title: At-Hv_3_4426.W

city: Cologne

first: Fantin

last: Mesny

address: Carl-von-Linné-Weg 10

department: Plant-Microbes interaction

institute: Max Planck Institute for Plant Breeding Research

description:
Pair of genomes mapped: Hv+At
Hv_fungalTranscriptome.csv
Hv_plantTranscriptome.csv

data_processing:
Raw-RNASeq reads were trimmed with Trimmomatic and parameters TRAILING:20 AVGQUAL:20 HEADCROP:10 MINLEN:100
Trimmed reads were mapped onto pairs of reference genomes using HiSat2
Per-gene read counts were retrieved from HiSat2 alignments using FeatureCounts
RPKM values were calculated from FeatureCounts data
Differential gene expression analyses were conducted with DESeq2, independently for plant and fungal transcriptomes
Genome_build: TAIR10.1
Genome_build: https://mycocosm.jgi.doe.gov/Chame1/Chame1.home.html
Genome_build: https://mycocosm.jgi.doe.gov/Parch1/Parch1.home.html
Genome_build: https://mycocosm.jgi.doe.gov/Phapo1/Phapo1.home.html
Genome_build: https://mycocosm.jgi.doe.gov/Truan1/Truan1.home.html
Genome_build: https://mycocosm.jgi.doe.gov/Macpha1/Macpha1.home.html
Genome_build: https://mycocosm.jgi.doe.gov/Zalva1/Zalva1.home.html
Supplementary_files_format_and_content: Files '_fungalTranscriptome.csv’ correspond to the DESeq2 differential expression analysis of fungal genes in planta vs. on medium. This file also provide RPKM values in control (mycelium grown on medium) and test (fungus in planta) conditions
Supplementary_files_format_and_content: Files '_plantTranscriptome.csv’ correspond to the DESeq2 differential expression analysis of  A. thaliana genes mock-inoculated vs. inoculated with mycelium. This file also provide RPKM values in control (mock-treated plants) and test (plant inoculated with mycelium) conditions

organism:
Arabidopsis thaliana
Halenospora varia

source_name: roots,mycelium

growth_protocol: Seven A. thaliana seeds (or 16 drops of 10µL crushed mycelium solution) were grown in a sterile plate gnotobiotic system filled with an agar medium (described in Gruber et al. 201 - 100µM inorganic Phosphate). Culture was carried out in growth cabinets for 28 days at 21 °C for 10 hours with light (intensity 4), and at 19 °C and 14 hours in the dark.

extract_protocol:
Total RNA was extracted from plant roots or mycelium grown on medium using Qiagen RNEasy Plant Mini Kit
An RNAseq library was prepared with the NEBNext Ultra™ II Directional RNA Library Prep Kit for Illumina (New England Biolabs) and then sequenced in single read mode on a HiSeq 3000 system

treatment_protocol: Prior to growth, plant seeds were inoculated with fungal mycelium or mock solution. For the control conditions, fungal inoculum were grown on the same agar-based culture medium.

value: 28 days post seed inoculation

tag: culture medium

value: 100µM Pi MS-Agar

tag: inoculation

value: Mycelium-inoculated seeds


title: neutrophil WT 30 rep1

status: Public on Nov 03 2021

type: SRA

city: Austin

first: Mijeong

last: Kim

state: Texas

address: 2500 Speedway

country: USA

institute: The University of Texas at Austin

library_source: transcriptomic

data_processing:
The reads were aligned to the mouse transcriptome (mm10) using a default setting of STAR (v.020201).
Aligned reads were counted using HTseq (v. 0.6.1p1).
Genome_build: mm10
Supplementary_files_format_and_content: Excel file include TPM values for each sample

molecule: total RNA

organism: Mus musculus

source_name: neutrophil

extract_protocol:
Mouse bone marrow neutrophils were enriched using a mouse neutrophil isolation kit (Miltenyi Biotec). Total RNAs were isolated using the RNeasy Plus Mini Kit (Qiagen)
300 ng of total RNA was used to generate RNA-seq library using the NEBNext Ultra II RNA Library Prep kit (NEB) according to the manufacturer’s instruction.

treatment_protocol: Bone marrow neutrophils isolated from WT and KO mice were treated without or with 20 ng/ml TNF-alpha for 30 or 120 minutes.

tag: strain

tag: genotype

value: wild type


title: neutrophil WT rep3


title: PFC_AAVGFP4_GlyGCC

city: New York

first: Jennifer

last: Blaze

state: New York

address: 1470 Madison Ave 9-202

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Library strategy: Bisulfite tRNA-seq
Bisulfite tRNA sequencing raw fastq files were analyzed using Bisamp publicly available web server.

source_name: Mouse prefrontal cortex

extract_protocol:
1ug of total RNA was used for bisulfite conversion with the EZ RNA Methylation kit according to manufacturer’s instructions (Zymo Research). Due to the strong secondary structure of tRNAs, the PCR step during bisulfite conversion was repeated 3 times consecutively, as previously reported to completely denature tRNAs.  Following bisulfite treatment and clean-up, we performed cDNA synthesis using the reverse primer for each tRNA isodecoder.  Targeted cDNA was then PCR-amplified with the tRNA-specific forward primer and products were size-verified on a 4% agarose gel. PCR amplicons (~120nt including tRNA amplicon and overhangs for adapter ligation) were then extracted and purified (Qiaquick Gel Extraction Kit, Qiagen).  We labelled each amplicon with a unique index (Nextera XT, Illumina) and pooled up to 20 amplicons in equimolar concentrations before next-gen sequencing. Note that only read 1 from paired end sequencing was used for analysis.
total RNA was extracted from mouse cortex using Trizol extraction and quantity was measured on Qubit fluorometer.  Quality of total RNA was checked on the Agilent Bioanalyzer using the RNA 6000 Pico Kit

tag: tissue type

value: Prefrontal cortex

value: WT C57BL/6, AAV-GFP injection

tag: developmental stage

value: Adult

tag: molecule

value: Bisulfite-treated total RNA


title: neutrophil WT rep2


title: At-Hv_2_4426.O

country: Germany


title: HealthyDonor_WholeBlood_Het_rep2

city: Ar-Rayyan, Doha,

first: Melanie

last: Makhlouf

address: Al Gharrafa Street,

country: Qatar

institute: Sidra Medicine

data_processing:
Reads were mapped using STAR_2.6.1d aligner.
FeatureCounts v2.0.0 was used to generate the raw counts.
Genome_build: human genome GRCh37.p13 (Genome Reference Consortium 622 Human Reference 37), INSDC Assembly GCA_000001405.14, Feb 2009
Supplementary_files_format_and_content: raw read count .txt file

molecule: polyA RNA

organism: Homo sapiens

source_name: Whole Blood

extract_protocol:
Total RNA from whole blood was extracted using the PAXgene Blood RNA Kit (PreAnalytiX).
mRNA was prepared for sequencing using the TruSeq stranded mRNA sample preparation kit (Illumina), with a selected insert size of 120–210 bp
mRNA libraries were pooled and paired-end 150-bp sequencing was performed on the Illumina HiSeq4000 platform.

tag: tissue

value: whole blood

tag: disease state

value: Healthy donor

tag: genotype_affected status

value: Heterozygous mutant


title: At-Hv_1_4426.G


title: HealthyDonor_WholeBlood_Homo_rep1

value: Homozygous non mutant


title: Patient_WholeBlood_rep4

value: Patient

value: Homozygous mutant


title: PFC_AAVNsun2_3_GlyGCC

value: WT C57BL/6, AAV-Nsun2 injection


title: Pc_3_4606.F

description:
Pair of genomes mapped: Pc+At
Pc_fungalTranscriptome.csv

organism: Paraphoma chrysanthemicola

source_name: mycelium

value: Mycelium inoculum deposited on medium


title: PFC_AAVNsun2_2_GlyGCC


title: P300KO_TET2KO_ATACseq_Rep4

city: Miami

first: Stephen

last: Nimer

state: FL

address: 1120 NW 14th ST

department: Sylvester Comprehensive Cancer Center

institute: University of Miami

library_source: genomic

data_processing:
Base calling using Illumina RTA 2.4.11
ATAC-Seq chromatin accessible regions were determined using ENCODE pipeline standards (https://github.com/ENCODE-DCC/atac-seq-pipeline; git commit 2b693ab)
Sequencing indices were trimmed from merged fastq files using cutadapt (v1.9.1) and then aligned to mm10 using bowtie2 (v2.2.6).
After de-duplication, reads were tn5 shifted, replicate peaks were called, and fold enrichment signal files were generated using macs2 (v2.1.0).
Genome_build: Encode: mm10_no_alt_analysis_set (ENCSR425FOI)
Supplementary_files_format_and_content: peak files from macs2

molecule: genomic DNA

source_name: HSPCs

growth_protocol: 200,000 HSPCs were sorted from mouse bone marrow samples. Each independent biological replicate was generated from HSPCs isolated from two mice of the same genotyping group and age-matched. Sorted HSPCs were cryopreserved in BAMBAKER Serum-free cell freezing medium (Wako Chemicals).

extract_protocol:
Cells were defrosted, washed twice in PBS and 50,000 viable HSPCs were then processed following the OMIM-ATAC-Seq protocol from Corces et al., Nature Methods 2017 with a dead cell pre-cleanup step with DNase I (Worthington cat#LS002007, 30 min at 37°C) followed by two cold PBS washes.
Libraries were prepared utilizing 2xTD buffer (15027866, Illumina) and Robust Tn5 Transposase (EMQZ1422, Creative Biogene) and cleaned up with a Zymo DNA Clean and Concentrator-5 kit (cat#D4014). OMIM-ATAC-Seq libraries were amplified with a total of 11 PCR cycles with ATAC-Seq primers (Buenrostro et al., 2015 (PMID: 25559105).
Paired-End, 100bp sequenced on an Illumina NOVASeq.

value: p300 Tet2 Knockout

tag: cell type

value: HSPCs


title: neutrophil WT rep1


title: Patient_WholeBlood_rep2


title: Pc_2_4606.E

value: 28 days post seed inoculation

value: 100µM Pi MS-Agar


title: PFC_AAVGFP3_GlyGCC


title: HealthyDonor_WholeBlood_Het_rep1


title: P300KO_TET2KO_ATACseq_Rep3


title: Pc_1_4606.D


title: PFC_AAVNsun2_4_GlyGCC


title: asthenozoospermia_58493

type: RNA

city: Prague

first: Lukáš

middle: Farhád

last: Mirchi

state: Czech Republic

address: Albertov 4

department: First Faculty of Medicine

country: Czech Republic

institute: Charles University

description: Gene expression data from sperm.

hyb_protocol: labelling was perfomermed using GeneAtlas® WT Expression Kit User Manual

scan_protocol: GeneChips were scanned using the GeneAtlas® Imaging station with GeneAtlas®Instrument Control Software 2.0.0.460

data_processing: The data were analyzed with PARTEK Genomics Suite 6.6 (Partek, Inc., Chesterfield, MO, USA) using GC-MRA as normalization method.

label: biotin

source_name: sperm sample with asthenozoospermia

extract_protocol: RNA extraction. Fresh sperm samples were resuspended and stored in RNAlater solution. Shipping was at room temperature with subsequent storage at -80°C. Immediately after thawing at room temperature, the samples were centrifuged at 16,000 x g for 10 minutes at 4°C The cell pellet was lysed by 1 ml Trizol (Invitrogen, Carlsbad, CA, USA). After chloroform extraction, the supernatant was mixed 1:1 with 96% ethanol and applied to RNeasy spin columns (Qiagen, Germantown, MD, USA). DNase I (Qiagen) was applied to the column according to the manufacturer´s protocol. Washing the column and DNA elution was according to the manufacturer´s protocol. DNase treatment or double column purification is necessary for removal of degraded DNA, which cannot be achieved by standard protocol.

tag: subject status

value: infertile; asthenozoospermia

tag: tissue/cell type

value: sperm


title: asthenozoospermia_60998

description: Gene expression data from sperm.

label_protocol: labelling was perfomermed using GeneAtlas® WT Expression Kit User Manual


title: asthenozoospermia_61186

description: Gene expression data from sperm.


title: PFC_AAVGFP1_GlyGCC

value: Prefrontal cortex

value: WT C57BL/6, AAV-GFP injection


title: LOCE_2_tyrosine

city: Leuven

first: Jasper

last: Wouters

address: ON IV Herestraat 49 - bus 602

country: Belgium

institute: KU Leuven - VIB

description:
raw_counts_tyrosine.tsv
norm_counts_tyrosine.tsv

data_processing:
RNA-seq reads were cleaned using fastq-mcf (ea-utils) and mapped to the genome (hg19) using STAR. Read counts per gene were obtained from the aligned reads using htseq-count. DESeq2 was used for normalization and differential gene expression analysis.
Genome_build: hg19
Supplementary_files_format_and_content: count matrix: raw count matrix as generated by htseq-count
Supplementary_files_format_and_content: normalized count matrix: count matrix normalized wth DeSeq2 using a multi-factor design (including the sample variable).

