title: Sample 4_MPA_04

description:
column header in processed data file:
1004

value: Male

value: placenta


title: KG-1-Control-Venet-100nM (2) [KHA101520_015]

status: Public on Aug 18 2021

type: SRA

city: Chicago

first: Leonid

last: Feferman

state: Illinois

address: 1737 West Polk St

department: Research Resources Center

country: USA

institute: University of Illinois at Chicago

description:
KG-1 human acute myeloid leukemia cell line, suspension myeloblast-like cells, transduced with control lentiviral particles from Sigma (pLKO.1-puro Non-Target, SHC016V-1EA) with subsequent selection with 4 ug/mL puromycin, treated with 100 nM of venetoclax for 48 hours, RNA purified immediately after treatment
312603367_KHA101520-015_S100_L001

library_source: transcriptomic

data_processing:
Raw reads were aligned to the reference genome using STAR.
ENSEMBL gene expression was quantified using FeatureCounts.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text tables

molecule: total RNA

organism: Homo sapiens

growth_protocol: Cells were grown in IMDM media with 10% FBS, 100 U/mL penicillin, and 100 ug/mL streptomycin

extract_protocol:
Cell culture samples were collected immediately after treatment and lysed in TRIzol. Phase separation was performed with chloroform according to manufacturer's instructions. Aqueous phase was collected and used for RNA purification with Invitrogen PureLink RNA Mini Kit with on-column DNAse treatment according to manufacturer's protocol.
Illumina RiboZerto HMR + TruSeq Stranded mRNA Sample Prep Kit

treatment_protocol: Cells were harvested by centrifugation, growth medium was aspirated from cell pellets and cells were resuspended in complete growth medium containing selected concentrations of treatment compounds. Cells were incubated in presence of treatment compounds in CO2 incubator at 37 degrees C for 24 or 48 hours

tag: cell line

tag: cell type

value: human acute myeloid leukemia cell line

tag: genotype/variation

value: Control

tag: treatment


title: Sample 7_MPA_07

city: Atlanta

first: Danielle

middle: A

last: Clarkson-Townsend

state: Georgia

address: 1518 Clifton Road

department: Environmental Health

institute: Emory University

description:
column header in processed data file:
1007

data_processing:
FastQC performed
Fastq files aligned using STAR v2.7 to the C57 mouse genome (Ensemble assembly GRCm38.p6)
Read counts derived with STAR v2.7 with "quantmode" command and default commands.
Count data were analyzed using DESeq2 for differential expression analysis
Genome_build: mm10
Supplementary_files_format_and_content: count data were generated using STAR 2.7 with the "quantmode" command

organism: Mus musculus

source_name: E15.5 Placenta

extract_protocol:
RNA isolated using Qiagen Allprep DNA/RNA Mini Kit and concentration and RIN score measured with Thermo Scientific NanoDrop and Agilent 2100 Bioanalyzer.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Female C57BL/6J mice were randomized into 2 different light treatments: standard control lighting (CL, 12:12 light:dark) schedule, or circadian disruption (inversions of the photoperiod every 3-4 days)). Females remained in this light treatment for 4 weeks of pre-dosing before timed breeding with male mice. Females remained in their light treatments until placental tissue collection at E15.5. Samples were collected from 6 pregnant mice in the CL group and 6 pregnant mice in the CD group. 2 placenta from each dam were selected for representation of a male and female sample (where possible) from each dam, for a total of 24 placenta samples. Isolated RNA were sequenced with PolyA RNA sequencing (paired-end) at a 30M read depth.

tag: strain

tag: developmental stage

value: Embryonic day 15.5 (E15.5)

tag: Sex

value: Circadian Disruption

tag: tissue


title: TCD_Host1_(API_183)

city: Brisbane

first: Dylan

middle: Patrick

last: Carter-Cusack

state: Queensland

address: 300 Herston Rd

department: Department of Immunology

country: Australia

institute: QIMR Berghofer Medical Research Institute

description:
API183SynHost1
stranded RNA

data_processing:
base calling performed with Illumina basecaller
Sequence reads were trimmed for adapter sequences using Cutadapt (version 1.9) and aligned using STAR (version 2.5.2a) to the Mus musculus GRCm38 assembly with the gene, transcript, and exon features of Ensembl (release 70) gene model. Quality control metrics were computed using RNA-SeQC (version 1.1.8)
Expression was estimated using RSEM (version 1.2.30)
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited tsv files include raw counts for each sample as well as differential expression analysis of each treatment vs the vehicle (DMSO).

source_name: Group 2 - Non-GVHD Host

growth_protocol: NA - didn't use any cultured cells

extract_protocol:
RNA was isolated using either the Qiagen Rneasy Mini Kit (74104) or the Quick-RNA Microprep Kit (Zymo)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Recipient mice received 1100-cGy split-dose total-body irradiation, followed by 5x10^6 T-cell depleted BM with or without 0.5x10^6 splenic T cells

value: microglia

value: Isolated microglia

tag: disease state

value: TCD (non GVHD control)


title: Sample 231

type: RNA

city: Syracuse

first: Vladimir

last: Kuznetsov

state: NY

address: 750 E Adams St

department: Urology / Biochemistry and Molecular Biology

institute: SUNY Upstate Medical University

description: human breast tumor RNA

hyb_protocol: standard

scan_protocol: Labelled cRNAs were fragmented to an average size of approximately 50–100 nucleotides by heating at 60 °C in the presence of 10 mM ZnCl2, added to a hybridization buffer containing 1 M NaCl, 0.5% sodium sarcosine, 50 mM MES, pH 6.5, and formamide to a final concentration of 30%, final volume 3 ml at 40 °C. Hu25K microarrays represented the 24,479 biological oligonucleotides plus 1,281 control probes. Sequences for microarrays were selected from RefSeq (a collection of non-redundant mRNA sequences; http://www.ncbi.nlm.nih.gov/LocusLink/refseq.html) and from expressed sequence tag (EST) contigs (http://www.phrap.org/est_assembly/human/gene_number_methods.html). Each mRNA or EST contig was represented on the Hu25K microarray by a single 60-polymer oligonucleotide chosen by the oligonucleotide probe design programme. After hybridization, slides were washed and scanned using a confocal laser scanner (Agilent Technologies). Fluorescence intensities on scanned images were quantified, corrected for background noise and normalized.

data_processing:
Normalization between the channels was accomplished by normalizing each channel to the mean intensities of all genes.
Batch effect correction using the Kolmogorov-Smirnov weighted mean method was used to reduce variability between patients. Patients were first categorized into batches. Then, for each probe, Kolmogorov-Smirnov statistics were calculated for every batch permutation. Weights were calculated by using the sum normalized sums of the KS distance matrix. Weights were used to calculate the weighted mean expression value of the given probe. Weighted average mean correction was then performed on each batch.

source_name: pool of individual breast tumors

label_protocol: cRNA was generated by in vitro transcription using T7 RNA polymerase on 5 µg total RNA and labelled with Cy3 or Cy5 (CyDye, Amersham Pharmacia Biotech). Five micrograms of Cy-labelled cRNA from one breast cancer tumour was mixed with the same amount of reverse colour Cy-labelled product from a pool, which consisted of an equal amount of cRNA from each individual sporadic patient

extract_protocol:
The criteria for the sporadic patients (n = 97) were: primary invasive breast carcinoma less than 5 cm (T1 or T2), no axillary metastases (N0), age at diagnosis less than 55 years, calendar year of diagnosis 1983–1996, no previous malignancies; all patients were treated by modified radical mastectomy (n = 35) or breast-conserving treatment (n = 62), including axillary lymph node dissection followed by radiotherapy. Five patients of the metastases group received adjuvant systemic therapy consisting of chemotherapy (n = 3) or hormonal therapy (n = 2), all other patients did not receive additional treatment. All patients were followed at least annually for a period of at least 5 years. The criteria for hereditary patients (n = 20) were: carriers of a germline mutation in BRCA1 or BRCA2, and primary invasive breast carcinoma; no other selection criterion was applied. This study was approved by the Medical Ethical Committee of the Netherlands Cancer Institute.
Tumour material was snap-frozen in liquid nitrogen within 1 h after surgery. A haematoxylin and eosin stained section was prepared before and after cutting slides for RNA isolation for assessment of the percentage of tumour cells. Only samples with greater than 50% tumour cells were selected, mean 67% and median 70% for all groups studied. Formalin-fixed, paraffin-embedded tumour tissue was used to evaluate the following: tumour type (according to the World Health Organisation classification), histological grade (grade 1–3), and the presence of angioinvasive growth and extensive lymphocytic infiltrate. ER expression was determined by immunohistochemical staining (negative when less than 10% of the nuclei showed staining, all others ER positive).
We used 30 sections of 30-µm thickness for total RNA isolation. Total RNA was isolated with RNAzolB, and finally dissolved in RNase-free H2O. Twenty-five micrograms of total RNA was treated with DNase using the Qiagen RNase-free DNase kit and RNeasy spin columns. Total RNA treated with DNase was dissolved in RNase-free H2O to a final concentration of 0.2 µg µl-1.

value: breast tumor

source_name: patient sample

tag: lypmph-nodes

value: LN-

tag: metastatis

value: Meta+

tag: death

value: Alive

tag: timesurvival(years)

tag: survival-years

tag: timerecurrence(years)

tag: recurrence-years

tag: timemeta

tag: metastasis-years

tag: estrogen-receptor

value: ER+

tag: nih

tag: stgallen

tag: conservflag


title: KG-1-shFOXM1-AraC-0.75uM (2) [KHA101520_014]

description:
KG-1 human acute myeloid leukemia cell line, suspension myeloblast-like cells, transduced with FOXM1-shRNA lentiviral particles from Sigma (SHCLNV-NM_021953) with subsequent selection with 4 ug/mL puromycin, treated with 0.75 uM of cytarabine for 48 hours, RNA purified immediately after treatment
312597237_KHA101520-014_S99_L001

tag: cell line

tag: cell type

tag: genotype/variation

tag: treatment


title: KG-1-Control-AraC-0.75uM (2) [KHA101520_013]

description:
KG-1 human acute myeloid leukemia cell line, suspension myeloblast-like cells, transduced with control lentiviral particles from Sigma (pLKO.1-puro Non-Target, SHC016V-1EA) with subsequent selection with 4 ug/mL puromycin, treated with 0.75 uM of cytarabine for 48 hours, RNA purified immediately after treatment
312602357_KHA101520-013_S98_L001


title: KG-1-shFOXM1-Venet-100nM (2) [KHA101520_016]

description:
KG-1 human acute myeloid leukemia cell line, suspension myeloblast-like cells, transduced with FOXM1-shRNA lentiviral particles from Sigma (SHCLNV-NM_021953) with subsequent selection with 4 ug/mL puromycin, treated with 100 nM of venetoclax for 48 hours, RNA purified immediately after treatment
312598195_KHA101520-016_S101_L001


title: Sample 3_MPA_03

description:
column header in processed data file:
1003

tag: strain

tag: developmental stage

tag: Sex

tag: tissue


title: Sample 224

description: human breast tumor RNA

tag: lypmph-nodes

tag: metastatis

value: Meta-

tag: death

tag: timesurvival(years)

tag: survival-years


title: Sample 228

description: human breast tumor RNA

value: Dead

tag: timerecurrence(years)

tag: recurrence-years

tag: timemeta

tag: metastasis-years

tag: estrogen-receptor

value: ER-


title: Sample 1_MPA_01

description:
column header in processed data file:
1001

value: Female

value: Control Light


title: KG-1-Control-STL-50uM [KHA101520_011]

description:
KG-1 human acute myeloid leukemia cell line, suspension myeloblast-like cells, transduced with control lentiviral particles from Sigma (pLKO.1-puro Non-Target, SHC016V-1EA) with subsequent selection with 4 ug/mL puromycin, treated with 50 uM of STL427944 for 48 hours, RNA purified immediately after treatment
312607322_KHA101520-011_S96_L001

tag: cell line

tag: cell type

value: human acute myeloid leukemia cell line


title: KG-1-Control-MK2206-30uM (2) [KHA101520_012]

description:
KG-1 human acute myeloid leukemia cell line, suspension myeloblast-like cells, transduced with control lentiviral particles from Sigma (pLKO.1-puro Non-Target, SHC016V-1EA) with subsequent selection with 4 ug/mL puromycin, treated with 30 uM of MK-2206 for 24 hours, RNA purified immediately after treatment
312609311_KHA101520-012_S97_L001

tag: genotype/variation

value: Control

tag: treatment


title: GVHD_Donor1_(API_183)

description:
API183GVHDDonor1
stranded RNA

source_name: Group 2 - GVHD Donor

value: bone marrow derived macrophage

value: Isolated macrophages

tag: disease state

value: GVHD


title: Sample 2_MPA_02

description:
column header in processed data file:
1002

tag: strain

tag: developmental stage

value: Embryonic day 15.5 (E15.5)

tag: Sex

value: placenta


title: Sample 227

description: human breast tumor RNA

tag: tissue

value: breast tumor

tag: lypmph-nodes

tag: metastatis

tag: nih

tag: stgallen

tag: conservflag


title: Sample 226

description: human breast tumor RNA

value: LN-

tag: death

tag: timesurvival(years)

tag: survival-years

tag: timerecurrence(years)

tag: recurrence-years

tag: timemeta


title: GVHD_Host1_(API_183)

description:
API183GVHDHost1
stranded RNA

source_name: Group 1 - GVHD Host

tag: cell type

value: microglia

value: Isolated microglia


title: GL261 and microenvironment in fibrin 3D-bioink, 2

city: Tel Aviv

first: Ronit

last: Satchi-Fainaro

address: Klatzkin 35

department: physiology and pharmacology

country: Israel

institute: Tel Aviv University

data_processing:
Data analysis was aligned to mice genome. RNA-seq reads were aligned using Kallisto (N. Bray, H. Pimentel, P. Melsted, L. Pachter. (ISSN)) to mouse genome version mm10, and expression levels were calculated using RSEM (B. Li, C. N. Dewey, RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC bioinformatics 12, 323 (2011)), followed by further processing using the Bioconductor package DESeq2 1.24.0 in R (S. Anders, W. Huber, Differential expression analysis for sequence count data. Nature Precedings, 1-1 (2010)).
The data were normalized using TMM normalization, and differentially expressed genes were defined using the differential expression pipeline on the raw counts with a single call to the function DESeq (FDR- adjusted P value < 0.05).
For global transcriptome quantification and comparison between the samples (2D culture, fibrin 3D-bioink and in-vivo,) we performed PCA analysis and calculated the Euclidean distance between each pair of transcriptional profiles.
Genome_build: mm10
Supplementary_files_format_and_content: Transcript count for each library was normalized to the median of the transcript counts across all cells. For PCA and clustering, we used a log-transformed expression matrix. The top 12 and 8 PCs were included for subsequent tSNE analysis, determined by a drop in the proportion of variance explained by subsequent PCs. We confirmed that the resulting analyses were not particularly sensitive to this choice.

