceptor nuclei, D50, ZT16, me3, rep3


title: Photoreceptor nuclei, D50, ZT16, me2, rep3


title: Human-U2OS-1

description: 24 commonly used cell lines samples

value: qMap-seq


title: Human-SY5Y-3

description: 24 commonly used cell lines samples


title: Human-U2OS-3

description: 24 commonly used cell lines samples


title: Human-SY5Y-2

description: 24 commonly used cell lines samples


title: Human-U2OS-2

description: 24 commonly used cell lines samples


title: Human-SW480-4

description: 24 commonly used cell lines samples


title: 0.83uM AD-EM-100ng 293-rep1

description: Testing adapter concentration


title: Human-SY5Y-4

description: 24 commonly used cell lines samples


title: Human-U2OS-4

description: 24 commonly used cell lines samples


title: Photoreceptor nuclei, D50, ZT16, me1, rep3


title: Human-SW480-2

description: 24 commonly used cell lines samples


title: Photoreceptor nuclei, D50, ZT16, me3, rep2


title: Human-MDA_MB_231-4

description: 24 commonly used cell lines samples


title: Human-MDA_MB_231-3

description: 24 commonly used cell lines samples


title: Photoreceptor nuclei, D50, ZT16, IgG, rep2


title: Human-MDA_MB_231-2

description: 24 commonly used cell lines samples


title: Human-SW480-1

description: 24 commonly used cell lines samples


title: Photoreceptor nuclei, D50, ZT16, me1, rep2


title: Human-MDA_MB_231-1

description: 24 commonly used cell lines samples


title: Human-MCF_7-4

description: 24 commonly used cell lines samples


title: Human-SY5Y-1

description: 24 commonly used cell lines samples


title: Photoreceptor nuclei, D50, ZT16, me2, rep1


title: Photoreceptor nuclei, D50, ZT16, me1, rep1


title: Human-MCF_7-3

description: 24 commonly used cell lines samples


title: Human-MCF_7-2

description: 24 commonly used cell lines samples


title: Photoreceptor nuclei, D50, ZT16, me3, rep1


title: Photoreceptor nuclei, D50, ZT16, me2, rep2


title: Photoreceptor nuclei, D50, ZT16, IgG, rep1


title: Photoreceptor nuclei, D50, ZT16, IgG, rep3


title: Photoreceptor nuclei, D50, ZT12, me3, rep2


title: Photoreceptor nuclei, D50, ZT12, me2, rep3


title: Human-K562-1

description: 24 commonly used cell lines samples


title: Human-MCF_7-1

description: 24 commonly used cell lines samples


title: Photoreceptor nuclei, D50, ZT12, me1, rep3


title: Photoreceptor nuclei, D50, ZT12, me3, rep3


title: Human-K562-4

description: 24 commonly used cell lines samples


title: Photoreceptor nuclei, D50, ZT12, IgG, rep3


title: Human-SW480-3

description: 24 commonly used cell lines samples


title: Human-K562-2

description: 24 commonly used cell lines samples


title: Human-K562-3

description: 24 commonly used cell lines samples


title: Photoreceptor nuclei, D50, ZT12, me2, rep2


title: Photoreceptor nuclei, D50, ZT12, me1, rep2


title: Photoreceptor nuclei, D50, ZT12, IgG, rep2


title: Human-Jurkat-2

description: 24 commonly used cell lines samples

value: Jurkat


title: Human-Jurkat-3

description: 24 commonly used cell lines samples


title: Photoreceptor nuclei, D50, ZT12, me3, rep1


title: Human-Jurkat-1

description: 24 commonly used cell lines samples


title: Photoreceptor nuclei, D50, ZT12, me2, rep1


title: Human-IOSE-3

description: 24 commonly used cell lines samples

value: IOSE


title: Photoreceptor nuclei, D50, ZT12, me1, rep1


title: Human-IOSE-4

description: 24 commonly used cell lines samples


title: Human-IOSE-2

description: 24 commonly used cell lines samples


title: Photoreceptor nuclei, D50, ZT08, me3, rep3


title: Human-IMR90-4

description: 24 commonly used cell lines samples


title: Photoreceptor nuclei, D50, ZT12, IgG, rep1


title: Photoreceptor nuclei, D50, ZT08, me2, rep3


title: Human-IMR90-3

description: 24 commonly used cell lines samples


title: Photoreceptor nuclei, D50, ZT08, IgG, rep2


title: Human-Huh7-3

description: 24 commonly used cell lines samples


title: Human-IOSE-1

description: 24 commonly used cell lines samples


title: Human-Jurkat-4

description: 24 commonly used cell lines samples


title: Human-Huh7-1

description: 24 commonly used cell lines samples


title: Photoreceptor nuclei, D50, ZT08, me2, rep1


title: Photoreceptor nuclei, D50, ZT04, me3, rep3


title: Human-HL60-4

description: 24 commonly used cell lines samples


title: Human-HL60-3

description: 24 commonly used cell lines samples


title: Photoreceptor nuclei, D50, ZT04, me1, rep3


title: Photoreceptor nuclei, D50, ZT04, me2, rep3


title: Human-HL60-1

description: 24 commonly used cell lines samples


title: Human-HT29-1

description: 24 commonly used cell lines samples


title: Human-HepG2-4

description: 24 commonly used cell lines samples


