title: ∆ve-1_M_Dark_R2 [VEG_MD2]

description:
RNA isolated from vegetative mycelium grown for 24h on vogel´s liquid flask under dark conditions with shaking (150 rpm)
VEG_MD2


title: ∆ve-1_M_Dark_R4 [VEG_MD4]

status: Public on Jul 20 2022

type: SRA

city: Sevilla

first: Gabriel

last: Gutierrez

address: PO BOX 1095

department: Genetics

country: Spain

institute: University of Seville

description:
RNA isolated from vegetative mycelium grown for 24h on vogel´s liquid flask under dark conditions with shaking (150 rpm)
VEG_MD4

library_source: transcriptomic

data_processing:
libraries were run on Illumina Genome Analyzer (Illumina HiSeqV4).
Single end-reads of 100 nucleotide each were mapped against the N. crassa OR74A genome by using Tophat 2.11
quality was checked using FastQC
automatic preprocessing of the reads was carried out with AFTERQC 0.9.6
SeqMonk was used for visualization and quantification
Supplementary_files_format_and_content: raw counts, matrix text format

molecule: total RNA

organism: Neurospora crassa

growth_protocol: dishes containing 25ml of Vogel´s liquid medium, were inoculated to a final concentration of 105 conidia/ml

extract_protocol:
Total RNA was isolated from frozen mycelia (approximately 100 mg) using 1g of Zirconia/Silica Beads (product number) with RLC extraction Buffer by using RNeasy Plant Mini Kit (Qiagen), following the manufacturer procedure. RNA was treated with on-column DNA digestion during RNA purification using RNAseq-free DNA set (Qiagen).
Poly-A selection and cDNA libraries preparation for RNA were prepared according to the Illumina mRNA Sample Preparation Guide

treatment_protocol: 48h at 22° in complete darkness.For light induction, cultures were exposed to white light for 30 min

tag: strain background

tag: genotype

tag: treatment

value: Dark

tag: tissue

value: mycelia


title: AML10-H3K27ac

city: Suzhou

first: Fang

last: Fang

state: Jiangsu

address: 92 Zhongnan street

country: China

institute: Children’s Hospital of Soochow University

library_source: genomic

data_processing:
Raw data of ChIP-Seq was aligned to the reference genome (UCSC hg38) using Bowtie2 (v 2.3.5)
Peaks were identified using MACS2 (v2.0.9)
Genome_build: hg38
Supplementary_files_format_and_content: peak text files

molecule: genomic DNA

organism: Homo sapiens

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions

tag: chip antibody

tag: disease

value: AML


title: Microdissected Rat Renal CCD, Sham Control_4_3Hr, RNA-Seq, Transcriptome 01

city: Taipei

first: Chih-Chien

last: Sung

state: Taipei

address: No 325, Section 2, Cheng-Kung Road,Neihu

department: Department of Medicine

country: Taiwan

institute: Tri-Service General Hospital, National Defense Medical Center

data_processing:
Sequenced reads were mapped to Ensembl rat gene set (Rnor_6.0) using STAR v2.7.3
Transcript abundances in TPM were caculated by RSEM/1.3.3
Genome_build: Rnor_6.0 (Ensembl)
Supplementary_files_format_and_content: tab-delimited text files include TPM  for each sample

molecule: polyA RNA

organism: Rattus norvegicus

source_name: Kidney

growth_protocol: Pathogen-free male Sprague-Dawley rats weighing 120-160 g had free access to ad libitum drinking water and normal rodent chow before experiment. The rats were housed one per cage, maintained on a 12:12-h light-dark cycle, and acclimated to the housing conditions for 2 days before the experimental procedures.

extract_protocol:
For bulk kidney, obstructed kidneys from animals were rapidly removed and be processed individually by homogenizing in Trizol, then transferred to a 2.0 mL microcentrifuge tube for RNA extraction and library construction (TruSeq Stranded mRNA Library Prep Kit, Illumina) according to the manufacturer’s protocol. For microdissecting cortical collecting duct and cortical TAL,  total RNA were extracted using the Direct-zol™ RNA Kits (Zymo Research) and cDNA was synthesized by SMARTer V4 Ultra Low RNA kit (Clontech). The cDNA was then amplified for 15 PCR cycles, purified by AmPure XP magnetic beads (Beckman Coulter Genomics), and eluted with 15 μL Elution Buffer. The purified cDNA was further quantified by Qubit. Library size distribution was determined using the Agilent 2100 bioanalyzer using High-Sensitive DNA kit. The Nextera XT DNA Library Preparation Kits (Illumina) was used to generate the libraries with input of 1 ng.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For the unilateral ureteral obstruction (UUO) group, rats were anesthetized and the left ureter was exposed and separated through a flank incision. The left ureter was ligated with 4-0 silk at near the renal pelvis. For the sham control group, surgical procedures were the same as for UUO animals except that the ureter was not ligated.

tag: strain

value: Sprague Dawley

value: Kidney

tag: group

value: sham


title: ∆ve-1_M_Dark_R3 [VEG_MD3]

description:
RNA isolated from vegetative mycelium grown for 24h on vogel´s liquid flask under dark conditions with shaking (150 rpm)
VEG_MD3


title: AML8-Input


title: AML11-H3K27ac


title: Microdissected Rat Renal cTALs, UUO_3_3Hr, RNA-Seq, Transcriptome 01

value: UUO


title: AML9-H3K27ac


title: T1003

city: Guangzhou

first: Jun

last: Ma

address: 651 Dongfeng Road East

institute: Sun Yat-sen University Cancer Center

data_processing:
For RNA sequencing, the libraries (2μg RNA) were constructed using the TruSeq RNA Sample Preparation Kit (Illumina, CA, USA) and sequenced on an Illumina NovaSeq 6000 platform at the PGEM Biotechnology Co., Ltd (Guangzhou, China).
Fragments were mapped to the human genome using Hisat2 (v2.0.5), and gene abundance was reported as read counts.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Human tissue

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tmn

tag: disease state

value: Nasopharyngeal carcinoma

value: High


title: T479

value: Low


title: ∆ve-1_M_Dark_R1 [VEG_MD1]

description:
RNA isolated from vegetative mycelium grown for 24h on vogel´s liquid flask under dark conditions with shaking (150 rpm)
VEG_MD1


title: Microdissected Rat Renal CCD, UUO_4_3Hr, RNA-Seq, Transcriptome 02


title: T798


title: Microdissected Rat Renal CCD, UUO_3_3Hr, RNA-Seq, Transcriptome 02


title: Microdissected Rat Renal CCD, UUO_3_3Hr, RNA-Seq, Transcriptome 01


title: Wt_VEG_Light_R2 [MYC_WL2]

description:
RNA isolated from vegetative mycelium grown for 47:30h on vogel´s liquid plates under dark conditions and exposed to 30 min light before being collected
MYC_WL2

value: Wild-type

value: Light


title: AML8-H3K27ac


title: Wt_VEG_Light_R1 [MYC_WL1]

description:
RNA isolated from vegetative mycelium grown for 47:30h on vogel´s liquid plates under dark conditions and exposed to 30 min light before being collected
MYC_WL1


title: AML7-H3K27ac


title: T661


title: T1147


title: AML6-H3K27ac


title: T596


title: Microdissected Rat Renal cTALs, Sham Control_3_3Hr, RNA-Seq, Transcriptome 01


title: Microdissected Rat Renal CCD, Sham Control_3_3Hr, RNA-Seq, Transcriptome 01


title: Wt_VEG_Dark_R2 [MYC_WD2]

description:
RNA isolated from vegetative mycelium grown for 48h on vogel´s liquid plates under dark conditions
MYC_WD2


title: AML5-H3K27ac


title: Microdissected Rat Renal cTALs, UUO_2_3Hr, RNA-Seq, Transcriptome 01


title: Ecl_5.VN

city: Pretoria

first: John

last: Osei Sekyere

state: Gauteng

address: 05 Bopheloweg Off Dr. Savage Road

department: Department of Medical Microbiology

country: South Africa

institute: University of Pretoria

description:
ST39
Samples were collected from Pregnant women who were at labour or just to have labour at the Steve Biko Academic Hospital. Rectal swabs were taken from the patients and brought to the laboratory for culturing and subsequent microbiological analysis

data_processing: All analysis was conducted within SMRTLINK v10.1

organism: Klebsiella pneumoniae

source_name: rectal swab of pregnant women

growth_protocol: isolates on the swabs were grown in an enrichment broth overnight prior to plating on a blood plate

extract_protocol:
Zymo DNA extraction kits were used to extract DNA for PCR confirmation of the resistance genes
HMW gDNA was isolated using NEB Mornach HMW DNA isolation kit (https://international.neb.com/protocols/2020/10/27/protocol-for-high-molecular-weight-dna-hmw-dna-extraction-from-bacteria). HMW gDNA was quantified using Qubit HS dsDNA Assay and qualified on Tapestation using genomics screentape. HMW gDNA was shared to ~10kb fragments using covaries g-Tubes and QC’d using the above method. SMRTbell libraries were performed using PacBio’s Microbial Multiplexing workflow (see attached)     The resulting libraries were size selected using BluePippin Size selection using U1 marker (10-18kb). QC was performed using the above method. Libraries were then prepared for sequencing following the online SMRTlink guided protocol (Binding kit 2.0 and Control 1.0, Sequel II Sequencing plate 2.0 and SMRT cell 8M.)
OTHER: size selection was done by Blue-Pippin and sequenced with PacBio for DNA WGS

treatment_protocol: The plates were impregnated with colistin and/ or carbapenems to inhibit all but carbapenem and/or colistin-resistant isolates

tag: source

value: Carbapenem and/or colistin resistant Enterobacterales isolated from pregnant women

tag: sample type

value: rectal swab isolate


title: Wt_VEG_Dark_R1 [MYC_WD1]

description:
RNA isolated from vegetative mycelium grown for 48h on vogel´s liquid plates under dark conditions
MYC_WD1


title: ∆ve-1_VEG_Light_R1 [MYC_ML1]

description:
RNA isolated from vegetative mycelium grown for 47:30h on vogel´s liquid plates under dark conditions and exposed to 30 min light before being collected
MYC_ML1


title: T591


title: ∆ve-1_VEG_Light_R2 [MYC_ML2]

description:
RNA isolated from vegetative mycelium grown for 47:30h on vogel´s liquid plates under dark conditions and exposed to 30 min light before being collected
MYC_ML2


title: T691


title: KPn_4.VN

description:
ST340
Samples were collected from Pregnant women who were at labour or just to have labour at the Steve Biko Academic Hospital. Rectal swabs were taken from the patients and brought to the laboratory for culturing and subsequent microbiological analysis


title: ∆ve-1_VEG_Dark_R2 [MYC_MD2]

description:
RNA isolated from vegetative mycelium grown for 48h on vogel´s liquid plates under dark conditions
MYC_MD2


title: Microdissected Rat Renal CCD, UUO_2_3Hr, RNA-Seq, Transcriptome 02


title: T524


title: Acetabular cartilage, DDH

city: Toon

first: Yuuki

last: Imai

state: Ehime

address: Shitsukawa

department: Proteo-Science Center

country: Japan

institute: Ehime University

description: combined total RNA from 5 individuals

data_processing:
Sequence data were mapped on the mouse genome (rn6) using Tophat and analyzed by Cufflinks.
Genome_build: rn6
Supplementary_files_format_and_content: Normal A vs DDH A.xlsx

source_name: Acetabular cartilage

growth_protocol: Newborn rats were divided into two groups.The control rats were raised without any restrictions. The DDH rats were fixed by swaddling, with the hind limbs immobilized in the position of hip adduction and extension and knee extension for 10 days after birth. After swaddling for 10 days, the rats were allowed to move freely. The acetabular cartilage was harvested from 3-week-old control and DDH rats.

extract_protocol:
Total RNA was extracted with Isogen (Nippon gene, Japan) and RNeasy spin column kit (Qiagen, USA). 1 µg of RNA samples with RNA integrity number (RIN) greater than 7 were used for library preparation.
RNA-Seq libraries were prepared using SMARTer Stranded Total RNA-Seq Kit - Pico Input Mammalian (Takara Bio Inc.) according to the manufacturer's instructions and subsequently validated for an average size of about 410-430 bp using a 2100 Bioanalyzer and the Agilent DNA1000 kit for the construction of sequencing libraries.