source_name: GL261 glioblastoma and murine primary astrocytes, microglia, pericytes and endothelial cells were grown in fibrin 3D-bioink

growth_protocol: For 2D culture and 3D-bioink models, a murine penta-culture composed of GL261 mCherry-labeled and freshly-isolated murine primary astrocytes, microglia, pericytes and endothelial cells was grown on a 2D petri dish, or in fibrin 3D-bioink GL261 cells were seeded at the concentration of 1x10^6 cells/ml (in fibrin 3D-bioink or in 2D culture) at the ratio of 1:1:2:0.1:0.1 creating the "penta-culture". mCherry-labeled murine GL261 GB cells (5x10^4) were stereotactically implanted into the striatum of 7 week-old male C57BL/6 immunocompetent mice (n=5, Envigo CRS), prior anesthesia using ketamine (150 mg/kg) and xylazine (12 mg/kg) injected intraperitoneally (IP). Mice were euthanized on day 14 post injection and the brains were resected for further evaluation of gene expression. For murine microenvironment cells isolation the following protocol was used: Brains from 6-10 week-old male C57BL/6 mice (Envigo CRS, Israel) were harvested, chopped and incubated in rotation with Collagenase IV/ Dispase II solution for 50 min at 37°C. Red blood-cells lysis was carried out followed by Percoll gradient for myelin separation. Cell suspension was then incubated with CD11b or CD31 microbeads for microglia or endothelial cells separation, respectively, and placed in MACS MS magnetic columns. Murine pericytes were isolated using anti-AN2 microbeads combined with anti- CD144 microbeads. The remaining cells collected following beads separation were astrocyte.

extract_protocol:
3D-bioink was cut into 1-2 mm fragments, digested with 600 U/ml collagenase II for 3 h and filtered with a 70 µm mesh prior RNA extraction. Total RNA was then isolated from all samples using EZ-RNA II total RNA isolation kit (Biological industries, California, USA), following the manufacturer’s protocol. RNA quality was evaluated by TapeStation® RNA Assay (Agilent Technologies).
Libraries were constructed with the NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina® (#E7760, NEB) using manufacturer’s instructions. Twenty-five to 75 ng RNA was amplified using 14 cycles of PCR. Final quality was evaluated by TapeStation® DNA HS Assay (Agilent Technologies). Equimolar pooling of libraries were performed based on Qubit® values and loaded (in triplicates) onto an Illumina® NextSeq 500 platform (Illumina, California, USA) in order to evaluate changes in gene expression between the tested groups.

tag: growth protocol

value: fibrin 3D-bioink


title: GL261 and microenvironment in fibrin 3D-bioink, 3

tag: strain

value: GL261 glioblastoma and murine primary astrocytes, microglia, pericytes and endothelial cells


title: KG-1-shFOXM1-DMSO [KHA101520_010]

description:
KG-1 human acute myeloid leukemia cell line, suspension myeloblast-like cells, transduced with FOXM1-shRNA lentiviral particles from Sigma (SHCLNV-NM_021953) with subsequent selection with 4 ug/mL puromycin, treated with 0.3% DMSO (vehicle) for 48 hours, RNA purified immediately after treatment
312607321_KHA101520-010_S95_L001

tag: cell line

tag: genotype/variation

tag: treatment

value: DMSO


title: Sample 220

description: human breast tumor RNA

tag: tissue

tag: lypmph-nodes

value: LN+

value: Meta-

value: Alive

tag: metastasis-years

tag: estrogen-receptor

value: ER+


title: Sample 222

description: human breast tumor RNA

tag: metastatis

value: Meta+

value: Dead

value: ER-

tag: nih

tag: stgallen

tag: conservflag


title: Sample 221

description: human breast tumor RNA

tag: death

tag: timesurvival(years)

tag: survival-years

tag: timerecurrence(years)


title: Sample 219

description: human breast tumor RNA

tag: recurrence-years

tag: timemeta


title: GL261 and microenvironment in 2D culture, 2

source_name: GL261 glioblastoma and murine primary astrocytes, microglia, pericytes and endothelial cells were grown on a 2D petri dish

tag: strain

tag: growth protocol

value: 2D petri dish


title: KG-1-Control-DMSO [KHA101520_009]

description:
KG-1 human acute myeloid leukemia cell line, suspension myeloblast-like cells, transduced with control lentiviral particles from Sigma (pLKO.1-puro Non-Target, SHC016V-1EA) with subsequent selection with 4 ug/mL puromycin, treated with 0.3% DMSO (vehicle) for 48 hours, RNA purified immediately after treatment
312592267_KHA101520-009_S94_L001

tag: cell line

tag: cell type

value: human acute myeloid leukemia cell line

tag: genotype/variation

value: Control

tag: treatment


title: KG-1-shFOXM1-Venet-100nM (1) [KHA101520_008]

description:
KG-1 human acute myeloid leukemia cell line, suspension myeloblast-like cells, transduced with FOXM1-shRNA lentiviral particles from Sigma (SHCLNV-NM_021953) with subsequent selection with 4 ug/mL puromycin, treated with 100 nM of venetoclax for 48 hours, RNA purified immediately after treatment
312605326_KHA101520-008_S93_L001


title: KG-1-shFOXM1-AraC-0.75uM (1) [KHA101520_006]

description:
KG-1 human acute myeloid leukemia cell line, suspension myeloblast-like cells, transduced with FOXM1-shRNA lentiviral particles from Sigma (SHCLNV-NM_021953) with subsequent selection with 4 ug/mL puromycin, treated with 0.75 uM of cytarabine for 48 hours, RNA purified immediately after treatment
312603360_KHA101520-006_S91_L001


title: KG-1-Control-MK2206-30uM (1) [KHA101520_004]

description:
KG-1 human acute myeloid leukemia cell line, suspension myeloblast-like cells, transduced with control lentiviral particles from Sigma (pLKO.1-puro Non-Target, SHC016V-1EA) with subsequent selection with 4 ug/mL puromycin, treated with 30 uM of MK-2206 for 24 hours, RNA purified immediately after treatment
312598190_KHA101520-004_S89_L001


title: Sample 218

description: human breast tumor RNA

tag: tissue

value: breast tumor

tag: lypmph-nodes

tag: metastasis-years

tag: estrogen-receptor


title: Whole tumor cells, 3

source_name: GL261 glioblastoma tumors in mice

value: Glioblastoma Tumor

value: control


title: Sample 215

description: human breast tumor RNA

value: LN-

tag: metastatis

tag: nih

tag: stgallen

tag: conservflag


title: KG-1-shFOXM1-DMSO [KHA101520_002]

description:
KG-1 human acute myeloid leukemia cell line, suspension myeloblast-like cells, transduced with FOXM1-shRNA lentiviral particles from Sigma (SHCLNV-NM_021953) with subsequent selection with 4 ug/mL puromycin, treated with 0.3% DMSO (vehicle) for 48 hours, RNA purified immediately after treatment
312608315_KHA101520-002_S87_L001


title: KG-1-Control-STL-50uM [KHA101520_003]

description:
KG-1 human acute myeloid leukemia cell line, suspension myeloblast-like cells, transduced with control lentiviral particles from Sigma (pLKO.1-puro Non-Target, SHC016V-1EA) with subsequent selection with 4 ug/mL puromycin, treated with 50 uM of STL427944 for 48 hours, RNA purified immediately after treatment
312593274_KHA101520-003_S88_L001


title: KG-1-Control-AraC-0.75uM (1) [KHA101520_005]

description:
KG-1 human acute myeloid leukemia cell line, suspension myeloblast-like cells, transduced with control lentiviral particles from Sigma (pLKO.1-puro Non-Target, SHC016V-1EA) with subsequent selection with 4 ug/mL puromycin, treated with 0.75 uM of cytarabine for 48 hours, RNA purified immediately after treatment
312595274_KHA101520-005_S90_L001


title: GL261 and microenvironment in fibrin 3D-bioink, 1

value: fibrin 3D-bioink


title: Sample 214

description: human breast tumor RNA

tag: death

tag: timesurvival(years)

tag: survival-years

tag: timerecurrence(years)


title: ATAC-seq_T1

city: Shanghai

first: Xuelong

last: Wang

address: No. 100 Banxia Road

country: China

institute: Chinese Academy of Sciences

library_source: genomic

data_processing:
ATAC-seq data sets were trimmed and aligned to hg19 genome using Bowtie2. Reads from RNA-seq experiments were aligned to hg19 genome using STAR.
Duplicate reads were removed with SAMtools.
MACS2 was used to identify regions of ATAC-seq peaks; The mRNA expression of a gene was quantified by FPKM based on RefSeq gene annotation using Cuffdiff and R packages.
The ATAC-seq peaks were used for known motif enrichment analysis, which were performed using HOMER (v4.9).
Genome_build: hg19
Supplementary_files_format_and_content: The bw (BigWig) files were generated using deepTools.
Supplementary_files_format_and_content: FPKM of all genes

molecule: genomic DNA

source_name: pituitary tumors

extract_protocol: Total RNA product was purified using RNeasy Mini Kit (QIAGEN, Germany) and run-on Agilent Bioanalyzer 4200 to assess RNA integrity. The total RNA‐seq library preparation from 1 μg of total RNA was performed with TruSeq RNA Sample Prep Kit (Illumina, USA) according to the manufacturer's instructions. The ATAC-seq assay was performed using 0.1 million cells isolated from normal or tumor tissues were lysed in 100μL lysis buffer per sample (10 mM Tris-HCl at pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630) for 10 min on ice to prepare the nuclei briefly. Immediately After 10 min, nuclei were spun for 5 min at 500 x g to remove the supernatant. Then nuclei were incubated at 37 °C with the tagmentation buffer and Tn5 transposome (Vazyme Biotech, China) for 30 min. After the 30 min, ended buffer was added directly into the reaction to quit the tagmentation. Products which were inputted to PCR were performed to amplify the library for 11 cycles using the following PCR conditions: 72 °C for 3 min; 98 °C for 30 s; and thermocycling at 98 °C for 15 s, 60 °C for 30 s and 72 °C for 3 min; following by 72 °C 5 min. After the PCR reaction, DNA libraries were purified with DNA Clean Beads (Vazyme Biotech, China) to remove invalid primer dimmers and quantitate used Qubit 2.0 Fluorimeter (Invitrogen, USA) to quantitate. All eligible DNA libraries were sequenced on the Illumina HiSeq X Ten with 150 bp paired-end reads.

value: pituitary tumors


title: KG-1-Control-Venet-100nM (1) [KHA101520_007]

description:
KG-1 human acute myeloid leukemia cell line, suspension myeloblast-like cells, transduced with control lentiviral particles from Sigma (pLKO.1-puro Non-Target, SHC016V-1EA) with subsequent selection with 4 ug/mL puromycin, treated with 100 nM of venetoclax for 48 hours, RNA purified immediately after treatment
312606322_KHA101520-007_S92_L001


title: ATAC-seq_N2

source_name: normal pituitary tissues

value: normal pituitary tissues


title: Whole tumor cells, 1

tag: strain

tag: growth protocol


title: RNA-seq_T6


title: GL261 and microenvironment in 2D culture, 1

value: GL261 glioblastoma and murine primary astrocytes, microglia, pericytes and endothelial cells


title: ATAC-seq_T2


title: KG-1-Control-DMSO [KHA101520_001]

description:
KG-1 human acute myeloid leukemia cell line, suspension myeloblast-like cells, transduced with control lentiviral particles from Sigma (pLKO.1-puro Non-Target, SHC016V-1EA) with subsequent selection with 4 ug/mL puromycin, treated with 0.3% DMSO (vehicle) for 48 hours, RNA purified immediately after treatment
312600217_KHA101520-001_S86_L001

tag: cell line

tag: cell type

value: DMSO


title: gut CD  vs. gut control

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

country: Germany

institute: Max-Planck-Institute for Infection Biology

hyb_protocol: Whole Human Genome (Agilent-012391) microarrays were hybridized and washed with a SSC wash protocol according to the supplier’s protocol (Agilent Technologies).

