title: UBKO rep1

city: Shanghai

first: Mingyang

last: Yuan

address: No. 573, Xujiahui Road, Huangpu District

institute: Shanghai Institute of Endocrine and Metabolic Diseases

description:
KO1E_FPKM
processed_data.xls

data_processing:
Illumina Casava1.7 software used for basecalling.
Paired-end sequence files (fastq) were mapped to the reference genome mm10 using Hisat2 (Hierarchical Indexing for Spliced Alignment of Transcripts, version 2.0.5). The output SAM (sequencing alignment/map) files were converted to BAM (binary alignment/map) files and sorted using SAMtools (version 1.3.1).
Differentially expressed genes were identified using Cuffdiff. The p-value significance threshold in multiple tests was set by the false discovery rate (FDR). The fold-changes were also estimated according to the FPKM in each sample.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample .

source_name: epididymal white adipose tissue

extract_protocol:
Total RNA was isolated using the RNeasy mini kit (Qiagen, Germany), after which the RNA concentration and quality were determined by the Qubit®2.0 Fluorometer (Life Technologies, USA) and the Nanodrop One spectrophotometer (Thermo Fisher Scientific Inc., USA). Integrity of total RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies Inc., USA), and samples with RNA integrity number (RIN) values above 7.0 were used for sequencing.
One micrograms of RNA were used as input material for the RNA sample preparations.Paired-end libraries were synthesized by using the TruSeq™ RNA Sample Preparation Kit (Illumina, USA) following TruSeq™ RNA Sample Preparation Guide

value: epididymal white adipose tissue

value: Ucp1-cre-driven Ctnnb1 knockout


title: CTC 19 WBM

status: Public on Mar 31 2023

type: SRA

city: Washington

first: Jerry

last: Xiao

state: DC

address: 3900 Reservoir Rd NW, PCS Bldg, Room GR10C

department: Tumor Biology

country: USA

institute: Georgetown University

description: total RNA from the whole blood of patient 19

library_source: transcriptomic

data_processing:
Base-calling was performed using salmon v0.14.
adapter were trimmed using trimmomatic
Reads were aligned to the human genome (Star Genecode v38) using STAR aligner v2.7.3a
reads were counted using feature counts in R annot.inbuilt='hg38' isPairedEnd = TRUE nthreads=23
Differential Expression was calculated using DESeq2 in R
Assembly: GRCH38.p13
Supplementary files format and content: raw and normalized gene counts (CSV) created from DESeq2

molecule: total RNA

organism: Homo sapiens

source_name: Patient 19

growth_protocol: CTC samples were extracted from patient samples using a Ficoll-based gradient selection. Cells were grown in hypoxia on ultra-low attachment plates using a modified conditional-reprogramming (CR)-based medium.

extract_protocol:
RNA was extracted using Invitrogen RNAqueous Micro-RNA kit following manufacturer protocol.
Psomagen was used to construct libraries based on an ultra-low input library preparation.