source_name: primary cell cultures

growth_protocol: Melanoma biopsies were obtained from surgical procedures. Tumor tissues were cut to very small pieces, which were incubated overnight in a medium containing dispase, collagenase, and supplemented with penicillin G, kanamycin sulphate, streptomycin sulphate, and gentamycin at standard concentrations (100μg/ml). Then the detached cells were washed and seeded in culture flasks. Melanoma primary cultures were propagated in the following culture media: Ham’s-F10, Ham’s F10 supplemented with 100μM of tyrosine and RPMI1640 (Lonza). All of these culture media were supplemented with 10% heat-inactivated fetal calf serum, L-glutamine, penicillin, and streptomycin at standard concentrations (Thermo Fisher Scientific).  Cell cultures were kept in a humidified incubator with 5% CO2 at 37°C. Cell culture medium was renewed every 2–3 days. Once the cells were at or near confluence they were subcultured. Melanoma primary cultures were regularly checked for mycoplasma contamination using MycoAlert® Mycoplasma Detection Kit (Lonza).

extract_protocol:
Total RNA was extracted using the innuPREP RNA mini kit (Analytik Jena), according to the manufacturer’s instructions.
RNA-seq libraries were prepared according to the Illumina Truseq stranded mRNA sample preparation guide. Final libraries were pooled and sequenced on a HiSeq4000 (LOCE#1 and #2 in Ham’s F10 and Ham’s F10 with tyrosine; Illumina) and NextSeq500 (LOCE#1 and #2 in Ham’s F10 and RPMI1640; Illumina).

treatment_protocol: Melanoma primary cultures were propagated in Ham’s-F10 culture medium, Ham’s F10 supplemented with 100μM of tyrosine or RPMI1640.

tag: culture

tag: treatment

value: extra tyrosine added


title: Xu142T3

city: Linyi

first: Lichen

last: Wang

address: shuangling Rd, middle section

country: China

institute: Linyi University

data_processing:
SOAPnuke software used for filtering.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Gossypium hirsutum_NAU genome using HISAT2 v2.1.0.
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated. Expression levels of genes and transcripts were calculated using RSEM.
Genome_build: Gossypium hirsutum_NAU genome
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample ...

organism: Gossypium hirsutum

source_name: ovules

growth_protocol: Feild growth

extract_protocol:
Ovules were removed and frozen immediately in liquid nitrogen, total RNA were extracted with a modified guanidine thiocyanate method.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: -3 and -1 dpa

value: Xuzhou142 wild type


title: TET2KO_ATACseq_Rep3

value: Tet2 Knockout


title: TET2KO_ATACseq_Rep4


title: Xu142T2


title: LOCE_2_Ctrl

value: control for tyrosine


title: P300KO_ATACseq_Rep4


title: P300KO_ATACseq_Rep3


title: Xu142T1


title: Patient_WholeBlood_rep3

value: whole blood

value: Patient


title: PFC_AAVNsun2_1_GlyGCC

value: WT C57BL/6, AAV-Nsun2 injection

value: Adult

value: Bisulfite-treated total RNA


title: KO4_GlyGCC

source_name: Mouse cortex

value: Cortex

value: Nsun2 floxed, Camk2a-Cre pos.


title: Xu142flT3


title: WT4_GlyGCC

value: Nsun2 floxed, Camk2a-Cre neg.


title: WT_ATACseq_Rep4

value: WT

value: HSPCs


title: LOCE_1_tyrosine


title: Xu142flT2


title: LOCE_1_Ctrl


title: KO3_GlyGCC


title: WT_ATACseq_Rep3


title: Homo NC-iPSCs

city: Shenzhen

first: Minglin

last: Ou

address: No.1017, Dongmen North Road, Luohu District

department: Clinical Medical Research Center of The Second Clinical Medical College

institute: Jinan University

data_processing:
Clean reads were obtained by removing adapter dimers,, junk, low complexity reads, common RNA families (rRNA, tRNA, snRNA, snoRNA), and repeats in the NCBI GenBank, Repbase, and Rfam databases.
Clean reads then were gathered and mapped to the human reference genome (GRCh38).
Differential expression analysis
Genome_build: GRCH38
Supplementary_files_format_and_content: Excel files include normalized expression values for each Sample.

source_name: The normal control human iPSCs (NC-iPSCs)  that were induced from urine of healthy donor by the same methods were purchased from Cellapy Biotechnology (Beijing, China).

extract_protocol:
Total RNA was extracted from the ADO2-iPSCs and NC-iPSCs using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s methods.
The urine-derived iPSCs were used for small RNA sequencing  library preparation according to the manufacturer's instruction.

tag: age

value: normal control iPSCs

value: urine


title: WT3_GlyGCC


title: Homo ADO2-iPSCs

source_name: The disease-specific ADO2-iPSCs with the mutation of CLCN7 (R286W) generated from urine of the proband in our previous studies.


title: Patient_WholeBlood_rep1

value: Homozygous mutant


title: SW872control3

city: Beijing

first: Chunyi

last: Hao

address: No. 52 Fucheng Road, Haidian District

department: Department of Hepato-Pancreato-Biliary Surgery

institute: Peking University Cancer Hospital & Institute

data_processing:
The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped clean data to human genome with STAR version 2.7.1a
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: liposarcoma cells

growth_protocol: SW872 cells was cultured with RPMI-1640（10%FBS）

extract_protocol:
Cells were digested and RNA was harvested using Trizol reagent.Ultrapure RNA Kit (CW0581S, 50 preps) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols (Hieff NGS® Ultima Dual-mode RNA Library Prep Kit for Illumina®)

treatment_protocol: SW872 cells were treated with Apatinib(18μM) for 24 h

tag: cell line

value: liposarcoma


title: P300KO_TET2KO_ATACseq_Rep2

data_processing:
Base calling using Illumina RTA 2.4.11
ATAC-Seq chromatin accessible regions were determined using ENCODE pipeline standards (https://github.com/ENCODE-DCC/atac-seq-pipeline; git commit 2b693ab)
Sequencing indices were trimmed from merged fastq files using cutadapt (v1.9.1) and then aligned to mm10 using bowtie2 (v2.2.6).
After de-duplication, reads were tn5 shifted, replicate peaks were called, and fold enrichment signal files were generated using macs2 (v2.1.0).
Final peaks were determined using IDR (v2.0.4) of true replicates.
Genome_build: Encode: mm10_no_alt_analysis_set (ENCSR425FOI)
Supplementary_files_format_and_content: Bigwig files contain fold change signal over background generated from macs2.

value: p300 Tet2 Knockout


title: WT2_GlyGCC


title: P300KO_TET2KO_ATACseq_Rep1


title: siTRIM56_2

first: Qiangzu

last: Zhang

address: Nan Hai Da Dao Chuang Shi Ji Bin Hai Hua Yuan Building9 9A , Nanshan District, Shenzhen City, Guangdong Province

institute: Lemondata BioTechnology Limited

data_processing:
Illumina hiseq4000 used for basecalling.
Sequence reads were trimmed for adaptor sequence and 3'-end was trimmed by quality, reads were filtered by quality and mapped to GRCh37 using the HISAT2 software
mapping QC by samtools and picard software
Quantification was done by using Cufflinks to produce gene-level expression values (FPKMs)
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: breast cancer cell

growth_protocol: cells were cultured in DMEM with 10% FBS.

extract_protocol:
The total RNA was extracted from cells by the qiagen RNA exaction kit
Libraries were prepared according to Illumina's instructions accompanying the RNA Sample Kit (Part# 0801-0303).

treatment_protocol: cells were treated with 50nM siTRIM56 or sicontrol

tag: tumor stage

value: 15-18 passage

value: 50nM siTRIM56


title: siTRIM56_3


title: SW872control1


title: SW872control2


title: KO1_GlyGCC


title: TET2KO_ATACseq_Rep2

value: Tet2 Knockout


title: SW872apatinib3

value: Incubate with apatinib (18uM) for 24 hours


title: SW872apatinib2


title: PFC_CreKO3_GlyGCC

value: Prefrontal cortex

value: Nsun2 floxed, PFC AAV-Cre injection


title: WT1_GlyGCC

value: Adult

value: Bisulfite-treated total RNA


title: sicontrol_3

value: 50nM scramble siRNA


title: P300KO_ATACseq_Rep2

value: p300 Knockout


title: PFC_AAVGFP2_GlyGCC

value: WT C57BL/6, AAV-GFP injection


title: siTRIM56_1


title: Xu142flT1

value: -3 and -1 dpa


title: sicontrol_2


title: PIM1 2

first: Michael

last: Garabedian

state: NY

address: 550 First Avenue

department: Microbiology

institute: NYU School of Medicine

description: PIM1 over-expressing LNCaP cells cultured in complete media with 24 hrs doxycycline treatment.

data_processing:
Data was analyzed by Rosalind (https://rosalind.onramp.bio/), with a HyperScale architecture developed by OnRamp BioInformatics, Inc. (San Diego, CA).
Reads were trimmed using cutadapt. Quality scores were assessed using FastQC.
Reads were aligned using STAR.
Individual sample reads were quantified using HTseq and normalized via Relative Log Expression (RLE) using DESeq2 R library.
DEseq2 was also used to calculate fold changes and p-values and perform optional covariate correction.
Functional enrichment analysis of pathways, gene ontology, domain structure and other ontologies was performed using HOMER.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: LNCaP p57 VO and p57 PIM1 RNA Seq_rawCounts.txt
Supplementary_files_format_and_content: LNCaP p57 VO and p57 PIM1 RNA Seq_normalizedCounts.txt

source_name: LNCaP cells

growth_protocol: LNCaP cell lines were maintained in RPMI-1640 supplemented with 10% fetal bovine serum (FBS) (Hyclone; Fisher Scientific) and 1% penicillin-streptomycin (Cellgro; Mediatech, Inc.)

extract_protocol:
Total RNA was extracted using RNeasy (Qiagen).
Libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina with polyA selection.

treatment_protocol: Cells were treated with 500 ng/mL doxycycline to induce empty vector or PIM1 over-expression.

value: LNCaP

value: prostate cancer

tag: phenotype

value: PIM1 overexpression

value: Doxycycline 500 ng/mL 24 hr


title: sicontrol_1


title: PFC_CreKO2_GlyGCC

tag: strain


title: WT_ATACseq_Rep2

description: WT.IDR.narrowpeak

tag: genotype

value: WT

value: HSPCs


title: MYBoe line 24 replicate 3

city: Milano

first: Raul

last: Pirona

address: Via Alfonso Corti 12

country: Italy

institute: IBBA-CNR

data_processing:
trimming, BBDuk software (JGI)
Alignment, Spliced Transcripts Alignment to a Reference (STAR) software
Filteiring, HTSfilter package
Differential expression analysis, edgeR package
Genome_build: Cynara cardunculus, version CcrdV1, Accession number GCA_001531365
Supplementary_files_format_and_content: text files, raw and fpkm data

organism: Cynara cardunculus

source_name: callus

growth_protocol: Undifferentiated wild type (WT) friable calluses were induced from leaves of cardoon plants  (“Spagnolo” genotype), following the method described in (Figueiredo et al., 1987), and gently provided for this study from Dr. M. De Palma (CNR-IBBR). Calluses were grown on Gamborg B5 agar medium including vitamins (Duchefa Biochemie, #G0209, www.duchefa-biochemie.com), supplied with 1 mg/L 2,4-dichlorophenoxyacetic acid (2,4-D), 1 mg/L adenine, 0.1 mg/L kinetin, 3% (w/v) sucrose, 7,5% (w/v) agar, adjusted to pH = 5.8. WT calluses were grown in the dark at 25°C, sub-cultured approximately every 30 days. Cell suspension cultures were started by inoculating 1.5 g of friable callus in a 250 mL Erlenmeyer flask containing 50 mL of liquid medium and kept on a gyratory shaker at 100 rpm in the dark at 25°C. To determine the cell growth, CVS was measured using 250 mL Erlenmeyer flasks with a graduated beak. This method has been shown to be a rapid and non-destructive one for the routine estimation of cell biomass, given how CVS is highly correlated with the fresh weight of cells (Blom et al., 1992). All measures were performed on biological triplicates.

extract_protocol:
For RNA extraction, 200 mg of callus were grinded under liquid nitrogen, lysed/homogenized with 1 mL of TRIzol (Thermo Fisher Scientific, #15596026) and, after addition of 0.2 mL of Phenol:Chloroform:Isoamyl-alcohol (25:24:1) and centrifugation (10 min, 13000 x g), the RNA was precipitated from the aqueous phase with 1 volume of isopropanol. Total RNA was treated using the Ambion TURBO DNA-free DNase (Thermo Fisher Scientific, #AM1907) and then reverse transcribed to cDNA using the High-Capacity cDNA Reverse Transcription Kit (Thermo Fisher Scientific, #4368814) according to the manufacturers’ instructions.
Sequencing libraries were prepared according to the manufacturer’s instructions using the Illumina TruSeq RNA Sample Prep kit and sequenced on NovaSeq 6000 Sequencing System (Illumina, www.illumina.com) to obtain 15-22M 150 bp paired-end reads per sample.