title: Photoreceptor nuclei, D50, ZT04, me2, rep2


title: Photoreceptor nuclei, D50, ZT08, me1, rep3


title: Photoreceptor nuclei, D50, ZT04, IgG, rep2


title: Human-HepG2-3

description: 24 commonly used cell lines samples


title: Photoreceptor nuclei, D50, ZT08, IgG, rep3


title: Human-IMR90-2

description: 24 commonly used cell lines samples


title: Photoreceptor nuclei, D50, ZT08, me3, rep2


title: Human-IMR90-1

description: 24 commonly used cell lines samples


title: Photoreceptor nuclei, D50, ZT08, me2, rep2


title: Human-HepG2-2

description: 24 commonly used cell lines samples


title: Human-Huh7-4

description: 24 commonly used cell lines samples


title: Human-HepG2-1

description: 24 commonly used cell lines samples


title: Photoreceptor nuclei, D50, ZT04, me3, rep1


title: Photoreceptor nuclei, D50, ZT08, me1, rep2


title: Human-Hela-4

description: 24 commonly used cell lines samples


title: Photoreceptor nuclei, D50, ZT08, me3, rep1


title: Human-Huh7-2

description: 24 commonly used cell lines samples


title: Photoreceptor nuclei, D50, ZT04, me2, rep1


title: Photoreceptor nuclei, D50, ZT08, IgG, rep1


title: Human-Hela-3

description: 24 commonly used cell lines samples


title: Photoreceptor nuclei, D50, ZT08, me1, rep1


title: Human-HT29-4

description: 24 commonly used cell lines samples


title: Human-HT29-2

description: 24 commonly used cell lines samples


title: Human-Hela-2

description: 24 commonly used cell lines samples


title: Human-HEK293T-4

description: 24 commonly used cell lines samples


title: Photoreceptor nuclei, D50, ZT00, me2, rep3


title: Human-Hela-1

description: 24 commonly used cell lines samples


title: Human-HEK293T-3

description: 24 commonly used cell lines samples


title: Human-HL60-2

description: 24 commonly used cell lines samples


title: Photoreceptor nuclei, D50, ZT04, me3, rep2


title: Photoreceptor nuclei, D50, ZT04, me1, rep2


title: Human-HT29-3

description: 24 commonly used cell lines samples


title: Photoreceptor nuclei, D50, ZT04, IgG, rep3


title: Photoreceptor nuclei, D50, ZT04, me1, rep1


title: Photoreceptor nuclei, D50, ZT00, me3, rep3


title: Photoreceptor nuclei, D50, ZT04, IgG, rep1


title: Photoreceptor nuclei, D50, ZT00, me2, rep2


title: Human-HEK293-3

description: 24 commonly used cell lines samples


title: Photoreceptor nuclei, D50, ZT00, me3, rep1


title: Photoreceptor nuclei, D50, ZT00, me1, rep3


title: Photoreceptor nuclei, D50, ZT00, me2, rep1


title: Human-HCT116-4

description: 24 commonly used cell lines samples


title: Human-HEK293-1

description: 24 commonly used cell lines samples


title: Human-HCT116-3

description: 24 commonly used cell lines samples


title: Photoreceptor nuclei, D50, ZT00, IgG, rep3


title: Photoreceptor nuclei, D10, ZT20, me2, rep3

value: Adult, day 10


title: Human-HEK293T-2

description: 24 commonly used cell lines samples


title: Photoreceptor nuclei, D50, ZT00, me3, rep2


title: Human-HEK293T-1

description: 24 commonly used cell lines samples


title: Photoreceptor nuclei, D10, ZT20, IgG, rep3


title: Human-DLD1-2

description: 24 commonly used cell lines samples


title: Human-HEK293-4

description: 24 commonly used cell lines samples


title: Photoreceptor nuclei, D50, ZT00, me1, rep2


title: Photoreceptor nuclei, D10, ZT20, me1, rep2


title: Human-A549-4

description: 24 commonly used cell lines samples


title: Photoreceptor nuclei, D50, ZT00, IgG, rep2


title: Photoreceptor nuclei, D50, ZT00, me1, rep1


title: Human-HEK293-2

description: 24 commonly used cell lines samples


title: Photoreceptor nuclei, D10, ZT20, me1, rep1


title: Human-HCT116-1

description: 24 commonly used cell lines samples


title: Photoreceptor nuclei, D10, ZT20, me3, rep3


title: Human-HCT116-2

description: 24 commonly used cell lines samples


title: Photoreceptor nuclei, D50, ZT00, IgG, rep1


title: Human-DLD1-4

description: 24 commonly used cell lines samples


title: Photoreceptor nuclei, D10, ZT16, me3, rep3


title: Photoreceptor nuclei, D10, ZT20, me1, rep3


title: Human-DLD1-3

description: 24 commonly used cell lines samples


title: Photoreceptor nuclei, D10, ZT16, me2, rep3


title: Human-Caco2-3

description: 24 commonly used cell lines samples


title: Photoreceptor nuclei, D10, ZT20, me3, rep2


title: Human-DLD1-1

description: 24 commonly used cell lines samples


title: Photoreceptor nuclei, D10, ZT20, me2, rep2


title: Human-Caco2-2

description: 24 commonly used cell lines samples


title: Photoreceptor nuclei, D10, ZT20, IgG, rep2


title: Human-A375-1

description: 24 commonly used cell lines samples


title: Photoreceptor nuclei, D10, ZT16, me3, rep2


title: Human-Caco2-1