tag: source

value: Patient Peripheral Blood

tag: disease state

value: Cancer

tag: tissue

value: Whole Blood


title: UBKO rep2

country: China

description:
KO36E_FPKM
processed_data.xls

organism: Mus musculus

tag: genotype

tag: treatment


title: UBKO rep3

description:
KO37E_FPKM
processed_data.xls


title: UBKO rep4

description:
KO39E_FPKM
processed_data.xls


title: CDX 26 Spleen

description: total RNA from CDX model derived from patient 26

source_name: Patient 26

value: CTC-derived Xenograft

value: Spleen


title: Control rep4

description:
con60E_FPKM
processed_data.xls

value: Control


title: CTC 19 TC

description: total RNA from the cultured CTCs of patient 19

value: CTC Culture

value: Tissue Culture


title: Control rep5

description:
con61E_FPKM
processed_data.xls


title: CTC 22 FFPE

description: total RNA from FFPE tissues of primary tumor from patient 22

source_name: Patient 22

value: Patient FFPE Tissue

value: FFPE


title: CDX 26 LN

value: Lymph Node


title: Control rep3

description:
con44E_FPKM
processed_data.xls


title: Control rep2

description:
con38E_FPKM
processed_data.xls


title: Control rep1

description:
con35E_FPKM
processed_data.xls


title: CDX 26 Liver

value: Liver


title: CDX 26 Tumor

value: Tumor


title: CDX 22 LN

description: total RNA from CDX model derived from patient 22


title: CDX 22 Liver


title: CDX 22 Lung

value: Lung


title: Macrophage Female OpnKI Mye NASH Diet#1

city: Chicago

first: Hui

last: HAN

state: IL

address: 909 S Wolcott Ave

institute: University of Illinois at Chicago

data_processing:
Data were aligned using RNA-Seq Alignment v.2.0.1 in basespce
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw count for each sample

source_name: Liver Resident Macrophage

extract_protocol:
Total liver RNA was isolated with illustra™ RNAspin Mini RNA Isolation Kit; macrophage RNA was isolated with Qiagen miRNeasy micro kit.
RNA libraries for RNA-seq were prepared using Illumina TruSeq Stranded mRNA library prep

treatment_protocol: Mice were fed diet for 24 weeks

value: Liver Resident Macrophage

tag: cell type

value: OpnKI Mye

tag: time

value: 24 weeks

value: NASH diet

tag: gender

value: Female


title: Macrophage Female OpnKI Mye NASH Diet#6


title: Macrophage Female OpnKI Mye NASH Diet#2


title: Macrophage Female OpnKI Mye NASH Diet#5


title: Macrophage Female OpnKI Mye NASH Diet#3


title: CDX 22 Spleen

value: Cancer


title: Macrophage Female OpnKI Mye Ctrl Diet#4

value: Control diet


title: Macrophage Female OpnKI Mye Ctrl Diet#3


title: CDX 21 Liver

description: total RNA from CDX model derived from patient 21

source_name: Patient 21

value: CTC-derived Xenograft


title: Macrophage Female OpnKI Mye Ctrl Diet#2


title: CDX 21 Spleen

value: Spleen


title: Macrophage Female WT NASH Diet#6


title: CDX 21 LN


title: CDX 19 Spleen

description: total RNA from CDX model derived from patient 19


title: CDX 22 Tumor


title: Macrophage Female OpnKI Mye Ctrl Diet#1


title: CDX 19 LN


title: CDX 19 Tumor


title: CDX 21 Tumor


title: Macrophage Female OpnKI Mye NASH Diet#4


title: Macrophage Female WT NASH Diet#4


title: Macrophage Female WT NASH Diet#5


title: Macrophage Female WT NASH Diet#2


title: Macrophage Female WT NASH Diet#1


title: Macrophage Female WT NASH Diet#3


title: eIF4A1, eIF4A2 and ASCC3 tKD HEK293T #2 TCP-seq replicate 2

city: Chikusa-ku, Nagoya, Aichi

first: Kazuya

last: Ichihara

address: Furo-cho

country: Japan

institute: Nagoya University

data_processing:
Adaptor sequences were trimmed from raw reads with the use of cutadapt.
Reads of low quality were discarded with the use of fastq_quality_trimmer and fastq_quality_filter of the FASTX-Toolkit.
Ribosomal RNA reads were removed by alignment with human rRNA sequences with the use of STAR, and the remaining reads were aligned with the human transcriptome (GRCh38.p13) and human genome (hg38) also with the use of STAR.
Read counting was performed with the use of featureCounts.
Assembly: hg38
Supplementary files format and content: Counts per transcript

source_name: HEK293T cells

growth_protocol: The cells were cultured under an atmosphere of 5% CO2 at 37°C in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum (Life Technologies) and antibiotics.