value: Wistar

value: Animal model of Developmental Dysplasia of the Hip

value: Acetabular cartilage


title: T476


title: Microdissected Rat Renal CCD, UUO_2_3Hr, RNA-Seq, Transcriptome 01


title: Acetabular cartilage, Normal

description: combined total RNA from 4 individuals

value: normal control


title: T456


title: Microdissected Rat Renal cTALs, Sham Control_2_3Hr, RNA-Seq, Transcriptome 01


title: Wt_15A_Light_R2 [CON_WL4]

description:
RNA isolated from aerial tissue developed for 14:30h on vogel´s solid plate under dark conditions and exposed to 30 min light before being collected
CON_WL4

value: mycelia


title: ∆ve-1_VEG_Dark_R1 [MYC_MD1]

description:
RNA isolated from vegetative mycelium grown for 48h on vogel´s liquid plates under dark conditions
MYC_MD1

value: Dark


title: T434


title: Microdissected Rat Renal CCD, Sham Control_3_3Hr, RNA-Seq, Transcriptome 02

value: Sprague Dawley


title: Microdissected Rat Renal CCD, Sham Control_2_3Hr, RNA-Seq, Transcriptome 02

value: Kidney


title: T571


title: Wt_15A_Light_R1 [CON_WL3]

description:
RNA isolated from aerial tissue developed for 14:30h on vogel´s solid plate under dark conditions and exposed to 30 min light before being collected
CON_WL3


title: T1440


title: Microdissected Rat Renal CCD, Sham Control_2_3Hr, RNA-Seq, Transcriptome 01

value: sham


title: Wt_15A_Dark_R2 [CON_WD2]

description:
RNA isolated from aerial tissue developed for 15h on vogel´s solid plate under dark conditions
CON_WD2


title: ∆ve-1_15A_Light_R2 [CON_ML4]

description:
RNA isolated from aerial tissue developed for 14:30h on vogel´s solid plate under dark conditions and exposed to 30 min light before being collected
CON_ML4


title: T1042


title: T11


title: Wt_15A_Dark_R1 [CON_WD1]

description:
RNA isolated from aerial tissue developed for 15h on vogel´s solid plate under dark conditions
CON_WD1


title: ∆ve-1_15A_Light_R1 [CON_ML3]

description:
RNA isolated from aerial tissue developed for 14:30h on vogel´s solid plate under dark conditions and exposed to 30 min light before being collected
CON_ML3


title: Microdissected Rat Renal cTALs, UUO_1_3Hr, RNA-Seq, Transcriptome 01

value: UUO


title: Icariin-treated BMSC

type: RNA

city: Shanghai

first: Hongmeng

last: Yu

address: No.83, Fenyang Road

department: Department of Otolaryngology

institute: Eye & ENT Hospital, Fudan University

description: The rat BMSC which Icariin-treated

hyb_protocol: NimbleGen Hybridization System

scan_protocol: Axon GenePix 4000B scanner

data_processing:
NimbleScan v2.5 software
Raw data normalization and low intensity filtering: Raw signal intensities were normalized in RMA method by NimbleScan v2.5, and low intensity genes were filtered (Genes that Intensity >= 100.0 in that at least 1 out of 2 samples were chosen for further analysis). Quality assessment of gene data after filtering: Contains Box Plot and Scatter Plot for genes after filtering.

source_name: Icariin-treated BMSC

label_protocol: NimbleGen One-Color DNA Labeling Kit

extract_protocol: The integrity of RNA can be assessed by electrophoresis on a denaturing agarose gel. Intact total RNA run on a denaturing gel will have sharp 28S and 18S rRNA bands (eukaryotic samples). The 28S rRNA band should be approximately twice as intense as the 18S rRNA band. This 2:1 intensity ratio indicates that the RNA is intact.

tag: cell type

value: BMSC

tag: gender

value: female

value: Icariin-treated


title: Microdissected Rat Renal CCD, UUO_1_3Hr, RNA-Seq, Transcriptome 01


title: Microdissected Rat Renal CCD, UUO_1_3Hr, RNA-Seq, Transcriptome 02


title: NB4-GNE987-1

description: NB4 sample with GNE987

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line


title: ∆ve-1_15A_Dark_R2 [CON_MD2]

description:
RNA isolated from aerial tissue developed for 15h on vogel´s solid plate under dark conditions
CON_MD2


title: NB4-GNE987-2

description: NB4 sample with GNE987


title: Microdissected Rat Renal CCD, Sham Control_1_3Hr, RNA-Seq, Transcriptome 02


title: NB4-NC-1 (GNE987 control)

description: NB4 sample with no treatment


title: Microdissected Rat Renal cTALs, Sham Control_1_3Hr, RNA-Seq, Transcriptome 01


title: ∆ve-1_15A_Dark_R1 [CON_MD1]

description:
RNA isolated from aerial tissue developed for 15h on vogel´s solid plate under dark conditions
CON_MD1


title: DMSO-treated BMSC

description: The rat BMSC which DMSO-treated

source_name: DMSO-treated BMSC

value: DMSO-treated


title: NB4-NC-2 (GNE987 control)

description: NB4 sample with no treatment


title: Microdissected Rat Renal CCD, Sham Control_1_3Hr, RNA-Seq, Transcriptome 01


title: NB4-Input

tag: treat

value: untreated


title: cell line-ELK3 sh control-2

city: Seongnam-si

first: Dae-keum

last: Lee

state: Gyeonggi-do

address: 335, Pangyo-ro,  Bundang-gu

country: South Korea

institute: CHA university

hyb_protocol: A hybridization mixture with controls, including control oligo B2, 20 X hybridization controls (bioB, bioC, bioD, cre), DMSO, 2 X hybridization buffer and water, was added to all six samples. 109 μl of this mixture was injected into a GeneChip MoGene 2.0 ST Array (Affymetrix, Santa Clara, California, USA) and placed in the Affymetrix GeneChip Hybridization Oven 640 at 45 °C and 60 rpm for 16 h overnight. Stain cocktails (stain cocktail 1 and stain cocktail 2 [GeneChip Hybridization, wash, and stain Kit, Lot No. 4343301]) were added to amplify signal intensities. Arrays were stained and washed in the Affymetrix GeneChip Fluidics Station 450 using the FS450_0002 fluidics protocol. All arrays were scanned with the Affymetrix GeneChip Scanner 3000 and raw analysis performed with Transcriptome Analysis ConsoleTM(TAC) software. The raw data images produced from the scanner were processed into CEL files, which contained measure intensities for each probe on the array

data_processing:
The raw analysis performed with Transcriptome Analysis ConsoleTM(TAC) software. The raw data images produced from the scanner were processed into CEL files, which contained measure intensities for each probe on the array
CEL files were imported into the Gene Expression Workflow in GeneSpring GX version 14.9.1 (Agilent Technologies Inc.,). The RMA algorithm (Background correction, log2 transformation, and probeset summarization) was performed using default settings in GeneSpring software. A Principal Component Analysis (PCA), which reduces the dimensionality of a data set consisting of a large number of interrelated variables, was performed using a covariance dispersion matrix as part of the quality control of the data. Differential expression (DE) between experimental group and control group was predicted at the gene-level (probesets summarized into transcript clusters/genes). Unpaired T-test was respectively used to compare the individual gene expression data with respect to experimental sample versus control. DE genes were defined based on an absolute fold change equal to or greater than 2.0 & a p-value less than or equal to 0.05. Input for the heatmap (TreeView Ver.1.1.6r4) was the log2 transformed DE genes with an absolute fold change equal to or greater than 2.0 & a p-value less than or equal to 0.05.

label: biotin

source_name: Human Breast cancer cell line

label_protocol: The RNA was labeled using the GeneChip 3'IVT PLUS Reagent kit (Affymetrix Inc., Santa Clara, CA, USA, Lot No.4335018). Samples were amplified using 3'IVT amplification reagents from GeneChip 3'IVT PLUS kit. Following amplification, cDNA samples were then purified using an Purification beads. Exactly 15 μg of cDNA was fragmented by uracil-DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease I (APE I) and labeled by terminal deoxynucleotidyl transferase (TDT) using the Affymetrix proprietary DNA Labeling Reagent.

growth_protocol: The human breast cancer cell line Hs578T was cultured in DMEM (Gibco) supplemented with 10% fetal bovine serum (Gibco), 1% penicillin-streptomycin (Gibco), and 0.01 mg/ml insulin (Sigma, I9278).

extract_protocol: RNA was extracted from cells using the Trizol reagent (Invitrogen, Carlsbad, CA, USA). cDNA synthesis was performed using SuperScript™ II Reverse Transcriptase (Invitrogen), and qPCR was performed using TOPreal™ qPCR 2X PreMIX (Enzynomics, Daejeon, Chungnam, Republic of Korea).

treatment_protocol: To generate stable ELK3-knockdown cells, shRNA lentiviruses (human ELK3, RHS4531-EG2004, Dharmacon Inc., Lafayette, CO, USA) were transduced into target cells with 10 μg/ml protamine sulfate.

value: Human Breast cancer cell line

value: ELK3 sh control


title: cell line-ELK3 sh control-1

scan_protocol: Arrays were stained and washed in the Affymetrix GeneChip Fluidics Station 450 using the FS450_0002 fluidics protocol. All arrays were scanned with the Affymetrix GeneChip Scanner 3000


title: cell line-ELK3 knockdown-5

value: ELK3 knockdown


title: AML2-Input

value: AML


title: PDAC cells transfected with siPCDH1, 3

city: Zhongshan

first: Junkai

last: Zhang

address: Zhongshan

institute: Zhongshan People's Hospital

description: This sample is prepared by transfecting with PCDH1 target siRNA

hyb_protocol: Labeled cRNA were purified by RNeasy mini kit (QIAGEN). Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Agilent technologies) in Hybridization Oven (Cat.# G2545A, Agilent technologies), according to the manufacturer’s instructions for 17 hours

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Agilent technologies) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies). Raw data were normalized by Quantile algorithm, GeneSpring Software 11.0 (Agilent technologies).

source_name: PDAC cells of PCDH1 knockdown group

label_protocol: RNA amplified and labeled by Low Input Quick Amp WT Labeling Kit (Agilent technologies), following the manufacturer’s instructions.

growth_protocol: PDAC cells were cultured in medium supplemented with 10% FBS.

extract_protocol: RNA was extracted using TRIzol Reagent (Invitrogen) according to manufacturer’s instructions, RNA quantity and quality were measured by Qubit 4 (Invitrogen). RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: PDAC cells were transfected with negative control siRNA or PCDH1 target siRNA.

value: pancreatic ductal adenocarcinoma (PDAC)

value: PDAC cells

value: PCDH1 knockdown


title: AML3-Input


title: AML1-Input


title: AML4-Input


title: AML4-H3K27ac


title: NB4-H3K27ac


title: 1SN

city: Homburg

first: Tanja

last: Stachon

address: Kirrergerstr. 100

department: Dr. Rolf  M. Schwiete Center

country: Germany

institute: Saarland University

hyb_protocol: The mRNA expression profile was determined using Agilent SurePrint G3 Human GE v3 8x60K Microarray according to the manufacturers recommendations

scan_protocol: Array´s were scanned with the Agilent Scanner with default settings.

data_processing: Raw expression values were extracted using the Feature Extraction Software. Data was quantil normalized and log transformed.

source_name: corneal stroma

extract_protocol: Total RNA including miRNAs was isolated using theQiagen miRNeasy Kit according to manufacturers recommendations.  RNA concentration was measured using NanoDrop2000 (ThermoScientific). RNA integrity was measured using the NanoRNA kit (Agilent) on a Bioanalyzer2100.