treatment_protocol: Cell suspensions of WT cardoon were set in 250 mL sterile flasks and kept in the dark at 25°C in gentle agitation, until the start of exponential growth (5 days); next, 5 mL of cell suspension and 10 mL of fresh liquid medium were added to a 100 mL sterile flask, and agitated for 5 additional days. Meanwhile, a single colony of recombinant Agrobacterium was used to start a 50 mL inoculum in LB medium, which was grown at 28°C with 200 rpm shaking until OD600 = 0.70 – 0.90 (approximately 48 h), then pelleted (15 min at 2000 x g) and re-suspended in Gamborg B5 liquid medium to a final OD600 = 0.80-0.85. Co-cultivation was performed adding 1 mL of Agrobacterium cells to each cell suspension in presence of 400 M acetosyringone (Sigma Aldrich, #D134406, www.sigmaaldrich.com), leaving flasks in the dark at 25°C in gentle agitation for 48 h. Afterwards, pelleted cells were washed three times with fresh Gamborg B5 medium supplied with 200 mg/L CFX and 10 mg/L PPT before spreading them on sterile filter paper to remove the liquid excess; cells were then moved to solid selective medium containing CFX and PPT. After 30 days, emerging resistant calluses were individually transferred to new plates and separately sub-cultured approximately every 21 days to fresh selective medium. PCR was used to confirm the presence of the transgene and to evaluate residual Agrobacterium contamination using AGL1 and EHA105 colonies as positive controls (Haas et al., 1995).

value: calus

tag: transgenic

value: Over-expressing MYB4


title: PIM1 1


title: PFC_GFP2_GlyGCC

tag: tissue type

value: Nsun2 floxed, PFC AAV-GFP injection

tag: developmental stage


title: PFC_CreKO1_GlyGCC

value: Prefrontal cortex

tag: molecule


title: MYBoe line 24 replicate 2

tag: tissue


title: VO 3

description: Control LNCaP cells cultured in complete media with 24 hrs doxycycline treatment.

value: control


title: WT_ATACseq_Rep1

description: WT.IDR.narrowpeak


title: WT_21d_full liver [022_41]

city: Copenhagen

first: Lars

middle: Roed

last: Ingerslev

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

country: Denmark

institute: Copenhagen University

data_processing:
STAR v2.7.2b was used to align sequence reads onto the GRCm38 mouse genome assembly, with the GENCODE version M22 gene model
reads were summarized onto genes by featureCounts v1.6.4 with the same gene model as when mapping, counting only fragments where both ends of the fragment were aligned
The quasi-likelihood tests found in the R package edgeR v3.26.0  was used for differential expression testing, using a two-way model of the form expression ~ Genotype * Age
Gene Ontology and Reactome enrichments were found by CAMERA
Genome_build: mm10
Supplementary_files_format_and_content: CSV file with counts of GENCODE vM22 genes

source_name: WT_21d_full liver

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Qiagen) according to the manufacturer’s protocol. Total RNA sequencing libraries were prepared using the Illumina TruSeq Stranded total RNA Gold protocol (Illumina). The total RNA (500ng) was depleted of rRNA by RiboZero beads, fragmented, and cDNA was synthesized using SuperScript III Reverse Transcriptase (Thermo Fisher Scientific). cDNA was adenylated to prime for adapter ligation and after a clean-up using AMPure beads (Beckman coulter), DNA fragments were amplified using PCR followed by a final clean-up.
Libraries were quality-controlled using a Bioanalyzer instrument (Agilent Technologies) and subjected to 51-bp paired-end sequencing on a NovaSeq 6000 system (Illumina). A total of 1.1 billion reads were generated.

tag: strain background

value: C57BL/6JBomTac (PMID 31320478)

tag: genotype/variation

value: wild-type (WT)

tag: Sex

value: female

value: 21 days

value: whole liver


title: VO 2

tag: cell type


title: TET2KO_ATACseq_Rep1

value: Tet2 Knockout


title: MYBoe line 24 replicate 1


title: PFC_GFP3_GlyGCC

value: Adult

value: Bisulfite-treated total RNA


title: PFC_GFP1_GlyGCC


title: KO_21d_full liver [022_40]

source_name: KO_21d_full liver

value: hepatocyte-specific NAMPT knockout (KO)


title: KO2_GlyGCC

value: Cortex

value: Nsun2 floxed, Camk2a-Cre pos.


title: MYBoe line 18 replicate 3


title: SW872apatinib1

value: liposarcoma

value: Incubate with apatinib (18uM) for 24 hours


title: WT3_YAMAT

description:
YAMATseq processed data.xlsx
4242_YAMAT

data_processing:
Library strategy: YAMAT-seq
Raw sequencing reads were processed using cutadapt to trim adaptor sequences and UMItools to extract UMIs from reads and perform deduplication.  Paired end reads were merged using Pear and differential expression analysis was performed using Deseq2, providing normalized counts for each sample.

extract_protocol:
5ug total RNA was deacetylated to remove amino acids from 3’ ends and demethylated to remove m1A, m1C, and m3C modifications using a proprietary demethylation mix (Arraystar, Inc).  40um of YAMAT forked linkers (Y-3-AD_UMI: 5'-P-GTATCCAGTNNNNTGGAATTCTCGGGTGCCAAGG-3'-ddC; Y-5-AD_UMI: 5’-GTTCAGAGTTCTACAGTCCGACGATCNNNNACTGGATACTGrGrN-3’) were then incubated with pure demethylated and deacetylated RNA followed by addition of 10X annealing buffer (50 mM Tris HCl pH 8, 100 mM MgCl2, 5 mM EDTA) and then overnight incubation with T4 RNA ligase 2.  Linker-ligated RNA was then incubated with RT Primer (TruSeq Small RNA Library Prep Kit, Illumina) and reverse transcription was performed with Superscript III RT (Invitrogen) followed by bead purification.  Libraries were amplified using Phusion Hotstart II Polymerase (Thermo Scientific) with primers and indexes from the TruSeq Small RNA kit (Illumina) for 11 PCR cycles.  Amplified libraries were then bead-purified and run on the Agilent Bioanalyzer for confirmation of library size and quantified with the Qubit Fluorometer (Invitrogen).
total RNA was extracted from mouse cortex using Trizol extraction and quantity was measured on Qubit fluorometer.  Quality of total RNA was checked on the Agilent Bioanalyzer using the RNA 6000 Pico Kit

value: Nsun2 floxed, Camk2a-Cre neg.

value: mature tRNA


title: VO 1

value: LNCaP

value: prostate cancer

value: Doxycycline 500 ng/mL 24 hr


title: KO4_YAMAT

description:
YAMATseq processed data.xlsx
4241_YAMAT


title: WT_21d_full liver [022_39]

value: C57BL/6JBomTac (PMID 31320478)

value: wild-type (WT)


title: MYBoe line 18 replicate 1

value: calus

value: Over-expressing MYB4


title: MYBoe line 18 replicate 2


title: KO_21d_full liver [022_38]

value: female

value: 21 days

value: whole liver


title: Vector pS213 AR 3

description: Control LNCaP cells cultured in complete media with 24 hrs doxycycline treatment, pS213 AR ChIP.

data_processing:
Data was analyzed by ROSALIND® (https://rosalind.onramp.bio/), with a HyperScale architecture developed by OnRamp BioInformatics, Inc. (San Diego, CA).
Reads were trimmed using cutadapt1. Quality scores were assessed using FastQC2. Reads were aligned to the Homo sapiens genome build hg19 using bowtie23.
Per-sample quality assessment plots were generated with HOMER4 and Mosaics5. Peaks were called using MACS26 (with input/IgG controls background subtracted, if provided).
Peak overlaps and differential binding were calculated using the DiffBind R library7. Differential binding was calculated at gene promoter sites.
Read distribution percentages, identity heatmaps, and FRiP plots were generated as part of the QC step using ChIPQC R library8 and HOMER.
HOMER was also used to generate known and de novo motifs and perform functional enrichment analysis of pathways, gene ontology, domain structure and other ontologies.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: bigWig files

extract_protocol:
Cell pellets were resuspended in nuclei isolation buffer (50 mM Tris–pH 8.0, 60 mM KCl, 0.5% NP40), nuclei collected, and resuspended in sonication buffer (RIPA buffer). Samples were sonicated in TPX PMP tubes (Diagenode) for 60 min (30 sec. on, 30 sec. off) in a Bioruptor sonicator (Diagenode). Inputs (10%) were collected and supernatants were then incubated overnight with the corresponding antibodies pre-incubated with Protein A and Protein G Dynabeads (Invitrogen). Immunocomplexes were then washed and cross-linking reversed overnight at 65 °C with 5 M NaCl. DNA was isolated with the Zymo Chip DNA Clean and Concentrator kit (Zymo Research).
Libraries were generated using NEBNext Ultra II DNA Library Prep Kit.

treatment_protocol: Cells treated with doxycycline (500 ng/mL) for 24 hours.

value: control

tag: chip antibody

value: pS213 AR (homemade)


title: P300KO_ATACseq_Rep1

value: p300 Knockout

value: HSPCs


title: KO_21d_full liver [022_37]

value: hepatocyte-specific NAMPT knockout (KO)


title: Vector pS213 AR 2

tag: treatment


title: MYBoe line 1 replicate 3


title: KO3_YAMAT

description:
YAMATseq processed data.xlsx
4236_YAMAT

value: Cortex

value: Nsun2 floxed, Camk2a-Cre pos.

value: Adult


title: Vector pS213 AR 1

value: LNCaP

value: prostate cancer


title: KO_12d_full liver [022_36]

source_name: KO_12d_full liver

value: C57BL/6JBomTac (PMID 31320478)

tag: age

value: 12 days


title: KO2_YAMAT

description:
YAMATseq processed data.xlsx
4222_YAMAT

value: mature tRNA


title: Vector MsRb IgG 3

description: Control LNCaP cells cultured in complete media with 24 hrs doxycycline treatment, IgG Control for AR.

tag: cell line

value: Doxycycline 500 ng/mL 24 hr

value: IgG mouse (Santa Cruz # sc-2025) and IgG rabbit (Sigma Aldrich, cat # 12-370)


title: MYBoe line 1 replicate 2

value: calus

value: Over-expressing MYB4


title: KO_12d_full liver [022_35]

value: female

value: whole liver


title: Vector MsRb IgG 2

value: control


title: MYBoe line 1 replicate 1


title: Widl type Replicate 3

value: Control


title: KO1_YAMAT

description:
YAMATseq processed data.xlsx
4217_YAMAT


title: WT_12d_full liver [022_33]

source_name: WT_12d_full liver

value: wild-type (WT)


title: WT1_YAMAT

description:
YAMATseq processed data.xlsx
4219_YAMAT

value: Cortex

value: Nsun2 floxed, Camk2a-Cre neg.


title: WT_12d_full liver [022_34]


title: Widl type Replicate 1


title: Widl type Replicate 2


title: Vector Input 3

description: Control LNCaP cells cultured in complete media with 24 hrs doxycycline treatment, input.

value: None (Input)


title: KO_6d_full liver [022_31]

source_name: KO_6d_full liver

value: hepatocyte-specific NAMPT knockout (KO)

value: 6 days


title: Vector MsRb IgG 1

value: LNCaP

value: prostate cancer


title: At-Ps_3_4426.S

description:
Pair of genomes mapped: Ps+At
Ps_fungalTranscriptome.csv
Ps_plantTranscriptome.csv

data_processing:
Raw-RNASeq reads were trimmed with Trimmomatic and parameters TRAILING:20 AVGQUAL:20 HEADCROP:10 MINLEN:100
Trimmed reads were mapped onto pairs of reference genomes using HiSat2
Per-gene read counts were retrieved from HiSat2 alignments using FeatureCounts
RPKM values were calculated from FeatureCounts data
Differential gene expression analyses were conducted with DESeq2, independently for plant and fungal transcriptomes
Genome_build: TAIR10.1
Genome_build: https://mycocosm.jgi.doe.gov/Chame1/Chame1.home.html
Genome_build: https://mycocosm.jgi.doe.gov/Parch1/Parch1.home.html
Genome_build: https://mycocosm.jgi.doe.gov/Phapo1/Phapo1.home.html
Genome_build: https://mycocosm.jgi.doe.gov/Truan1/Truan1.home.html
Genome_build: https://mycocosm.jgi.doe.gov/Macpha1/Macpha1.home.html
Genome_build: https://mycocosm.jgi.doe.gov/Zalva1/Zalva1.home.html
Supplementary_files_format_and_content: Files '_fungalTranscriptome.csv’ correspond to the DESeq2 differential expression analysis of fungal genes in planta vs. on medium. This file also provide RPKM values in control (mycelium grown on medium) and test (fungus in planta) conditions
Supplementary_files_format_and_content: Files '_plantTranscriptome.csv’ correspond to the DESeq2 differential expression analysis of  A. thaliana genes mock-inoculated vs. inoculated with mycelium. This file also provide RPKM values in control (mock-treated plants) and test (plant inoculated with mycelium) conditions

organism:
Arabidopsis thaliana
Phaeosphaeria sp.