scan_protocol: Scanning of the arrays was performed at 5µm resolution using a DNA microarray laser scanner (Agilent Technologies).

data_processing: Features were extracted from raw image data using the Agilent Technologies image analysis software (G2567AA Feature Extraction Software, Version A7.5.1) and default settings. Background subtraction was accomplished by 'spacial detrend'. The arrays were normalized using rank consistency filtering of normalization feature selection, together with a combination linear and LOWESS curve fitting method. Ratios were calculated by most conservative estimate between a universal error model and propagated error. The extracted MAGE-ML files were analyzed with the Rosetta Resolver Biosoftware (Rosetta Biosoftware). The extracted txt files were analyzed further using R and the associated BioConductor limma package.

source_name: gut UC

label_protocol: RNA labeling was performed with the Low RNA Input Linear Amp Kit   (Agilent Technologies) according supplier's instructions.

growth_protocol: Colonic tissue was isolated and cut into pieces.

extract_protocol: Total RNA was isolated by the Trizol (Invitrogen) method according the manufacturer´s protocol.

tag: subject status

value: Ulcerative colitis

value: gut

source_name: gut control

value: healthy control


title: C84

city: Lausanne

first: Yun-Tsan

last: Chang

address: Avenue de Beaumont 29

department: Dermatology

country: Switzerland

institute: CHUV

description:
clonal (malignant T cell)
C84

data_processing:
The wells which do not contain a single cell or contained less than one million reads or less than 30% of the reads which map to protein coding regions were excluded.
Gene expression was quantified using Kallisto
The reads from each cell were mapped to the Homo Sapiens genome (Ensembl archive GRCh37) to produce the gene expression in transcripts per million (TPM)
Genome_build: GRCh37
Supplementary_files_format_and_content: Matrix table with TPM for every transcripe and every cell

source_name: skin T cell

extract_protocol:
Capture and processing of single skin T cells from patient with mycosis fungoides was performed using the Fluidigm C1 Autoprep system. Cells were loaded at a concentration of 2,000 cells/μL onto C1 integrated fluidic circuits (IFC) chips for 5-10 μm cells. All C1 capture sites were microscopically inspected to determine the sites containing only a single cell. Empty sites and those with multiple cells were excluded from further analysis. ERCC (External RNA Controls Consortium) spike-in RNAs were added and served as a control. SMARTer Ultra Low RNA Kit (Clontech) was used for reverse transcription and cDNA preamplification.
The cDNA products from each cell were then used to prepare Illumina sequencing libraries and then sequenced on Illumina HiSeq2500 using single-end 100-base reads.

value: skin T cell

tag: patient diagnosis

value: mycosis fungoides

tag: cell disease state

value: malignant T cell


title: Sample 217

description: human breast tumor RNA

tag: tissue

tag: lypmph-nodes

value: LN+

value: Meta+

value: Dead

tag: recurrence-years

tag: timemeta

tag: metastasis-years

value: ER-


title: GL261 and microenvironment in 2D culture, 3

value: 2D petri dish


title: gut UC  vs. gut control


title: C67

description:
clonal (malignant T cell)
C67


title: Whole tumor cells, 2

value: Glioblastoma Tumor

value: control


title: TPC1 + miR-NC

city: Bruxelles

first: Alice

last: Augenlicht

address: 808 route de Lennik

department: IRIBHM

country: Belgium

institute: Université Libre de Bruxelles

description: TPC1 cells transfected with negative control miR-NC

hyb_protocol: Gene expression analysis using the Human Genome U133 plus 2.0 arrays.

scan_protocol: Standard Affymetrix protocol.

data_processing: The .cel files were processed using a preprocessed GenePattern program to create mRNA expression files and to perform a log2 transformation of the data. Normalization was performed based on the expression profiles of cells transfected with the negative control.

label: Biotin

source_name: TPC1 cell line

label_protocol: Affymetrix 3’IVT plus labellig kit.

growth_protocol: Both cell lines were cultured at 37°C in 5% CO2 with RPMI 1640 (Invitrogen) supplemented with 10% fetal bovine serum.

extract_protocol: Total RNA extraction was performed using QIAzol reagent (Qiagen) and miRNeasy Mini kit (Qiagen).

treatment_protocol: Cells were transiently transfected with miRIDIAN microRNA mimics miR-7-5p (#C-300546-07-0005) or negative control cel-miR-67 (#CN-001000-01-05) using DharmaFECT 2 (Dharmacon) according to the manufacturer’s protocol. Transfected miRNA mimics and negative control miRNA were used at a concentration of 2nM. RNA extraction and hybridization on Affymetrix microarrays are performed 4 days after transfection.

value: TPC1 cell line derived from a human RET/PTC1-positive PTC


title: RNA-seq_T2

value: pituitary tumors


title: RNA-seq_T3


title: HTori-3 + miR-NC

description: HTori-3 cells transfected with negative control miR-NC

source_name: Htori-3 cell line

value: Htori-3 cell line derived from SV40-immortalized human thyrocytes


title: N96

description:
non-clonal (benign T cell)
N96

value: benign T cell


title: TPC1 + miR-7-5p

description: TPC1 cells transfected with miR-7-5p


title: HTori-3 + miR-7-5p

description: HTori-3 cells transfected with miR-7-5p


title: C59

description:
clonal (malignant T cell)
C59


title: C47

description:
clonal (malignant T cell)
C47


title: gut control vs. gut UC

value: Ulcerative colitis


title: RNA-seq_T4


title: C71

description:
clonal (malignant T cell)
C71


title: ATAC-seq_N1

value: normal pituitary tissues


title: RNA-seq_T5


title: C89

description:
clonal (malignant T cell)
C89


title: C29

description:
clonal (malignant T cell)
C29


title: C44

description:
clonal (malignant T cell)
C44


title: RNA-seq_N6


title: RNA-seq_N2


title: gut control vs. gut CD

value: healthy control

value: gut


title: C21

description:
clonal (malignant T cell)
C21

value: skin T cell

value: mycosis fungoides


title: RNA-seq_N5


title: WT_1

city: Göttingen

first: Katherine

last: Bohnsack

address: Humboldtallee 23

institute: University Medical Centre Göttingen

data_processing:
Library strategy: CRAC-seq
Sequencing reads for each experimental sample were demultiplexed using their 5' barcode sequences and barcodes were then clipped
Reads of identical sequence that contained identical 5-nucleotide random barcodes were collapsed
Reads were trimmed and quality controlled using flexbar and aligned to the S.cerevisiae genome by Bowtie2 (version 2.2.4).

organism: Saccharomyces cerevisiae

source_name: BY4741 yeast strain

growth_protocol: Wild-type BY4741 yeast cells or yeast cells expressing C-terminally His-Tev-ProtA tagged Has1, Mak5 or Spb4 from their genomic loci were grown in exponential phase in low uracil media supplemented with 4-thiouracil as previously described (Baejen et al., 2014; Brüning et al., 2018).

extract_protocol:
Crosslinked RNA-protein complexes were purified under denaturing conditions and RNAs associated with His-ProtA-tagged proteins were trimmed (Bohnsack et al., 2012).
3' and 5' adapters were ligated and a cDNA library was prepared by reverse transcription and amplified by PCR (Bohnsack et al., 2012).

treatment_protocol: Cells were crosslinked in vivo using light at 365 nm

tag: tagged protein

value: no tag

tag: background strain


title: h293_m5C-RIP_mRNA_IP_rep2

city: Guangzhou

first: Zhang

last: Zhang

state: Guangdong

address: Xingangxi Roda 135#

institute: Sun Yat-sen University

data_processing:
RNA-seq analyses for endogenous mRNA and IVT RNA samples: Raw reads were first trimmed to get rid of sequencing adaptors using cutadapt (v1.15) and mapped to reference genome using Hisat2 (v2.1.0) with the parameters ‘--rna-strandness RF’. Integrative Genomics Viewer (IGV) was used for data visualization.
MeRIP-seq data analyses: After removing the adaptor and mapping to reference genome, the sam file was sorted and converted to bam file using samtools (v1.6). Two extensively used software, exomePeak2 (v1.3.7) and Macs2 (v2.1.2), were applied for m6A peak calling. The parameters ‘p_cutoff=0.00001, log2FC_cutoff=1, fragment_length=150’ were set for exomePeak2; and the parameters ‘--keep-dup all -f BAM --nomodel --extsize 150 -q 0.05 --fe-cutoff 2’ were set for Macs2.
m6A-REF-seq data analyses: The raw reads of m6A-REF-seq was firstly removed adaptors using cutadaptor (v1.15) and mapped to reference genome using Hisat2 (v2.1.0). The IVT RNA library reflected the gene signature and expression level of cellular mRNA but was modification-free. Therefore, high confidence m6A sites had undigested reads in endogenous samples but less or none undigested reads in IVT RNA samples. We defined the false positive rate (FPR) and conduct fisher exact test to evaluate each putative m6A site. The false positive rate (FPR) is the ratio of the number of false positive results to the number of total positive results. For each candidate m6A site, the false-positive rate (FPR) was defined as dividing the undigested rate (undigested reads/total reads at each site) in IVT RNA to that in cellular mRNA. Fisher’s exact test was applied to calculate significance. High confidence m6A sites were identified using the following criteria: 1) undigested reads in IVT RNA samples were significantly less than those in cellular mRNA samples (fisher exact test p-value ≤ 0.05); 2) the false positive rate (FPR) ≤ 0.2; 3) reads coverage ≥ 10; 4) reproducible in two replicates.
m5C BS-seq data analyses: To increase the credibility of m5C identification from BS-seq data, a stringent pipeline from published literature (https://github.com/SYSU-zhanglab/RNA-m5C) was adopted.  High confidence m5C sites were determined using IVT RNA as negative control. The false-positive rate (FPR) was defined as the ratio of false-positive results to total positive results, which was calculated by dividing non-conversion rate of IVT RNA sample to that of the endogenous sample. Fisher exact test was applied to calculate significance. In sum, the high confidence m5C sites were identified using the following criteria: 1) the false positive rate (FPR) ≤ 0.2; 2) p-value ≤ 0.05 (fisher exact test); 3) non-conversion rate ≥ 0.05; 4) sequencing coverage ≥ 10; 5) non-conversion read depth ≥ 5; 6) reproducible in two replicates.
Genome_build: GRCh37 (human), mm10 (mouse)
Supplementary_files_format_and_content: RNA-seq processed data was tdf file generated by IGV. RIP-seq processed data was peak file in bed format. Processed data of m6A-REF-seq and m5C BS-seq were detected high confidence sites in text file.

molecule: polyA RNA

source_name: human HEK293T cell line

growth_protocol: Human HEK293T cell line was cultured with DMEM (Corning) supplemented with 10% (v/v) FBS (Gibco) at 37℃ in the presence of 5% CO2, and tested to be negative for mycoplasma contamination. Wild type (WT) of mouse 129 embryonic stem cells (mESCs) and Mettl3 knockout (KO) mESCs were provided by Dr. Jiekai Chen (Guangzhou Institutes of Biomedicine and Health, CAS).