tag: age

value: M

value: healthy control


title: PDAC cells transfected with siPCDH1, 2


title: cell line-ELK3 knockdown-1


title: PDAC cells transfected with siNC, 3

description: This sample is prepared as control group by transfecting with siNC

source_name: PDAC cells of negative control group

value: negative control


title: 8SN

label_protocol: The mRNA expression profile was determined using Agilent SurePrint G3 Human GE v3 8x60K Microarray according to the manufacturers recommendations


title: AML3-H3K27ac


title: 7SN

value: F


title: UMSCC6 input ChIP-seq

city: Madison

first: Scot

middle: Carson

last: Callahan

state: WI

address: 600 highland ave

country: USA

institute: UW Health

description: Genomic DNA

data_processing:
Raw fastq reads for all ChIP-seq experiments were processed using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and aligned to the hg19 reference genome using Bowtie version 1.1.2 with the following criteria: -m 1 --best --strata. Duplicate reads were marked using SAMBLASTER before compression to BAM files.  Uniquely mapped reads for each mark were normalized by total reads per condition, sorted and indexed using samtools version 1.9
Model based analysis of ChIP-seq (MACS) version 1.4.2 peak calling algorithm with a p-value threshold of 1e-5 to identify H3K27ac enrichment over “input” background
deepTools version 1.5.11 was used to generate bigWig files by scaling the bam files to reads per kilobase per million (RPKM).
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files and bed peak files

growth_protocol: Human HNSCC cell lines were acquired and characterized as previously described [59]. Briefly, cell lines were cultured in DMEM supplemented with 10% FBS, L-glutamine, sodium pyruvate, nonessential amino acids, vitamins, and 1% penicillin-streptomycin. All cell lines were cultured at 37 °C in an atmosphere of 5% CO2

extract_protocol:
Cells were crosslinked with both 0.75% formaldehyde and glycine. Chromatin was sheared to 300-700 bp using a Diagenode Bioruptor.
DNA were end-repaired, adapter-ligated using NEBNext Ultra II DNA library prep kit from Illumina and sequenced by Illumina HiSeq2000 at SR-50.

value: head and neck squamous cell carcinoma cell line


title: UMSCC6 H3K27ac ChIP-seq

description: ChIP DNA

value: H3K27ac Abcam ab4729


title: PDAC cells transfected with siPCDH1, 1


title: normal control_peripheral blood NB3

city: Kuala Lumpur

first: Ivyna

middle: PN

last: Bong

state: Kuala Lumpur

address: Jalan Pahang

department: Cancer Research Centre

country: Malaysia

institute: Institute for Medical Research

description: Gene expression healthy volunteer

hyb_protocol: 600 ng  of labeled cRNAs (specific activity >6.0 pmol Cy3/ug cRNAs) were combined with Blocking Agent and Fragmentation Buffer and incubated at 60°C for 30 min in the dark. The mixture was then added with 25 μl of GEx Hybridisation Buffer HI-RPM. 40 ul of mixture was applied to SurePrint G3 Human GE 8x60K V2 Microarray Kit and the array was hybridised at 65°C for 17 h. After incubation, the slides were washed with GE wash buffer 1 and GE wash buffer 2 according to manufacturer's recommendation.

scan_protocol: slides were scanned immediately after washing with Agilent DNA Microarray Scanner  (G2505C) using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Agilent Feature Extraction Software Version 10.7.3.1. Microarray data were analysed using GeneSpring software version 13.0.

source_name: peripheral blood, normal

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100ng of total RNAs using the one colour Agilent’s Low Input Quick Amp Labeling kit according to manufacturer's recommendation. Labeled cRNAs were purified with RNeasy mini spin columns (Qiagen Rneasy mini kit) to wash off unincorporated dyes. The quantity and specific activity of cRNAs were determined on Nanodrop ND-1000 UV–VIS spectrophotometer.

growth_protocol: cell lines were grow in RPM1640 medium supplemented with 10-15% of FBS in culture flasks at 37°C and 5% CO2 incubator

extract_protocol: Total RNAs were extracted from the samples by using Qiagen miRNeasy mini kit according to manufacturer's protocol.  On-column DNase digestion was performed using Qiagen DNAse I kit. Total RNAs were quantified using a NanoDrop-1000 spectrophotometer and RNA integrity number was assessed with the Agilent 2100 Bioanalyzer.

value: male


title: PDAC cells transfected with siNC, 2


title: normal control_peripheral blood NB1

description: Gene expression healthy volunteer

value: female


title: 1SKC

source_name: KC corneal stroma

value: KC

tag: Stage


title: 4SKC


title: multiple myeloma_cell line MM.1S

description: Cell line

source_name: cell line, multiple myeloma

value: cell line


title: 7SKC


title: multiple myeloma_cell line KMS-12BM

description: Cell line


title: normal control_peripheral blood NB2

description: Gene expression healthy volunteer


title: PDAC cells transfected with siNC, 1

tag: genotype


title: 5SN


title: UMSCC4 input ChIP-seq

description: Genomic DNA


title: AML2-H3K27ac


title: AML1-H3K27ac


title: UMSCC4 H3K27ac ChIP-seq

description: ChIP DNA


title: UMSCC25 input ChIP-seq

description: Genomic DNA


title: multiple myeloma_cell line KMS-20

description: Cell line


title: 5SKC


title: HN4 low GR50 – rep 3

data_processing:
raw reads were aligned to the hg19 genome using STAR v2.7.2b and quality checked using FastQC v0.11.8
Counts were generated using featureCounts from subread v1.6.3 80
Downstream normalization and differential expression analysis were performed using DESeq2, with size factors being calculated using data-driven housekeeping gene method as implemented in the CustomSelection R package
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file with raw gene counts for every gene and every sample. Samples as columns, genes as rows.

extract_protocol:
RNA extraction was performed using an RNeasy Mini Kit per manufacturer’s instructions (Qiagen). Isolation of mRNA was performed using NEBNext Poly(A) mRNA Magnetic Isolation Module
libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep kit (New England BioLabs). Library quality was checked on an Agilent TapeStation 4150 and quantified by Qubit 2000 fluorometer (Invitrogen). Libraries were pooled in equimolar ratios and sequenced on Illumina NovaSeq6000 SP runs with paired-end 100-bp reads at the The Advanced Technology Genomics Core (ATGC) at MD Anderson Cancer Center.

treatment_protocol: For the PLX51107 treatment RNA-seq experiments, representative cell lines were selected for the Atypical subtype (HN4) and a non-Atypical subtype (MDA1186, Classical subtype) and were treated with DMSO, GR50 of the MDA1186, or GR50 of HN4 for 24 hours prior to RNA isolation.

tag: treatment

value: PLX51107 low GR50 24hr


title: multiple myeloma_cell line KMS-28BM

description: Cell line


title: UMSCC19 input ChIP-seq

description: Genomic DNA


title: HN4 low GR50 – rep 1


title: UMSCC25 H3K27ac ChIP-seq

description: ChIP DNA


title: 6SN


title: UMSCC19 H3K27ac ChIP-seq

description: ChIP DNA


title: multiple myeloma_cell line RPMI-8226

description: Cell line


title: UMSCC17A  input ChIP-seq

description: Genomic DNA


title: multiple myeloma_cell line IM-9

description: Cell line


title: HN4 low GR50 – rep 2


title: HN4 DMSO – rep 1

value: DMSO 24 hr


title: HN4 high GR50 – rep 1

value: PLX51107 high GR50 24hr


title: HN4 DMSO – rep 2


title: UMSCC17A   H3K27ac ChIP-seq

description: ChIP DNA


title: UMSCC14B  input ChIP-seq

description: Genomic DNA


title: 3SN


title: multiple myeloma_cell line U-266

description: Cell line


title: HN4 DMSO – rep 3


title: multiple myeloma_clinical specimen MM18

description: Gene expression before treatment, newly diagnosed patient

source_name: bone marrow, multiple myeloma


title: 2SN


title: multiple myeloma_clinical specimen MM17


title: multiple myeloma_clinical specimen MM16


title: 3SKC


title: 6SKC


title: 8SKC

value: A4 B4 C2 D3


title: 4EN

source_name: corneal epithelium


title: multiple myeloma_clinical specimen MM19


title: MDA1196 DMSO – rep 1


title: 2SKC


title: HN4 high GR50 – rep 2


title: HN4 high GR50 – rep 3


title: TR146   input ChIP-seq

description: Genomic DNA


title: UMSCC14B  H3K27ac ChIP-seq

description: ChIP DNA


title: UMSCC10A input ChIP-seq

description: Genomic DNA


title: 2EN


title: UMSCC10A H3K27ac ChIP-seq

description: ChIP DNA


title: multiple myeloma_clinical specimen MM15


title: TR146  H3K27ac ChIP-seq

description: ChIP DNA


title: 3EN


title: MDA1196 DMSO – rep 2


title: multiple myeloma_clinical specimen MM13


title: 1EN


title: multiple myeloma_clinical specimen MM12


title: MDA1186 low GR50 – rep 2


title: MDA1186 low GR50 – rep 3


title: MDA1196 DMSO – rep 3


title: multiple myeloma_clinical specimen MM11

description: Gene expression after treatment, relapsed patient


title: 8EKC

source_name: KC corneal epithelium


title: SCC61  H3K27ac ChIP-seq

description: ChIP DNA


title: SCC61   input ChIP-seq

description: Genomic DNA


title: PCI24  input ChIP-seq

description: Genomic DNA


title: MDA1186 low GR50 – rep 1


title: PE/CA-PJ34  H3K27ac ChIP-seq

description: ChIP DNA


title: MDA1586 PRO-seq rep 2

description: nascent RNA

data_processing:
Fastq files from PRO-seq experiments were processed using the previously described PEPPRO pipeline (Smith et al., 2021).
The aligned, sorted bam files for these samples were used as input for downstream analysis using the previously described NRSA downstream analysis pipeline (Wang et al., 2018)
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files containing (respectively): results of differential eRNA expression from NRSA, normalized eRNA counts, raw eRNA counts, and enhancer information

extract_protocol:
Nuclei were isolated from approximately 10 million cells. Precision nuclear run-on reaction, nuclei were resuspended in 100l of freezing buffer and added to 100l of NRO-reaction mix - NRO-reaction buffer (10mM Tris-HCl pH 8.0, 5mM MgCl2, 300mM KCl), 1mM DTT, 100U/ml SUPERase-In, 1% Sarkosyl, 250M ATP, 250M GTP, 50M biotin-11-UTP, 50M biotin-11-CTP. RNA was extracted using TRIzol. RNA was purified using Streptavidin C1 beads.
isolated RNA samples were dephosphorylated by FastAP (ThermoFisher) and T4 Polynucleotide kinase (NEB). Samples were cleaned up using MyONE Silane beads and RNA was isolated with RLT buffer. RNA was then reverse transcribed with AR17 primer and AffinityScript reverse transcriptase (Agilent). cDNA samples were then PCR amplified using NEBNext® Ultra™ II Q5® Master Mix. Libraries were size selected and purified using SPRI beads and sequenced on a NovaSeq6000 with 100nt paired-end format

value: untreated


title: PE/CA-PJ34   input ChIP-seq

description: Genomic DNA


title: 5EKC


title: multiple myeloma_clinical specimen MM10


title: 8EN


title: 6EKC


title: MDA1586 PRO-seq rep 1

description: nascent RNA


title: 7EKC


title: multiple myeloma_clinical specimen MM7


title: 7EN


title: multiple myeloma_clinical specimen MM8


title: multiple myeloma_clinical specimen MM9


title: MDA1186 PRO-seq rep 1

description: nascent RNA


title: OSC19  input ChIP-seq

description: Genomic DNA


title: multiple myeloma_clinical specimen MM6


title: 6EN


title: 183 PRO-seq rep 1

description: nascent RNA


title: UMSCC14B PRO-seq rep 2

description: nascent RNA


title: multiple myeloma_clinical specimen MM4


title: multiple myeloma_clinical specimen MM5


title: OSC19 H3K27ac ChIP-seq

description: ChIP DNA


title: PCI24 H3K27ac ChIP-seq

description: ChIP DNA


title: multiple myeloma_clinical specimen MM14


title: MDA886LN H3K27ac ChIP-seq

description: ChIP DNA


title: HN4 PRO-seq rep 2

description: nascent RNA


title: MDA886LN  input ChIP-seq

description: Genomic DNA


title: Swim3

city: shanghai

first: weiyi

last: wang

address: No. 1111 Xianxia Road, Changning District, Shanghai, PR China

department: Department of Endoscopy

institute: Shanghai Tong Ren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China

description: Swimming pretreatment significantly inhibited the shortening of colonic length and colitis-induced tumorigenicity.