source_name: roots,mycelium

value: 28 days post seed inoculation

tag: culture medium

value: 100µM Pi MS-Agar

tag: inoculation

value: Mycelium-inoculated seeds


title: Vector Input 2

tag: phenotype

value: Doxycycline 500 ng/mL 24 hr


title: WT2_YAMAT

description:
YAMATseq processed data.xlsx
4238_YAMAT

tag: strain

value: Adult

value: mature tRNA


title: miRNA-seq_DP_4

city: Ithica

first: Praveen

last: Sethupathy

address: Cornell University College of Veterinary Medicine, Box 17

institute: Cornell University

description:
HepG2-GFP cells that serve as a control
FLC-DP_DESeq_normalized_miR_counts.csv

data_processing:
Sequencing was aligned and quantiitated using miRquant2.0 (small RNAseq) or aligned and quantified using STAR/Salmon.
Both sequencing types were processed with DESeq2.
Genome_build: hg19 (small RNAseq) or hg38 (RNAseq)
Supplementary_files_format_and_content: DESeq normalized counts

source_name: FLC-DP cell line sample #4

extract_protocol: Libraries were prepared according to the TriLink CleanTag Small RNA Library Preparation Kit protocol

value: liver

tag: molecule subtype

value: small RNA


title: miRNA-seq_DP_2

source_name: FLC-DP cell line sample #2


title: Vector Input 1

value: control


title: KO_6d_full liver [022_30]

value: C57BL/6JBomTac (PMID 31320478)

value: female

value: whole liver


title: KO_12d_full liver [022_32]

value: 12 days


title: miRNA-seq_DP_3

source_name: FLC-DP cell line sample #3


title: At-Ps_2_4426.K

extract_protocol:
Total RNA was extracted from plant roots or mycelium grown on medium using Qiagen RNEasy Plant Mini Kit
An RNAseq library was prepared with the NEBNext Ultra™ II Directional RNA Library Prep Kit for Illumina (New England Biolabs) and then sequenced in single read mode on a HiSeq 3000 system


title: At-Ps_1_4426.C


title: Vector AR 2

description: Control LNCaP cells cultured in complete media with 24 hrs doxycycline treatment, AR ChIP.

value: AR 441 mouse monoclonal (Santa Cruz, cat # sc-7305) and AR D6F11 rabbit monoclonal (Cell Signaling Technology, cat # 5153)


title: KO_6d_full liver [022_29]

value: hepatocyte-specific NAMPT knockout (KO)

value: 6 days


title: Vector AR 3

value: LNCaP

value: prostate cancer


title: miRNA-seq_Control_4

source_name: Control for FLC-DP cell line sample #4


title: WT_6d_full liver [022_28]

source_name: WT_6d_full liver

value: wild-type (WT)


title: At-Pc_2_4426.J

description:
Pair of genomes mapped: Pc+At
Pc_fungalTranscriptome.csv
Pc_plantTranscriptome.csv

organism:
Arabidopsis thaliana
Paraphoma chrysanthemicola

value: 28 days post seed inoculation

value: 100µM Pi MS-Agar

value: Mycelium-inoculated seeds


title: miRNA-seq_Control_2

source_name: Control for FLC-DP cell line sample #2


title: At-Pc_3_4426.R


title: WT_6d_full liver [022_27]


title: Vector AR 1

value: Doxycycline 500 ng/mL 24 hr


title: miRNA-seq_Control_3

source_name: Control for FLC-DP cell line sample #3

value: liver


title: Vector 20 Rb IgG 3

description: Control LNCaP cells cultured in complete media with 24 hrs doxycycline treatment, IgG Control for pS213 AR.

value: IgG rabbit (Sigma Aldrich, cat # 12-370)


title: At-Pc_1_4426.B


title: Vector Abcam 14-3-3 z

description: Control LNCaP cells cultured in complete media with 24 hrs doxycycline treatment,14-3-3 ζ ChIP.

value: control


title: WT_3d_full liver [022_26]

source_name: WT_3d_full liver

value: C57BL/6JBomTac (PMID 31320478)

value: 3 days


title: miRNA-seq_DP_1

source_name: FLC-DP cell line sample #1

value: small RNA


title: WT_3d_full liver [022_25]

value: female

value: whole liver


title: miRNA-seq_Control_1

source_name: Control for FLC-DP cell line sample #1


title: WT_3d_full liver [022_24]


title: Vector 20 Rb IgG 2

source_name: LNCaP cells


title: KO_3d_full liver [022_23]

source_name: KO_3d_full liver

value: hepatocyte-specific NAMPT knockout (KO)


title: miRNA-seq_FLC90_T

description:
Fibrolamellar tissue biopsy from a fibrolamellar carcinoma patient
DESeq_normalized_miR_counts.csv

source_name: Fibrolamellar carcinoma tissue sample #26


title: miRNA-seq_FLC89_T

source_name: Fibrolamellar carcinoma tissue sample #25


title: miRNA-seq_FLC90_N

description:
Non-malignant liver tissue biopsy from a fibrolamellar carcinoma patient
DESeq_normalized_miR_counts.csv

source_name: Non-malignant liver tissue #7


title: Vector 20 Rb IgG 1


title: KO_3d_full liver [022_22]


title: DNeg_rep2

city: Los Angeles

first: Juliet

last: Girard

state: CA

address: 610 Charles E Young Dr E

institute: University of California Los Angeles

description:
Double Negative biological replicate 2
dnlsDNeg2_S11

data_processing:
Illumina software for basecalling
Sequencing data was analyzed using Partek Flow, a web-based software platform. Sequences were aligned to the Drosophila melanogaster reference genome r6.22 (Flybase) using STAR aligner with default parameters. Read counts were normalized by counts per million (CPM). Differential genes expression analysis was performed using ANOVA with a fold change cutoff of 2 and FDR<0.05 (see Supplementary file 3 Tables 1 and 2).
Genome_build: r6.22

organism: Drosophila melanogaster

source_name: domeMESO-GFP.nls HmlΔ-DsRed.nls_DNeg

growth_protocol: 20 virgin females and 10 males were mated in each vial at 25 degrees C. Eggs were laid in the vials for a 6 hour and then adults were transferred to a new vial. Vials were placed back at 25 degrees for 90-96 hours until larvae reached early thrid instar. Larvae were thoroughly washed in DEPC-treated water prior to dissection.

extract_protocol:
Lymph glands were dissected out of early 3rd instar larvae, their anterior lobes were removed, and the primary lobes were transferred to a watchglass filled with dissecting buffer on ice. After dissection, the lymph glands were dissociated as previously described with some modifications (Harzer et al. 2013; Khan et al. 2016). After being washed with MDS buffer twice, these tissues were transferred to 1.5 mL DNA LoBind tubes (Eppendorf) and incubated with 200 µL of dissociation solution containing 1 mg/mL of papain (Sigma, P4762) and 1 mg/mL of collagenase (Sigma, C2674) in Schneider’s medium. They were dissociated for 15 minutes in a shaking incubator at 25°C, 300 rpm. Next, 500 µL of cold Schneider’s medium was added and the suspension was gently pipetted up and down using a low-binding 1000 µL tip (Olympus Plastics) 20 times for mechanical dissociation. After centrifugation at 3000 rpm for 5 minutes, cells were resuspended and washed with 500 µL of 1X PBS (Corning, MT21040CV) containing 0.04% of UltraPure BSA (Invitrogen, AM2616) and then passed through a 35 micrometer cell strainer (Falcon 352235). , Dissociated, live lymph gland cells were sorted using the BD FACSARIA-H. Gates and compensation were based on single color controls. Cells were sorted into 300 µL of DNA/RNA Shield (Zymo) in DNA LoBind tubes and frozen at -80°C prior to RNA extraction. Total RNA was extracted from each sample using the Quick-RNA Microprep Kit (Zymo). RNA quality control was performed using the Agilent 4150 TapeStation system.
3' mRNA capture: cDNA libraries were prepared using KAPA Stranded mRNA-seq kit (KAPA Biosystems)

treatment_protocol: Experiment was done on untreated wild-type larvae.

tag: line

value: domeMESO-GFP.nls Hml{delta}-DsRed.nls

value: 90-96 hours after egg lay (25 degrees C)

tag: tissue/cell type

value: lymph gland blood cells

tag: cell population

value: Double Negative


title: DNeg_rep3

description:
Double Negative biological replicate 3
dnlsDNeg3_S12


title: WT_21d_full liver [022_21]

source_name: WT_21d_full liver

value: wild-type (WT)

value: 21 days

tag: tissue


title: Vector 10 Rb IgG

description: Control LNCaP cells cultured in complete media with 24 hrs doxycycline treatment, IgG Control for 14-3-3 ζ.

value: LNCaP

value: prostate cancer


title: miRNA-seq_FLC89_N

source_name: Non-malignant liver tissue #6

value: liver


title: DNeg_rep1

description:
Double Negative biological replicate 1
dnlsDNeg1_S10


title: PIM1 pS213 AR 3

description: PIM1 over-expressing LNCaP cells cultured in complete media with 24 hrs doxycycline treatment, pS213 AR ChIP.

value: PIM1 over-expression

value: Doxycycline 500 ng/mL 24 hr

value: pS213 AR (homemade)


title: CZ_rep3

description:
CZ biological replicate 3
dnlsDsRed3_S6

source_name: domeMESO-GFP.nls HmlΔ-DsRed.nls_CZ

value: cortical zone (CZ)


title: miRNA-seq_FLC88_T

source_name: Fibrolamellar carcinoma tissue sample #24

value: small RNA


title: CZ_rep1

description:
CZ biological replicate 1
dnlsDsRed1_S4


title: PIM1 pS213 AR 2


title: PIM1 pS213 AR 1


title: WT_21d_full liver [022_20]

tag: strain background

value: C57BL/6JBomTac (PMID 31320478)

value: female


title: PIM1 MsRb IgG 3

description: PIM1 over-expressing LNCaP cells cultured in complete media with 24 hrs doxycycline treatment, IgG control for AR.

value: IgG mouse (Santa Cruz # sc-2025) and IgG rabbit (Sigma Aldrich, cat # 12-370)


title: miRNA-seq_FLC85_T

source_name: Fibrolamellar carcinoma tissue sample #23


title: PIM1 MsRb IgG 2


title: IZ_rep2

description:
IZ biological replicate 2
dnlsDPos2_S8

source_name: domeMESO-GFP.nls HmlΔ-DsRed.nls_IZ

value: domeMESO-GFP.nls Hml{delta}-DsRed.nls

value: intermediate zone (IZ)


title: miRNA-seq_FLC84_T

source_name: Fibrolamellar carcinoma tissue sample #22


title: KO_21d_full liver [022_18]

description:
Failed QC
022_18_S17

source_name: KO_21d_full liver

tag: genotype/variation

value: hepatocyte-specific NAMPT knockout (KO)

value: whole liver


title: KO_21d_full liver [022_17]

description:
Failed QC
022_17_S16

tag: Sex


title: IZ_rep1

description:
IZ biological replicate 1
dnlsDPos1_S7

value: 90-96 hours after egg lay (25 degrees C)

value: lymph gland blood cells


title: WT_12d_full liver [022_16]

source_name: WT_12d_full liver

value: wild-type (WT)

value: 12 days


title: miRNA-seq_FLC83_T

source_name: Fibrolamellar carcinoma tissue sample #21

value: liver


title: PIM1 Input 3

description: PIM1 over-expressing LNCaP cells cultured in complete media with 24 hrs doxycycline treatment, input.

value: LNCaP

tag: cell type

value: prostate cancer

value: PIM1 over-expression

value: None (Input)


title: miRNA-seq_FLC83_N

source_name: Non-malignant liver tissue #4

value: small RNA


title: MZ_rep3

description:
MZ biological replicate 3
dnlsGFP3_S3

source_name: domeMESO-GFP.nls HmlΔ-DsRed.nls_MZ

value: medullary zone (MZ)


title: PIM1 MsRb IgG 1

source_name: LNCaP cells

value: Doxycycline 500 ng/mL 24 hr

tag: chip antibody


title: CZ_rep2

description:
CZ biological replicate 2
dnlsDsRed2_S5

value: cortical zone (CZ)


title: WT_12d_full liver [022_14]

value: C57BL/6JBomTac (PMID 31320478)

value: female


title: WT_12d_full liver [022_15]


title: MZ_rep2

description:
MZ biological replicate 2
dnlsGFP2_S2

value: domeMESO-GFP.nls Hml{delta}-DsRed.nls


title: PIM1 Input 2

tag: treatment


title: PIM1 Input 1


title: miRNA-seq_FLC87_N

source_name: Non-malignant liver tissue #5


title: IZ_rep3

description:
IZ biological replicate 3
dnlsDPos3_S9

tag: age

value: intermediate zone (IZ)


title: miRNA-seq_FLC82_T

source_name: Fibrolamellar carcinoma tissue sample #20


title: WT_21d_full liver [022_19]

value: 21 days

value: whole liver


title: MZ_rep1

description:
MZ biological replicate 1
dnlsGFP1_S1

value: 90-96 hours after egg lay (25 degrees C)

value: lymph gland blood cells


title: miRNA-seq_FLC58L_T

source_name: Fibrolamellar carcinoma tissue sample #19

value: liver


title: miRNA-seq_FLC57_T

source_name: Fibrolamellar carcinoma tissue sample #18


title: KO_12d_full liver [022_13]

source_name: KO_12d_full liver

value: hepatocyte-specific NAMPT knockout (KO)

value: 12 days


title: KO_12d_full liver [022_12]


title: PIM1 AR 3

description: PIM1 over-expressing LNCaP cells cultured in complete media with 24 hrs doxycycline treatment, AR ChIP.