extract_protocol:
Total RNA was extracted using TRIzol reagent (Thermo Fisher Scientific, 15596026) and the mRNA was purified using Dynabeads mRNA Purification Kit (Thermo Fisher Scientific,  61006). mRNA was treated by TURBO DNase (Thermo Fisher, AM2238) at 37 ℃ for 30 min and purified by ethanol precipitation or RNA Clean & Concentrator-5 kit (Zymo Research, R1015) to remove genomic DNA.
IVT RNA generation:  The 100 ng (in 3ul volume at most) extracted mRNA was first annealed with 1ul PolyT primer (12 uM) for 3 min at 75 ℃ and 2 min at 42 ℃. Then we prepared the first strand cDNA mix by adding 2ul 5× First-Strand buffer of SMARTScribe Reverse Transcriptase (Takara, 639536), 0.5 ul 100 mM DTT, 0.5 ul RNase inhibitor (Takara, 2313A), 1ul TSO T7 Primer (10uM), 1ul 50× Advantage UltraPure PCR Deoxynucleotide Mix (Takara, 639125) and 1ul SMARTScribe Reverse Transcriptase (Takara, 639536). After adding the first strand cDNA mix to the mRNA/PolyT Primer mixture, the reaction mixture was incubated at 42 ℃ for 1.5 h and stopped by heating at 68 ℃ for 10min for first strand cDNA synthesis. The primer extension was conducted by adding 10 ul 10× Advantage 2 PCR buffer and 1ul Advantage 2 PCR Polymerase mix (Takara, 639207), 2 ul 50× Advantage UltraPure PCR Deoxynucleotide Mix, 2 ul T7 Extension Primer (10 uM), 2ul RNaseH (NEB, M0297) and RNase-free water to 100 ul. The reaction was conducted at 37 ℃ for 15 min, 95 ℃ for 2 min, 60 ℃ for 1 min and 68 ℃ for 10 min. The double-strand cDNA was purified using NucleoSpin PCR cleanup (MACHEREY-NAGEL, 740609.50). The in vitro transcription step was performed using HiScribe™ T7 High Yield RNA Synthesis Kit (NEB, E2040) and NTPs from Takara (cat. 6140). The sample was subjected to TURBO DNase (Thermo Fisher, AM2238) treatment at 37 ℃ for 30 min and purified by RNA Clean & Concentrator-5 kit (Zymo Research, R1015) to remove dsDNA. The concentration of IVT RNA was determined by Qubit RNA HS Assay kit (Thermo Fisher, Q32852).
MeRIP-seq: Cellular mRNA and IVT RNA were fragmented by using Thermo Fisher’s Fragmentation Kit (Thermo Fisher Scientific, AM8740) at 94 °C for 30s and then purified by ethanol precipitation. The commercial antibodies of NEB (EpiMark® N6-Methyladenosine Enrichment Kit, E1610S), SYSY (202003) and Abcam (ab190886) were used in m6A immunoprecipitation. The 25 ul protein G beads (Thermo Fisher Scientific, 1004D) were washed three times with Reaction buffer (150mM NaCl, 10mM pH 7.4 Tris-HCl, 0.1% Igepal CA-630 in nuclease free H2O). Then the protein G beads were resuspended in 250 ul Reaction buffer and 2 ul anti-m6A antibody was added. After incubation with orbital rotation at 4 ℃ for 1 h, the antibody-protein G beads mixture was washed twice with Reaction buffer. A total of 1ul mRNA for each sample was added to the mixture and then incubated with rotation at 4 ℃ for 3 h. After washed with Reaction buffer twice, the mRNA-antibody-protein G mixture was washed low salt buffer (50 mM NaCl, 10 mM pH 7.4 Tris-HCl, 0.1% Igepal CA-630 in nuclease-free H2O) and high salt buffer (500 mM NaCl, 10 mM pH 7.4 Tris-HCl, 0.1% Igepal CA-630 in nuclease-free H2O) twice, respectively. The IP products were eluted with 130 ul Elution buffer (150 mM NaCl, 10 mM pH 7.4 Tris-HCl, 0.1% Igepal CA-630, 6.7 mM m6A in nuclease-free H2O) at 37 °C, 1000 rpm for 1.5 hours. After purified by ethanol precipitation, the IP products and input sample kept before IP were used to constructed the NGS library using NEBNext® Ultra II Directional RNA Library Prep (NEB, E7760S).
m6A-REF-seq: We followed the experimental procedural of m6A-RFE-seq in Zhang et al., (2019) and used IVT RNA as negative control. After heated at 85°C for 5 min and chilled on ice for 2 min, the equivalent endogenous mRNA and IVT RNA were incubated with MazF (Takara, 2415A) in the MazF reaction buffer at 37 °C for 30 min. After purified by RNA Clean & Concentrator-5 kit (Zymo Research, R1015), the fragment mRNA was end-repaired by T4 polynucleotide kinase (T4PNK; Vazyme Biotech). Then the fragment mRNA was purified by RNA Clean & Concentrator-5 kit, and the NGS libraries were constructed by using the VAHTS Small RNA Library Prep Kit (Vazyme Biotech, NR801) with 10 ng of fragmented RNA.
m5C BS-seq: Cellular mRNA and IVT RNA samples were conducted bisulfite treatment following the instruction in Huang et al., (2019) using EZ RNA methylation kit (Zymo Research, R5001). High-stringency conditions: Total among of 1 ug cellular mRNA and IVT RNA were treated with three cycles of 70 °C for 10 min and 64 °C for 45 min in sulfonation step and then 37 °C for 30 min in desulfonation step. The NGS libraries were constructed by using NEBNext Ultra II Directional RNA Library Prep Kit (NEB, E7760S).
RNA-seq, MeRIP-seq and m5C BS-seq libraries were constructed by using NEBNext Ultra II Directional RNA Library Prep Kit (NEB, E7760S). The m6A-REF-seq libraries were constructed by using the VAHTS Small RNA Library Prep Kit (Vazyme Biotech, NR801) with 10 ng of fragmented mRNA.

tag: sample type

value: cellular mRNA

tag: sequence type

tag: treatment

value: m5C-IP, Cell Signaling Technology (28692)


title: RNA-seq_T1


title: h293_m5C-RIP_mRNA_input_rep2


title: RNA-seq_N3


title: h293_m5C-RIP_mRNA_input_rep1


title: C14

description:
clonal (malignant T cell)
C14

value: malignant T cell


title: C61

description:
clonal (malignant T cell)
C61


title: WT_2


title: Dbp7-HTP_1


title: N16

description:
non-clonal (benign T cell)
N16


title: C41

description:
clonal (malignant T cell)
C41


title: RNA-seq_N1


title: C04

description:
clonal (malignant T cell)
C04


title: liver, Tm, 6500

city: Bonn

first: Elvira

last: Mass

address: Carl-Troll str

institute: LIMES

description:
Pharmacological in vivo model for non-alcoholic fatty liver induction
Drug-induced ER stress

data_processing:
base calling and de-multipexing using CASAVA version 1.8
Alignment with TopHat2 v2.0.11 and SAMtools version 1.4 using the default parameters
Quantification with Partek Genomics Suite V6.6
reads mapped to each transcript against the RefSeq Hg19 annotation download on May 2015
Normalization using DeSeq2
Genome_build: hg19
Supplementary_files_format_and_content: Comma separated file includes DeSeq2 rlog counts for each Sample.

source_name: liver

extract_protocol:
RNA was isolated using the Nucleospin RNA II kit (Macherey & Nagel) according to the manufacturer’s instructions
According to the manufacturer´s instructions in the Tru-Seq RNA library preparation kit v2, 10 ng of RNA was converted into cDNA libraries

tag: genetic background

value: Creld2 eGFP/eGFP

value: Tm

value: liver


title: liver, Tm, 6499


title: not5Del_2

city: Geneve

first: George

last: Allen

state: Geneve

address: Rue Michel-Servet 1

institute: University of Geneva

description:
Not5 deletion ribosome footprinting
RPKMS_WT_NOT4_Not5.xlsx

data_processing:
For the Ribo-Seq samples, all fastq files were adapter stripped using cutadapt. Only trimmed reads were retained, with a minimum length of 20 and a quality cutoff of 2 reads were retained if the trimmed size was between 28 and 31.
Reads were mapped, using default parameters, with HISAT2  to R64-1-1, using Ensembl release 84 gtf for transcript definitions. For the mapping, only primary alignments were retained and reads were removed if they mapped to rRNA, tRNA and dubious ORFs or non-genic regions. Reads mapping to UTRs were retained.
A full set of 6692 CDS sequences were established for R64-1-1 Ensembl release 84 and extended by  UTR sequences. The filtered reads were then mapped to this transcriptome with bowtie2, using default parameters.
The P-site position of each read was predicted by riboWaltz and confirmed by inspection (reads were generally shifted 15 bases from the 3’ end). Counts were made by aggregating P-sites overlapping with the CDS and RPKMs were then generated through normalising by CDS length and total counts for the sample.
Genome_build: R64-1-1
Supplementary_files_format_and_content: RPKM

source_name: saccharomyces cerevisiae cells

growth_protocol: Yeast were grown in YPD to mid-log phase in accordance with standard protocols.

extract_protocol:
Libraries were constructed exactly as described in Subtelny et al., 2014 (GSE52809)
Libraries were constructed exactly as described in Subtelny et al., 2014 (GSE52809)

treatment_protocol: Cells were harvested and extracts were perpared and processed as described for S. pombe samples in Subtelny et al., 2014 (GSE52809)

tag: strain

tag: genotype/variation


title: C23

description:
clonal (malignant T cell)
C23

tag: cell type


title: h293_m5C-RIP_mRNA_IP_rep1

tag: cell line


title: not4Del_1

description:
Not4 deletion ribosome footprinting
RPKMS_WT_NOT4_Not5.xlsx


title: Dbp7-HTP_2


title: RNA-seq_N4


title: cgl2_c5

city: Taipei City

first: Yen-Hua

last: Huang

address: No. 155, Sec. 2, Li-Nong St., Beitou Dist

department: Institute of Biomedical Informatics

country: Taiwan

institute: National Yang-Ming University

description: young adult

data_processing:
FastQC v0.11.8 was used for quality assessment of raw FASTQ sequencing data
Trimmomatic 0.38 trim and crop Illumina (FASTQ) data
STAR 2.7.1a was used for reads mapping to the human GRCh38 genome assembly (Homo_sapiens.GRCh38.98)
TMM (the weighted trimmed mean of M-values method) values were calculated by edgeR (v3.28.0)
Genome_build: Homo_sapiens.GRCh38.98 (Ensembl)

source_name: PBMC

growth_protocol: PBMC of 14 participants were ioslated from whole blood by Lymphoprep™.

extract_protocol:
RNeasy Micro Kit extract total RNA by combining the stringency of guanidine-isothiocyanate lysis with the speed and purity of silica-membrane purification
prepared library Illumina TruSeq Stranded Total RNA Library Prep Globin + limited cycles of PCR by KAPA HiFi Polymerase

treatment_protocol: No treatment

tag: age

value: 17 years 6 months


title: cgl2_c4

description: young adult

value: 19 years 2 months


title: cgl2_c3

description: child

value: 4 years 6 months


title: h293_m5C_mRNA_med_rep1

description: h293_m5C_diff_conditions_ERCC_conversion_rate.txt

data_processing:
Library strategy: m5C-BS-seq
RNA-seq analyses for endogenous mRNA and IVT RNA samples: Raw reads were first trimmed to get rid of sequencing adaptors using cutadapt (v1.15) and mapped to reference genome using Hisat2 (v2.1.0) with the parameters ‘--rna-strandness RF’. Integrative Genomics Viewer (IGV) was used for data visualization.
MeRIP-seq data analyses: After removing the adaptor and mapping to reference genome, the sam file was sorted and converted to bam file using samtools (v1.6). Two extensively used software, exomePeak2 (v1.3.7) and Macs2 (v2.1.2), were applied for m6A peak calling. The parameters ‘p_cutoff=0.00001, log2FC_cutoff=1, fragment_length=150’ were set for exomePeak2; and the parameters ‘--keep-dup all -f BAM --nomodel --extsize 150 -q 0.05 --fe-cutoff 2’ were set for Macs2.
m6A-REF-seq data analyses: The raw reads of m6A-REF-seq was firstly removed adaptors using cutadaptor (v1.15) and mapped to reference genome using Hisat2 (v2.1.0). The IVT RNA library reflected the gene signature and expression level of cellular mRNA but was modification-free. Therefore, high confidence m6A sites had undigested reads in endogenous samples but less or none undigested reads in IVT RNA samples. We defined the false positive rate (FPR) and conduct fisher exact test to evaluate each putative m6A site. The false positive rate (FPR) is the ratio of the number of false positive results to the number of total positive results. For each candidate m6A site, the false-positive rate (FPR) was defined as dividing the undigested rate (undigested reads/total reads at each site) in IVT RNA to that in cellular mRNA. Fisher’s exact test was applied to calculate significance. High confidence m6A sites were identified using the following criteria: 1) undigested reads in IVT RNA samples were significantly less than those in cellular mRNA samples (fisher exact test p-value ≤ 0.05); 2) the false positive rate (FPR) ≤ 0.2; 3) reads coverage ≥ 10; 4) reproducible in two replicates.
m5C BS-seq data analyses: To increase the credibility of m5C identification from BS-seq data, a stringent pipeline from published literature (https://github.com/SYSU-zhanglab/RNA-m5C) was adopted.  High confidence m5C sites were determined using IVT RNA as negative control. The false-positive rate (FPR) was defined as the ratio of false-positive results to total positive results, which was calculated by dividing non-conversion rate of IVT RNA sample to that of the endogenous sample. Fisher exact test was applied to calculate significance. In sum, the high confidence m5C sites were identified using the following criteria: 1) the false positive rate (FPR) ≤ 0.2; 2) p-value ≤ 0.05 (fisher exact test); 3) non-conversion rate ≥ 0.05; 4) sequencing coverage ≥ 10; 5) non-conversion read depth ≥ 5; 6) reproducible in two replicates.
Genome_build: GRCh37 (human), mm10 (mouse)
Supplementary_files_format_and_content: RNA-seq processed data was tdf file generated by IGV. RIP-seq processed data was peak file in bed format. Processed data of m6A-REF-seq and m5C BS-seq were detected high confidence sites in text file.

value: cellular mRNA, ERCC

value: Bisulfite, medium-strigency


title: C08

description:
clonal (malignant T cell)
C08

tag: patient diagnosis

tag: cell disease state


title: liver, Tm, 6496

tag: tissue


title: h293_m5C_mRNA_low_rep1

value: Bisulfite, low-strigency


title: h293_m5C-RIP_IVT_IP_rep1

value: in vitro transcribed (IVT) RNA


title: h293_m5C-RIP_IVT_IP_rep2


title: liver, Tm, 6493

value: Creld2 WT/WT


title: h293_m5C-RIP_IVT_input_rep1


title: N17

description:
non-clonal (benign T cell)
N17

value: skin T cell

value: benign T cell


title: not4Del_2


title: h293_m5C_mRNA_med_rep2


title: h293_m5C_IVT_med_rep2

value: in vitro transcribed (IVT) RNA, ERCC


title: liver, Tm, 6498


title: cgl2_c6

description: young adult

value: 15 years 9 months


title: not5Del_1


title: liver, Tm, 6497


title: liver, Tm, 6491


title: h293_m5C_IVT_low_rep2


title: liver, Tg, 6490

value: Tg


title: liver, Tg, 6489


title: h293_m5C-RIP_IVT_input_rep2


title: cgl2_p6

description: young adult

tag: disease

value: congenital generalized lipodystrophy type 2

value: 16 years 4 months

tag: health state

value: Diabetes mellitus, intellectual disability


title: liver, Tm, 6494

value: Tm

value: liver


title: cgl2_c1

description: child

value: 6 years 1 months


title: cgl2_c7

description: young adult

value: 13 years 8 months


title: liver, Tg, 6488

value: Creld2 eGFP/eGFP


title: liver, Tm, 6495


title: cgl2_p7

description: young adult

value: hyperlipidemia,Diabetes mellitus,  intellectual disability


title: BEAS-2B-EV_48h

city: San Francisco

first: Tsukasa

last: Kadota

state: CA

address: 513 Parnassus Ave.