data_processing:
CLC Genomics Workbenchv 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to NCBI_GRCm38.p6 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Mus musculus

source_name: Colorectal tissue

extract_protocol:
Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following the manufacturer’s protocol.
Then the libraries were constructed using TruSeq Stranded mRNALTSample Prep Kit(Ilumina,San Diego, CA, USA) . 1 ug of total RNA was used for the construction of sequencing libraries.

tag: tissue

value: Colorectal tissue

value: AOM/DSS treated+swimming pretreatment


title: Swim2


title: HN4 PRO-seq rep 1

description: nascent RNA


title: MDA1386TU  input ChIP-seq

description: Genomic DNA


title: Botrytis cinerea BcSpd1 treated rep3

city: Changchun

first: Shouan

last: Liu

address: Xi-An-Da Road 5333

institute: Jilin University

description:
Botrytis cinerea BcSpd1 treated rep3
BcSpd1_3

data_processing:
Illumina Casava1.7 software used for basecalling.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Arabidopsis thaliana

source_name: Botrytis cinerea BcSpd1 treated rep3

growth_protocol: The Arabidopsis thaliana Col-0 were grown in soil under a microbe free climate chamber with the 10 h light and 14 h dark.The plants were watered once a week and kept growing for about 4 weeks.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The B. cinerea B05.10 and BcSfp1 was grown in PDA (200 g potato, 20 g glucose, 20 g agar and 1 L water) plate to produce the conidia spores. For incubation, the plant leaves were spray infected with 5*105 spores mL-1. The buffer without any spores were sprayed as untreated control (CK). All leaves were harvest at 14 hours and frozen at -80℃ for RNA sequencing.

tag: ecotype

value: leaf

value: 4 weeks old


title: Botrytis cinerea BcSpd1 treated rep2

description:
Botrytis cinerea BcSpd1 treated rep2
BcSpd1_2

source_name: Botrytis cinerea BcSpd1 treated rep2


title: multiple myeloma_clinical specimen MM2


title: 3EKC

tag: disease


title: Swim1


title: multiple myeloma_clinical specimen MM3


title: Botrytis cinerea BcSpd1 treated rep1

description:
Botrytis cinerea BcSpd1 treated rep1
BcSpd1_1

source_name: Botrytis cinerea BcSpd1 treated rep1


title: MDA1386TU H3K27ac ChIP-seq

description: ChIP DNA

tag: chip antibody


title: 5EN

value: healthy control


title: UMSCC25 H3K27ac HiChIP

data_processing:
Paired-end reads were processed using HiC-Pro (Servant et al., 2015), peaks were called using HiChIP-Peaks (Shi et al., 2020), and loops were called using HiChipper software (http://hichipper.readthedocs.io/en/latest/index.html).
Genome_build: hg19
Supplementary_files_format_and_content: bedpe files, bed peak files, and mango files

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 minutes, then quenched with 0.125M glycine for 5 minutes. In situ Hi-C contacts were generated with MboI restriction enzyme, followed with biotin-dATP filling and ligation. H3K27Ac ChIP was performed on them. Further, DNA elution with biotin capture was done.
Libraries were prepared using the nextera Tn5 transposase and sequenced on a Novaseq6000 with 100-bp paried-end reads.


title: 4EKC

value: M


title: MDA686LN  input ChIP-seq

description: Genomic DNA

value: head and neck squamous cell carcinoma cell line


title: HN4 H3K27ac HiChIP

value: H3K27ac Abcam ab4729


title: UMSCC14B PRO-seq rep 1

description: nascent RNA


title: 1EKC

value: F


title: Model2

description: AOM/DSS induced significantly the shortening of colonic length and colitis-induced tumorigenicity.

value: AOM/DSS treated


title: Botrytis cinerea B0510 treated rep3

description:
Botrytis cinerea B0510 treated samples replicate 3
Bc0510_3


title: Model3


title: MDA686LN H3K27ac ChIP-seq

description: ChIP DNA


title: multiple myeloma_clinical specimen MM1

value: female


title: CAL27 H3K27ac HiChIP


title: Botrytis cinerea B0510 treated rep2

description:
Botrytis cinerea B0510 treated samples replicate 2
Bc0510_2


title: 2EKC

value: KC


title: MDA1186 H3K27ac HiChIP


title: Ctrl_Swim4

description: Natural colorectal morphology

value: swim only


title: MDA1386LN  input ChIP-seq

description: Genomic DNA


title: CK rep3

description:
uninfected control samples replicate 3
CK_3

source_name: uninfected control samples replicate 3


title: Ctrl_Swim3

description: Natural colorectal morphology


title: MDA1986LN H3K27ac ChIP-seq

description: ChIP DNA


title: sELK1_CD371P_GMP_rep3

city: chengdu

first: Yong

last: Dong

state: sichuan

address: Xindu road 783, Xindu district

department: Immunology

institute: Chengdu medical college

data_processing:
The clean fastq files were provied by Novogene company. All the fastq files were mapped to human genomic hg38 by Hisat2 program to generate .sam files. FeatureCounts program was used to calculate the gene expression raw counts.
The gene expression raw counts were normalized by edgeR or DESeq2 R package. The raw count data of in vitro culture single cells RNAseq was converted into cpm value. 10x genomic data of in vivo BM Lin-CD371+CD123+ cells was processed by  cell ranger4.0.4 software
Supplementary_files_format_and_content: The gene expression cpm value normalized data for each group was uploaded.

source_name: Sorted CD34+CD123+CD38+CD371+CD115-GMPs

growth_protocol: Human cord blood derived GMPs or CD371+GMPs were cultured in 10%FBS IMDM medium plus with SCF, FLT3L, IL-3, IL-6, TPO, GM-CSF, G-CSF, EPO for 3 days. CD115-CD371+CD34+CD15- NbP1, CD115-CD371+CD34mid CD15mid NbP2 were sorted to generated dsDNA as reported.

extract_protocol:
The cDNA of treated 2000-cell aliquots were generated and amplified, as described previously(PMID:29434353, 31443434)
Then qualities of the amplified cDNA were examined by qPCR analysis of housekeeping genes (B2m, Actb, Gapdh). Samples that passed quality control were used for subsequent sequencing library preparation, 1ng of dsDNA was used to generate the library using Vazyme TruePrepTM DNA library Prep Kit V2 for Illumina (TD-503). All libraries were sequenced by Illumina Novaseq6000 system (Novogene Co., Ltd. ).

treatment_protocol: The sorted NbP1 and NbP2 were cultured with 25 μg/ml alpha lipoic acid (ALA) or not(Ctrl) for 48 hours. As for the ELK1 or sELK1 overexpression CD371+GMP cells, the ELK1, sELK and GFP virus transduced CD123+CD38+CD34+CD115-CD371+cells were sorted.

value: CD34+HSPC derived


title: CK rep2

description:
uninfected control samples replicate 2
CK_2

source_name: uninfected control samples replicate 2


title: Ctrl_Swim2

description: Natural colorectal morphology


title: Ctrl3

description: Natural colorectal morphology

value: NC


title: MDA1386LN H3K27ac ChIP-seq

description: ChIP DNA


title: MDA1986LN input ChIP-seq

description: Genomic DNA


title: Botrytis cinerea B0510 treated rep1

description:
Botrytis cinerea B0510 treated samples replicate 1
Bc0510_1


title: sELK1_CD371P_GMP_rep2


title: JHU029  input ChIP-seq

description: Genomic DNA


title: sELK1_CD371P_GMP_rep1


title: JHU029 H3K27ac ChIP-seq

description: ChIP DNA


title: CK rep1

description:
uninfected control samples replicate 1
CK_1

source_name: uninfected control samples replicate 1


title: ELK1_CD371P_GMP_rep2


title: ELK1_CD371P_GMP_rep1


title: Model1


title: BMAd-Pnpla2-/- CR, rep3

city: Ann Arbor

first: Ziru

last: Li

state: MI

address: 2800 Plymouth Rd.

department: Molecular & Integrative Department

institute: University of Michigan

data_processing:
The quality of the raw reads data was checked using FastQC (v.0.11.9).
The filtered reads were aligned to reference genome (UCSC mm10) using STAR with default parameters.
All samples passed the post-alignment quality check (QualiMap (v.2.2.1).
The DEseq2 method was used for differential expression analysis.
Genome_build: UCSC mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Bone marrow adipose tissue

growth_protocol: Mice were housed in a 12 h light/dark cycle in the Unit for Laboratory Animal Medicine at the University of Michigan, with free access to water. Mice were fed ad libitum or underwent caloric restriction, as indicated.

extract_protocol:
Distal tibiae were collected and cut ends. Bone marrow plugs were flushed out and homoginized with RNAStat60 reagent. DNA-free™ Kit was used to remove DNA before submitting for QC and RNAseq.
RNA libraries were prepared for sequencing using P_Stranded Library&Seq (PE100).

treatment_protocol: 30% Caloric restriction (CR). After acclimation to single-housing for 2 weeks, and control diet (D17110202; Research Diets) for a week, daily food intake was measured for another week. Mice were then fed a 30% caloric restriction diet (D19051601; Research Diets) daily at ~6 pm, prior to onset of the dark cycle.

tag: strain

tag: Sex

value: male

value: Bone marrow adipose tissue

value: 24 weeks old

value: Caloric restriction


title: BMAd-Pnpla2-/- CR, rep2


title: Ctrl1

description: Natural colorectal morphology

value: Colorectal tissue


title: ATF7IP-KO_WGBS

city: Utrecht

first: Tuncay

last: Baubec

address: Padualaan 8

department: Department of Biology

country: Netherlands

institute: Utrecht University

description: WGBS

data_processing:
Sequencing reads were pre-processed and trimmed using trim_galore v0.6.6 with -q 20 --length 20 --hardtrim5 50 or --hardtrim5 30
Trimmed reads were mapped against the mm9 mouse assembly BSgenome.Mmusculus.UCSC.mm9 using QuasR in R with qAlign() parameters: aligner="Rbowtie",     bisulfite = "dir".
methylation calling was done using QuasR qMeth() with standard parameters.
Assembly: mm9
Supplementary files format and content: Processed tab delimited file contains following information: chromosome, start, end, average methylation, reported methylated cytosines, reported unmethylated cytosines

source_name: Mouse Embryonic Stem Cells

growth_protocol: ES cells were were cultivated on feeder cells or 0.2% gelatine coated dishes. ES cell growth medium consisted of DMEM (Invitrogen) supplemented with 15% foetal calf serum (Invitrogen), 1x non-essential amino acids (Invitrogen), 1mM L-glutamine, LIF and 0.001% beta-mercaptoethanol.

extract_protocol:
Genomic DNA extraction, followed by phenol/chloroform extraction and ethanol precipitation. RNaseA treatment was performed for 30 min at 37C
10 µg of genomic DNA was sonicated to a length of approximately 400-500 base pairs. For each sample, 2 µg of sheared genomic DNA was mixed with 10 ng of equimolar pooled sonicated methylated phage T7 and unmethylated phage Lambda DNA. Adapter-ligation was carried out with the NEBNext Ultra II kit (NEB E7645L) using methylated adaptors (NEB E7535S), prior to bisulfite conversion using the Qiagen Epitect bisulfite conversion kit, according to the manufacturer’s instructions. After conversion, libraries were amplified for 10 cycles using the Pfu TurboCx Hotstart DNA polymerase (Agilent) and the NEB dual index primers (NEB E7600S). PCR reactions were run with the following parameters:  95°C for 2 min, 98°C for 30 s, followed by 10 cycles of 98°C for 15 s, 65°C for 30 s and 72°C for 3 min, ending with 5 min at 72°C. The PCR reactions were cleaned up using 1.2 x AMPure XP beads (Beckman Coulter) and eluted in 20 µl EB buffer (Qiagen). Library quality was checked on an Agilent TapeStation and sequencing was done on an Illumina NovaSeq machine.