tag: cell line

value: LNCaP

value: prostate cancer

value: PIM1 over-expression

value: AR 441 mouse monoclonal (Santa Cruz, cat # sc-7305) and AR D6F11 rabbit monoclonal (Cell Signaling Technology, cat # 5153)


title: KO_12d_full liver [022_11]


title: PIM1 AR 2

value: Doxycycline 500 ng/mL 24 hr


title: PIM1 AR 1


title: miRNA-seq_FLC56_N

source_name: Non-malignant liver tissue #3

value: small RNA


title: WT_6d_full liver [022_10]

source_name: WT_6d_full liver

value: C57BL/6JBomTac (PMID 31320478)

value: wild-type (WT)

value: 6 days


title: PIM1 Abcam 14-3-3 z

description: PIM1 over-expressing LNCaP cells cultured in complete media with 24 hrs doxycycline treatment, 14-3-3 ζ ChIP.


title: miRNA-seq_FLC55_T

source_name: Fibrolamellar carcinoma tissue sample #16


title: WT_6d_full liver [022_8]

value: female


title: PIM1 20 Rb IgG 3

description: PIM1 over-expressing LNCaP cells cultured in complete media with 24 hrs doxycycline treatment, IgG control for pS213 AR.

value: IgG rabbit (Sigma Aldrich, cat # 12-370)


title: miRNA-seq_FLC34_YROP

source_name: Fibrolamellar carcinoma tissue sample #15


title: KO_6d_full liver [022_7]

source_name: KO_6d_full liver

value: whole liver


title: KO_6d_full liver [022_6]


title: miRNA-seq_FLC34_PMVV

source_name: Non-malignant liver tissue #2


title: PIM1 20 Rb IgG 1


title: miRNA-seq_FLC33_NYTS

source_name: Fibrolamellar carcinoma tissue sample #14


title: WT_3d_full liver [022_5]

source_name: WT_3d_full liver

value: 3 days


title: miRNA-seq_FLC56_T

source_name: Fibrolamellar carcinoma tissue sample #17


title: KO_3d_full liver [022_4]

source_name: KO_3d_full liver


title: miRNA-seq_FLC32_UOTX

source_name: Fibrolamellar carcinoma tissue sample #13


title: PIM1 10 Rb IgG

description: PIM1 over-expressing LNCaP cells cultured in complete media with 24 hrs doxycycline treatment, IgG control for 14-3-3 ζ.

source_name: LNCaP cells


title: miRNA-seq_FLC31_OTOK

source_name: Fibrolamellar carcinoma tissue sample #12


title: PBMC from sample HB250

city: Barcelona

first: Ferran

last: Aguilar

state: Barcelona

address: Travessera de Gràcia, 11

country: Spain

institute: EF-CLIF

description: PBMC from sample HB250

data_processing:
enumerated and resuspended in RPMI 1640 medium containing penicillin (100 U/ml),
streptomycin (100 U/ml) and L-glutamine (4 mM) without fetal bovine serum (FBS).
Genome_build: Human genome (hg38)
Supplementary_files_format_and_content: RSEM expected counts

source_name: PBMC

extract_protocol:
PBMCs and PMNs were isolated from 20 ml of EDTA blood. Blood samples were centrifuged at
200 g for 10 min to collect plasma and sedimented cells were diluted with DPBS -/- up to a volume
of 20 ml. Diluted blood was layered over 13.3 ml of Ficoll-Hypaque and centrifuged at 500 g for
25 min with the break off. PBMCs were obtained from the mononuclear cell layer, washed with
Dulbecco’s PBS -/- and centrifuged again at 400 g for 5 min. Pelleted PMNs were incubated with

value: PBMC

tag: disease state

value: HV


title: KO_3d_full liver [022_3]

value: hepatocyte-specific NAMPT knockout (KO)


title: PBMC from sample HB249

description: PBMC from sample HB249


title: Mv1Lu cells cholesterol depleted rep2

city: Tel Aviv

first: Guy

last: Shapira

address: Chaim Levanon 30

country: Israel

institute: Tel Aviv University

description:
raw_counts.csv
cd2

data_processing:
Trimmed and filtered using fastp 0.20.1 (default parameters)
Aligned to mink genome assembly (NNQGG.v01) using STAR 2.7.2a
Normalization and differential expression analysis were performed in R 4.0.3 using the package DESeq2 1.30.1
Genome_build: NNQGG.v01
Supplementary_files_format_and_content: Normalized gene expression files, normalized by DESeq2
Supplementary_files_format_and_content: Raw count file (supplementry) detailing reads per gene (STAR aligner output)

organism: Neogale vison

source_name: Lung

growth_protocol: According to the ATCC instructions.

extract_protocol:
RNA was harvested from the cells using EZ-RNA (cat. #20-400-100, Biological Industries Beit Haemek).
Libraries were prepared using NEBNext® Poly(A) mRNA Magnetic Isolation Module (cat. #E7490, New England Biolabs). One ng cDNA was used for preparation of sequencing libraries using the Nextera XT DNA Sequencing kit (NextSeq 500/550 high output kit v2.5, cat. #20024906, Illumina). Samples were analyzed on a NextSeq500 sequencer (Illumina).
mRNA-seq

treatment_protocol: Mv1Lu cells were subjected to cholesterol depletion by statin-mediated metabolic inhibition of HMG-CoA reductase. The cells were incubated (16 h) with 50 μM lovastatin and 50 μM mevalonate in medium supplemented with 10% lipoprotein-deficient fetal calf serum (LPDS).

value: Lung

value: Mv1Lu, ATCC cat. #CRL-6584

value: cholesterol depleted


title: miRNA-seq_FLC30_KPKS

source_name: Fibrolamellar carcinoma tissue sample #11

value: liver


title: PIM1 20 Rb IgG 2

value: LNCaP

value: prostate cancer

value: PIM1 over-expression


title: KO_3d_full liver [022_2]

value: C57BL/6JBomTac (PMID 31320478)


title: Mv1Lu cells cholesterol depleted rep1

description:
raw_counts.csv
cd1


title: KDM6B siRNA, biological rep1

city: Memphis

first: JUN

last: YANG

state: TN

address: 262 Danny Thomas Place

department: Surgery

institute: St Jude Children's Research Hospital

description: Gene expression data from BE2 cells treated with KDM6B siRNA

hyb_protocol: The WT Plus assay from Affymetrix fragments and labels 5.5 ug of ss-cDNA which is hybridized on the Clariom S human array with a constant temperature of 45° C for 16 hours while rotating at 60 rpm.

scan_protocol: The samples were the stained and washed using the Affymetrix Fluidics 450 stations and  recommended protocol. Then the Clariom Shuman arrays were then scanned by the Affymetrix GeneChip Scanner 3000 7G

data_processing: Data from Affymetrix GeneChip arrays is acquired and analyzed using GeneChip Operating System (GCOS)

label: Biotin

source_name: BE2 cells transfected with KDM6B siRNA

label_protocol: The protocol used for the samples run on the Clariom S human arrays was the Whole Transcript Plus assay from Affymetrix.  The initial input of RNA was 125 ng.

growth_protocol: BE2C cells cultured in standard RMPI media with 10% FBS, 1% Glutamine.

extract_protocol: RNeasy minikit from QIAGEN was used for RNA extraction according to the manufacturer's instructions.

treatment_protocol: BE2C cells  were treated with 0.1% DMSO or 2.5mM of GSK-J4 for 24h. For siRNA knockdown, BE2C cells were transfected with 30nM of siRNA controls or KDM6B siRNAs for 48h.

value: neuroblastoma cell line


title: KDM6B siRNA, biological rep2


title: miRNA-seq_FLC29_QLXW

source_name: Fibrolamellar carcinoma tissue sample #10

value: small RNA


title: PBMC from sample HB246

description: PBMC from sample HB246


title: GSK-J4 treatment, biological rep 1

description: Gene expression data from BE2 cells treated with2.5mM GSK-J4

source_name: BE2C cells treated with GSK-J4


title: GSK-J4 treatment, biological rep 2


title: Treatment control, biological rep 2

description: Gene expression data from BE2 cells treated with 0.1% DMSO

source_name: BE2C cells treated with DMSO control


title: WT_3d_full liver [022_1]

value: wild-type (WT)

value: female


title: siRNA control, biological rep2

description: Gene expression data from BE2 cells treated with siRNA control

source_name: BE2 cells transfected with siRNA control


title: siRNA control, biological rep1


title: Treatment control, biological rep 1


title: miRNA-seq_FLC28_RKXK

description:
Fibrolamellar tissue biopsy from a fibrolamellar carcinoma patient
DESeq_normalized_miR_counts.csv

source_name: Fibrolamellar carcinoma tissue sample #9


title: Mv1Lu cells untreated rep3

description:
raw_counts.csv
con3

value: control


title: PBMC from sample HB222

description: PBMC from sample HB222


title: Mv1Lu cells cholesterol depleted rep3

description:
raw_counts.csv
cd3


title: Mv1Lu cells untreated rep2

description:
raw_counts.csv
con2


title: PBMC from sample HB20

description: PBMC from sample HB20


title: miRNA-seq_FLC25_BCRB

source_name: Fibrolamellar carcinoma tissue sample #8


title: Mv1Lu cells untreated rep1

description:
raw_counts.csv
con1


title: miRNA-seq_FLC24_DJZW

source_name: Fibrolamellar carcinoma tissue sample #7


title: PBMC from sample AD9

description: PBMC from sample AD9

value: AD


title: wt_hfd_2

city: Columbus

first: Federica

last: Accornero

state: OH

address: 473 W 12th Ave.

institute: Ohio State University Medical Center

description: FVB/N; αMHC tTA

data_processing:
sequencing alignment, hisat2 v2.2.0
read count matrix formation, htseq v2.0
differential analysis, DEseq2 v1.32.0
Genome_build: mm10
Supplementary_files_format_and_content: count matrix (.txt), DEseq2 analysis (.csv). DEseq2 analysis was carried out comparing all 4 groups. Nomenclature example: 'ctl_tgf_vs_wt.csv' compares TGFb overexpression to TGFb wildtype under control diet conditions.

source_name: visceral white adipose tissue

growth_protocol: High fat diet treatment was performed in 8-10 weeks old TGF-b1 gain-of-function mice and littermate controls for either 2 or 6 weeks (Research Diets Inc. D12492; 60% kcal fat, 20% kcal carbohydrate, 20% kcal protein, 5.21 kcal/g). Normal mouse chow (Envigo Teklad 7912; containing only 17% kcal fat and a total of 3.1 kcal/g) was used as control.

extract_protocol:
RNA was extracted using a Zymo Research Quick-RNA MiniPrep kit (catalog no. R1055).
DNBseq preparation method (BGI)

tag: genotype

value: FVB/N; alphaMHC tTA

tag: diet

value: high fat diet


title: miRNA-seq_FLC20_ZDNV

source_name: Fibrolamellar carcinoma tissue sample #6


title: PBMC from sample AD6

description: PBMC from sample AD6

value: PBMC


title: wt_hfd_3

description: FVB/N; αMHC tTA


title: miRNA-seq_FLC18_WSVW

source_name: Fibrolamellar carcinoma tissue sample #5


title: wt_hfd_1

description: FVB/N; αMHC tTA


title: miRNA-seq_FLC06_UFNW

source_name: Fibrolamellar carcinoma tissue sample #3


title: wt_ctl_3

description: FVB/N; αMHC tTA

value: control diet


title: miRNA-seq_FLC18_QFZD

source_name: Fibrolamellar carcinoma tissue sample #4


title: wt_ctl_2

description: FVB/N; αMHC tTA


title: PHHs,  biological rep3

city: Laurel

first: Xiugong

last: Gao

state: MD

address: 8301 Muirkirk Rd

department: HFP/OLOAS/OCT/DT

institute: US FDA

description: Gene expression data for PHHs

hyb_protocol: Hybridization, wash, and staining were carried out using the Affymetrix GeneChip Hybridization, Wash, and Stain Kit on an Affymetrix Fluidics Station 450 following the manufacturer’s protocols.

scan_protocol: The chips were scanned on Affymetrix GeneChip Scanner 3000 7G and the image (.DAT) files were preprocessed using the Affymetrix GeneChip Command Console (AGCC) software v.4.0 to generate cell intensity (.CEL) files.

data_processing: The values of individual probes belonging to one probe set in .CEL files were summarized using the robust multi-array average (RMA) algorithm embedded in the Expression Console software v.1.3 (Affymetrix), which comprises of convolution background correction, quantile normalization, and median polish summarization.

source_name: PHHs

label_protocol: The total RNA samples (100 ng each) were labeled using the GeneChip 3’ IVT PLUS Reagent Kit (Affymetrix) following the manufacturer’s protocol.

growth_protocol: Human iPSCs were maintained as a single-cell culture (no colony formation) on COAT-1 coated 6-well tissue culture plate in Cellartis DEF-CS Culture System (Takara) at 37 °C, 5% CO2.

extract_protocol: HLCs were lysed in RLT buffer (Qiagen) supplemented with β-mercaptoethanol, homogenized by QIAshredder (Qiagen), and kept in a -80 °C freezer until further processing. Total RNA was isolated on the EZ1 Advanced XL (Qiagen) automated RNA purification instrument using the EZ1 RNA Cell Mini Kit (Qiagen) following the manufacturer’s protocol, including an on-column DNase digestion.