description: 24 commonly used cell lines samples


title: Photoreceptor nuclei, D10, ZT20, me2, rep1


title: Photoreceptor nuclei, D10, ZT20, me3, rep1


title: Carboplatin treated MCF-7 cells_3

city: Wuhan

first: Xiang

last: Li

address: Youyi Road

institute: Hubei University

data_processing:
Through removing low quality, ploy-N, and adapter contained reads by in-house perl scripts, high-quality clean data were used for further analysis.
After building index of the reference genome (GRCh38), paired-end clean reads were aligned to the mouse genome using Hisat (v2.0.5).
For the quantification of gene expression, featureCounts (v1.5.0–p3) was used to count the clean reads numbers mapped to each gene, and the FPKM (fragments per kilobase of transcript per million mapped reads) value of each gene was obtained according to the gene length and reads count.
Assembly: GRCh38
Supplementary files format and content: Text file include all FPKM values for each Sample

source_name: breast

growth_protocol: MCF-7 (ATCC® HTB-22) cells were obtained from American Type Culture Collection and cultured in DMEM (Gibco; C11995500BT) at 37 oC with a saturating humidity atmosphere containing 5% CO2. DMEM contained 10% FBS (Gibco; 26140079), and 1% penicillin/streptomycin (Gibco; 15140122).

extract_protocol:
RNA was harvested using TRIzolTM Reagent (Thermo, 15596026). 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs, E7530S) according to manufacturer’s recommendations.

treatment_protocol: Here, mRNA-Seq on the MCF-7 cells treated with or without 0.5 mM carboplatin. NC group: Normal MCF-7 cells, C group: carboplatin treated MCF-7 cells.

value: breast

value: human breast cancer cells

value: cancer cell

value: Carboplatin


title: Human-A549-3

description: 24 commonly used cell lines samples


title: MCF-7 cells_2

value: Control


title: Photoreceptor nuclei, D10, ZT20, IgG, rep1


title: MCF-7 cells_1


title: Human-A375-4

description: 24 commonly used cell lines samples


title: Human-A549-1

description: 24 commonly used cell lines samples


title: Human-A375-3

description: 24 commonly used cell lines samples


title: Human-A549-2

description: 24 commonly used cell lines samples


title: Human-A375-2

description: 24 commonly used cell lines samples


title: Photoreceptor nuclei, D10, ZT16, IgG, rep3


title: Carboplatin treated MCF-7 cells_1


title: Photoreceptor nuclei, D10, ZT16, me2, rep1


title: Photoreceptor nuclei, D10, ZT16, IgG, rep2


title: MCF-7 cells_3


title: Undifferentiated LipD1 preadipocytes, 7, LF_25

city: Leipzig

first: Linnaeus

middle: Tapia

last: Bundalian

address: 15 Albert-Scwheitzer Str.

institute: Universitatklinikum Leipzig

data_processing:
nf-core rnaseq pipeline
extract counts from DESeq2 dds object from the final output of the pipeline
Assembly: GRCh38
Supplementary files format and content: comma separetd values of normalized counts extracted from dds object
Supplementary files format and content: comma separetd values of normalized counts extracted from dds object

source_name: adipose tissue

growth_protocol: We used PTEN–haploinsufficient lipoma cells (LipPD1) isolated from a pediatric patient diagnosed with PTEN Hamartoma Tumor Syndrome (PHTS) and SGBS cells. These cells have been established as a valid human adipocyte cell models and their isolation and culture methods have been described in previous studies. Cells were cultured in Dulbecco's Modified Eagle's medium (DMEM/F12) supplemented with 10% fetal calf serum (FCS), 1% glutamine, 8 mg/L biotin and 4 mg/L pantothenic acid.

extract_protocol:
RNeasy Mini Kit (QIAGEN, #74106)
TruSeq RNA Library Prep Kit v2

treatment_protocol: Transfection was conducted using the Neon Transfection System 100 µl Kit (Invitrogen, Thermo Fisher Scientific). Preadipocytes were seeded in 15 cm diameter cell culture dishes (250,000 cells/20 ml culture medium) 24 hours prior to transfection. After harvesting and washing with PBS, cell pellets were treated with either scrambled control siRNA (Silencer Negative Control No.1 siRNA, #AM4611, Ambion, Thermo Fisher Scientific) or a combination of two leptin siRNAs (Silencer Select Pre-designed siRNA #s8135 and #s8133, Ambion, Thermo Fisher Scientific) resulting in a final RNA concentration of 10 nM in the culture medium after transfection. Subsequently, the pellet was resuspended in 100 µl R-buffer for transfection and electroporated at 1,300 V with 2 pulses of 20 ms. Transfected cells were transferred to prewarmed culture medium and plated for functional assays as described below. LEP KD efficiency was confirmed for the following experiments by measuring LEP mRNA expression in the control and LEP KD group using RT-qPCR.