value: embryonic stem cells


title: ZMYM2-KO_WGBS

description: WGBS


title: GFP_CD371P_GMP_rep1


title: HN5  input ChIP-seq

description: Genomic DNA


title: HN4 H3K27ac ChIP-seq

description: ChIP DNA


title: BMAd-Pnpla2-/- AL, rep3

value: Ad libitum


title: HN31  input ChIP-seq

description: Genomic DNA


title: ELK1_CD371P_GMP_rep3


title: BMAd-Pnpla2-/- AL, rep2


title: BM_CD371P_GMP_rep2

value: Bone marrow derivedCD371+GMP


title: GFP_CD371P_GMP_rep2


title: BMAd-Pnpla2+/+ CR, rep4


title: BMAd-Pnpla2+/+ CR, rep3


title: HN31 H3K27ac ChIP-seq

description: ChIP DNA

value: head and neck squamous cell carcinoma cell line


title: HN4  input ChIP-seq

description: Genomic DNA


title: BMAd-Pnpla2-/- CR, rep1


title: Ctrl2

description: Natural colorectal morphology


title: BM_MoP_rep2

source_name: Monocyte progeintors(MoP)

value: Bone marrow derived monocyte progenitors


title: HN30  input ChIP-seq

description: Genomic DNA


title: GFP_CD371P_GMP_rep3


title: BMAd-Pnpla2+/+ CR, rep2


title: Pde6c_GSK

city: Perth

first: Livia

last: Carvalho

state: Western Australia

address: 2 Verdun St

country: Australia

institute: Lions Eye Institute

description:
This line contains the Pde6ccpfl1 mutation along with eGFP driven by Chrnb4 promoter
The fastq read names include the well ID for each cell.

data_processing:
Reads were quality-filtered and passed through a demultiplexing tool to assign reads to individual wells and to the 3’end and 5’ end; Reads for the individual single-cells were demultiplexed using plate-ID (30 nt) and cell barcode (6 nt).
Reads were further demultiplexed as either 3’ or 5’ using primer sequence (30 nt), with the remaining 45 nt sequences aligned to the GRCh38 Mus-Musculus reference genome (Ensembl rel. 97) using the CLC Genomics Workbench (CLC Bio) (v.20, QIAGEN Bioinformatics).
An eight-nucleotide UMI tag and mapping coordinates were used to remove PCR-duplicate reads. Gene-specific read counts were calculated using RSubread:featureCount using Gencode M17 (2018) annotations and the 3’ and 5’ counts were summed.
Genome_build: GRCh38 Mus-Musculus reference genome (Ensembl rel. 97)
Supplementary_files_format_and_content: Matrix table containing raw gene counts for every gene in each sample well

source_name: Retina

extract_protocol: RNA was isolated using the RNeasy Mini Kit (Qiagen) and processed as per manufacturer’s instructions. Libraries were prepared using TruSeq adapaters and Kapa Universal qPCR library kit, according to the manufacturer’s instructions.

treatment_protocol: P14 mice received a single intravitreal injection containing 10 micromolar GSK-J4; retinas were collected 10 days later, processed for FACS using papain-based dissociation and single cone cells collected in a 96-well plate.

value: GSK-J4 treated

value: Retina

value: cone photoreceptor

value: Pde6ccpfl1 crossed with Chrnb4.eGFP mouse line


title: BM_MoP_rep1


title: BMAd-Pnpla2+/+ CR, rep1


title: HN30 H3K27ac ChIP-seq

description: ChIP DNA

value: H3K27ac Abcam ab4729


title: CCND1T3

city: Fuzhou

state: China

address: Department of Medical Oncology, Fujian Medical University Cancer Hospital & Fujian Cancer Hospital, Fuzhou, Fujian Province, China

data_processing:
Basecalls performed using Solexa pipeline v1.8.
The trimmed reads (trimmed 5',3'-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 (2.1.0) software.
The transcript abundances for each sample was estimated with StringTie (1.3.3).
The FPKM value for gene and transcript level were calculated with R package Ballgown (v2.10.0).
Genome_build: GRCh37
Supplementary_files_format_and_content: Expression_Transcript.txt: Tab-delimited text file contains the FPKM values of genes in every sample.

source_name: tumor of B16 with CCND1 overexpression

extract_protocol:
The tumor tissues were washed by phosphate buffer saline. The tissues were used in following study, RNA was harvested using Trizol reagent. RNA quality and quantity were measured by using Nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis.
Libraries were prepared by using KAPA Stranded RNA-Seq Library Prep Kit (Illumina). Briefly, total RNA of each sample was used to prepare the RNA sequencing library 1) RNA fragment; 2) Random primed first strand cDNA synthesis; 3) dUTP based second strand cDNA synthesis; 4) Adaptor ligation and PCR amplification.

value: Tumor of B16 with CCND1 overexpression


title: BMAd-Pnpla2-/- AL, rep1


title: CCND1T2

institute: Fujian Medical University Cancer Hospital & Fujian Cancer Hospital


title: CAL27 H3K27ac ChIP-seq

description: ChIP DNA


title: CAL27  input ChIP-seq

description: Genomic DNA


title: BMAd-Pnpla2+/+ AL, rep4


title: BMAd-Pnpla2+/+ AL, rep3


title: MDA686TU H3K27ac ChIP-seq

description: ChIP DNA


title: BM_NbP2_rep1

source_name: Neutrophil bias progeintors(NbP2)

value: Bone marrow derived neutrophil bias progenitors


title: CCND1C4

source_name: tumor of B16 Ctrl

value: Tumor of B16 Ctrl


title: CCND1T1


title: BM_NbP3_rep1

source_name: Neutrophil bias progeintors(NbP3)


title: BMAd-Pnpla2+/+ AL, rep2

value: male

value: Bone marrow adipose tissue


title: Pde6c_untreated

value: Untreated


title: BM_CD371P_GMP_rep1


title: CCND1C2


title: BM_NbP1_rep2

source_name: Neutrophil bias progeintors(NbP1)


title: 183 input ChIP-seq

description: Genomic DNA


title: BM_NbP1_rep1


title: 584A2  input ChIP-seq

description: Genomic DNA


title: CCND1C1


title: 584A2 H3K27ac ChIP-seq

description: ChIP DNA


title: BM_NbP3_rep2


title: Culture_MoP_rep3

value: GMP derived monocyte progenitors


title: MDA686TU  input ChIP-seq

description: Genomic DNA


title: 183 H3K27ac ChIP-seq

description: ChIP DNA


title: HA36_WT_ES

description: bsPCR-amplicons

data_processing:
Sequencing reads were pre-processed and trimmed using trim_galore v0.6.6 with --paired --clip_R1 10 --clip_R2 10 --nextseq 20
Trimmed reads were mapped against the mm10 mouse assembly using Bismark v0.23.0 bismark with --non_directional
methylation calling was done with Bismark v0.23.0 bismark_methylation_extractor with --bedgraph
Genome_build: mm10
Supplementary_files_format_and_content: Processed tab delimited file contains bismark coverage report with following information: chromosome, start, end, average methylation, reported methylated cytosines, reported unmethylated cytosines

extract_protocol:
Genomic DNA extraction, followed by phenol/chloroform extraction and ethanol precipitation. RNaseA treatment was performed for 30 min at 37C
Gemomic DNA was converted using the Qiagen Epitect bisulphite conversion kit. After conversion, two separate PCR amplifications per target were performed at 50 ˚C and 58 ˚C annealing temperature with the PhusionU polymerase (Thermo Scientific) for 45 cycles of 1 min 95 ˚C denaturation, 1 min for annealing, and 1 min 72 ˚C for extension. PCR products were run on a 1.2 % agarose gel, extracted, quantified and pooled at equimolar ratios. Library preparation was done with 10 ng of input material using the NEBNext Ultra II kit protocol and cleaned up using Ampure XP beads (Beckman Coulter).
targeted bisuphite PCR- seq

value: embryonic stem cells

value: wild type


title: BM_NbP2_rep2


title: MDA1586 input ChIP-seq

description: Genomic DNA


title: BMAd-Pnpla2+/+ AL, rep1

value: 24 weeks old

value: Ad libitum


title: 9_3T3+TNFa

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

country: France

institute: Lille University

description: TNFa treated 3T3 cells

hyb_protocol: Agilent-074809 SurePrint G3 Mouse GE v2 8x60K Microarrays were scanned on an Agilent G2505B scanner.

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

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

source_name: TNFa

label_protocol: manufacturer's instructions

growth_protocol: MEFs were cultured in DMEM Glutamax supplemented with FCS, penicillin, and streptomycin (all from Thermofisher). MEFs (105 cells) alone or stimulated were seeded in 12-well plates for 24 or 72 hours.

extract_protocol: Total RNA extracted using manufacturer's instructions

treatment_protocol: For MEFs stimulation, cells were incubated either with 5 ng/ml of recombinant TGFβ1 or with 10 ng/ml of recombinant TNFa or  IL1β (1ng/mL) ou IL6/sIL6Rα (20ng/mL–25ng/ml)

value: MEFs


title: MDA1586 H3K27ac ChIP-seq

description: ChIP DNA

value: head and neck squamous cell carcinoma cell line


title: HN5 H3K27ac ChIP-seq

description: ChIP DNA


title: HA36_ATF7IP-KO_ES

description: bsPCR-amplicons


title: TR-246-WT-m6A-IP_8

city: Aarhus

first: Ulf

middle: Vang

last: Ørom

state: Aarhus

address: Aarhus University

department: MBG

country: Denmark

institute: Aarhus University

data_processing:
fastq files were aligned to mouse reference genome mm9 using the STAR aligner(2.7.3a).
bam files were filterd in two steps 1) Uniquely mapped reads are considered 2) mouse blacklist regions are removed
peak calling of corresponding input and IP (immuniprecipitated) samples were performed using MACS (2.2.6)
reproducibility between replicates were performed using IDR (2.0.3)
Differentially expressed genes (p-value < 0.05) were identified by diffbind (2.8.0). Further, annotation was performed with mm9.knownGene.ID.proID.sym_mm9.knownGene.bed using bedtools intersect
Genome_build: mm9

source_name: Hippocampus

growth_protocol: The animals were housed  with ad libitum access to food and water in a colony room kept at 19°C to 22°C and 40%–60% humidity, under a 12-hour light/12-hour dark cycle.

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (Qiagen) and processed as per manufacturer’s instructions.
Library construction were performed following the instructions provided by the SMARTer® Stranded Total RNA-Seq kit v2- Pico Input Mammalian (Takara Bio®, cat nº 634412). Libraries were then pooled volumetrically and sequenced on the NovaSeq platform (Illumina®)

treatment_protocol: In order to induce hippocampal neuronal activity, 5 and 8 months old WT and KI mice (that is, mice at pre-symptomatic and symptomatic cognitive stages, respectively), were subjected to the object-place exploration task. For this purpose, mice were habituated to an open field in the absence of objects and spatial cues for 2 consecutive days (10 min/day). This open field consisted of a white open-top squared arena with the following dimensions: 45 x 45 cm sides, 40 cm high. The third day, the mice were placed in the open field, which now contained 2 identical objects located in the centre zone as well as 4 different black spatial cues on each wall, which they were allowed to explore for 10 minutes. After the ten-minute training, mice were returned to the cage to allow for molecular brain changes to happen and sacrificed 30 minutes after the training task through cervical dislocation. During the whole procedure, the temperature was kept at 19-22 ºC, with a humidity of 40-60%. The open field was rigorously cleaned with 70% ethanol between each animal to avoid any bias caused by odours.