treatment_protocol: In M1, activin A, BMP4, and FGF2 were applied to guide hepatic specification of definitive endoderm (DE), and HGF and OSM were further utilized to promote cell maturation into HLCs. In M2, DMSO and HGF were employed to guide the hepatic specification, followed by hepatic maturation promoted by DEX, dihexa, and OSM.

value: PHHs


title: PBMC from sample ACLF9

description: PBMC from sample ACLF9

source_name: PBMC

value: ACLF


title: miRNA-seq_FLC06_SLVP

description:
Non-malignant liver tissue biopsy from a fibrolamellar carcinoma patient
DESeq_normalized_miR_counts.csv

source_name: Non-malignant liver tissue #1

value: liver


title: PBMC from sample AD14

description: PBMC from sample AD14


title: wt_ctl_1

description: FVB/N; αMHC tTA


title: PBMC from sample ACLF7

description: PBMC from sample ACLF7


title: miRNA-seq_FLC06_DZIS

source_name: Fibrolamellar carcinoma tissue sample #2


title: tgf_hfd_3

description: FVB/N; αMHC tTA x αMHC TGFb

value: FVB/N; alphaMHC tTA x alphaMHC TGFb


title: PBMC from sample ACLF32

description: PBMC from sample ACLF32


title: F4e_1390G3_iPSC_2

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

country: Japan

institute: Kyoto University, Graduate school of medicine

data_processing:
The read processing, mapping, and estimation of the methylated C levels were performed as described previously (Shirane et al., 2016). Single-end reads were processed with the Trim_galore program (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) to remove four bases from the 5’‐ends, one base from the 3’‐ends, adaptor sequences, and low‐quality reads (quality score < 20).
The processed reads were aligned to the human genome (GRCh38.p2, chromosome 1 to 22 and X) with the bismark program from Bismark v0.17.0 with the “–pbat” option (Krueger & Andrews, 2011). Mapped data (BAM format) were converted to methylation levels using the bismark_methylation_extractor program from Bismark. SAMtools v1.3 (Li et al., 2009).
Only CpGs in which the read depth is between 4 and 200 are used for % methylated C (mC) calculations. Only regions in which CpG (read depth ≥ 4) counts were four or more within genome‐wide 2 kb bins were used for calculating averages. For the analysis on CpA, CpC, and CpT methylations, percent methylations were calculated as % mC per kb as follows: The numbers of methylation call over genome-wide 1 kb bins were summed and divided by the sum of the numbers of unmethylation calls in the same region. The methylation levels per kb for CpA, CpC, and CpT were calculated separately throughout the whole genome.
Genome_build: GRCh38.p2
Supplementary_files_format_and_content: bismark report txt

source_name: hiPSC

growth_protocol: The human iPSC lines (Table S1) were maintained under a feeder-free condition (StemFit AK03 or AK03N [Ajinomoto] medium on recombinant LAMININ511 [iMatrix-511; Nippi]-coated cell culture plates) (Nakagawa et al., 2014). For single-cell dissociation for the passage, the cells were treated with 0.5x TryPLE Select (Life Technologies) solution in 0.5 mM EDTA/PBS for 8-10 min at 37˚C and harvested with cell scrapers. 10 uM of Rho-associated coiled-coil forming kinase (ROCK) inhibitor (Y-27632; Wako Pure Chemical Industries) was added and the treatment was continued for 24 h after seeding.

extract_protocol:
Genomic DNA of iPSCs (~4 × 10^5) was purified using an All Prep DNA/RNA mini kit (QIAGEN) following manufacturer’s guidelines.
Whole Genome Bisulfite Sequence (WGBS): Unmethylated lambda phage DNA (1/200 of the estimated gDNA mass) (Promega) was spiked into the samples, and then the samples were subjected to bisulfite conversions and library constructions for amplification-free WGBS analyses (Miura et al., 2012).

value: Human induced pluripotent stem cells (hiPSCs)


title: HLCs generated by M2 at D21, biological rep2

description: Gene expression data for HLCs generated by M2 at D21

source_name: HLCs generated by M2 at D21

value: HLCs

tag: method

tag: time


title: PBMC from sample AD7

description: PBMC from sample AD7


title: PHHs,  biological rep2

description: Gene expression data for PHHs


title: PHHs,  biological rep1

description: Gene expression data for PHHs


title: HLCs generated by M2 at D17, biological rep3

description: Gene expression data for HLCs generated by M2 at D17

source_name: HLCs generated by M2 at D17


title: HLCs generated by M2 at D17, biological rep2


title: tgf_hfd_2

description: FVB/N; αMHC tTA x αMHC TGFb


title: PBMC from sample ACLF25

description: PBMC from sample ACLF25


title: F5e_1390C1_iPSC_2


title: PBMC from sample ACLF23

description: PBMC from sample ACLF23


title: tgf_ctl_3

description: FVB/N; αMHC tTA x αMHC TGFb


title: HLCs generated by M2 at D21, biological rep3


title: PBMC from sample ACLF24

description: PBMC from sample ACLF24


title: tgf_ctl_2

description: FVB/N; αMHC tTA x αMHC TGFb


title: PBMC from sample AD11

description: PBMC from sample AD11


title: F5e_1390C1_iPSC_1


title: F1_201B7_iPSC_2


title: PBMC from sample ACLF11

description: PBMC from sample ACLF11


title: HLCs generated by M1 at D21, biological rep3

description: Gene expression data for HLCs generated by M1 at D21

source_name: HLCs generated by M1 at D21


title: HLCs generated by M2 at D21, biological rep1


title: HLCs generated by M1 at D17, biological rep3

description: Gene expression data for HLCs generated by M1 at D17

source_name: HLCs generated by M1 at D17


title: PBMC from sample ACLF10

description: PBMC from sample ACLF10


title: HLCs generated by M1 at D21, biological rep2


title: HLCs generated by M1 at D21, biological rep1


title: HLCs generated by M2 at D17, biological rep1


title: tgf_ctl_1

description: FVB/N; αMHC tTA x αMHC TGFb


title: F1_201B7_iPSC_1


title: BH1 Re2

status: Public on Nov 02 2021

city: Shanghai

first: Yi

last: Kan

address: Fenglin

institute: Center for Excellence in Molecular Plant Sciences ,CAS

data_processing:
the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated
clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated.
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0)
Genome_build: IRGSP ftp://ftp.ensemblgenomes.org/pub/release-42/plants/fasta/oryza_sativa/dna
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Oryza sativa

source_name: aerial organs

growth_protocol: NILs plants were normally grown at 28°C

extract_protocol:
Total RNA were extracted using RNeasy Plant Mini Kit (Cat 74904, Qiagen).Illumina TruSeq RNA sample prep Kit (Cat#FC-122-1001) was used with 1ug of total RNA for construction
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: NILs plants were treated at 28°C or 42.5°C for 20 hours

value: developing aerial tissues

value: 20-hr heat treatment

value: loss-of-function TT2

tag: true name


title: BH1 Re3


title: F4e_1390G3_iPSC_1


title: tgf_hfd_1

description: FVB/N; αMHC tTA x αMHC TGFb


title: AH1 Re3

value: wild type


title: BQ3 Re3

value: normal conditions


title: BH1 Re1


title: BQ1 Re1


title: AQ3 Re3


title: AQ1 Re1


title: AQ2 Re2


title: BQ2 Re2


title: NL-IP-KIAA_KD, MeRIP-Seq

city: La Jolla

last: Li

state: California

address: 9500 Gilman Dr

department: Pediatrics

institute: University of California, San Diego

data_processing:
Basecalls performed using FastQC v0.11.8
RNA-seq reads and MeRIP reads were aligned to hg38 genome assembly using STAR aligner
Data were filtered using cutadapt: Phred quality score > 30 and remove adapters
peaks were called by MACS2 using the following configuration:  q<0.05 --nomodel --extsize 200.
Raw read gene counts are generated using htseq-count; normalized read gene counts are generated by DESeq2.
Genome_build: hg38
Supplementary_files_format_and_content: xlsx: contains normalized gene expression by DESeq2; bigwig: contains peaks detecting by MACS2

source_name: KIAA1429 KD MDA-MB-231 breast cancer cells

growth_protocol: The human breast cancer cells MDA-MB-231 were cultured in high-glucose DMEM (Thermo Fisher Scientific) supplemented with 10% fetal bovine serum (FBS; Gibco) and 50 U/ml penicillin-streptomycin (Gibco) in a humidified 5% CO2 atmosphere

extract_protocol:
mRNA from KIAA1429 KD MDA-MB-231 cells were extracted and purified for IP of MeRIP-Seq
Total RNA was extracted from cultured cells using Quick-RNA Miniprep Plus Kit (Zymo Research) following the manufacturer’s instructions. All RNAs were treated with on-column DNase I digestion. cDNAs were synthesized using an iScript cDNA synthesis kit (Bio-Rad) according to the manufacturer’s instructions.  RNA sequencing (RNA Seq) of control and KIAA1429/VIRMA KO MDA-MB-231 cells was performed by HiSeq 4000 at the IGM Genomics Center, UCSD. Data analysis of RNA-Seq was performed in La Jolla bioinformatics core. MeRIP-Seq was performed as previously reported (Li et al., 2020). Briefly, total RNA was extracted from control and KIAA1429/VIRMA depleted MDA-MB-231 cells. mRNA was isolated from 300 µg total RNA by using Magnetic mRNA Isolation Kit (NEB, S1550S). Purified mRNA was fragmented to 100–200 nucleotides using Ambion RNA Fragmentation Reagent (AM8740, Life Technologies).  Purify fragmented mRNA by ethanol precipitation. An input sample (10% of total fragmented mRNA) from each group was reserved. The remaining fragmented mRNA was used for IP by incubating with 10 μl rabbit anti-m6A polyclonal Ab (ab151230, Abcam) in IP binding buffer (10 mM Tris-HCl, 150 mM NaCl, 0.1% NP-40, pH 7.4) for 2 h at 4°C.  50 μl protein A/G magnetic beads (Thermo Fisher) were then added to the mixture and incubated for 2 h at 4°C, and the beads were collected and washed once in IP binding buffer and twice in IP wash buffer (10 mM Tris-HCl, 1 M NaCl, 0.1% NP-40, pH 7.4). Bound mRNAs were eluted from the beads by using fresh prepared m6A elution buffer (10 mM Tris-HCl, 1 M NaCl, 0.1% NP-40, 25 mM m6A, pH 7.4).  Eluted mRNAs were purified by RNA Clean & Concentrator kit (Zymo Research) according to the manufacturer’s instructions. m6A-containing mRNAs were dissolved in water and then processed for library generation using a TruSeq mRNA library preparation kit (Illumina). Sequencing was performed by HiSeq 4000 at the IGM Genomics core, UCSD.
Total RNA, the immunoprecipitated m6A-containing mRNAs and the input RNAs were proceeded for library generation by TruSeq mRNA library prep kit (Illumina).

treatment_protocol: Infected cells lentivirus for non-targeting control (NTC) and KIAA1429 depletion and selected, stable cell lines for control (NTC) and KIAA1429 KD/KO were generated.

value: Human breast cancer cells

value: KIAA1429 KD

tag: passages

tag: merip antibody

value: anti-m6A polyclonal antibody (ab151230, abcam)


title: NL-IP-NTC, MeRIP-Seq

source_name: Control (NTC) MDA-MB-231 breast cancer cells

extract_protocol:
mRNA from control (NTC) MDA-MB-231 cells were extracted and purified for IP of MeRIP-Seq
Total RNA was extracted from cultured cells using Quick-RNA Miniprep Plus Kit (Zymo Research) following the manufacturer’s instructions. All RNAs were treated with on-column DNase I digestion. cDNAs were synthesized using an iScript cDNA synthesis kit (Bio-Rad) according to the manufacturer’s instructions.  RNA sequencing (RNA Seq) of control and KIAA1429/VIRMA KO MDA-MB-231 cells was performed by HiSeq 4000 at the IGM Genomics Center, UCSD. Data analysis of RNA-Seq was performed in La Jolla bioinformatics core. MeRIP-Seq was performed as previously reported (Li et al., 2020). Briefly, total RNA was extracted from control and KIAA1429/VIRMA depleted MDA-MB-231 cells. mRNA was isolated from 300 µg total RNA by using Magnetic mRNA Isolation Kit (NEB, S1550S). Purified mRNA was fragmented to 100–200 nucleotides using Ambion RNA Fragmentation Reagent (AM8740, Life Technologies).  Purify fragmented mRNA by ethanol precipitation. An input sample (10% of total fragmented mRNA) from each group was reserved. The remaining fragmented mRNA was used for IP by incubating with 10 μl rabbit anti-m6A polyclonal Ab (ab151230, Abcam) in IP binding buffer (10 mM Tris-HCl, 150 mM NaCl, 0.1% NP-40, pH 7.4) for 2 h at 4°C.  50 μl protein A/G magnetic beads (Thermo Fisher) were then added to the mixture and incubated for 2 h at 4°C, and the beads were collected and washed once in IP binding buffer and twice in IP wash buffer (10 mM Tris-HCl, 1 M NaCl, 0.1% NP-40, pH 7.4). Bound mRNAs were eluted from the beads by using fresh prepared m6A elution buffer (10 mM Tris-HCl, 1 M NaCl, 0.1% NP-40, 25 mM m6A, pH 7.4).  Eluted mRNAs were purified by RNA Clean & Concentrator kit (Zymo Research) according to the manufacturer’s instructions. m6A-containing mRNAs were dissolved in water and then processed for library generation using a TruSeq mRNA library preparation kit (Illumina). Sequencing was performed by HiSeq 4000 at the IGM Genomics core, UCSD.
Total RNA, the immunoprecipitated m6A-containing mRNAs and the input RNAs were proceeded for library generation by TruSeq mRNA library prep kit (Illumina).