value: adipose tissue

value: preadipocytes

value: LEP Knockdown


title: Photoreceptor nuclei, D10, ZT12, me3, rep3

value: Outer photoreceptors


title: Photoreceptor nuclei, D10, ZT16, me2, rep2


title: Photoreceptor nuclei, D10, ZT12, me1, rep3


title: Photoreceptor nuclei, D10, ZT12, me2, rep3


title: Photoreceptor nuclei, D10, ZT16, me1, rep3


title: Photoreceptor nuclei, D10, ZT16, me1, rep1


title: Photoreceptor nuclei, D10, ZT16, me1, rep2


title: Undifferentiated LipD1 preadipocytes, 7, LF_24


title: Carboplatin treated MCF-7 cells_2


title: Photoreceptor nuclei, D10, ZT16, me3, rep1


title: Photoreceptor nuclei, D10, ZT16, IgG, rep1


title: Differentiated LipD1 preadipocytes, 7, LF_27


title: Differentiated LipD1 preadipocytes, 7, LF_26


title: Differentiated LipD1 preadipocytes, 6, LF_22


title: Photoreceptor nuclei, D10, ZT12, me3, rep2


title: Differentiated LipD1 preadipocytes, 5, LF_19


title: Undifferentiated LipD1 preadipocytes, 6, LF_20


title: Differentiated LipD1 preadipocytes, 4, LF_16


title: Photoreceptor nuclei, D10, ZT12, IgG, rep2


title: Differentiated LipD1 preadipocytes, 4, LF_15


title: Photoreceptor nuclei, D10, ZT12, me1, rep2


title: Photoreceptor nuclei, D10, ZT12, me2, rep1


title: Photoreceptor nuclei, D10, ZT12, me2, rep2


title: Photoreceptor nuclei, D10, ZT12, IgG, rep3


title: Photoreceptor nuclei, D10, ZT12, me1, rep1


title: Differentiated LipD1 preadipocytes, 5, LF_18


title: Differentiated LipD1 preadipocytes, 6, LF_23


title: Undifferentiated LipD1 preadipocytes, 5, LF_17


title: Differentiated LipD1 preadipocytes, 3, LF_12


title: Undifferentiated LipD1 preadipocytes, 4, LF_13


title: Photoreceptor nuclei, D10, ZT12, IgG, rep1


title: Photoreceptor nuclei, D10, ZT08, me1, rep3


title: Photoreceptor nuclei, D10, ZT08, IgG, rep3


title: Photoreceptor nuclei, D10, ZT08, me3, rep3


title: Photoreceptor nuclei, D10, ZT08, me2, rep3


title: Differentiated LipD1 preadipocytes, 2, LF_08


title: Differentiated LipD1 preadipocytes, 2, LF_07


title: Photoreceptor nuclei, D10, ZT08, me3, rep1


title: Undifferentiated LipD1 preadipocytes, 3, LF_09


title: Undifferentiated LipD1 preadipocytes, 2, LF_06


title: Undifferentiated LipD1 preadipocytes, 3, LF_10


title: Photoreceptor nuclei, D10, ZT08, me2, rep2


title: Photoreceptor nuclei, D10, ZT08, me3, rep2


title: Photoreceptor nuclei, D10, ZT04, me2, rep3


title: Differentiated LipD1 preadipocytes, 1, LF_04


title: Photoreceptor nuclei, D10, ZT12, me3, rep1


title: Undifferentiated LipD1 preadipocytes, 2, LF_05


title: Photoreceptor nuclei, D10, ZT04, me1, rep3


title: Undifferentiated LipD1 preadipocytes, 4, LF_14


title: Photoreceptor nuclei, D10, ZT08, IgG, rep2


title: Differentiated LipD1 preadipocytes, 3, LF_11


title: Photoreceptor nuclei, D10, ZT08, me1, rep2


title: Photoreceptor nuclei, D10, ZT04, me3, rep2


title: Undifferentiated LipD1 preadipocytes, 1, LF_01


title: Photoreceptor nuclei, D10, ZT08, me1, rep1


title: Photoreceptor nuclei, D10, ZT08, IgG, rep1


title: Test-input

first: linlin

last: feng

state: 未选择

address: Dongqing Road

institute: Guizhou Medical University

data_processing:
The data sequence was contaminated and low quality, and the filtered reads were compared to the reference genome and counted, and each read was allowed up to 3 base mismatches. The hydroxymethylation peak (peak) was based on the whole genome processed sequences by MACS software, the results of each sample were obtained, and the distribution on gene elements (upstream2k, 5 'UTR, CDS, Intron, 3' UTR, downstream2k) was counted for comparative analysis.
The hMeDIP enriched regions (peaks) associated with LncRNA, mRNA and Small ncRNA were annotated using the latest UCSC RefSeq database. Hydroxymethylated regions (differentially hydroxymethylated regions, DhMRs) within LncRNA, mRNA and Small ncRNA promoter were analyzed by diffrep software, cutoff value: log2FC 1, p-value 10 3.
Intergenic regions of hydroxymethylation associated with Enhancer and Super Enhancer were annotated using the UCSC RefSeq database.
Finally, the differential genes between the two samples were subjected to GO functional enrichment analysis and KEGG functional analysis.
Assembly: hg38
Supplementary files format and content: bigwig