department: Medicine

institute: UCSF

data_processing:
Paired-end sequenced reads were checked by FastQC and aligned to the reference genome, human GRCh38, using TopHat.
Cuffdiff was performed to define FPKM values for genes.
Genome_build: hg38
Supplementary_files_format_and_content: .xls file was generated by Qiagen online primary data analysing tool: (http://ngsdataanalysis.sabiosciences.com/QIAseqmiRNA).

source_name: primary lung fibroblast treated with BEAS-2B-EVs for 48h

growth_protocol: Primary lung fibroblast were cultured in Dulbecco’s modified Eagle medium (DMEM; Invitrogen, CA, USA) with 10% fetal bovine serum and a 1% antibiotic–antimycotic solution (AA, Invitrogen) at 37 °C in 5% CO2.

extract_protocol:
Total RNA was extracted using QIAzol and the miRNeasy Mini Kit (Qiagen, Hilden, Germany) according to manufacturer’s protocols. RNA was quantified using a NanoDrop-1000 spectrophotometer and a Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, Calif.).
The mRNA sequencing library was prepared using theTruSeq Stranded mRNA Sample Prep Kit

treatment_protocol: Primary lung fibroblasts were treated with EVs derived from human bronchial epithelial cells (10 μg/mL), BEAS-2B cells (10 μg/mL) or PBS (-)  and cultured for 24 hours or 48 hours. To prepare the EVs, conditioned medium from each cell was ultracentrifuged at 35,000 rpm using a SW41Ti rotor for 70 min at 4°C. The pellets were washed with PBS, ultracentrifuged at 35,000 rpm using the SW41Ti rotor for 70 min at 4°C and resuspended in PBS.

value: Primary human lung fibroblast

tag: teatment

value: BEA2B EVs

tag: time point

value: 48 hours


title: h293_m5C_mRNA_high_rep1

value: cellular mRNA, ERCC

value: Bisulfite, high-strigency


title: h293_m6A-REF_mRNA_1ul

description: h293_m6A-REF_diff_treat_ERCC_undigested_rate.txt

value: MazF (Takara, 2415A), 1ul (20U)


title: cgl2_p2

description: child

value: 6 years 5 months

value: severe intellectual disability


title: h293_m5C_mRNA_low_rep2

value: Bisulfite, low-strigency


title: HBEC-EV_48h

source_name: primary lung fibroblast treated with HBEC-EVs for 48h

value: HBEC EVs


title: cgl2_c2

description: child


title: liver, Tg, 6484

value: Creld2 WT/WT

value: Tg


title: cgl2_p3

description: child

value: congenital generalized lipodystrophy type 2

value: 3 years 11 months


title: h293_m5C_mRNA_high_rep2


title: h293_m5C_IVT_high_rep1

value: in vitro transcribed (IVT) RNA, ERCC


title: h293_m6A-REF_IVT_1ul


title: liver, Tm, 6492

value: Tm

value: liver


title: liver, Tg, 6483


title: h293_m6A-REF_IVT_1_2ul


title: cgl2_p5

description: young adult

value: 17 years 10 months


title: liver, Tg, 6481


title: h293_m6A-REF_mRNA_1_25ul


title: h293_m6A-REF_IVT_1_25ul


title: HBEC-EV_24h

source_name: primary lung fibroblast treated with HBEC-EVs for 24h

value: Primary human lung fibroblast

value: 24 hours


title: h293_m5C_IVT_med_rep1

value: Bisulfite, medium-strigency


title: NC_48h

source_name: primary lung fibroblast treated with PBS(-) for 48h

value: PBS(-)

value: 48 hours


title: liver, Sucrose, 6476

value: Creld2 eGFP/eGFP

value: Sucrose


title: h293_miCLIP_mRNA

value: cellular mRNA

value: miCLIP-seq

value: miCLIP, Abcam (ab190886)


title: BEAS-2B-EV_24h

source_name: primary lung fibroblast treated with BEAS-2B-EVs for 24h

value: BEA2B EVs


title: liver, Tg, 6486

value: Tg


title: h293_m5C_IVT_low_rep1

value: Bisulfite, low-strigency


title: liver, Tg, 6482

value: Creld2 WT/WT


title: liver, Sucrose, 6474


title: cgl2_p4

description: young adult

value: congenital generalized lipodystrophy type 2

value: 19 years 5 months

value: hyperlipidemia, Diabetes mellitus, severe intellectual disability


title: liver, Sucrose, 6480

value: liver


title: h293_m5C_IVT_high_rep2

value: in vitro transcribed (IVT) RNA, ERCC

value: Bisulfite, high-strigency


title: liver, Tg, 6487


title: liver, Sucrose, 6479


title: h293_m6A-REF_mRNA_1_2ul

value: cellular mRNA, ERCC


title: S41

city: Amsterdam

first: Brendon

middle: P.

last: Scicluna

address: Meibergdreef 9

country: Netherlands

institute: Amsterdam UMC Locatie AMC

description: size selected RNA (<200 bp)

data_processing:
Sequence read quality was assessed by means of the FastQC methods and Trimmomatic was used to trim the Illumina adapters containing, poor-quality bases and ambiguous nucleotide-containing sequences.
Reads were used to align against the Genome Reference Consortium Human Genome Build 38 patch release 7 (GRCh38.p7) using TopHat 2 (version 2.1.1). Count data were generated by means of the featureCounts method.
DESEq2 was used for differential expression analysis using a detection threshold of greater than 2 count
Genome_build: Genome Reference Consortium Human Genome Build 38 patch release 7 (GRCh38.p7)
Supplementary_files_format_and_content: tab-delimited text files including DESeq2 normalized values

source_name: Patient

extract_protocol:
Small RNA (<200 nucleotides) were isolated by means of the miRNeasy RNA isolation kit (Qiagen, Venlo, The Netherlands) according to the manufacturer’s instructions.
Sequencing libraries were prepared by means of the Illumina TrueSeq small RNA-Seq preparation kit as per manufacturer’s instructions

value: plasma

tag: diagnosis

value: community-acquired pneumonia (CAP)

tag: gender

value: male


title: cgl2_p1

description: child

value: 5 years 7 months

value: hyperlipidemia, intellectual disability


title: liver, Sucrose, 6475

value: Sucrose


title: liver, Sucrose, 6478

value: Creld2 eGFP/eGFP


title: liver, Sucrose, 6473


title: NC_24h

source_name: primary lung fibroblast treated with PBS(-) for 24h

value: Primary human lung fibroblast

value: PBS(-)

value: 24 hours


title: S39

description: size selected RNA (<200 bp)

value: female


title: h293_miCLIP_IVT_rep2

description: h293_miCLIP_IVT_2reps_highconf_peaks.bed

tag: sample type

value: in vitro transcribed (IVT) RNA

tag: sequence type

value: miCLIP-seq

value: miCLIP, Abcam (ab190886)


title: h293_m6A-REF_IVT_rep2

tag: treatment

value: MazF (Takara, 2415A), 20U


title: h293_m6A-REF_mRNA_rep2

value: cellular mRNA


title: liver, Sucrose, 6477

tag: genetic background

value: liver


title: S25

description: size selected RNA (<200 bp)

value: plasma


title: h293_miCLIP_IVT_rep1


title: h293_m5C_mRNA_rep1

value: Bisulfite, high-strigency


title: h293_MeRIP_SYSY_mRNA_IP_rep2

description: h293_MeRIP_SYSY_mRNA_rep2_Macs2_peaks.bed

value: MeRIP-seq


title: h293_MeRIP_SYSY_mRNA_input_rep2


title: h293_m5C_IVT_rep1


title: liver, Recovery, 6468

description:
Dietary in vivo model for non-alcoholic fatty liver induction
High-fat diet

value: Recovery


title: h293_m6A-REF_IVT_rep1


title: h293_m5C_mRNA_rep2


title: S43

description: size selected RNA (<200 bp)

value: community-acquired pneumonia (CAP)


title: liver, Tg, 6485

value: Creld2 WT/WT

value: Tg


title: S35

description: size selected RNA (<200 bp)


title: S28

description: size selected RNA (<200 bp)

value: male


title: S22

description: size selected RNA (<200 bp)


title: liver, Sucrose, 6472

value: Sucrose


title: liver, Recovery, 6469

value: Creld2 eGFP/eGFP


title: liver, Recovery, 6470


title: S19

description: size selected RNA (<200 bp)

value: female


title: S21

description: size selected RNA (<200 bp)


title: liver, Sucrose, 6471


title: h293_m6A-REF_mRNA_rep1


title: liver, Recovery, 6466


title: h293_m5C_IVT_rep2

value: in vitro transcribed (IVT) RNA


title: liver, Recovery, 6467


title: S18

description: size selected RNA (<200 bp)


title: liver, Recovery, 6465


title: liver, Recovery, 6464


title: S17

description: size selected RNA (<200 bp)


title: liver, Recovery, 6463


title: h293_MeRIP_SYSY_mRNA_input_rep1

description: h293_MeRIP_SYSY_mRNA_rep1_Macs2_peaks.bed


title: h293_MeRIP_SYSY_IVT_input_rep2

description: h293_MeRIP_SYSY_IVT_rep2_Macs2_peaks.bed


title: liver, Recovery, 6461


title: H36

description: size selected RNA (<200 bp)

source_name: Healthy

value: Healthy


title: liver, Recovery, 6462


title: h293_MeRIP_SYSY_mRNA_IP_rep1


title: liver, HFD, 6460

value: HFD


title: h293_MeRIP_NEB_mRNA_input_rep2

description: h293_MeRIP_NEB_mRNA_rep2_Macs2_peaks.bed


title: H31

description: size selected RNA (<200 bp)


title: h293_MeRIP_SYSY_IVT_IP_rep2


title: h293_MeRIP_SYSY_IVT_input_rep1

description: h293_MeRIP_SYSY_IVT_rep1_Macs2_peaks.bed


title: h293_MeRIP_SYSY_IVT_IP_rep1


title: h293_MeRIP_NEB_mRNA_IP_rep1

description: h293_MeRIP_NEB_mRNA_rep1_Macs2_peaks.bed

value: m6A-IP, NEB (EpiMark® N6-Methyladenosine Enrichment Kit, E1610S)


title: H45

description: size selected RNA (<200 bp)


title: liver, HFD, 6458


title: S16

description: size selected RNA (<200 bp)


title: S20

description: size selected RNA (<200 bp)


title: h293_MeRIP_NEB_mRNA_IP_rep2

value: cellular mRNA


title: H30

description: size selected RNA (<200 bp)


title: H26

description: size selected RNA (<200 bp)


title: liver, HFD, 6459

value: liver


title: h293_MeRIP_NEB_mRNA_input_rep1


title: RNAseq_PCa_spheres_rep1

city: Zurich

first: Raffaella

last: Santoro

address: Winterthurerstrasse 190

department: Dep. of Molecular Mechanisms  of Disease

institute: University of Zurich

data_processing:
RNAseq reads were aligned to the reference genome (hg38) with Subread (i.e. subjunc, version 1.4.6-p4; (Liao et al., 2013)) allowing up to 16 alignments per read (options: –trim5 10 –trim3 15 -n 20 -m 5 -B 16 -H –allJunctions). Count tables were generated with Rcount (Schmid and Grossniklaus, 2015) with an allocation distance of 10bp for calculating the weights of the reads with multiple alignments, considering the strand information, and a minimal number of 5 hits. Variation in gene expression was analyzed with a general linear model in R with the package edgeR (version 3.12.0; (Robinson and Oshlack, 2010)) according to a crossed factorial design with two explanatory factors (i) siRNA against Tip5 and a mock sequence and (ii) expression pattern of PCa spheres versus PC3 cells. Genes differentially expressed between specific conditions were identified with linear contrasts using trended dispersion estimates and Benjamini-Hochberg multiple testing corrections. For subsequent analyses only refseq transcripts were taken into account. Genome_build: GRCh38/hg38
Genome_build: GRCh38/hg38

source_name: Prostate cancer progenitors/CSC

growth_protocol: PC3 cells were cultured in RPMI 1640 medium and Ham's F12 medium (1:1; Gibco) containing 10% FBS (Gibco) and 1% penicillin-streptomycin (Gibco).