value: Control


title: NL-Input-NTC, MeRIP-Seq

extract_protocol:
mRNA from control (NTC) MDA-MB-231 cells were extracted and purified for input of MeRIP-Seq
Total RNA was extracted from cultured cells using Quick-RNA Miniprep Plus Kit (Zymo Research) following the manufacturer’s instructions. All RNAs were treated with on-column DNase I digestion. cDNAs were synthesized using an iScript cDNA synthesis kit (Bio-Rad) according to the manufacturer’s instructions.  RNA sequencing (RNA Seq) of control and KIAA1429/VIRMA KO MDA-MB-231 cells was performed by HiSeq 4000 at the IGM Genomics Center, UCSD. Data analysis of RNA-Seq was performed in La Jolla bioinformatics core. MeRIP-Seq was performed as previously reported (Li et al., 2020). Briefly, total RNA was extracted from control and KIAA1429/VIRMA depleted MDA-MB-231 cells. mRNA was isolated from 300 µg total RNA by using Magnetic mRNA Isolation Kit (NEB, S1550S). Purified mRNA was fragmented to 100–200 nucleotides using Ambion RNA Fragmentation Reagent (AM8740, Life Technologies).  Purify fragmented mRNA by ethanol precipitation. An input sample (10% of total fragmented mRNA) from each group was reserved. The remaining fragmented mRNA was used for IP by incubating with 10 μl rabbit anti-m6A polyclonal Ab (ab151230, Abcam) in IP binding buffer (10 mM Tris-HCl, 150 mM NaCl, 0.1% NP-40, pH 7.4) for 2 h at 4°C.  50 μl protein A/G magnetic beads (Thermo Fisher) were then added to the mixture and incubated for 2 h at 4°C, and the beads were collected and washed once in IP binding buffer and twice in IP wash buffer (10 mM Tris-HCl, 1 M NaCl, 0.1% NP-40, pH 7.4). Bound mRNAs were eluted from the beads by using fresh prepared m6A elution buffer (10 mM Tris-HCl, 1 M NaCl, 0.1% NP-40, 25 mM m6A, pH 7.4).  Eluted mRNAs were purified by RNA Clean & Concentrator kit (Zymo Research) according to the manufacturer’s instructions. m6A-containing mRNAs were dissolved in water and then processed for library generation using a TruSeq mRNA library preparation kit (Illumina). Sequencing was performed by HiSeq 4000 at the IGM Genomics core, UCSD.
Total RNA, the immunoprecipitated m6A-containing mRNAs and the input RNAs were proceeded for library generation by TruSeq mRNA library prep kit (Illumina).


title: AH1 Re2

tag: tissue


title: KIAA-sg2-3, RNA-Seq

description: Summary analysis NTC KIAA1429 KO -231.xlsx

source_name: KIAA1429 KO MDA-MB-231 breast cancer cells

extract_protocol:
Total RNA from KIAA1429 KD (KIAA-sg2) cells were extracted and purified
Total RNA was extracted from cultured cells using Quick-RNA Miniprep Plus Kit (Zymo Research) following the manufacturer’s instructions. All RNAs were treated with on-column DNase I digestion. cDNAs were synthesized using an iScript cDNA synthesis kit (Bio-Rad) according to the manufacturer’s instructions.  RNA sequencing (RNA Seq) of control and KIAA1429/VIRMA KO MDA-MB-231 cells was performed by HiSeq 4000 at the IGM Genomics Center, UCSD. Data analysis of RNA-Seq was performed in La Jolla bioinformatics core. MeRIP-Seq was performed as previously reported (Li et al., 2020). Briefly, total RNA was extracted from control and KIAA1429/VIRMA depleted MDA-MB-231 cells. mRNA was isolated from 300 µg total RNA by using Magnetic mRNA Isolation Kit (NEB, S1550S). Purified mRNA was fragmented to 100–200 nucleotides using Ambion RNA Fragmentation Reagent (AM8740, Life Technologies).  Purify fragmented mRNA by ethanol precipitation. An input sample (10% of total fragmented mRNA) from each group was reserved. The remaining fragmented mRNA was used for IP by incubating with 10 μl rabbit anti-m6A polyclonal Ab (ab151230, Abcam) in IP binding buffer (10 mM Tris-HCl, 150 mM NaCl, 0.1% NP-40, pH 7.4) for 2 h at 4°C.  50 μl protein A/G magnetic beads (Thermo Fisher) were then added to the mixture and incubated for 2 h at 4°C, and the beads were collected and washed once in IP binding buffer and twice in IP wash buffer (10 mM Tris-HCl, 1 M NaCl, 0.1% NP-40, pH 7.4). Bound mRNAs were eluted from the beads by using fresh prepared m6A elution buffer (10 mM Tris-HCl, 1 M NaCl, 0.1% NP-40, 25 mM m6A, pH 7.4).  Eluted mRNAs were purified by RNA Clean & Concentrator kit (Zymo Research) according to the manufacturer’s instructions. m6A-containing mRNAs were dissolved in water and then processed for library generation using a TruSeq mRNA library preparation kit (Illumina). Sequencing was performed by HiSeq 4000 at the IGM Genomics core, UCSD.
Total RNA, the immunoprecipitated m6A-containing mRNAs and the input RNAs were proceeded for library generation by TruSeq mRNA library prep kit (Illumina).

value: KIAA1429 KO


title: HLCs generated by M1 at D17, biological rep2


title: KIAA-sg2-2, RNA-Seq


title: AH1 Re1


title: KIAA-sg2-1, RNA-Seq


title: KIAA-sg1-2, RNA-Seq

extract_protocol:
Total RNA from KIAA1429 KD (KIAA-sg1) cells were extracted and purified
Total RNA was extracted from cultured cells using Quick-RNA Miniprep Plus Kit (Zymo Research) following the manufacturer’s instructions. All RNAs were treated with on-column DNase I digestion. cDNAs were synthesized using an iScript cDNA synthesis kit (Bio-Rad) according to the manufacturer’s instructions.  RNA sequencing (RNA Seq) of control and KIAA1429/VIRMA KO MDA-MB-231 cells was performed by HiSeq 4000 at the IGM Genomics Center, UCSD. Data analysis of RNA-Seq was performed in La Jolla bioinformatics core. MeRIP-Seq was performed as previously reported (Li et al., 2020). Briefly, total RNA was extracted from control and KIAA1429/VIRMA depleted MDA-MB-231 cells. mRNA was isolated from 300 µg total RNA by using Magnetic mRNA Isolation Kit (NEB, S1550S). Purified mRNA was fragmented to 100–200 nucleotides using Ambion RNA Fragmentation Reagent (AM8740, Life Technologies).  Purify fragmented mRNA by ethanol precipitation. An input sample (10% of total fragmented mRNA) from each group was reserved. The remaining fragmented mRNA was used for IP by incubating with 10 μl rabbit anti-m6A polyclonal Ab (ab151230, Abcam) in IP binding buffer (10 mM Tris-HCl, 150 mM NaCl, 0.1% NP-40, pH 7.4) for 2 h at 4°C.  50 μl protein A/G magnetic beads (Thermo Fisher) were then added to the mixture and incubated for 2 h at 4°C, and the beads were collected and washed once in IP binding buffer and twice in IP wash buffer (10 mM Tris-HCl, 1 M NaCl, 0.1% NP-40, pH 7.4). Bound mRNAs were eluted from the beads by using fresh prepared m6A elution buffer (10 mM Tris-HCl, 1 M NaCl, 0.1% NP-40, 25 mM m6A, pH 7.4).  Eluted mRNAs were purified by RNA Clean & Concentrator kit (Zymo Research) according to the manufacturer’s instructions. m6A-containing mRNAs were dissolved in water and then processed for library generation using a TruSeq mRNA library preparation kit (Illumina). Sequencing was performed by HiSeq 4000 at the IGM Genomics core, UCSD.
Total RNA, the immunoprecipitated m6A-containing mRNAs and the input RNAs were proceeded for library generation by TruSeq mRNA library prep kit (Illumina).


title: KIAA-sg1-3, RNA-Seq


title: NTC-2, RNA-Seq

extract_protocol:
Total RNA from control (NTC-2) MDA-MB-231 cells were extracted and purified
Total RNA was extracted from cultured cells using Quick-RNA Miniprep Plus Kit (Zymo Research) following the manufacturer’s instructions. All RNAs were treated with on-column DNase I digestion. cDNAs were synthesized using an iScript cDNA synthesis kit (Bio-Rad) according to the manufacturer’s instructions.  RNA sequencing (RNA Seq) of control and KIAA1429/VIRMA KO MDA-MB-231 cells was performed by HiSeq 4000 at the IGM Genomics Center, UCSD. Data analysis of RNA-Seq was performed in La Jolla bioinformatics core. MeRIP-Seq was performed as previously reported (Li et al., 2020). Briefly, total RNA was extracted from control and KIAA1429/VIRMA depleted MDA-MB-231 cells. mRNA was isolated from 300 µg total RNA by using Magnetic mRNA Isolation Kit (NEB, S1550S). Purified mRNA was fragmented to 100–200 nucleotides using Ambion RNA Fragmentation Reagent (AM8740, Life Technologies).  Purify fragmented mRNA by ethanol precipitation. An input sample (10% of total fragmented mRNA) from each group was reserved. The remaining fragmented mRNA was used for IP by incubating with 10 μl rabbit anti-m6A polyclonal Ab (ab151230, Abcam) in IP binding buffer (10 mM Tris-HCl, 150 mM NaCl, 0.1% NP-40, pH 7.4) for 2 h at 4°C.  50 μl protein A/G magnetic beads (Thermo Fisher) were then added to the mixture and incubated for 2 h at 4°C, and the beads were collected and washed once in IP binding buffer and twice in IP wash buffer (10 mM Tris-HCl, 1 M NaCl, 0.1% NP-40, pH 7.4). Bound mRNAs were eluted from the beads by using fresh prepared m6A elution buffer (10 mM Tris-HCl, 1 M NaCl, 0.1% NP-40, 25 mM m6A, pH 7.4).  Eluted mRNAs were purified by RNA Clean & Concentrator kit (Zymo Research) according to the manufacturer’s instructions. m6A-containing mRNAs were dissolved in water and then processed for library generation using a TruSeq mRNA library preparation kit (Illumina). Sequencing was performed by HiSeq 4000 at the IGM Genomics core, UCSD.
Total RNA, the immunoprecipitated m6A-containing mRNAs and the input RNAs were proceeded for library generation by TruSeq mRNA library prep kit (Illumina).


title: WB_Gt042

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

description:
RNASeq_Counts
cohort details: Whole blood, peripheral blood (PBMC) and other immune subpopulations for this study were collected from healthy donors enrolled in the Genetic and Epigenetic Signatures of Translational Aging Laboratory Testing study (GESTALT) (Protocol# 15-AG-0063). GESTALT participants (age range 22-83 years) were selected to be free of major diseases, except for controlled hypertension or a history of cancer that had been clinically silent for at least 10 years, were not chronically on medications,had no  physical or cognitive impairment , weighed more than 110 lbs and had BMI less than 30 kg/m2, and were not professional athletes.