source_name: LX -2

growth_protocol: DMEM (4.5 g/L glucose) supplemented with 10% FBS and penicillin/streptomycin at 37°C, 5% CO2 and 95% humidity

extract_protocol:
cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covans)
1 µg of each fragmented sample was connected to Illumina's genomic adapters with the Genomic DNA Sample Kit (#FC-102-1002, Illumina) following the manufacturer's protocol. Next, DNA fragments of 300–900 bp were denatured at 95°C to form single-stranded DNA, followed by immunoprecipitation using rabbit anti-5hmC. Next, The DNA enrichment was followed by PCR amplification and purification using AMPure XP beads. Quality control (QC) was conducted to evaluate the integrity of the hMeDIP experiments. The DNA fragment mixture library is denatured by 0.1M NaOH to generate single-stranded DNA molecules, which are loaded into the flow cell channels at a concentration of 8 pM, and then amplified in situ.
Sequencing was performed using an Illumina NovaSeq 6000, according to the manufacturer’s instructions. Sequencing was performed by running 300 cycles using the NovaSeq 6000 S4 Reagent Kit (#2012866, Illumina).

treatment_protocol: TET3 overexpression, knockdown, or control vectors were infected into LX-2 cells when the cells reached approximately 70–80% confluency; the procedures were carried out in compliance with the instructions provided by the manufacturer. Transfected cells were cultured with 5 ng/mL of TGF-β (containing serum-free DMEM) medium for 24h prior to the experiments.

value: LX -2

value: human hepatic stellate cell line

tag: chip antibody


title: Undifferentiated LipD1 preadipocytes, 1, LF_02


title: Test-1-3

value: Oe-TET3,5 ng/ml TGF-β 24h


title: Photoreceptor nuclei, D10, ZT04, me3, rep3

value: male


title: stable THP-1 cell line selected after transfection with an vector expressing ELDR  (Lego-lnc-ELDR) rep1 C3

city: Montreal

first: Tarik

last: Moroy

state: QC

address: 110, West Pine Avenue, 597

country: Canada

institute: Institut de recherches cliniques de Montréal

data_processing:
The quality of the raw reads was assessed with FASTQC v0.11.8. After examining the quality of the raw reads, trimming was performed with TRIMMOMATIC v0.36.
The reads were aligned to the GRCh38 reference genome (release 102) with BOWTIE2 v2.2.6 with mean of 77 % of reads uniquely mapped.
Alignments were post-processed to remove PCR duplicates (Picard tool v2.4.1) and reads mapping to mitochondrial DNA (samtools v1.8). In order to represent the real Tn5 transposase binding sites of 9bp, the coordinates of the reads were shifted by +4bp for the plus strand and by -5bp for the minus strand, using Deeptools v3.0.1. The former was also used to remove ENCODE's blacklisted regions (signal artefact regions) and convert Bam files to BEDPE format.
MACS2 was used to identify significant peaks. Diffbind v2.10.0 R package was used to generate the count matrix of Tn5 insertion site numbers for each consensus peak (peaks that were present in all samples for each condition). Differentially accessibility regions (DARs) were identified between conditions within each cell type and controlling for the effect of gender, using DESeq2 v1.30.0 R package. DARs were annotated with their closest feature and different transcription binding motifs identified with HOMER v4.8.0. A non biaised motif search was also performed with HOMER, in order to identify all known motifs and de novo motifs in these regions.
Assembly: GRCh38
Supplementary files format and content: bigWig, DESEQ2 diff results

source_name: AML cell line THP-1

extract_protocol:
ATAC-seq was carried out with 50,000 cells washed once with 50μl of cold 1X PBS buffer. Spin down at 500g for 5 min, 4 °C. Gently pipetted to resuspend the cell pellet in 50μl of cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). Cells were spin down immediately at 500g for 10 min, 4°C and lysed with non-ionic detergent to enrich nuclei.
Pellets of 50,000 nuclei were tagmented for 30 minutes at 37°C (TDE1 Transposase, Illumina) and tagmented DNA was purified on column DNA clean-5 (Zymo Research). Illumina UDP Indexes were integrated by PCR-enrichment (11 cycles) and final libraries were purified and size selected (L=1.1; R=0.6) with ampure beads (KAPA, Roche Diagnotics). Library size distribution was assessed on a 2100 bioanalyzer (Agilent Technologies) and libraries were quantified by qPCR

value: AML cell line THP-1

value: myeloid


title: Photoreceptor nuclei, D10, ZT04, me1, rep2


title: Photoreceptor nuclei, D10, ZT04, IgG, rep2

value: IgG for H3K4me


title: Differentiated LipD1 preadipocytes, 1, LF_03


title: CON-input


title: Test-1-2


title: Photoreceptor nuclei, D10, ZT08, me2, rep1

value: Adult, day 10


title: CON-1-2

value: Oe-NC, 5 ng/ml TGF-β 24h


title: CON-1-3


title: stable THP-1 cell line selected after transfection with an vector expressing ELDR  (Lego-lnc-ELDR) rep2 C3


title: Photoreceptor nuclei, D10, ZT04, me3, rep1


title: Photoreceptor nuclei, D10, ZT04, me2, rep1


title: stable THP-1 cell line selected after transfection with an empty vector (Lego-lnc) rep2