extract_protocol:
Ribo-seq protocol: HEK293T cells were seeded at a density of 2.0 × 106 per 10-cm dish and the following analyses were performed 48 h after siRNA transfection. The medium was aspirated, and the cells were immediately placed on ice, washed once with ice-cold phosphate-buffered saline (PBS), and lysed with lysis buffer [50 mM Tris-HCl (pH 7.5), 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 1% Triton X-100, and EDTA-free protease inhibitor] supplemented with CHX (100 μg/ml). The lysates were then incubated with TURBO DNase on ice for 10 min and centrifuged at 15,000 rpm for 10 min at 4°C, and the resulting supernatants were collected carefully, assayed for RNA concentration with a Qubit RNA BR assay kit, incubated with RNase I (20 U per 10 μg of RNA, Epicentre) for 45 min at 25°C, and placed on ice before the addition of SUPERase•In RNase inhibitor (Invitrogen). The samples were then loaded on a 1 M sucrose cushion buffer [20 mM Tris-HCl (pH 7.5), 150 mM NaCl, 5 mM MgCl2, SUPERase•In (10 U/ml), 1 mM DTT, and CHX (100 μg/ml)], and the gradients were centrifuged at 100,000 rpm for 1 h at 4°C in a Beckman TLA110 rotor. The resulting pellets were suspended in ribosome splitting buffer [20 mM Tris-HCl (pH 7.5), 300 mM NaCl, 5 mM EDTA, SUPERase•In (20 U/ml), 1 mM DTT, 1% Triton X-100] and subjected to purification with the use of an Amicon Ultra filtration device (100-kDa cutoff, Millipore) to deplete rRNAs.
TCP-seq and Sel-TCP-seq protocol: Cells were seeded at a density of 8.0 × 106 cells per 15 cm dish, with 8 to 18 dishes per assay, and cultured for 2 days. Then, the subconfluent cells were treated for 10 min at room temperature with phosphate-buffered saline (PBS) containing 0.25% formalin, after which glycine was added to a final concentration of 125 mM and the cells were collected. The cells were washed three times with ice-cold PBS, lysed in lysis buffer [50 mM Tris-HCl (pH 7.5), 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 1% Triton X-100, cOmplete EDTA-free protease inhibitor (Roche)] supplemented with cycloheximide (CHX) (100 μg/ml), and incubated for 10 min on ice. The lysates were centrifuged at 20,380 × g for 10 min at 4°C, and the resulting supernatants were collected carefully, assayed for RNA concentration with a Qubit RNA BR assay kit, incubated with RNase I (20 U per 10 μg of RNA, Thermo Fisher Scientific) at 25°C for 45 min, and then placed on ice before the addition of 200 U SUPERase•In RNase inhibitor (Invitrogen). The samples were loaded on a 5% to 30% sucrose gradient buffer [20 mM Tris-HCl (pH 7.5), 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, CHX (100 μg/ml), SUPERase•In (10 U/ml)] and centrifuged at 38,200 rpm (180,000 × g) for 4 h at 4°C in a Himac P40ST rotor. The gradient was fractionated with the use of a TRIAX gradient-profiling system and AC-5700P microcollector. Polysome profiles were determined by measurement of absorbance at 260 nm. Dynabeads Protein G were conjugated with antibodies to FLAG by incubation overnight at 4°C in lysis buffer supplemented with 0.5% bovine serum albumin, and they were washed three times with lysis buffer before use. Small aliquots of the small ribosomal subunits (SSU) or large ribosomal subunits (LSU) fractions were stored for input or TCP-seq, and the remaining aliquots were incubated with the beads for 90 min at 4°C, and the resulting immunoprecipitates were washed four times with wash buffer [50 mM Tris-HCl (pH 7.5), 300 mM NaCl, 1 mM DTT, 0.1% Triton X-100]. For Sel-TCP-seq analysis, 250 μl of decrosslinking buffer [1% SDS, 10 mM EDTA, 10 mM Tris-HCl (pH 7.5), 10 mM glycine], 750 μl of ISOGEN LS, and 200 μl of chloroform were added to the beads, and incubated for 45 min at 65°C, and RNA was then purified by precipitation with isopropanol.
Ribo-seq protocol: The purified RNA was subjected to selection on the basis of a size range of 17 to 34 nt by electrophoresis through a 15% polyacrylamide and Tris-borate-EDTA (TBE)–urea gel (SuperSep RNA, Fujifilm). The footprint fragments were treated with T4 PNK to repair the 2x-3x cyclic phosphates, a DNA linker including barcode sequences (NI-810 to NI-817) was ligated with the use of T4 RNA Ligase 2, truncated K227Q (New England Biolabs), and the resulting products were purified on a 15% polyacrylamide and TBE-urea gel. Ribosomal RNAs were further depleted with the use of RiboZero Gold (Illumina). Reverse transcription was performed with the NI-802 primer, and the resulting products were purified on a 15% polyacrylamide and TBE-urea gel. The purified cDNAs were circularized with circLigase II (Lucigen), and index sequences were then added by amplification in a PCR reaction with the common primer (NI-798) and primers including index sequences (NI-799 and NI-822 to NI-826). Products of the desired size were purified on a 15% polyacrylamide nondenaturing gel (SuperSep DNA, Fujifilm), and the libraries were sequenced with a NovaSeq 6000 system (Illumina).
TCP-seq and Sel-TCP-seq protocol: The purified RNA was selected according to size in the range of 17 to 100 nt by electrophoresis in a 15% polyacrylamide and TBE-urea gel, and subjected to dephosphorylation, DNA linker ligation, and rRNA depletion with RiboZero Gold as described for the Ribo-seq protocol. Reverse transcription was performed with the use of the SI-019 primer, and the resulting products were purified on a 15% polyacrylamide and TBE-urea gel. The second linker (SI-018) was ligated by incubation overnight at 25°C with T4 RNA Ligase 1 (ssRNA Ligase), High Concentration (New England Biolabs). The products were then amplified in a PCR reaction with the same primers as used for the Ribo-seq protocol, and those of the desired size were purified by electrophoresis through a 15% polyacrylamide nondenaturing gel. The libraries were sequenced with a NovaSeq 6000 system.