data_processing:
Single-read sequencing was performed for 138 cycles and Real-Time Analysis (RTA) v1.18.66.3 generated the base-call files (BCL files).
BCL files were demultiplexed and converted to standard FASTQ files using bcl2fastq program (v2.17.1.14).
After adapter removal and end trimming of raw FASTQ files using cutadapt program(Martin, 2011),the quality of reads was checked using FastQC software (Andrews, 2010). A quality threshold of Q30 was used in cutadapt for trimming low quality reads.
The reads were aligned to hg19 genome using STAR aligner (Dobin et al., 2013). STAR was used with default parameters (10 mismatches) in total. The output BAM files were then processed into read-count files using featureCounts tool.
Genes with low read counts (<10 reads in 4 or more samples) were filtered out and pseudogenes were further excluded from the analysis. Differentially expressed transcripts in each cell type were identified using the DESeq2 software package(Love et al., 2014).
Genome_build: hg19
Supplementary_files_format_and_content: Text files containing gene counts

source_name: Whole Blood

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) were isolated from cytapheresis packs by density gradient centrifugation using Ficoll-Paque Plus (GE Healthcare, NJ, USA). For isolation of specific immune cells, total B, CD4 and CD8 cells were enriched by negative selection using EasySep Negative Human kits specific for each cell type; monocytes were negatively enriched using “EasySep Human Monocyte Enrichment Kit w/o CD16” (StemCell Technologies, Vancouver, Canada) following the manufacturer’s instructions. Natural killer cells were negatively enriched by depleting PBMCs with antibodies directed against CD3, CD4, CD14, CD19 and Glycophorin-A in HBSS buffer. Enriched cell populations were further purified by flow cytometry following Human Immunophenotyping Consortium (HIPC) phenotyping panels (Maecker et al., 2012).  Gating strategies and post-sort purity were analyzed by FlowJo software. Granulocytes were positively selected from whole blood using EasySep™ Human Whole Blood CD66b Positive Selection Kit
Total RNA was prepared from 2 million cells using miRNeasy mini kit (Qiagen Inc, CA) according to the manufacturer’s recommendations. RNA quality and quantity were checked using RNA-6000 nano kits on the Agilent 2100-Bioanalyzer and 500ng of the total RNA was used for ribosomal RNA (rRNA) depletion using GeneRead rRNA Depletion Nano Kit (Qiagen Inc, CA). 50ng of the rRNA depleted RNA was used for cDNA synthesis followed by single primer isothermal amplification (SPIA) using Ovation RNA–Seq System V2 kits according to manufacturer’s protocol (Nugen Technologies Inc, CA). 375ng of amplified cDNA sheared to an average size of 150–250 bases, was used to prepare the libraries using Illumina ChIP-Seq kits (Illumina Inc, CA) according to the manufacturer’s protocol, followed by sequencing using Illumina Hiseq2500 sequencer with V4 reagents

tag: donor id

tag: phase


title: WB_Gt035


title: WB_Gt045


title: HLCs generated by M1 at D17, biological rep1


title: WB_Gt033


title: WB_Gt032


title: WB_Gt029


title: NL-Input-KIAA_KD, MeRIP-Seq

extract_protocol:
mRNA from KIAA1429 KD MDA-MB-231 cells were extracted and purified for input of MeRIP-Seq
Total RNA was extracted from cultured cells using Quick-RNA Miniprep Plus Kit (Zymo Research) following the manufacturer’s instructions. All RNAs were treated with on-column DNase I digestion. cDNAs were synthesized using an iScript cDNA synthesis kit (Bio-Rad) according to the manufacturer’s instructions.  RNA sequencing (RNA Seq) of control and KIAA1429/VIRMA KO MDA-MB-231 cells was performed by HiSeq 4000 at the IGM Genomics Center, UCSD. Data analysis of RNA-Seq was performed in La Jolla bioinformatics core. MeRIP-Seq was performed as previously reported (Li et al., 2020). Briefly, total RNA was extracted from control and KIAA1429/VIRMA depleted MDA-MB-231 cells. mRNA was isolated from 300 µg total RNA by using Magnetic mRNA Isolation Kit (NEB, S1550S). Purified mRNA was fragmented to 100–200 nucleotides using Ambion RNA Fragmentation Reagent (AM8740, Life Technologies).  Purify fragmented mRNA by ethanol precipitation. An input sample (10% of total fragmented mRNA) from each group was reserved. The remaining fragmented mRNA was used for IP by incubating with 10 μl rabbit anti-m6A polyclonal Ab (ab151230, Abcam) in IP binding buffer (10 mM Tris-HCl, 150 mM NaCl, 0.1% NP-40, pH 7.4) for 2 h at 4°C.  50 μl protein A/G magnetic beads (Thermo Fisher) were then added to the mixture and incubated for 2 h at 4°C, and the beads were collected and washed once in IP binding buffer and twice in IP wash buffer (10 mM Tris-HCl, 1 M NaCl, 0.1% NP-40, pH 7.4). Bound mRNAs were eluted from the beads by using fresh prepared m6A elution buffer (10 mM Tris-HCl, 1 M NaCl, 0.1% NP-40, 25 mM m6A, pH 7.4).  Eluted mRNAs were purified by RNA Clean & Concentrator kit (Zymo Research) according to the manufacturer’s instructions. m6A-containing mRNAs were dissolved in water and then processed for library generation using a TruSeq mRNA library preparation kit (Illumina). Sequencing was performed by HiSeq 4000 at the IGM Genomics core, UCSD.
Total RNA, the immunoprecipitated m6A-containing mRNAs and the input RNAs were proceeded for library generation by TruSeq mRNA library prep kit (Illumina).


title: WB_Gt024


title: WB_Gt025


title: WB_Gt022


title: WB_Gt020


title: WB_Gt017


title: WB_Gt018


title: WB_Gt026


title: KIAA-sg1-1, RNA-Seq


title: NTC-3, RNA-Seq

extract_protocol:
Total RNA from control (NTC-3) MDA-MB-231 cells were extracted and purified
Total RNA was extracted from cultured cells using Quick-RNA Miniprep Plus Kit (Zymo Research) following the manufacturer’s instructions. All RNAs were treated with on-column DNase I digestion. cDNAs were synthesized using an iScript cDNA synthesis kit (Bio-Rad) according to the manufacturer’s instructions.  RNA sequencing (RNA Seq) of control and KIAA1429/VIRMA KO MDA-MB-231 cells was performed by HiSeq 4000 at the IGM Genomics Center, UCSD. Data analysis of RNA-Seq was performed in La Jolla bioinformatics core. MeRIP-Seq was performed as previously reported (Li et al., 2020). Briefly, total RNA was extracted from control and KIAA1429/VIRMA depleted MDA-MB-231 cells. mRNA was isolated from 300 µg total RNA by using Magnetic mRNA Isolation Kit (NEB, S1550S). Purified mRNA was fragmented to 100–200 nucleotides using Ambion RNA Fragmentation Reagent (AM8740, Life Technologies).  Purify fragmented mRNA by ethanol precipitation. An input sample (10% of total fragmented mRNA) from each group was reserved. The remaining fragmented mRNA was used for IP by incubating with 10 μl rabbit anti-m6A polyclonal Ab (ab151230, Abcam) in IP binding buffer (10 mM Tris-HCl, 150 mM NaCl, 0.1% NP-40, pH 7.4) for 2 h at 4°C.  50 μl protein A/G magnetic beads (Thermo Fisher) were then added to the mixture and incubated for 2 h at 4°C, and the beads were collected and washed once in IP binding buffer and twice in IP wash buffer (10 mM Tris-HCl, 1 M NaCl, 0.1% NP-40, pH 7.4). Bound mRNAs were eluted from the beads by using fresh prepared m6A elution buffer (10 mM Tris-HCl, 1 M NaCl, 0.1% NP-40, 25 mM m6A, pH 7.4).  Eluted mRNAs were purified by RNA Clean & Concentrator kit (Zymo Research) according to the manufacturer’s instructions. m6A-containing mRNAs were dissolved in water and then processed for library generation using a TruSeq mRNA library preparation kit (Illumina). Sequencing was performed by HiSeq 4000 at the IGM Genomics core, UCSD.
Total RNA, the immunoprecipitated m6A-containing mRNAs and the input RNAs were proceeded for library generation by TruSeq mRNA library prep kit (Illumina).


title: NTC-1, RNA-Seq

extract_protocol:
Total RNA from control (NTC-1) MDA-MB-231 cells were extracted and purified
Total RNA was extracted from cultured cells using Quick-RNA Miniprep Plus Kit (Zymo Research) following the manufacturer’s instructions. All RNAs were treated with on-column DNase I digestion. cDNAs were synthesized using an iScript cDNA synthesis kit (Bio-Rad) according to the manufacturer’s instructions.  RNA sequencing (RNA Seq) of control and KIAA1429/VIRMA KO MDA-MB-231 cells was performed by HiSeq 4000 at the IGM Genomics Center, UCSD. Data analysis of RNA-Seq was performed in La Jolla bioinformatics core. MeRIP-Seq was performed as previously reported (Li et al., 2020). Briefly, total RNA was extracted from control and KIAA1429/VIRMA depleted MDA-MB-231 cells. mRNA was isolated from 300 µg total RNA by using Magnetic mRNA Isolation Kit (NEB, S1550S). Purified mRNA was fragmented to 100–200 nucleotides using Ambion RNA Fragmentation Reagent (AM8740, Life Technologies).  Purify fragmented mRNA by ethanol precipitation. An input sample (10% of total fragmented mRNA) from each group was reserved. The remaining fragmented mRNA was used for IP by incubating with 10 μl rabbit anti-m6A polyclonal Ab (ab151230, Abcam) in IP binding buffer (10 mM Tris-HCl, 150 mM NaCl, 0.1% NP-40, pH 7.4) for 2 h at 4°C.  50 μl protein A/G magnetic beads (Thermo Fisher) were then added to the mixture and incubated for 2 h at 4°C, and the beads were collected and washed once in IP binding buffer and twice in IP wash buffer (10 mM Tris-HCl, 1 M NaCl, 0.1% NP-40, pH 7.4). Bound mRNAs were eluted from the beads by using fresh prepared m6A elution buffer (10 mM Tris-HCl, 1 M NaCl, 0.1% NP-40, 25 mM m6A, pH 7.4).  Eluted mRNAs were purified by RNA Clean & Concentrator kit (Zymo Research) according to the manufacturer’s instructions. m6A-containing mRNAs were dissolved in water and then processed for library generation using a TruSeq mRNA library preparation kit (Illumina). Sequencing was performed by HiSeq 4000 at the IGM Genomics core, UCSD.
Total RNA, the immunoprecipitated m6A-containing mRNAs and the input RNAs were proceeded for library generation by TruSeq mRNA library prep kit (Illumina).


title: WB_Gt014


title: WB_Gt013


title: WB_Gt005


title: WB_Gt007


title: WB_Gt015


title: WB_Gt027


title: WB_Gt001


title: WB_Gt002


title: WB_Gt030


title: WB_Gt003


title: PBMC_Gt045

source_name: Peripheral Blood


title: WB_Gt004


title: PBMC_Gt042


title: WB_Gt016


title: PBMC_Gt035


title: PBMC_Gt030


title: PBMC_Gt032


title: PBMC_Gt027


title: PBMC_Gt026


title: PBMC_Gt029


title: WB_Gt011


title: PBMC_Gt025


title: PBMC_Gt024


title: PBMC_Gt022


title: PBMC_Gt020


title: PBMC_Gt018


title: PBMC_Gt017


title: PBMC_Gt016


title: PBMC_Gt015


title: PBMC_Gt014


title: PBMC_Gt007


title: PBMC_Gt011


title: PBMC_Gt005


title: PBMC_Gt001


title: PBMC_Gt002


title: NK_Gt045

source_name: Natural Killer cells


title: NK_Gt033


title: NK_Gt035


title: NK_Gt042


title: NK_Gt030


title: NK_Gt029


title: NK_Gt025


title: NK_Gt022


title: NK_Gt020


title: NK_Gt018


title: NK_Gt026


title: NK_Gt017


title: NK_Gt016


title: NK_Gt015


title: NK_Gt013


title: NK_Gt014


title: NK_Gt011


title: NK_Gt004


title: NK_Gt005


title: NK_Gt003


title: NK_Gt007


title: PBMC_Gt033


title: NK_Gt002


title: NK_Gt001


title: MONOCYTES_Gt042

source_name: Monocytes


title: NK_Gt032


title: NK_Gt027


title: MONOCYTES_Gt032


title: MONOCYTES_Gt033


title: MONOCYTES_Gt030


title: NK_Gt024


title: MONOCYTES_Gt029


title: MONOCYTES_Gt026


title: MONOCYTES_Gt025


title: MONOCYTES_Gt027


title: Conditioned failed 3 RNA-seq

city: Rehovot

first: Igor

last: Ulitsky

state: Central

address: 234 Hertzl St.

institute: Weizmann Institute of Science

description: Con. unsuccessful extinction SFCpExtpminus-LS18

data_processing:
RNA-seq: Raw reads were aligned to the mouse genome (mm10) using HiSAT and StringTie (Pertea et al., 2016) for transcript-based analysis or STAR aligner for count based analysis (Dobin et al., 2013). The program Ballgown was used to perform differential expression analysis based on FPKM values. Two other count-based strategies were performed since count-based differential expression analysis is more robust. For the first strategy, count data was calculated from the Ballgown data using an additional pipeline available, prepDE.PY. For the second strategy, the whole mapping was repeated using RNA STAR and the count data calculated using the HTseq pipeline. Both these count-based data were used to calculate differential expression of genes as well as transcripts using DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig read coverage files are provided for all samples

source_name: brain septum

extract_protocol:
Total RNA and protein were isolated from mouse brain septum using the NucleoSpin miRNA kit (Macherey-Nagel GmbH & Co KG) according to the manufacturer’s protocol for animal tissues.
Libraries for total RNA-seq were prepared using the Ovation SoLo RNA-Seq System, Mouse (#0501-32, NuGEN Technologies) according to the manufacturer’s protocol with an RNA starting concentration of 0.8 ng/µl.

value: brain septum

tag: aso

tag: histone mark


title: Conditioned failed 1 RNA-seq

description: Con. unsuccessful extinction SFCpExtpminus-LS4


title: MONOCYTES_Gt024


title: Conditioned successful 3 RNA-seq

description: Con. successful extinction SFCpExtpplus-LS20


title: Conditioned successful 2 RNA-seq

description: Con. successful extinction SFCpExtpplus-LS19


title: MONOCYTES_Gt022