title: Photoreceptor nuclei, D10, ZT04, me2, rep2


title: Photoreceptor nuclei, D10, ZT00, me2, rep3


title: Photoreceptor nuclei, D10, ZT04, me1, rep1


title: Photoreceptor nuclei, D10, ZT04, IgG, rep1


title: stable THP-1 cell line selected after transfection with an vector expressing ELDR  (Lego-lnc-ELDR) rep2 C1


title: CON-1-1


title: stable THP-1 cell line selected after transfection with an vector expressing ELDR  (Lego-lnc-ELDR) rep1 C1


title: Photoreceptor nuclei, D10, ZT00, me3, rep3


title: Photoreceptor nuclei, D10, ZT04, IgG, rep3


title: non transfected THP-1 cells rep2


title: Photoreceptor nuclei, D10, ZT00, me3, rep2


title: Test-1-1


title: stable THP-1 cell line selected after transfection with an vector expressing ELDR C1 (Lego-lnc-ELDR)

data_processing:
The quality of the raw reads was assessed with FASTQC v0.11.9.
The reads were aligned to the human reference genome with STAR v2.7.9a
The raw counts were calculated with FeatureCounts v2.0.3 based on the human reference genome (release 102).DESeq2 R package was used to compute FPKM values and logFC.
Assembly: GRCh38
Supplementary files format and content: DESEQ2 FPKM/log2FC

extract_protocol:
RNA was extracted using RNeasy Mini Kit (Qiagen)
Ribodepletion and library preparation were performed with Zymo-Seq RiboFree Total RNA Library Kit (Zymo Research). Library size distribution was assessed on a 2100 bioanalyzer (Agilent Technologies) and libraries were quantified by qPCR.


title: stable THP-1 cell line selected after transfection with an empty vector expressing NO ELDR (Lego-lnc)

description: WT


title: R0135

first: Peng

last: Jin

address: Ruijin Rd. II

department: Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics

institute: Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

library_source: transcriptomic single cell

data_processing:
Single-cell expression matrices were derived from raw sequence data (FASTQ) using Cell Ranger software (v6.0.2) with the GRCh38 reference genome. These expression matrices were subsequently processed individually in R (v4.1.3) utilizing the CreateSeuratObject function from Seurat (v4.4.0). The resulting objects were then merged. We excluded cells with < 1,000 or > 6,000 unique feature counts, as well as those with over 15% of transcripts originating from mitochondrial genes. To identify and eliminate cells from empty droplets and remove barcode-swapped pseudo-cells from the gene expression matrices, we employed the emptyDrops function of DropletUtils (v1.18.1). Additionally, DoubletFinder (v2.0.3) was utilized to identify and remove doublets, based on the expected doublet rate derived from the loading rate.
Assembly: GRCh38
Supplementary files format and content: H5 files include the raw count

source_name: Bone marrow

extract_protocol:
Bone marrow mononuclear cells from AML patients were isolated after Ficoll–Isopaque density gradient centrifugation.
Single-cell RNA-sequencing was performed on two primary AML patient BMs with the Chromium 10x Genomics 3’ gene expression kit version 3.1 according to the manufacturer’s instructions.

value: Bone marrow


title: R0134


title: stable THP-1 cell line selected after transfection with an empty vector (Lego-lnc) rep1


title: non transfected THP-1 cells rep1


title: Photoreceptor nuclei, D10, ZT00, me1, rep3


title: Photoreceptor nuclei, D10, ZT00, me2, rep2


title: Photoreceptor nuclei, D10, ZT00, me1, rep2


title: R0133


title: Photoreceptor nuclei, D10, ZT00, IgG, rep2


title: ATAC Day 50 ZT20 rep 3

data_processing:
For CUT&RUN and ATAC: Read trimming with trimmomatic
Alignment with Bowtie2, dovetail mates considered concordant for CUT&RUN
Indexing, generation of BAM files using Samtools
CPM-normalized bigWigs generated with deepTools
Assembly: BDGP6.46
Supplementary files format and content: bigWig files, CPM-normalized

value: Adult, day 50


title: AML_302

data_processing:
Trim-galore was employed to remove the adapter sequences.
The clean reads were aligned with STAR and quantified with HT-Seq using the GRCh38 human assembly.
The differential expression assessment was conducted using the DESeq2 package.
Gene expression levels were normalized to Transcripts Per Kilobase of exon model per Million mapped reads (TPM) using a customed script.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text files include raw count values for each Sample

extract_protocol:
Bone marrow mononuclear cells from AML patients were isolated after Ficoll–Isopaque density gradient centrifugation. Genomic mRNA were extracted from the patients’ BM using the AllPrep PowerFecal RNA Kit in accordance with the manufacturer’s instructions.
Libraries were prepared using the KAPA RNA HyperPrep kit in accordance with the manufacturer’s instructions (KAPA). High-throughput sequencing was performed on the NovaSeq 6000 platform in accordance with the manufacturer’s protocol (paired-end 2 × 150 bp).