extract_protocol: Total RNA was purified with TRIzol reagent (Life Technologies). DNA contaminants were removed by treating RNA with 2U Turbo-DNaseI (Invitrogen) for 1h at 37°C and the RNA samples were re-purified using TRIzol. The quality of the isolated RNA was determined by Bioanalyzer 2100 (Agilent, Waldbronn, Germany). Only those samples with a 260nm/280nm ratio between 1.8–2.1 and a 28S/18S ratio within 1.5–2 were further processed. The TruSeq RNA Sample Prep Kit v2 (Illumina, Inc, California, USA) was used in the succeeding steps. Briefly, total RNA samples (100-1000ng) were poly A enriched and then reverse-transcribed into double-stranded cDNA. The cDNA samples was fragmented, end-repaired and polyadenylated before ligation of TruSeq adapters containing the index for multiplexing Fragments containing TruSeq adapters on both ends were selectively enriched with PCR. The quality and quantity of the enriched libraries were validated using Qubit® (1.0) Fluorometer and the Caliper GX LabChip® GX (Caliper Life Sciences, Inc., USA). The product is a smear with an average fragment size of approximately 260bp. The libraries were normalized to 10nM in Tris-Cl 10mM, pH8.5 with 0.1% Tween 20. The TruSeq SR Cluster Kit HS4000 (Illumina, Inc, California, USA) was used for cluster generation using 10pM of pooled normalized libraries on the cBOT. Sequencing was performed on the Illumina HiSeq 2500 single end 100bp using the TruSeq SBS Kit HS2500 (Illumina, Inc, California, USA).

tag: cancer status

value: Pca progenitor - Cancer stem cells

value: Prostate

value: Prostate cancer progenitors/CSC

value: RNAseq


title: h293_MeRIP_NEB_IVT_input_rep1

value: MeRIP-seq


title: h293_MeRIP_Abcam_mRNA_IP_rep2

description: h293_MeRIP_Abcam_mRNA_rep2_Macs2_peaks.bed

value: m6A-IP, Abcam (ab190886)


title: wild type INPUT

city: La Jolla

first: Stephen

middle: M

last: Blazie

address: 9500 Gilman Drive

institute: UC San Diego

description:
wild type
N2_CLIP.normed.compressed.bed

data_processing:
Barcode removal: Sequenced reads were removed of inline barcodes and reformatted to include randomers in read headers with eclipdemux (v0.0.1). Args: --length 10. Reads were then trimmed with cutadapt (1.9.1). Args: --match-read-wildcards -O 1 --times 1 -e 0.1 --quality-cutoff 6 -m 18 -g g_adapters.fasta -A A_adapters.fasta -a a_adapters.fasta (fasta sequences generated from parsebarcodes.sh within the eclip 0.1.5+ pipeline). Reads were then trimmed once more with cutadapt (1.9.1) to remove double-ligation events. Args: --match-read-wildcards -O 5 --times 1 -e 0.1 --quality-cutoff 6 -m 18 -A A_adapters.fasta (fasta sequences generated from parsebarcodes.sh within the eclip 0.1.5+ pipeline)
Mapping and duplicate removal: • Trimmed reads were then mapped with STAR (2.4.0i) against a repeat element database (RepBase 18.05). Args: --runThreadN 16 \ --genomeDir repbase \ --readFilesIn path/to/read1 path/to/read2 \ --outFileNamePrefix out_prefix \ --outReadsUnmapped Fastx \ --outSAMtype BAM Unsorted \ --outSAMattributes All \ --outSAMunmapped Within \ --outSAMattrRGline ID:foo \ --outFilterType BySJout \ --outFilterMultimapNmax 30 \ --outFilterMultimapScoreRange 1 \ --outFilterScoreMin 10 \ --alignEndsType EndToEnd. Unmapped reads filtered of repeat elements were then mapped with STAR (2.4.0i) against a C. elegans genome (ce10). Args: --runThreadN 16 \ --genomeDir genomedir \ --readFilesIn /path/to/read1 /path/to/read2 \ --outFileNamePrefix out_prefix \ --outReadsUnmapped Fastx \ --outSAMtype BAM Unsorted \ --outSAMattributes All \ --outSAMunmapped Within \ --outSAMattrRGline ID:foo \ --outFilterType BySJout \ --outFilterMultimapNmax 1 \ --outFilterMultimapScoreRange 1 \ --outFilterScoreMin 10 \ --alignEndsType EndToEnd. Aligned reads were sorted with samtools (1.4.1). Sorted reads were collapsed with barcodecollapsepe.py included in eclip 0.1.5+ pipelines. Args: -o preRmDup.bam -m metrics_file -b rmDup.bam. PCR de-duped reads from each inline barcode were then merged with samtools (1.4.1) merge (merged.bam). • Merged alignments were split to keep just read2 using samtools (1.4.1) view. Args: -h -b -f 128
Peak (read cluster) identification and annotation: Read2 BAM files were used to identify peak clusters with Clipper (1.2.2). Args: --species ce10 --bam path/to/input.bam --timeout 3600000 --maxgenes 1000000 --save-pickle --outfile path/to/output.bam. Peak clusters were normalized using read2 BAM files for IP against read2 BAM files for INPUT with peaksnormalize.pl(overlap_peakfi_with_bam_PE.pl), included in eclip 0.1.5+. Overlapping normalized peak regions were merged with compress_l2foldenrpeakfi_for_replicate_overlapping_bedformat.pl, included within eclip-0.1.5+. Normalized peak files were ranked by entropy score (make_informationcontent_from_peaks.pl included within the merge_peaks pipeline) and used as inputs to IDR (2.0.2) to determine reproducible peaks. Peaks were annotated by overlapping peak regions with WS235 annotations.
Genome_build: ce10
Supplementary_files_format_and_content: .bed and .bw files output from CLIPPER

organism: Caenorhabditis elegans

source_name: negative (IgG) control

growth_protocol: Mixed stage worms were grown on ~12 large (30 cm) NGM plates

extract_protocol:
Worms were resuspenced in 4ml lysis buffer [150mM NaCl, 1M HEPES, 100mM DTT, 6.25µl RNAsin (Promega) per 10ml, 10% glycerol, 10% Triton X-100, 1 protease inhibitor tablet per 10ml] and split into two tubes for each replicate. The resuspension was disrupted on an XL-2000 sonicator (QSonica, Newtown, CT) with 7 pulses (powersetting=11, 10 seconds each, 50 seconds on ice in between) and immediately spun at 4,750 RPM for 5 minutes at 4°C.
Libraries constructed according to seCLIP protocol (PMID: 28766298).

treatment_protocol: Worms were washed twice with M9, spinning at 1,500 rpm between washes. Worms were resuspended in M9 media and rocked on a rotator for 10 minutes and washed again at 1,500 rpm. Worms were then crosslinked on a Spectrolinker XL-1000 on NGM plates (without the plate lids)  with UV-B at 3kJ/m2 (Energy Settings: 3000). Worms were then collected in M9 buffer and then spun for 1min at 1500rpm.

tag: seclip antibody

value: seCLIP INPUT control

tag: genotype

value: wild type (+)

tag: strain


title: h293_MeRIP_NEB_IVT_input_rep2

tag: cell line


title: h293_MeRIP_NEB_IVT_IP_rep2


title: liver, HFD, 6456


title: 3xFLAG::EIF-3.G(∆RRM)_CLIP_replicate 1

description:
3xFLAG::EIF-3.G(∆RRM) expressed in the cholinergic motor neurons via Punc-17β
623_1_CLIP.normed.compressed.bed

source_name: cholinergic motor neurons

value: anti-FLAG M2 (Sigma #M8823)


title: liver, HFD, 6457

value: Creld2 eGFP/eGFP


title: RNAseq_PC3_rep2

source_name: PC3 cells

value: Metastatic

tag: cell type

value: PC3 cells


title: wild type CLIP

description:
wild type
N2_CLIP.normed.compressed.bed


title: RNAseq_PCa_spheres_rep2

tag: tissue


title: RNAseq_PC3_rep1


title: h293_MeRIP_NEB_IVT_IP_rep1

value: in vitro transcribed (IVT) RNA


title: RNAseq_PC3_siTIP5_rep2

treatment_protocol: cells were transfected with the indicated siRNAs and collected 3 days post transfection.


title: RNAseq_PC3_siTIP5_rep1


title: liver, CD, 6455

value: CD


title: liver, CD, 6454


title: liver, CD, 6453


title: RNAseq_PC3_siCTL_rep1

value: siRNA-CTL


title: liver, CD, 6452


title: liver, CD, 6451


title: 3xFLAG::EIF-3.G(∆RRM)_CLIP_replicate 2

description:
3xFLAG::EIF-3.G(∆RRM) expressed in the cholinergic motor neurons via Punc-17β
623_2_CLIP.normed.compressed.bed


title: RNAseq_PC3_siCTL_rep2


title: liver, HFD, 6449

value: Creld2 WT/WT

value: HFD


title: 3xFLAG::EIF-3.G(C130Y)_CLIP_replicate 2

description:
3xFLAG::EIF-3.G(C130Y) expressed in the cholinergic motor neurons via Punc-17β
565_2_CLIP.normed.compressed.bed


title: h293_MeRIP_Abcam_IVT_IP_rep2

description: h293_MeRIP_Abcam_IVT_rep2_Macs2_peaks.bed


title: liver, HFD, 6450

value: liver


title: h293_MeRIP_Abcam_IVT_input_rep2


title: h293_MeRIP_Abcam_mRNA_input_rep2

value: cellular mRNA


title: 3xFLAG::EIF-3.G(∆RRM)_INPUT_replicate 1


title: h293_MeRIP_Abcam_mRNA_input_rep1

description: h293_MeRIP_Abcam_mRNA_rep1_Macs2_peaks.bed


title: 3xFLAG::EIF-3.G(C130Y)_CLIP_replicate 1

description:
3xFLAG::EIF-3.G(C130Y) expressed in the cholinergic motor neurons via Punc-17β
565_1_CLIP.normed.compressed.bed


title: liver, HFD, 6446


title: 3xFLAG::EIF-3.G(∆RRM)_INPUT_replicate 2


title: h293_RNA-seq_IVT_rep2


title: h293_MeRIP_Abcam_mRNA_IP_rep1


title: 3xFLAG::EIF-3.G(+)_INPUT_replicate 2

description:
3xFLAG::EIF-3.G(+) expressed in the cholinergic motor neurons via Punc-17β
494_2_CLIP.normed.compressed.bed


title: RpoB_2

first: Ye

last: Gao

address: 9500 Gilman Dr.

institute: UCSD

data_processing:
library strategy: ChIP-exo
The base calling was done using Illumina’s Real-Time Analysis (RTA) v2.7.7; data was converted to fastq and demultiplexed using Illumina’s bcl2fastq2 Conversion Software v2.20;
Sequence reads generated from the study were mapped onto each reference genome using bowtie with default options to generate SAM output files
MACE software (https://code.google.com/p/chip-exo/) was used to detect peaks with aligned output from bowtie mapping.
Read count was calculated for each genomic position from sequence alignment, and 5% strongest intensity was used as background intensity. For each peak deteced with MACE, binding intensity was calculated by averaging read counts from two biological replicates and dividing by background intensity.
Genome_build: the reference genome ( MG1655 =  NC_000913.3 )
Supplementary_files_format_and_content: Tab-delimited text files in gff format which has 8 columns: sequence id, source(empty), feature (+/- strand), start position, end position, intensity score, strand(+/-), frame(.), attribute(.).

organism: Escherichia coli K-12

source_name: bacteria cells

growth_protocol: glycerol stocks of E. coli myc-tagged strains were inoculated into M9 minimal media with 0.2% (w/v) glucose. The culture was incubated at 37 degree overnight with agitation, and then was used to inoculate the fresh media (1/200 dilution). The volume of the fresh media was 150 mL for each biological replicate. The fresh culture was incubated at 37 degree with agitation to the mid-log phase (OD600 ≈ 0.5).

extract_protocol:
Lysates were clarified from sonicated TFs-DNA complexes, and then were isolated with myc antibody.
The experiments were performed following the procedures:  to identify each TF candidate binding maps in vivo, we isolated the DNA bound to each TF from formaldehyde cross-linked E. coli cells by chromatin immunoprecipitation (ChIP) with the specific antibodies that specifically recognizes myc tag (9E10, Santa Cruz Biotechnology), and Dynabeads Pan Mouse IgG magnetic beads (Invitrogen). ChIP materials (chromatin-beads) were used to perform on-bead enzymatic reactions. Briefly, the sheared DNA of chromatin-beads was repaired by the NEBNext End Repair Module (New England Biolabs) followed by the addition of a single dA overhang and ligation of the first adaptor (5’-phosphorylated) using dA-Tailing Module (New England Biolabs) and NEBNext Quick Ligation Module (New England Biolabs), respectively. Nick repair was performed by using PreCR Repair Mix (New England Biolabs). Lambda exonuclease- and RecJf exonuclease-treated chromatin was eluted from the beads and the protein-DNA cross-link was reversed by overnight incubation at 65 degree. RNAs- and Proteins-removed DNA samples were used to perform primer extension and second adaptor ligation. The DNA samples incubated for primer extension were treated with dA-Tailing Module (New England Biolabs) and NEBNext Quick Ligation Module (New England Biolabs) for second adaptor ligation. The DNA sample purified by GeneRead Size Selection Kit (Qiagen) was enriched by polymerase chain reaction (PCR) using Phusion High-Fidelity DNA Polymerase (New England Biolabs). The amplified DNA samples were purified again by GeneRead Size Selection Kit (Qiagen) and quantified using Qubit dsDNA HS Assay Kit (Life Technologies). Quality of the DNA sample was checked by running Agilent High Sensitivity DNA Kit using Agilent 2100 Bioanalyzer (Agilent) before sequenced using HiSeq (Illumina) in accordance with the manufacturer’s instructions. The experiments were performed in biological duplicate.