value: Hippocampus

value: HdhQ7/7 (wild-type)

value: 8 months

value: Trained


title: TR-294-KI-input_8

value: HdhQ7/Q111 (KI)

value: input


title: Culture_MoP_rep1


title: 4_3T3+TNFa

description: TNFa treated 3T3 cells


title: Culture_NbP3_rep4

value: GMP derived erly neutrophil bias progenitors


title: MDA1186 input ChIP-seq

description: Genomic DNA


title: Culture_NbP3_rep3


title: Culture_NbP3_rep2


title: MDA1186 H3K27ac ChIP-seq

description: ChIP DNA

value: H3K27ac Abcam ab4729


title: Culture_MoP_rep2


title: TR-241-KI-m6A-IP_8


title: TR-294-KI-m6A-IP_8


title: 14_3T3+TNFa

description: TNFa treated 3T3 cells


title: Culture_NbP3_rep1


title: 7_3T3+TGF

description: TGF treated 3T3 cells


title: 8_3T3+IL6+IL6R

description: IL6+IL6R treated 3T3 cells


title: 2_3T3+TGF

description: TGF treated 3T3 cells


title: TR-241-KI-input_8


title: 12_3T3+TGF

description: TGF treated 3T3 cells


title: Culture_NbP2_rep3


title: TR-231-KI-m6A-IP_8


title: TR-246-WT-input_8


title: TR-231-KI-input_8


title: Culture_NbP2_rep2


title: TR-230-WT-m6A-IP_8


title: TR-230-WT-input_8


title: Culture_NbP1_rep4


title: Culture_NbP2_rep1


title: Culture_NbP1_rep3


title: 3_3T3+IL6+IL6R

description: IL6+IL6R treated 3T3 cells


title: Culture_NbP1_rep1


title: Lung, OVA+PM3

city: Sao Paulo

first: Alexis Germán

last: Murillo Carrasco

email: agmurilloc@gmail.com, agmurilloc@usp.br

state: Sao Paulo

address: Av. Dr. Arnaldo 251, Sao Paulo

country: Brazil

institute: ICESP

description: Gene expression data from Mus musculus treated with 10 µg ovalbumin and exposed to  600 µg.m-3 PM2.5 for 1 hour daily

hyb_protocol: The hybridization was performed onto the GeneChip Mouse Gene 2.0 ST Array (Thermo Scientific, Massachusetts, USA), following manufacturer’s protocol. After hybridization, the arrays were washed and stained using the GeneChip Hybridization Wash and Stain Kit in the GeneChip Fluidics Station 450 under standard conditions.

scan_protocol: Then, they were scanned using Affymetrix GeneChip Scanner 3000 7G. We used Expression Console software (Thermo Scientific, Massachusetts, USA) for quality assessment.

data_processing: The background correction, normalization and summarization of raw data (CEL files) by Robust Multi-Array Average (RMA) method were performed in two software: Transcriptome Analysis Console (TAC) software version 4.0.2 (Thermo Scientific, Massachusetts, USA) and R software version 4.0.2 (released on 2020-06-22).

source_name: Lung, OVA+PM

label_protocol: The microarray analysis was performed using three RNA samples for each studied group (Control, OVA, PM2.5, OVA+PM2.5), totalizing 12 samples. One hundred nanograms of total RNA was ampliﬁed with the Ambion WT Expression Kit.

extract_protocol: Total RNA of lung samples (n=3 animals per group) was extracted using RNeasy Mini Kit (Qiagen, Hilden, Germany), according to manufacturer's instructions.

treatment_protocol: Five-day-old male mice were immunized intraperitoneally (i.p.) with 10 µg of ovalbumin (OVA) (Advanced Nutrition, Rio de Janeiro, Brazil) in 1 mg of aluminum hydroxide (Al(OH)3) in 0.1 ml of phosphate-buffered saline (PBS). This procedure was repeated at the 7th day of life. Animals from the control group received i.p. injection of PBS only.   After the sensitization protocol, animals were challenged three more times with aerosolized 3% OVA solution or PBS only using an ultrasonic nebulizer (Pulmoclear II Luxo - Soniclear, São Paulo, Brazil) for 15 min a day for 3 consecutive days. The first challenge occurred from the 9th to 11th day, the second from 24th to 26th day and the third from 37th to 39th day. At the 40th day, animals were euthanized.   The HAPC system consists of three virtual impactors to concentrate particles of the ambient air with aerodynamic diameter smaller than 2.5 microns and it is located on the campus of the University of São Paulo School of Medicine (23°33′18.1”S 46°40′15.0”W) closer to a high traffic density road.   Mass concentrations of PM was measured using an airborne particulate monitor (two-wavelength nephelometer DataRam DR-4000, Thermo Fisher Scientific, Waltham, MA, USA) and our target dose were 600 µg.m-3 for 1 hour daily that is the equivalent to the to a  24-h mean PM2.5 concentration of 25 μg.m−3 .   Mice were exposed to either ambient PM2.5 or filtered air from the 5th to the 39th day of life, using an ambient particle concentrator developed at the Harvard School of Public Health (HAPC).

value: Ovalbumin

tag: exposure


title: Culture_NbP1_rep2


title: TR-2216-WT-m6A-IP_5

value: 5 months


title: Lung, OVA+PM2


title: Lung, PM3

description: Gene expression data from Mus musculus exposed to  600 µg.m-3 PM2.5 for 1 hour daily

source_name: Lung, PM

value: No ovalbumin


title: Lung, OVA+PM1


title: 13_3T3+IL6+IL6R

description: IL6+IL6R treated 3T3 cells


title: 6_3T3_CTRL

description: control  3T3 cells

source_name: CTRL


title: TR-2216-WT-input_5


title: Lung, PM2


title: 10_3T3+IL1B

description: IL1B treated 3T3 cells


title: 5_3T3+IL1B

description: IL1B treated 3T3 cells


title: whole kidney UUOO_12Hr Transriptome

city: Taipei

first: Chih-Chien

last: Sung

address: No 325, Section 2, Cheng-Kung Road,Neihu

institute: Tri-Service General Hospital, National Defense Medical Center

data_processing:
Sequenced reads were mapped to Ensembl rat gene set (Rnor_6.0) using STAR v2.7.3
Transcript abundances in TPM were caculated by RSEM/1.3.3
Genome_build: Rnor_6.0 (Ensembl)
Supplementary_files_format_and_content: tab-delimited text files include TPM  for each sample

source_name: Kidney

extract_protocol:
For bulk kidney, obstructed kidneys from animals were rapidly removed and be processed individually by homogenizing in Trizol, then transferred to a 2.0 mL microcentrifuge tube for RNA extraction and library construction (TruSeq Stranded mRNA Library Prep Kit, Illumina) according to the manufacturer’s protocol. For microdissecting cortical collecting duct and cortical TAL,  total RNA were extracted using the Direct-zol™ RNA Kits (Zymo Research) and cDNA was synthesized by SMARTer V4 Ultra Low RNA kit (Clontech). The cDNA was then amplified for 15 PCR cycles, purified by AmPure XP magnetic beads (Beckman Coulter Genomics), and eluted with 15 μL Elution Buffer. The purified cDNA was further quantified by Qubit. Library size distribution was determined using the Agilent 2100 bioanalyzer using High-Sensitive DNA kit. The Nextera XT DNA Library Preparation Kits (Illumina) was used to generate the libraries with input of 1 ng.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Sprague Dawley

value: Kidney

tag: group

value: UUO


title: 15_3T3+IL1B

description: IL1B treated 3T3 cells


title: NbP2_D2_ALA4


title: TR-2214-KI-m6A-IP_5


title: Lung, OVA2

description: Gene expression data from Mus musculus treated with 10 µg ovalbumin

source_name: Lung, OVA

value: No PM2.5


title: Lung, PM1


title: whole kidney sham control_12Hr Transriptome

value: sham


title: TR-2214-KI-input_5


title: 1_3T3_CTRL

description: control  3T3 cells

value: MEFs


title: Lung, OVA3


title: whole kidney UUO_6Hr Transriptome


title: TR-220-WT-m6A-IP_8

value: Hippocampus


title: whole kidney sham control_6Hr Transriptome


title: TR-220-WT-input_8

value: HdhQ7/7 (wild-type)


title: NbP2_D2_ALA2


title: NbP2_D2_ALA1


title: Lung, OVA1


title: Lung, Control2

description: Gene expression data from Mus musculus with no treatment

source_name: Lung, Control


title: whole kidney UUO_3Hr Transriptome


title: Lung, Control3


title: NbP2_D2_Ctrl4


title: small RNAs in P16 leptotene and zygote spermatocytes

city: Nagoya

first: Kenji

last: Ichiyanagi

address: Furo-cho, Chikusa-ku

department: Graduate School of Bioagricultural Sciences

institute: Nagoya University

description: P16 LZ spermatocytes

data_processing:
Adaptor sequences were removed from the reads by Trim Galore.
The reads were mapped to the mouse genome by hisat2.
Uniquly mapped reads were counted for each piRNA cluster.
Assembly: mm10
Supplementary files format and content: comma-separated text file containing expression levels (RPKM, reads per kilobase per million mapped reads) of piRNA clusters.

source_name: leptotene and zygotene spermatocytes

extract_protocol:
Leptotene and zygote spematocytes were  purified by cell sorting using Hochyst staining.  RNAs were extracted by isogene, and used for small RNA library preparation
NEBNext small RNA library prep set was used.

value: leptotene and zygotene spermatocytes

value: wild type

value: 16 days


title: whole kidney sham control_3Hr Transriptome


title: NbP2_D2_ALA3


title: NbP2_D2_Ctrl3


title: NbP2_D2_Ctrl1


title: TR-2209-WT-input_5

value: Trained

value: input


title: TR-2202-KI-input_5

value: HdhQ7/Q111 (KI)


title: TR-2202-KI-m6A-IP_5


title: whole kidney sham control 0Hr Transriptome


title: whole kidney UUO 0Hr Transriptome


title: LNA TUG1 3

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

data_processing:
Quality, adapter content and duplication rates were accessed by FastQC.
Trimming of reads was achieved by employing Trimmomatic version 0.39 after a quality drop below a mean of Q20 in a window of 10 nucleotides (34). Reads of at least 15 nucleotides were approved for subsequent analyses.
Read mapping was done with STAR aligner using default settings with the option --outSAMtype BAM SortedByCoordinate (Dobin, 2013) with default settings.
For known transcript models we used GRCh38.R21 annotations downloaded from Gencode repository (Frankish et al., 2021). Counting reads over gene model was carried out using GenomicFeatures Bioconductor package (Lawrence, 2013). All transcripts with read counts less than 10 were excluded. For normalization of read counts and identification of differentially expressed genes we used DESeq2 with padj < 0.05 cutoff (Love, 2014).
Assembly: hg38
Supplementary files format and content: DEseq2 normalitzed count table

source_name: HUVEC cell lysate

growth_protocol: HUVECs were grown in 6-well plates with Endothelial Cell Growth medium from Lonza

extract_protocol:
Total RNA was isolation with Direct-zol RNA miniprep kit (Zymo Research) according to the manufacturer’s instructions including DNase digest.
The library was generated by using the SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian (Takara Bio) with 1 µg RNA as input

treatment_protocol: HUVECs were transfected with Control or TUG1 LNA GapmeRs. Total RNA was isolated at confluent state after 48 h with QIazol (Qiagen)

value: human umbilical vein endothelial cells; pooled


title: LNA TUG1 2


title: LNA TUG1 1


title: Lung, Control1


title: ECl_1.VN

city: Pretoria

first: John

last: Osei Sekyere

address: 05 Bopheloweg Off Dr. Savage Road

institute: University of Pretoria

description:
MLST unknown
Samples were collected from Pregnant women who were at labour or just to have labour at the Steve Biko Academic Hospital. Rectal swabs were taken from the patients and brought to the laboratory for culturing and subsequent microbiological analysis

data_processing: All analysis was conducted within SMRTLINK v10.1

organism: Enterobacter cloacae

source_name: rectal swab of pregnant women

extract_protocol:
Zymo DNA extraction kits were used to extract DNA for PCR confirmation of the resistance genes
HMW gDNA was isolated using NEB Mornach HMW DNA isolation kit (https://international.neb.com/protocols/2020/10/27/protocol-for-high-molecular-weight-dna-hmw-dna-extraction-from-bacteria). HMW gDNA was quantified using Qubit HS dsDNA Assay and qualified on Tapestation using genomics screentape. HMW gDNA was shared to ~10kb fragments using covaries g-Tubes and QC’d using the above method. SMRTbell libraries were performed using PacBio’s Microbial Multiplexing workflow (see attached)     The resulting libraries were size selected using BluePippin Size selection using U1 marker (10-18kb). QC was performed using the above method. Libraries were then prepared for sequencing following the online SMRTlink guided protocol (Binding kit 2.0 and Control 1.0, Sequel II Sequencing plate 2.0 and SMRT cell 8M.)
OTHER: size selection was done by Blue-Pippin and sequenced with PacBio for DNA WGS

tag: source

value: Carbapenem and/or colistin resistant Enterobacterales isolated from pregnant women