value: AML

value: Others


title: Photoreceptor nuclei, D10, ZT00, me3, rep1


title: Photoreceptor nuclei, D10, ZT00, me2, rep1


title: AML_304


title: AML_303


title: ATAC Day 50 ZT16 rep 2


title: Photoreceptor nuclei, D10, ZT00, IgG, rep1


title: ATAC Day 50 ZT20 rep 2


title: ATAC Day 50 ZT20 rep 1


title: AML_301


title: Photoreceptor nuclei, D10, ZT00, IgG, rep3


title: AML_299


title: AML_300


title: ATAC Day 50 ZT16 rep 3


title: ATAC Day 50 ZT12 rep 2


title: ATAC Day 50 ZT16 rep 1


title: Photoreceptor nuclei, D10, ZT00, me1, rep1


title: ATAC Day 50 ZT12 rep 1


title: ATAC Day 50 ZT8 rep 3


title: AML_298


title: ATAC Day 50 ZT12 rep 3


title: AML_297

value: Venetoclax-based


title: AML_296


title: ATAC Day 50 ZT8 rep 1


title: AML_294

value: Supportive care


title: R0132


title: ATAC Day 50 ZT8 rep 2


title: stable THP-1 cell line selected after transfection with an vector expressing ELDRC3 (Lego-lnc-ELDR)