treatment_protocol: HEK293T cells were transfected with 10 nM small interfering RNAs (siRNAs) with the use of Lipofectamine RNAiMAX (Invitrogen).

tag: protocol

value: TCP-seq

value: WT

value: eIF4A1, eIF4A2 and ASCC3 tKD

tag: ip antibody


title: Macrophage Female WT Ctrl Diet#3


title: Macrophage Female WT Ctrl Diet#2


title: eIF4A1, eIF4A2 and ASCC3 tKD HEK293T #2 TCP-seq replicate 1


title: eIF4A1, eIF4A2 and ASCC3 tKD HEK293T #1 TCP-seq replicate 1


title: siControl HEK293T TCP-seq replicate 4

value: siControl


title: Macrophage Female WT Ctrl Diet#1


title: eIF4A1, eIF4A2 and ASCC3 tKD HEK293T #1 TCP-seq replicate 2


title: siControl HEK293T TCP-seq replicate 3


title: Macrophage Male OpnKI Mye NASH Diet#5

value: Male


title: Macrophage Male OpnKI Mye NASH Diet#4


title: Macrophage Female WT Ctrl Diet#4


title: Macrophage Male OpnKI Mye NASH Diet#3


title: Macrophage Male OpnKI Mye NASH Diet#1


title: Macrophage Male OpnKI Mye NASH Diet#2


title: eIF4A1, eIF4A2 and ASCC3 tKD HEK293T #1 RNA-seq replicate 1

value: RNA-seq


title: eIF4A1, eIF4A2 and ASCC3 tKD HEK293T #1 RNA-seq replicate 2


title: siControl HEK293T RNA-seq replicate 3


title: siControl HEK293T RNA-seq replicate 4


title: Macrophage Male OpnKI Mye Ctrl Diet#3


title: eIF4A1, eIF4A2 and ASCC3 tKD HEK293T #2 RNA-seq replicate 1


title: Macrophage Male OpnKI Mye Ctrl Diet#4


title: RPL7A-HA RS IP replicate 2

value: Sel-TCP-seq

value: RPL7A-HA KI

value: HA


title: Macrophage Male OpnKI Mye Ctrl Diet#1

value: Liver Resident Macrophage

value: OpnKI Mye


title: RPL7A-HA RS IP replicate 1


title: Macrophage Male OpnKI Mye Ctrl Diet#2

value: 24 weeks


title: Newborn2_c.leave

city: Granada

first: Martin

last: Munoz-Lopez

state: GRANADA

address: C/ Ilustración

country: Spain

institute: GENYO

library_source: genomic

data_processing:
Library strategy: RC-seq (Retrotransposon Capture Sequencing)
Computational analysis of reads was implemented according to the RC-seq pipeline described by Shuckla et al. (Shukla et al., 2013). Briefly, the RC-seq pipeline is conducted to search for split reads that represent a L1-insertion junction, being constituted by an L1-end and a flanking DNA sequence. Flanking DNA sequences are aligned to the Human Genome Reference Sequence (hg19) using SOAP (Li et al., 2009) (parameters –M 4 –v 2 –r 1 –p 8) and the L1-end characterized by mapping to the human active L1 consensus sequences (L1Hs-Ta/L1Hs-preTa) using LAST (Kielbasa et al., 2011) (parameters –s 2 –l 11 –d 30 –q 3 –e 30) (alignment at >95% identity and spanning at least 33 nucleotides of the read end). To assess the reliability of RC-seq, we