tag: genotype/variation

value: myc-tagged

tag: chip-exo antibody

value: anti-RpoB mouse monoclonal IgG2a, NT63, Biolegend


title: ChIPseq_HA-TIP5-BRDmut_PC3

data_processing:
ChIPseq reads from Ilumina HiSeq to the human hg38 reference genome using Bowtie2 (version 2.2.5). Duplicated sequences were removed with samtools-1.9. Read counts were computed and normalized using “bamCoverage” from deepTools (version 2.0.1; (Ramirez et al., 2014)) using a bin size of 50bp in order to generate bigwig files. Enriched regions (peaks) were calulated with MACS 2.0 (default settings). For HA-TIP5 ChIPs, enriched regions were calcutated with p-val <0.01. Genomic annotation of ChIPseq peaks was done with ChIPseeker (Yu et al., 2015). Genome_build: GRCh38/hg38
Genome_build: GRCh38/hg38

growth_protocol: PC3 cells were cultured in RPMI 1640 medium and Ham's F12 medium (1:1; Gibco) containing 10% FBS (Gibco) and 1% penicillin-streptomycin (Gibco). PCa spheres were cultured in serum free DMEM/F12 medium (1:1, Gibco) supplemented with 20ng/ml of basic human FGF (Sigma), 20ng/ml of EGF (Sigma), 3μg/ml of Insulin (Sigma) and 1x B-27 (Gibco). 1x104 cells were seeded in low adhesion petri dishes (Greiner) and cultured for 6 to 8 days. About 20% of media was changed every 2 days. All cells were regularly tested for mycoplasma contamination.

extract_protocol: ChIP experiments were performed as previously described (Leone et al., 2017). Briefly, 1% formaldehyde was added to cultured cells to cross-link proteins to DNA. Isolated nuclei were then lysed (50 mM Tris-HCl pH 8.1, 10 mM EDTA and 1% SDS) and sonicated using a Bioruptor ultrasonic cell disruptor (Diagenode) to shear genomic DNA to an average fragment size of 200 bp. 20 μg of chromatin was diluted tenfold with ChIP buffer (16.7 mM Tris-HCl pH 8.1, 167 mM NaCl, 1.2 mM EDTA, 0.01% SDS and 1.1% Triton X-100) and precleared for 2h with 10ul of packed Sepharose beads for at least 2h at 4°C. Immunoprecipitation was done overnight with the indicated antibodies. Pulldowns were done with Dynabeads protein-A (or -G, Millipore) for 4h at 4°C. For HA-TIP5 ChIPs, preclearing and pulldowns were done with beads block with BSA (50μg) and ytRNA (50μg), per 400ul of Dynabeads protein-A. After washing, elution and reversion of cross-links, eluates were treated with RNAse A (1μg). DNA was purified with phenol-chloroform, ethanol precipitated and quantified by quantitative PCR. The quantity and quality of the isolated DNA was determined with a Qubit® (1.0) Fluorometer (Life Technologies, California, USA) and a Bioanalyzer 2100 (Agilent, Waldbronn, Germany). The NEBNext® Ultra™ II DNA Library Prep Kit from NEB (New England Biolabs, Ipswich, MA) was used in the succeeding steps. ChIP samples (1ng) were end-repaired and adenylated.  Adapters containing the index for multiplexing were ligated to the fragmented DNA samples. Fragments containing adapters on both ends were enriched by PCR.  The quality and quantity of the enriched libraries were measured using Qubit® (1.0) Fluorometer and the Tapestation (Agilent, Waldbronn, Germany). The product is a smear with an average fragment size of approximately 300 bp. The libraries were normalized to 10nM in Tris-Cl 10 mM, pH8.5 with 0.1% Tween 20. The TruSeq SR Cluster Kit v4-cBot-HS (Illumina, Inc, California, USA) was used for cluster generation using 8 pM of pooled normalized libraries on the cBOT. Sequencing was performed on the Illumina HiSeq 2500 ot Hiseq 4000 single end 125 bp using the TruSeq SBS Kit v4-HS (Illumina, Inc, California, USA).

value: Prostate

value: ChIPseq

tag: chip antibody

value: HA-tag (Abcam ab9110)


title: liver, CD, 6444


title: ChIPseq_HA-TIP5-BRDmut_input

value: none (input)


title: 3xFLAG::EIF-3.G(+)_CLIP_replicate 1

description:
3xFLAG::EIF-3.G(+) expressed in the cholinergic motor neurons via Punc-17β
494_1_CLIP.normed.compressed.bed

value: anti-FLAG M2 (Sigma #M8823)


title: RpoD_2

value: ArcA myc-tagging cells

value: anti-sigma factor D mouse monoclonal IgG1, lot#2G10, Biolegend


title: liver, CD, 6442


title: h293_MeRIP_Abcam_IVT_input_rep1

description: h293_MeRIP_Abcam_IVT_rep1_Macs2_peaks.bed

source_name: human HEK293T cell line

value: MeRIP-seq


title: ChIPseq_HA-TIP5_PC3_input

value: Metastatic

value: PC3 cells


title: h293_MeRIP_Abcam_IVT_IP_rep1

value: in vitro transcribed (IVT) RNA

value: m6A-IP, Abcam (ab190886)


title: liver, HFD, 6448

source_name: liver

value: Creld2 WT/WT

value: HFD


title: liver, CD, 6441

value: CD

value: liver


title: 3xFLAG::EIF-3.G(C130Y)_INPUT_replicate 1

value: seCLIP INPUT control


title: 3xFLAG::EIF-3.G(C130Y)_INPUT_replicate 2


title: ChIPseq_HA-TIP5_PC3

value: Prostate


title: 3xFLAG::EIF-3.G(+)_CLIP_replicate 2


title: liver, CD, 6445


title: liver, CD, 6443


title: RpoB_1

value: myc-tagged

value: anti-RpoB mouse monoclonal IgG2a, NT63, Biolegend


title: h293_RNA-seq_mRNA_rep2

value: cellular mRNA

value: RNAseq


title: liver, HFD, 6447


title: RpoD_1

value: ArcA myc-tagging cells


title: h293_RNA-seq_mRNA_rep1


title: Blood_healthy_rep6

status: Public on Aug 17 2021

first: Ting

last: Zhou

address: No.6600, Nanfeng highway, Fengxian District

institute: Fengxian Hospital, Southern Medical University

description: gene ecpression in healthy people

hyb_protocol: After purification the labeled RNAs were hybridized onto the microarray.

scan_protocol: After washing, the arrays were scanned with the Agilent Scanner G2505C (Agilent Technologies)

data_processing: Feature Extraction software (version10.7.1.1, Agilent Technologies) was used to analyze array images to get raw data. Next, Genespring software (version 14.8, Agilent Technologies) was employed to finish the basic analysis with the raw data. To begin with, the raw data was normalized with the quantile algorithm.

source_name: Peripheral Blood,healthy

label_protocol: total RNA were dephosphorylated, denaturated and then labeled with Cyanine-3-CTP.

extract_protocol: Total RNA was extracted and purified usingPAXgeneTM  Blood RNA Kit (Cat#762174, QIAGEN, GmBH, Germany) following the manufacturer’s instructions.Then quantified by the NanoDrop ND-2000 (Thermo Scientific)and the RNA integrity was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies).

treatment_protocol: Ethylenediaminetetraacetic acid (EDTA)-treated whole blood samples from  depression patients and healthy volunteers were collected.

value: whole blood

value: female

tag: age


title: 3xFLAG::EIF-3.G(+)_INPUT_replicate 1


title: h293_RNA-seq_IVT_rep1


title: Blood_healthy_rep4

description: gene ecpression in healthy people

value: male


title: Blood_depression_rep1

description: gene ecpression in depressed patients

source_name: Peripheral Blood,depression


title: Blood_healthy_rep1

description: gene ecpression in healthy people


title: Blood_healthy_rep2

description: gene ecpression in healthy people


title: Blood_depression_rep2

description: gene ecpression in depressed patients


title: Blood_depression_rep6

description: gene ecpression in depressed patients


title: Blood_healthy_rep3

description: gene ecpression in healthy people


title: Blood_depression_rep4

description: gene ecpression in depressed patients


title: Blood_depression_rep3

description: gene ecpression in depressed patients


title: T2D_HGI_36h_i06

city: Copenhagen

first: Ali

last: Altintas

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

country: Denmark

institute: Copenhagen University

description:
counts.tsv.gz
logCPM_batchCorrected.tsv.gz

data_processing:
1) Reads were trimmed using Trim_Galore! (v0.4.3) on default settings
2) Trimmed reads were aligned using STAR (v2.5.3a) aligner with Ensembl human annotation (GRCh38, release 92)
3) Gene read coverages were counted using featureCounts from subread (v1.5.2) package
4) The lowly expressed genes were discarded from downstream analysis using filterByExpr function from edgeR package (v3.32.1) resulting 18,482 genes for downstream analysis
5) Batch effect caused by "individuals" are removed from CPM values by using removeBatchEffect function from limma (v3.46.0)
6) Batch effect removed logCPM values are used for rhythmicity and differential rhythmicity analysis by RAIN (v1.20.0) and DODR (v0.99.3), respectively
Genome_build: hg38
Supplementary_files_format_and_content: Text file in tab separated format with gene coverages in units of read counts and logCPM (log counts per million) values (batch effect caused by individuals are removed)

source_name: Primary myotubes from vastus lateralis

growth_protocol: Primary myoblasts from skeletal muscle biopsies from men with NGT and T2D were grown in DMEM/F12+Glutamax with 16% FBS and 1% Antibiotic-Antimycotic (100X). Differentiation was induced at 80% confluence, by incubating the cells for 4-5 days in fusion medium consisting of 76% DMEM Glutamax with 25 mmol/l glucose, 20% M199 (5.5 mmol/l), 2% HEPES and 1% Antibiotic-Antimycotic (100X), with 0.03 μg/ml zinc sulfate and 1.4 mg/ml Vitamin B12, with a further addition of 100 μg/ml apo-transferrin and 0.286 IU/ml insulin prior to use. Experiments were performed on differentiated myotubes after an additional 3-5 days incubation in the same media containing 2% FBS (post fusion media).

extract_protocol:
Cells were lysed and RNA extracted using E.Z.N.A.® Total RNA Kit I (SKU: R6834-01, Omega Bio-tek, GA, USA). RNA was checked for quality using the Agilent RNA 600 nano kit and Bioanalyser instrument (Agilent Technologies, Santa Clara, CA). Aliquots of RNA (1 µg) were analyzed using the Illumina TruSeq Stranded Total RNA with Ribo-Zero Gold protocol (Illumina).
Ribosomal RNA was removed from the sample using 35 µl rRNA removal beads (Illumina) on a magnetic plate followed by clean-up of the ribosomal-depleted RNA with 193 µl Agencourt RNAClean XP beads (Beckman Coulter), 70% ethanol wash and elution into 10 µl Elution buffer (Illumina). The RNA sample was fragmented for 4 min at 94°C in Elute, Prime, Fragment High Mix (Illumina) and then subjected to first strand cDNA synthesis with 1 µl Superscript III reverse transcriptase (Life Technologies) per sample using a thermocycler programmed to 25°C for 10 min, 50°C for 15 min and 70°C for 15 min. Second strand cDNA was synthesized by addition of Second Strand Marking Master Mix and samples were incubated at 16°C for 60 min. Samples were subject to another bead clean up prior to A-tailing and ligation of adapters as per kit instructions (Illumina). Following a third bead clean-up, samples were enriched for DNA fragments by amplification using the Illumina PCR Primer Cocktail and PCR Master Mix, subjected to 98°C for 30 min, followed by a pre-defined cycle (98°C for 10 s, 60°C for 30 s and 72°C for 30 s) that was repeated 3-15 times, based on each individual sample, and finally incubated for 5 min at 72°C. Samples were cleaned, and validated for DNA concentration using the Qubit dsDNA HS assay kit (Invitrogen) and for base pair size and purity using the Agilent High Sensitivity DNA chip and Bioanalyser instrument.
Libraries were subjected to 100-bp single-end sequencing on the X Ten platform (Illumina) at the Beijing Genomics Institute (BGI), Hong Kong, China. Approximately 20 million reads/sample were assigned to genes with 18,482 genes surviving the expression threshold.

treatment_protocol: After post fusion, DMEM with 5.5 mmol/l glucose was used in the post fusion medium to create a low glucose condition. After 22 hrs, cells were synchronized by serum shock (media containing 50% FBS, 2 hrs) and then switched back to low glucose media. Skeletal muscle myotubes from men with either T2D or NGT were lysed at 6-hr intervals from 12 hrs to 54 hrs. Zeit-time (ZT) was determined as time after synchronization.  All transfections were performed using 250ng of plasmid DNA total. Treatment conditions: all cells received 5uM Rosiglitazone 48hrs post-transfection.