title: AML_295


title: ATAC Day 50 ZT4 rep 3


title: AML_291


title: AML_290


title: AML_289


title: AML_288


title: AML_287


title: ATAC Day 50 ZT0 rep 3


title: ATAC Day 50 ZT0 rep 2


title: AML_286


title: AML_285


title: AML_284


title: ATAC Day 50 ZT0 rep 1


title: ATAC Day 10 ZT20 rep 2


title: ATAC Day 10 ZT20 rep 1


title: ATAC Day 10 ZT16 rep 3


title: AML_283


title: ATAC Day 10 ZT16 rep 2


title: ATAC Day 10 ZT16 rep 1


title: AML_279


title: ATAC Day 10 ZT12 rep 3


title: AML_293


title: ATAC Day 10 ZT20 rep 3


title: ATAC Day 10 ZT12 rep 2


title: AML_278


title: AML_281


title: AML_292


title: ATAC Day 50 ZT4 rep 1


title: AML_277


title: ATAC Day 10 ZT12 rep 1


title: AML_275


title: AML_282


title: ATAC Day 10 ZT8 rep 2


title: AML_274


title: AML_276


title: ATAC Day 10 ZT8 rep 1


title: ATAC Day 10 ZT4 rep 3


title: AML_273


title: AML_272


title: ATAC Day 10 ZT4 rep 2


title: ATAC Day 10 ZT4 rep 1


title: AML_271


title: AML_280


title: ATAC Day 10 ZT0 rep 3


title: AML_270


title: ATAC Day 50 ZT4 rep 2


title: AML_268


title: ATAC Day 10 ZT0 rep 2


title: AML_269


title: AML_266


title: AML_267


title: CUT&RUN Day 50 ZT20 PolII rep 3

value: RNA PolII


title: ATAC Day 10 ZT0 rep 1

value: Outer photoreceptors


title: AML_265


title: CUT&RUN Day 50 ZT20 PolII rep 2


title: CUT&RUN Day 50 ZT20 IgG rep 2

value: IgG for RNA PolII


title: AML_264


title: ATAC Day 10 ZT8 rep 3


title: AML_263


title: AML_261


title: AML_262


title: CUT&RUN Day 50 ZT20 IgG rep 1


title: CUT&RUN Day 50 ZT16 PolII rep 3


title: AML_260


title: AML_259


title: CUT&RUN Day 50 ZT16 PolII rep 2


title: AML_258


title: CUT&RUN Day 50 ZT20 PolII rep 1


title: AML_257


title: CUT&RUN Day 50 ZT16 IgG rep 3


title: CUT&RUN Day 50 ZT16 IgG rep 2


title: AML_256


title: CUT&RUN Day 50 ZT16 PolII rep 1


title: CUT&RUN Day 50 ZT20 IgG rep 3


title: AML_255


title: AML_253


title: CUT&RUN Day 50 ZT16 IgG rep 1


title: CUT&RUN Day 50 ZT12 IgG rep 3


title: CUT&RUN Day 50 ZT12 PolII rep 3


title: CUT&RUN Day 50 ZT12 IgG rep 2


title: AML_254


title: CUT&RUN Day 50 ZT12 PolII rep 2


title: AML_252


title: CUT&RUN Day 50 ZT12 IgG rep 1


title: CUT&RUN Day 50 ZT12 PolII rep 1


title: AML_248


title: CUT&RUN Day 50 ZT8 PolII rep 3


title: AML_249


title: AML_246


title: CUT&RUN Day 50 ZT8 IgG rep 3


title: CUT&RUN Day 50 ZT8 IgG rep 2


title: AML_245


title: AML_242


title: AML_244


title: CUT&RUN Day 50 ZT4 IgG rep 3


title: CUT&RUN Day 50 ZT8 IgG rep 1


title: AML_243


title: CUT&RUN Day 50 ZT4 PolII rep 2


title: CUT&RUN Day 50 ZT4 PolII rep 3


title: AML_241


title: CUT&RUN Day 50 ZT4 IgG rep 2


title: AML_251


title: AML_240


title: AML_239


title: CUT&RUN Day 50 ZT4 PolII rep 1


title: CUT&RUN Day 50 ZT4 IgG rep 1


title: AML_238


title: AML_235


title: CUT&RUN Day 50 ZT8 PolII rep 2


title: CUT&RUN Day 50 ZT0 IgG rep 2


title: AML_233


title: AML_250


title: CUT&RUN Day 50 ZT0 PolII rep 3


title: AML_237


title: AML_236


title: CUT&RUN Day 50 ZT0 IgG rep 3


title: AML_231


title: AML_230


title: CUT&RUN Day 10 ZT20 PolII rep 2


title: CUT&RUN Day 10 ZT20 IgG rep 2


title: AML_247


title: CUT&RUN Day 50 ZT0 PolII rep 2


title: AML_228


title: CUT&RUN Day 10 ZT20 IgG rep 1


title: CUT&RUN Day 50 ZT8 PolII rep 1


title: AML_234


title: AML_224


title: CUT&RUN Day 50 ZT0 PolII rep 1


title: AML_232


title: AML_223


title: CUT&RUN Day 50 ZT0 IgG rep 1


title: AML_220


title: CUT&RUN Day 10 ZT20 PolII rep 3


title: CUT&RUN Day 10 ZT20 IgG rep 3


title: CUT&RUN Day 10 ZT12 PolII rep 3


title: CUT&RUN Day 10 ZT12 PolII rep 2


title: CUT&RUN Day 10 ZT12 IgG rep 3


title: AML_217


title: CUT&RUN Day 10 ZT16 IgG rep 1


title: AML_229


title: AML_227


title: AML_226


title: AML_216


title: CUT&RUN Day 10 ZT20 PolII rep 1


title: CUT&RUN Day 10 ZT12 IgG rep 2


title: CUT&RUN Day 10 ZT16 PolII rep 3


title: AML_225


title: CUT&RUN Day 10 ZT16 IgG rep 3


title: AML_213


title: AML_214


title: AML_222


title: CUT&RUN Day 10 ZT16 IgG rep 2


title: AML_210


title: CUT&RUN Day 10 ZT8 IgG rep 2


title: AML_209


title: CUT&RUN Day 10 ZT16 PolII rep 1


title: AML_221


title: CUT&RUN Day 10 ZT8 IgG rep 1


title: AML_208


title: CUT&RUN Day 10 ZT12 IgG rep 1


title: CUT&RUN Day 10 ZT4 IgG rep 3


title: CUT&RUN Day 10 ZT4 PolII rep 3


title: CUT&RUN Day 10 ZT4 PolII rep 2


title: AML_219


title: AML_218


title: CUT&RUN Day 10 ZT16 PolII rep 2


title: CUT&RUN Day 10 ZT4 PolII rep 1


title: AML_203


title: CUT&RUN Day 10 ZT0 PolII rep 3


title: AML_200


title: CUT&RUN Day 10 ZT12 PolII rep 1


title: AML_215


title: AML_205


title: AML_198


title: CUT&RUN Day 10 ZT0 IgG rep 2


title: CUT&RUN Day 10 ZT8 PolII rep 3


title: AML_197


title: AML_212


title: AML_196


title: CUT&RUN Day 10 ZT8 IgG rep 3


title: CUT&RUN Day 10 ZT0 IgG rep 1


title: vil1-1 12°C RNA-seq (replicate 3)

city: Austin

first: Sibum

last: Sung

institute: University of Texas at Austin

data_processing:
Reads generated by Illumina NovaSeq platform were checked for quality using FastQC
After quality assessment, reads were aligned on TAIR10 genome using HISAT2 for RNA-seq and Bowtie2 for ChIP-seq
SAM files generated from mapping were then converted into BAM files and sorted using Samtools
For the gene counting bedtools program was used which generates raw count using BAM files
Raw count was then fed into R for differential gene expression analysis using edgeR and data visualization
Assembly: TAIR10
Supplementary files format and content: Excel file containing raw read count of each sample and RPKM normalized read count of each sample

organism: Arabidopsis thaliana

source_name: Whole rosettes

extract_protocol:
RNA was extracted using Qiagen, Rneasy Plant Mini kit.
Library was prepared using NEB illumina library preparation kit

value: Whole rosettes

value: Continous 12°C in short-day


title: CUT&RUN Day 10 ZT8 PolII rep 2

value: male


title: AML_211


title: CUT&RUN Day 10 ZT0 IgG rep 3


title: AML_207


title: AML_206


title: AML_199


title: CUT&RUN Day 10 ZT8 PolII rep 1


title: AML_194


title: vil1-1 12°C RNA-seq (replicate 1)


title: AML_192


title: vil1-1 22°C RNA-seq (replicate 3)

value: Continous 22°C in short-day


title: CUT&RUN Day 10 ZT0 PolII rep 1

value: RNA RNA PolII


title: vil1-1 22°C RNA-seq (replicate 2)


title: AML_191


title: CUT&RUN Day 10 ZT4 IgG rep 2


title: AML_204


title: AML_201


title: AML_202


title: CUT&RUN Day 10 ZT4 IgG rep 1


title: Col-0 12°C RNA-seq (replicate 3)


title: CUT&RUN Day 10 ZT0 PolII rep 2


title: vil1-1 12°C RNA-seq (replicate 2)


title: AML_188


title: AML_179


title: AML_178