determined the percentage of L1Hs copies annotated in hg19 (available from euL1db at http://eul1db.unice.fr/, contains 1544 reference L1Hs copies annotated) that were detected by RC-seq in the different WGA-gDNA samples. As an additional control, we also compared recovered insertions in H9-hESCs and hEMBs with the L1Hs-Ta subset of reference L1Hs (485 copies). Finally, L1-insertions were further filtered with respect to reference L1-insertions annotated in hg19 and to reported polymorphic L1-insertions (from euL1db database (Mir et al., 2015) and from recent publications not included yet in this database (Tubio et al., 2014)).

molecule: genomic DNA

source_name: chorion leave

extract_protocol:
Genomic DNA purification from extraembryonic tissues was carried out using the Blood & Cell Culture DNA Midi Kit (Qiagen) following the manufacturer’s instructions. Genomic DNA from blood samples was purified using the QIAamp DNA Blood Mini Kit (Qiagen) following the manufacturer’s instructions.
Multiplexed Illumina libraries were prepared using the KAPA Library Preparation Kit (NimbleGen) and following the manufacture’s instruction; we used Illumina adapters from the SeqCap Adapter Kit (NimbleGen)

value: chorion leave


title: RPL7A-HA SSU IP replicate 2


title: Newborn2_blood-mother

source_name: blood

value: blood


title: RPL7A-HA SSU IP replicate 1


title: Macrophage Male WT NASH Diet#5

value: NASH diet


title: eIF4A1, eIF4A2 and ASCC3 tKD HEK293T #2 RNA-seq replicate 2


title: Macrophage Male WT NASH Diet#4


title: Macrophage Male WT NASH Diet#3


title: RPL7A-HA RS input replicate 1


title: Newborn2_amnion

source_name: amnion

value: amnion


title: Newborn2_blood


title: Newborn1_c.frondosum

source_name: chorion frondosum

value: chorion frondosum


title: RPL7A-HA RS input replicate 2


title: Macrophage Male WT NASH Diet#2


title: RPL7A-HA SSU input replicate 2


title: Macrophage Male WT NASH Diet#1


title: Newborn1_blood


title: Macrophage Male WT Ctrl Diet#3

value: Control diet


title: Macrophage Male WT Ctrl Diet#4


title: RPL7A-HA SSU input replicate 1


title: Macrophage Male WT Ctrl Diet#2


title: Newborn1_blood-mother


title: E6.C1

description:
whole genome amplification
Multiple Displacement Amplification

source_name: blastocyst

extract_protocol:
Whole Genome Aamplification reactions were performed within 48 hours after single-cell extraction, using the GenomiPhi v2 DNA Amplification Kit (GE Healthcare)
Multiplexed Illumina libraries were prepared using the KAPA Library Preparation Kit (NimbleGen) following the manufacture’s instruction; we used Illumina adapters from the SeqCap Adapter Kit (NimbleGen)