tag: disease

value: HGI

tag: group

tag: time

tag: individual


title: T2D_HGI_12h_i06

tag: treatment


title: NGT_HGI_48h_i08

value: NGT


title: NGT_HGI_30h_i08


title: T2D_CTL_54h_i06

value: CTL


title: NGT_HGI_54h_i08


title: T2D_HGI_48h_i06


title: NGT_HGI_24h_i08


title: NGT_HGI_18h_i08


title: NGT_HGI_12h_i08


title: NGT_HGI_36h_i08


title: T2D_CTL_30h_i06


title: T2D_CTL_42h_i06


title: T2D_HGI_24h_i06


title: T2D_CTL_18h_i06


title: Blood_depression_rep5

description: gene ecpression in depressed patients

tag: gender


title: NGT_HGI_42h_i08


title: NGT_HGI_30h_i12


title: T2D_HGI_54h_i06


title: NGT_HGI_30h_i09


title: NGT_HGI_42h_i09


title: Blood_healthy_rep5

description: gene ecpression in healthy people


title: T2D_CTL_48h_i06


title: NGT_HGI_42h_i12


title: NGT_HGI_18h_i12


title: T2D_CTL_12h_i06


title: T2D_HGI_42h_i02


title: NGT_HGI_54h_i09


title: T2D_CTL_24h_i06


title: T2D_HGI_18h_i06


title: T2D_CTL_36h_i06


title: DM_5

city: Harbin

first: Ping

state: Heilongjiang

address: Harbin Medical University

institute: Harbin Medical University

description: smallRNA

data_processing: The tools for genome alignment was "Bowtie2" and the alignment tools for Non-coding RNA was "AASRA". "cmsearch" was used to align with the Rfam database.

source_name: blood

extract_protocol:
Clinical serum samples were collected by utilizing residual specimens from patients undergoing routine medical care. Each blood sample is 4-6ml. Samples were then centrifuged and the supernatant was stored at −80°C in the centrifuge tube.
Filter Small RNA: Use the 200ng-1μg of RNA sample, then separate RNA segment of different size by PAGE gel, select 18-30nt (14-30 ssRNA Ladder Marker, TAKARA) stripe and recycle.

value: blood

tag: diagnosis

value: DM

tag: height(cm)

tag: weight(kg)

tag: medical history(year)

tag: iief-5 score

tag: bp(mmhg)

tag: fbg(mmol/l)

tag: ts(g/ml)

tag: cre(umol/l)

tag: bu(mmol/l)

tag: tsh(uiu/ml)

tag: tg(mmol/l)

tag: cho(tc)(mmol/l)

tag: alt(u/l)

tag: ast(u/l)

tag: sas

tag: sds


title: T2D_HGI_42h_i06

tag: disease

tag: treatment

tag: group

tag: time

tag: individual


title: T2D_HGI_30h_i06


title: DM_9

description: smallRNA

tag: tissue

tag: diagnosis

tag: age

tag: height(cm)

tag: weight(kg)

tag: medical history(year)

tag: iief-5 score

tag: bp(mmhg)


title: T2D_HGI_24h_i02


title: T2D_HGI_48h_i02


title: T2D_HGI_18h_i02


title: T2D_CTL_54h_i02


title: T2D_HGI_30h_i02


title: T2D_CTL_18h_i02


title: DM_10

description: smallRNA

tag: fbg(mmol/l)

tag: ts(g/ml)

tag: cre(umol/l)

tag: bu(mmol/l)

tag: tsh(uiu/ml)

tag: tg(mmol/l)

tag: cho(tc)(mmol/l)

tag: alt(u/l)


title: T2D_CTL_30h_i02

tag: disease

tag: treatment

tag: group

tag: time

tag: individual


title: DM_1

description: smallRNA

tag: tissue

tag: diagnosis

tag: age

tag: height(cm)

tag: weight(kg)

tag: ast(u/l)

tag: sas

tag: sds


title: DM_8

description: smallRNA

tag: medical history(year)

tag: iief-5 score

tag: bp(mmhg)

tag: fbg(mmol/l)

tag: ts(g/ml)

tag: cre(umol/l)

tag: bu(mmol/l)

tag: tsh(uiu/ml)


title: T2D_HGI_54h_i02

tag: disease

tag: treatment

tag: group

tag: time

tag: individual


title: T2D_CTL_42h_i02


title: DM_7

description: smallRNA

tag: tissue

tag: diagnosis

tag: age

tag: height(cm)

tag: weight(kg)

tag: tg(mmol/l)

tag: cho(tc)(mmol/l)

tag: alt(u/l)


title: DMED_9

description: smallRNA

value: DMED

tag: medical history(year)

tag: iief-5 score

tag: bp(mmhg)

tag: fbg(mmol/l)

tag: ts(g/ml)

tag: ast(u/l)

tag: sas

tag: sds


title: DMED_8

description: smallRNA

tag: cre(umol/l)

tag: bu(mmol/l)

tag: tsh(uiu/ml)


title: DM_3

description: smallRNA

tag: tissue

tag: diagnosis

tag: age


title: T2D_CTL_12h_i02

tag: disease

tag: treatment

tag: group

tag: time

tag: individual


title: T2D_HGI_36h_i02


title: DMED_6

description: smallRNA

tag: height(cm)

tag: weight(kg)

tag: medical history(year)

tag: iief-5 score

tag: bp(mmhg)

tag: tg(mmol/l)

tag: cho(tc)(mmol/l)

tag: alt(u/l)


title: T2D_HGI_54h_i03


title: DMED_10

description: smallRNA

tag: fbg(mmol/l)

tag: ts(g/ml)

tag: cre(umol/l)

tag: bu(mmol/l)

tag: tsh(uiu/ml)

tag: ast(u/l)

tag: sas

tag: sds


title: DM_2

description: smallRNA

tag: tissue

tag: diagnosis

tag: age


title: T2D_CTL_36h_i02

tag: disease

tag: treatment

tag: group

tag: time

tag: individual


title: T2D_CTL_48h_i02


title: T2D_HGI_30h_i03


title: DM_6

description: smallRNA

tag: height(cm)

tag: weight(kg)

tag: medical history(year)

tag: iief-5 score

tag: bp(mmhg)

tag: tg(mmol/l)

tag: cho(tc)(mmol/l)

tag: alt(u/l)


title: DM_4

description: smallRNA

tag: fbg(mmol/l)

tag: ts(g/ml)

tag: cre(umol/l)

tag: bu(mmol/l)

tag: tsh(uiu/ml)

tag: ast(u/l)

tag: sas

tag: sds


title: T2D_CTL_24h_i02

tag: disease

tag: treatment

tag: group

tag: time

tag: individual


title: DMED_7

description: smallRNA

tag: tissue

tag: diagnosis

tag: age

tag: height(cm)

tag: weight(kg)

tag: medical history(year)

tag: iief-5 score

tag: bp(mmhg)


title: T2D_HGI_42h_i03


title: T2D_HGI_12h_i02


title: DMED_1

description: smallRNA

tag: fbg(mmol/l)

tag: ts(g/ml)

tag: cre(umol/l)

tag: bu(mmol/l)

tag: tsh(uiu/ml)

tag: tg(mmol/l)

tag: cho(tc)(mmol/l)

tag: alt(u/l)


title: T2D_HGI_18h_i03

tag: disease

tag: treatment

tag: group

tag: time

tag: individual


title: DMED_4

description: smallRNA

tag: tissue

tag: diagnosis

tag: age

tag: height(cm)

tag: weight(kg)

tag: ast(u/l)

tag: sas

tag: sds


title: DMED_3

description: smallRNA

tag: medical history(year)

tag: iief-5 score

tag: bp(mmhg)

tag: fbg(mmol/l)

tag: ts(g/ml)

tag: cre(umol/l)

tag: bu(mmol/l)

tag: tsh(uiu/ml)


title: DMED_5

description: smallRNA

tag: tg(mmol/l)

tag: cho(tc)(mmol/l)

tag: alt(u/l)


title: DMED_2

description: smallRNA

tag: tissue

tag: diagnosis

tag: age


title: NGT_HGI_24h_i09

tag: disease

tag: treatment

tag: group

tag: time

tag: individual


title: T2D_CTL_30h_i03


title: T2D_CTL_54h_i03


title: T2D_CTL_42h_i03


title: NGT_HGI_12h_i09


title: T2D_CTL_18h_i03


title: NGT_HGI_36h_i09


title: C9P3_T2_0.5mM

city: State College

first: Aswathy

last: Sebastian

address: University Park

institute: PennState

data_processing:
Illumina Truseq Stranded mRNA Librarykit was used and data was sequnced using Illumina HiSeq2500. Base calling was done using bcl2fastq v2.20.0  software and quality reports were generated using fastqc.
Raw data was mapped to chicken reference genome using hisat2 (v.2.1.0)
Mapping was visualized  and inspected in IGV.
Gene-level read counts were obtained using featureCounts
Differential expression analysis was done using DESeq2
Genome_build: Gallus_gallus.GRCg6a
Supplementary_files_format_and_content: Gene-level raw read counts
Supplementary_files_format_and_content: Normalized counts and differential expression results

organism: Gallus gallus

source_name: COVCAR cells designated as C9 in 3rd passage

growth_protocol: COVCAR cells were cultured on gelatinized 75cm cell culture flasks at 37ºC under 5% CO2 atmosphere.  When the COVCAR cells reached 100% confluence, the cells were dissociated from the flask using 0.05% trypsin (Invitrogen) and used for metformin treatment.

extract_protocol:
Cells and spheres following the metformin treatment were harvested by centrifugation followed by resuspension in Trizol and stored at -80C until RNA extraction.  Total RNA was extracted using the RNeasy Micro kit (Qiagen) using the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Approximately 200,000 COVCAR cells from each of 4 primary ovarian cancer lines designated as C5, C7, C9, and C11 were treated with 0, 0.5, 1, or 2 mM metformin dissolved in serum-free medium [SCM, X-VIVO 20 culture medium supplemented with 5 µg/ml bovine insulin, 20 ng/ml recombinant human epidermal growth factor and antibiotic-antimycotic solution] in 24-well ultra-low attachment plate for 24 h at 37ºC under 5% CO2 atmosphere.

tag: cell line

value: COVCAR

tag: cell type

value: Ovarian cancer cells derived fom ascites of chickens with ovarian cancer

tag: tumor type

value: Ovarian endometrioid adenocarcinoma

value: 0.5mM metfromin


title: C5P3_T4_2.0mM

source_name: COVCAR cells designated as C5 in 3rd passage

value: 2mM metformin


title: C11P2_T2_0.5mM

source_name: COVCAR cells designated as C11 in 2ndpassage


title: C9P3_T4_2.0mM


title: C7P3_T4_2.0mM

source_name: COVCAR cells designated as C7 in 3rd passage


title: C9P3_T3_1.0mM

value: 1mM metformin


title: C11P2_T4_2.0mM

source_name: COVCAR cells designated as C11 in 2nd passage


title: NGT_HGI_30h_i10


title: C7P3_T3_1.0mM


title: C5P3_T3_1.0mM


title: C11P2_T1_0.0mM

value: untreated


title: NGT_HGI_18h_i10


title: C11P2_T3_1.0mM


title: C7P3_T1_0.0mM


title: C7P3_T2_0.5mM


title: NGT_HGI_48h_i12


title: C5P3_T1_0.0mM


title: NGT_HGI_42h_i10


title: NGT_HGI_54h_i10


title: C5P3_T2_0.5mM


title: NGT_HGI_36h_i12


title: 73899: ino4delta pRS316-GPDprom-Mga2deltaTM-mCh Replicate3

city: Vienna

first: Alwin

last: Köhler

state: Vienna

address: Dr. Bohr-Gasse 9/3

department: Medical Biochemistry

country: Austria

institute: Max Perutz Labs, Medical University of Vienna

data_processing:
The reads were mapped to the Saccharomyces cerevisiae Ensembl R64-1-1 reference genome with STAR (version 2.5.1b).
The read counts for each gene were detected using HTSeq (version 0.5.4p3).
The counts were normalised using the TMM normalization from edgeR package in R.
Prior to statistical testing the data was voom transformed and then the differential expression between the sample groups was calculated with limma package in R.
Genome_build: Saccharomyces cerevisiae Ensembl R64-1-1 reference genome
Supplementary_files_format_and_content: xlsx files containing raw and normalized count values for each sample

source_name: Exponentially growing yeast cells

growth_protocol: Yeast cells were grown in synthetic media and expenentially growing cells were harvested.

extract_protocol:
Total RNA was extracted from 12 mL of an exponentially growing yeast cell cultures using the hot phenol method.
For RNA sequencing, total RNA was depleted from ribosomal RNA and then reverse transcribed using random oligomer primers (RiboZero, NEB). Sequencing was performed on an Illumina platform

tag: strain

tag: plasmid

tag: growth media

value: SDC-URA


title: NGT_HGI_48h_i09


title: 73897: mga2delta pRS316-GPDprom-Mga2deltaTM-mCh Replicate3


title: 73892: ino4delta pRS316-GPDprom-Mga2deltaTM-mCh Replicate2


title: NGT_HGI_12h_i12


title: 73894: WT pRS316-GPDprom-Ole1-mCh Replicate3

value: wild-type (BY4741)


title: 73893: WT SDC+All Replicate3

value: SDC+All


title: 73889: mga2delta pRS316-GPDprom-Mga2-mCh Replicate2


title: 73888: mga2delta SDC+All Replicate2


title: C9P3_T1_0.0mM


title: NGT_HGI_54h_i04


title: 73891: ino4delta SDC+All Replicate2


title: 73890: mga2delta pRS316-GPDprom-Mga2deltaTM-mCh Replicate2


title: NGT_HGI_42h_i04


title: NGT_HGI_30h_i04


title: 73896: mga2delta pRS316-GPDprom-Mga2-mCh Replicate3


title: 73898: ino4delta SDC+All Replicate3


title: 73887: WT pRS316-GPDprom-Ole1-mCh Replicate2


title: NGT_HGI_18h_i04


title: NGT_HGI_24h_i12


title: 73886: WT SDC+All Replicate2