tag: sample type

value: rectal swab isolate


title: TR-2181-KI-m6A-IP_5

value: 5 months


title: NbP1_D2_ALA4

value: GMP derived erly neutrophil bias progenitors


title: Zymo_S4

city: Tartu

first: Kaspar

last: Valgepea

state: Tartu

address: Nooruse 1, room 520

department: Institute of Technology

country: Estonia

institute: University of Tartu

data_processing:
The quality of NextSeq raw reads was verified using MultiQC (Ewels et al., 2016) and adapter sequences were trimmed using the Cutadapt package (version 2.10; Martin 2011)
Sequencing reads were aligned and mapped to the genome of C. autoethanogenum DSM 10061 (NC_022592.1) using the Rsubread package (version 2.4.2; Liao et al., 2019).
Genomic features were assigned using the featureCounts functions within Rsubread
Raw library sizes were normalized and transcript abundances in reads per kilobase of transcript per million mapped reads (RPKM) were estimated from feature counts and gene lengths using edgeR (version 3.32.1; Robison et al., 2010).
Assembly: NC_022592.1
Supplementary files format and content: RPKM value tab-delimited text files

organism: Clostridium autoethanogenum

source_name: bacteria cell

growth_protocol: Clostridium autoethanogenum was grown on syngas or CO in chemically defined medium anaerobically at 37C and a pH of 5 in chemostats at dilution rate ~1 and 2.0 day-1

extract_protocol:
Frozen pellets were thawed and total RNA was extracted using cellular lysis in RNase-free acid-washed glass beads (Merck) and RNeasy mini kit (Qiagen) with off-column DNase treatment followed by enrichment and purification using RNA Clean & ConcentratorTM (Zymo Research).
Ribosomal RNA were removed as follows: samples referred to as “NuGEN” were processed with Prokaryotic AnyDeplete™ (0363; NuGEN), “Qiagen” samples with QIAseq® FastSelect™ Kit (335925; Qiagen), and “Zymo” samples with Zymo-Seq RiboFree™ Total RNA Library Kit (R3000; Zymo Research)
Stranded mRNA libraries were prepared for NuGEN samples with Universal Prokaryotic RNA-Seq, Prokaryotic AnyDeplete™ (0363; NuGEN); for Qiagen samples with QIAseq® Stranded RNA Lib Kit (180743; Qiagen); for Zymo with Zymo-Seq RiboFree™ Total RNA Library Kit (R3000; Zymo Research). Constructed mRNA libraries were prepared for sequencing using the MiSeq v3 150 cycles sequencing kit (MS-102-3001; Illumina).

treatment_protocol: Culture was pelleted by rapid centrifugation (5,000 × g for 3 min at 4C) followed by resuspension in 5 mL of RNAlater (Qiagen). Samples were stored at 4C overnight, centrifuged (4000 × g for 10 min at 4C) and the pellets stored at -80C.

tag: physiological state

value: Syngas chemostat at 1 day-1


title: TR-2209-WT-m6A-IP_5


title: TR-2181-KI-input_5


title: LNA Ctrl 3

tag: cell type


title: LNA Ctrl 2


title: small RNAs in P11 leptotene and zygote spermatocytes

description: P11 LZ spermatocytes

value: 11 days


title: Zymo_S3

value: CO chemostat at 2 day-1


title: NbP2_D2_Ctrl2

tag: cell line


title: NbP1_D2_ALA3


title: NbP1_D2_ALA2


title: NbP1_D2_ALA1


title: TR-2175-WT-input_5

tag: age


title: Zymo_S1

value: CO chemostat at 1 day-1


title: Zymo_S2

value: Syngas chemostat at 2 day-1


title: Qiagen_S4


title: Ctrl-271-KI-m6A-IP_8

value: Hippocampus

value: 8 months

value: Naive (not trained)


title: NbP1_D2_Ctrl3


title: Ctrl-372-KI-m6A-IP_8


title: NbP1_D2_Ctrl4


title: R3_HCC827_Illumina

city: Parkville

first: Matthew

last: Ritchie

state: Victoria

address: 1G Royal Parade

institute: The Walter and Eliza Hall Institute of Medical Research

data_processing:
MinKNOW PromethION Release 19.12.9 (ONT)
Base calling and quality scoring (Illumina): Real-Time Analysis on board software v2.4.6. Base calling (ONT): Guppy 4.2.2, with the PromethION model, in high-accuracy mode.
Circular consensus sequence generation (PacBio): ccs 4.0.0 (commit SL-release-8.0.0).
FASTQ file generation and de-multiplexing (Illumina): bcl2fastw conversion software v2.15.0.4. De-multiplexing (PacBio): lima 1.10.0 (commit SL-release-8.0.0).
Refining and clustering (PacBio): isoseq3 3.2.2 (commit SL-release-8.0.0)
Sequenced reads were mapped to the GRCh38 reference genome and RNA Sequin decoy chromosome combined sequences using the align function in the Rsubread package (version 1.34.7, Liao et al. Nucleic Acids Research, 2013) with default parameters (Illumina),  minimap2 version 2.17 with arguments -ax splice -uf -k14 -L (ONT) and pbmm2 1.1.0 (commit SL-release-8.0.0) (PacBio).
Gene-level counts were obtained using the featureCounts function (Liao et al. Bioinformatics, 2014) from the Rsubread package (version 1.34.7) using the GENCODE v33 annotation and RNA sequin annotation 2.4 combined GTF file (Illumina) and the GENCODE v29 annotation and RNA sequin annotation 2.4 combined GTF file (ONT, PacBio) .
Genome_build: GrCh38 and RNA sequin decoy chromosome 2.4 combined sequences
Supplementary_files_format_and_content: Tab-delimited text files with columns representing Ensembl IDs and the number of reads mapping to that gene.

source_name: Human lung cancer cell line HCC827

growth_protocol: The cell lines were retrieved from the ATCC (https://www.atcc.org/) and cultured in Roswell Park Memorial Institute (RPMI) 1640 medium with 10% fetal calf serum and 1% penicillin-streptomycin. The cells were grown independently at 37°C with 5% carbon dioxide until near 100% confluency.

extract_protocol:
The mRNA was extracted using a Qiagen RNA miniprep kit and purified using the NEBNext® Poly(A) mRNA Magnetic Isolation Module (E7490).
3.75ng purified mRNA spiked with sequins were used for the NEBNext Ultra II Directional RNA Library Prep Kit (Illumina). Fragmentation was done for 15 minutes at 94°C, and final amplification with 11 PCR cycles. The libraries were sequenced in 75PE on NextSeq 500. The cRNA-PCR Barcoding (SQK-PCS109 with SQK-PBK004) kit was used with the supplied protocol (ONT). Amplication for 1.5ng purified mRNA spiked with sequins was done with 14 PCR cycles with a 2 minutes and 30 seconds extension step. Pooled barcoded libraries were sequenced on 5 PromethION R9 flow cells. Iso-Seq libraries were prepared and sequenced by Novogene on Sequel II (PacBio). Libraries were prepared according to the manufacturer's specifications from total RNA spiked in with sequins. Size selection was performed for the standard ~2kb target. The total number of PCR cycles is 12.

treatment_protocol: Cells were dissociated into single cell suspensions in FACS buffer, centrifuged and frozen at -80 °C.

value: Human lung cancer cell line

tag: replicate


title: Ctrl-372-KI-input_8

tag: genotype


title: NbP1_D2_Ctrl2


title: 11_ 3T3_CTRL

description: control  3T3 cells

value: MEFs


title: NbP1_D2_Ctrl1


title: Qiagen_S2


title: R2_HCC827_Illumina


title: Ctrl-271-KI-input_8

tag: treatment

value: input


title: LNA Ctrl 1


title: TR-2175-WT-m6A-IP_5

tag: tissue

value: HdhQ7/7 (wild-type)

value: Trained


title: R3_H1975_Illumina

source_name: Human lung cancer cell line NCI-H1975


title: Ctrl-247-WT-input_8


title: Ctrl-247-WT-m6A-IP_8


title: R2_H1975_Illumina


title: NuGEN_S2


title: Ctrl-245-KI-input_8

value: HdhQ7/Q111 (KI)


title: Qiagen_S3


title: Fibro-iPSC.2_IFN

city: Montréal

first: Claude

last: Perreault

state: Québec

address: 2950, Chemin de Polytechnique

country: Canada

institute: Institute for Research in Immunology and Cancer

data_processing:
Basecalls performed using Illumina RTA 2.4.11.
Samples demultiplexed using bcl2fastq 2.20 allowing 1 mismatch in the index.
Sequenced reads were trimmed for sequencing adapters and low quality extrimities and mapped to the reference genome using STAR version 2.5.1b
Readcounts were computed by STAR during sequence alignment based on annotations from Gencode version 26, based on Ensembl version 88
Genome_build: GRCh38
Supplementary_files_format_and_content: Readcounts: Tab-delimited file where columns are Ensembl gene identifier, counts for unstranded RNA, counts for 1st strand aligned, counts for 2nd strand aligned

source_name: adult dermal fibroblasts

growth_protocol: hiPSCs were grown in mTeSR1 medium (STEMCELL) on Matrigel or in DEF-CS™ 500 Basal Medium with Additives (Takara Bio) on coated (COAT-1, Takara Bio) cell culture vessels

extract_protocol:
Total RNA extraction was done using TRIzol (Invitrogen) and further purification with the RNeasy Micro Kit (QIAGEN) from 3 x 10^6 Fibro-iPSC.2 and Fibro-iPSC.2_IFN cells, and from 5 x 10^6 cells for all other samples.
cDNA library preparation was done using 1000 ng RNA for hiPSC22_IFN and 4000 ng RNA for all other samples, using the KAPA Hyperprep RNAseq stranded kit (KAPA) with polyA capture. 9 and 7 PCR cycles for hiPSC22_IFN and all other iPSC samples, respectively, were used for library amplification. All libraries were diluted to 10 nM and normalized by qPCR using the KAPA library quantification kit (KAPA). Libraries were pooled to equimolar concentration. Sequencing was performed with the Illumina Nextseq500 using the Nextseq High Output 150 cycles (2x80bp for hiPSC22 and hiPSC22_IFN, and 2x75bp for all other iPSCs) using 2 pM of the pooled libraries.

treatment_protocol: For treated hiPSCs: 40 ng/mL recombinant human IFN-γ (Gibco) for 72 hours

value: human induced pluripotent stem cells (hiPSCs)

value: IFN-g treatment (40 ng/mL for 72h)

tag: culture medium

value: mTeSR1 medium (STEMCELL) on Matrigel

tag: reprogramming method

value: lentivirus


title: Fibro-iPSC.1_IFN


title: Ctrl-232-WT-m6A-IP_8


title: ATP6_4

city: Athens

first: Jingwen

last: Song

state: Ohio

address: 172 Water Tower Drive, 101 Konner Bldg.25, The Rideges

department: biological Sciences

institute: Ohio university

data_processing:
Preparation of clean sequence reads  Constructed sequencing libraries were subject to sequencing with Illumina NovaseqTM 6000 platform (paired-end, 150 bp). Prior to assembly, reads containing sequencing adaptors, reads containing sequencing primers, and sequences with q quality score lower than 20 were removed.
Alignment of reads  The cleaned sequencing reads were aligned to reference genome [https://www.ncbi.nlm.nih.gov/genome/guide/human/] using HISAT2 package. Multiple alignments were allowed for each read sequence (up to 20 by default), with a maximum of two mismatches allowed. HISAT2 also built a database of potential splice junctions.
Transcript abundance estimation and differential expression analysis  Aligned reads of individual samples were assembled using StringTie. Transcriptomes from all samples were then merged to reconstruct a comprehensive transcriptome using a proprietary Perl script of LC Sciences (Houston, Texas, U.S.A.). Following transcriptome reconstruction, FPKM reads were evaluated by StringTie, and differential expressed genes were evaluated by edgeR. The differentially expressed mRNAs and genes were selected with log2 (fold change) ≥1 or log2 (fold change) ≤-1, and with p values < 0.05.

source_name: lung

growth_protocol: Human non-small lung cancer cell line A549 cells were purchased from ATCC. A549 cells were cultured in standard Dulbecco’s Modified Eagle Medium (DMEM contains 25mM glucose) supplemented with 10% fetal bovine serum, 1% penicillin, and 50ug/ml streptomycin in a humidified atmosphere of 5% CO2 at 37℃.

extract_protocol:
The total RNA was extracted using GeneJET RNA Purification Kit (Thermo Scientific™) following manufacture’s instruction.
Poly(A) RNA sequencing library was prepared following Illumina’s TruSeq-stranded-mRNA sample preparation protocol. RNA integrity was checked with Agilent Technologies 2100 Bioanalyzer.

treatment_protocol: A549 cells which grown on 100mm plates (1*10^6 cells) were individually treated with 0.5mM ATP, 10ng/ml TGF-β for 2h and 6h.

value: human non-small lung cancer cell line A549

value: 0.5mM ATP 6h treatment


title: Ctrl-232-WT-input_8


title: TGF6_2

value: 10ng/ml TGF-β 6h treatment


title: ATP6_3


title: NuGEN_S4

value: Syngas chemostat at 1 day-1


title: hiPSC22_IFN

value: DEF-CS 500 Basal Medium with Additives (Takara Bio) on coated (COAT-1, Takara Bio) cell culture vessels

value: retrovirus


title: NuGEN_S3

value: CO chemostat at 2 day-1


title: ATP6_2


title: Ctrl-245-KI-m6A-IP_8

value: Hippocampus

value: 8 months

value: Naive (not trained)


title: R1_HCC827_Illumina

value: Human lung cancer cell line


title: Ctrl-222-WT-input_8

value: HdhQ7/7 (wild-type)

value: input


title: Ctrl-2210-WT-m6A-IP_5

value: 5 months


title: hiPSC22_2

value: human induced pluripotent stem cells (hiPSCs)

value: no treatment


title: ATP6_1


title: Fibro-iPSC.1

value: mTeSR1 medium (STEMCELL) on Matrigel

value: lentivirus


title: TGF6_1

value: human non-small lung cancer cell line A549


title: TGF2_4

value: 10ng/ml TGF-β 2h treatment


title: Ctrl-2210-WT-input_5


title: R1_H1975_Illumina


title: hiPSC22_1


title: Ctrl-222-WT-m6A-IP_8


title: Ctrl-2201-KI-input_5

value: HdhQ7/Q111 (KI)


title: Lepr_KO_LPS_1h

city: Beijing

first: Ziyi

last: Guo

state: Beijing

address: Medicial Science Building, Tsinghua University

department: School of Medicine

institute: Institute for Immunology

data_processing:
Base-calling was performed using CASAVA v1.8
Data were filtered by using SOAPnuke (developed by BGI) v1.4.0. The parameters were -l 15 -q 0.2 -n 0.1. Sequenced reads were trimmed for adaptor sequence, unknown base >5% and low-quality reads. These reads were clean reads.
HISAT v2.1.0 was used for mapping clean reads to reference genome (mm10). The parameters were --dta --phred64 unstranded --new-summary -x index -1 read_r1 -2 read_r2(PE).
Bowtie2 v2.2.5 was used for alignment to reference gene sequence. The parameters were -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200. Gene expression level was calculated by RSEM.
Genome_build: mm10
Supplementary_files_format_and_content: The processed data dile is xls format and includes FPKM values in each sample.

source_name: Alveolar macrophages

growth_protocol: Alveolar macrophages were isolated by collecting BALF cells. Cells were attached to plate.

extract_protocol:
RNA was extracted by TRIzol reagent.
Libraries were prepared by using standard Illumina protocols.

treatment_protocol: After cells were attached to the plate, LPS was added at the final concentration of 10ng/ml for 1h or cells were left unstimulated.

value: BALF-derived alveolar macrophages

value: Leprfl/fl, Lyz2-Cre


title: Lepr_KO_0

value: untreated


title: hiPSC22_3

value: DEF-CS 500 Basal Medium with Additives (Takara Bio) on coated (COAT-1, Takara Bio) cell culture vessels

value: retrovirus


title: TGF2_2


title: Ctrl-2201-KI-m6A-IP_5

value: Hippocampus

value: Naive (not trained)


title: Ctrl-2199-WT-m6A-IP_5

value: HdhQ7/7 (wild-type)


title: ATP2_4

value: 0.5mM ATP 2h treatment


title: ATP2_3


title: TGF2_1


title: Ctrl-2199-WT-input_5

value: 5 months

value: input


title: WT_0

value: Lepr+/+, Lyz2-Cre


title: WT_LPS_1h


title: ATP2_2


title: Ctrl-2184-KI-input_5


title: TGF2_3


title: Ctrl-2184-KI-m6A-IP_5


title: liver tumor cells_Myc_p53_3

city: New York

first: Yu-Jui

last: Ho

state: New York

address: 417 E 68th St

department: Cancer Biology & Genetics Program

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Trimmomatic (v0.36) was used to remove adaptor sequences. RNAseq reads were aligned to (GRCm38 - mm10) with STAR (v2.5.3a)
Genome wide transcript counting was performed by featureCounts (v1.6.3) to generate raw count table
Differential expression analysis was performed with DESeq2 (v1.20.0) package in R
Genome_build: GRCm38 - mm10
Supplementary_files_format_and_content: csv text file includes raw count value for each sample

source_name: liver cells

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit (Qiagen) and Rnase-Free Dnase Set (Qiagen) in accordance to manufacturer’s protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

value: primary liver cancer cell lines


title: liver tumor cells_Myc_p53_2


title: ATP2_1


title: Copra mannooligosaccharide Test 2 R2

city: Mysuru

first: Mukesh

last: Kapoor

state: Karnataka

address: CFTRI

department: Protein Chemistry and Technology

country: India

institute: CSIR-Central Food Technological Research Institute

description: Gene expression in presence of purified copra β-mannooligosaccharide

hyb_protocol: Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Agilent Technologies, Part Number 5188-5327)

scan_protocol: Scanned using Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D).

data_processing: Data extraction from Images was done using Feature Extraction software  and Normalization of the data was done in GeneSpring GX  : 50th percentile shift  method

organism: Bifidobacterium adolescentis

source_name: Minimal media late log phase

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). The total RNA were reverse transcribed at 40°C using oligo dT primer tagged to a T7 polymerase promoter and converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

growth_protocol: Bifidobacterium adolescentis ATCC-15703 was passaged anaerobically 3 times in minimal media containing copra β-manno-oligosaccharides (mix and bio-gel P2 purified),  glucose and galactose (0.5 % w/v, 37 C, static, 36 h) as sole carbon source to reduce carryover between indivual sugars. The cells from 2nd passage were innoculated (1 % v/v, OD600 ~ 0.2) in the minimal medium (30 ml) containing respective sugars in duplicates, and were grown till the late log phase (OD600 ~0.8, 36 h, 37 C, static). The cells were then harvested by centrifugation (3000 rpm, 10 min, 4C), supernatant was discarded, and the pellet was washed once with phosphate buffer saline (10 ml) to remove the residual medium component Bifidobacterium adolescentis ATCC-15703 grown under different sugars were stored in RNA later (Sigma) overnight at 44C and then stored in -80C till RNA extration.

extract_protocol: Total RNA extracted using Qiagen Rneasy Mini Kit following manufacturer's instructions.

treatment_protocol: Bifidobacterium adolescentis ATCC-15703 was passaged anaerobically 3 times in minimal media containing copra β-manno-oligosaccharides (mix and bio-gel P2 purified), mannose, glucose and galactose (0.5 % w/v, 37 C, static, 36 h) as sole carbon source to reduce carryover between indivual sugars. The cells from 2nd passage were inoculated (1 % v/v, OD600 ~ 0.2) in the minimal medium (30 ml) containing respective sugars in duplicates, and were grown till the late log phase (OD600 ~0.8, 36 h, 37 C, static). The cells were then harvested by centrifugation (3000 rpm, 10 min, 4C), supernatant was discarded, and the pellet was washed once with phosphate buffer saline (10 ml) to remove the residual medium component Bifidobacterium adolescentis ATCC-15703 grown under different sugars were stored in RNA later (Sigma) overnight at 44C and then stored in -80 C till RNA extration.

tag: growth medium

value: Minimal media late log phase

value: Probiotic strain

value: purified copra β-mannooligosaccharide


title: Copra mannooligosaccharide Test 2 R1

tag: strain


title: Cont_4

value: human non-small lung cancer cell line A549

value: Control without treatment


title: Ctrl-2183-WT-m6A-IP_5

source_name: Hippocampus


title: Copra mannooligosaccharide Test 1 R2

description: Gene expression in presence of mixed copra β-mannooligosaccharide

value: mixed copra β-mannooligosaccharide


title: Ctrl-2183-WT-input_5


title: liver tumor cells_Myc_p53_1


title: TGF6_4

value: 10ng/ml TGF-β 6h treatment


title: Galactose control 1 R2

description: Gene expression in presence of Galactose

value: Galactose


title: liver tumor cells_Myc_Utx_2D


title: Cont_3


title: Copra mannooligosaccharide Test 1 R1


title: Ctrl-2172-KI-m6A-IP_5

value: HdhQ7/Q111 (KI)


title: liver tumor cells_Myc_Utx_2B


title: Cont_2


title: Ctrl-2172-KI-input_5

value: Hippocampus


title: liver tumor cells_Myc_Utx_2A


title: Galactose control 1 R1


title: Cont_1


title: Glucose control 1 R2

description: Gene expression in presence of Glucose

value: Glucose


title: Glucose control 1 R1

description: Gene expression in presence of Glucose


title: HeLa, HLA-G, 4

status: Public on Jul 19 2022

city: Linhai

first: Hui-Hui

last: Xu

state: Zhejiang province

institute: Taizhou Hospital

data_processing:
BGISEQ-500
Sequence reads were trimmed for adaptor sequence/low-quality sequence (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using BGISEQ-500 genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using BGISEQ-500 genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

source_name: HeLa

growth_protocol: The human cervical carcinoma cell lines HeLa were maintained in DMEM supplemented with 10% heat-inactivated fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

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-seq were prepared using BGI Kit following manufacturer's protocols.

treatment_protocol:
transfected with the recombinant pVITRO2-mcs vector (InvivoGen, NY, USA) containing HLA-G cDNA or empty vector by Lipofectamine 3000 reagent (InvitroGen, NY, USA) according to the manual instructions.
The transfectants were selected with 50 μg/ml hygromycin B (InvitroGen, NY, USA)

value: HeLa

value: human cervical carcinoma cell

value: HLA-G overexpression

value: pVITRO2-hygro-mcs_HLA-G transfection


title: SiHa, HLA-G, 6

source_name: SiHa

growth_protocol: The human cervical carcinoma cell lines SiHa were maintained in DMEM supplemented with 10% heat-inactivated fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

value: SiHa


title: SiHa, HLA-G, 4


title: SiHa, pv, 1

value: control

value: pVITRO2-hygro-mcs vector transfection


title: SiHa, HLA-G, 5


title: HeLa, HLA-G, 6


title: HeLa, pv, 2


title: HeLa, pv, 3


title: SiHa, pv, 2


title: P_T3_2

city: Madrid

first: ANTONIO

last: CASTRILLO

address: Arturo Duperier 4

department: metabolism and cellular signaling

country: Spain

institute: Instituto Investigaciones Biomedicas Alberto Sols CSIC

data_processing:
Low quality reads (More than 20% of the bases qualities are lower than 10), reads with adaptors and reads with unknown bases (N bases more than 5%) were filtered to get the clean reads. Sequences were mapped to mm10 genome using  Bowtie2 with the following parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant  -p 1 -k 200
Gene expression levels were determined with software RSEM
Assembly: mm10
Supplementary files format and content: tab-delimited text files include Entrez Gene ID and Log2 Fold Change values for differential expression of case vs control

source_name: Macrophages

growth_protocol: Primary bone marrow derived macrophages (P-BMDMs) differentiated with complete 10% FCS and M-CSF were trypsinized and plated in 6-well plates (1million cells/well) in complete medium. Immortalized macrophages (I-BMDMs) were plated in complete medium (containing 10% FCS), similar to P-BMDMs

extract_protocol:
Total RNA was extracted using the NucleoSpin RNA/Protein kit (Macherey-Nagel, Düren, Germany). Qualitative analysis of total RNAs were performed in a bioanalizer Agilent 2100.
RNA libraries were prepared for sequencing using standard BGI protocols

treatment_protocol: P-BMDM and I-BMDM were treated with thyroid hormone (10 nM) or vehicle.

value: Immortal bone marrow derived macrophages

value: thyroid hormone T3


title: P_T3_3


title: P_T3_1