value: blastocyst

tag: developmental stage

value: day +5

tag: origin

value: single-cell

tag: embryo


title: Liver Female NASH Diet#4

source_name: Total liver

value: Total liver

value: Liver tissue lysate

value: Female


title: E6.T

value: remaining blastocyst


title: Liver Female NASH Diet#3


title: E3.C4

value: day +6


title: E3.C6


title: Liver Female NASH Diet#2


title: Newborn1_amnion


title: OEANO1, Kras, 3

city: Jilin

first: Meiyan

last: Sun

address: 5 Jilin Ave, Fengman District

institute: Jilin Medical University

data_processing:
Quality control through in house perl scripts
Reads mapping 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
DESeq2 was used for defferential expression analysis
Assembly: hg19
Supplementary files format and content: tab-delimited text files include gene ID, gene name, raw counts and fpkm of a group of samples (3 replicates per group)

source_name: pancreas

extract_protocol:
Cells in trizol were shipped overnight to Novogene (Beijing, China) on dry ice, the total RNA was extracted by following an in house protocol
Library from total RNA was prepared by Novogene (Beijing, China) by following an in house protocol

value: pancreas

tag: cell line

value: epithelial

value: ANO1 overexpression and oncogenic KRAS


title: OEANO1, Kras, 2


title: Liver Female WT Ctrl Diet#4

value: 24 weeks


title: E6.C3


title: Liver Female NASH Diet#1


title: OncoKras, 3

description: OncoKras.txt

value: Oncogenic KRAS


title: Treat 125x rep 4

city: Liège

first: Marc

last: Muller

address: B34 Sart Tilman

department: Life Sciences

country: Belgium

institute: Université de Liège

description: POP mix 125x

data_processing:
The sequencing reads were processed through the Nf-core rnaseq pipeline 3.0 (Ewels, P. A., et al.,  Nat Biotechnol 2020, 38, (3), 276-278) with default parameters and using the zebrafish reference genome (GRCz11) and the annotation set from Ensembl release 103 (www.ensembl.org).
Differential gene expression analysis was performed using DESeq2 pipeline
Assembly: zebrafish reference genome (GRCz11) and the annotation set from Ensembl release 103
Supplementary files format and content: Table_POP1_Control_5dpf.csv  and Table_POP2_Control_5dpf.csv files containing: Ensembl gene ID, gene name, baseMean, log2FoldChange, lfcSE, stat, pvalue, padj, control-baseMean, Treated_baseMean
Supplementary files format and content: 5dpf_Table_Counts.csv: individual sample count files. Ensembl gene ID,Gene name,BaseMean,control rep 1,control rep 2,control rep 4,Treat 75x rep 2,Treat 75x rep 3,Treat 75x rep 4,Treat 125x rep 1,Treat 125x rep 2,Treat 125x rep 3,Treat 125x rep 4

organism: Danio rerio

source_name: whole larvae

growth_protocol: Zebrafish (Danio rerio) of the AB strain were obtained from breeding facilities at the GIGA-Institute, Liege, Belgium. The water characteristics were as follows: pH = 7.4 and temperature = 28°C. The lighting was 14/10-h light/dark. Embryos were used and staged as described [28, 29]. Fish were mated and spawning was stimulated by the onset of light. The day before breeding, adult male and female zebrafish were set up in several breeding tanks, separated by a clear plastic wall. After the light was turned on the next morning, walls are removed, and eggs are generated by natural mating and then collected from 30 minutes to 2 hours after spawning. After sorting, fertilized clean eggs are moved to Petri dishes and incubated at 28°C in E3 medium (5 mM Na Cl, 0.17 mM KCl, 0.33 mM CaCl2, 0.33 mM MgSO4, 0.00001% Methylene Blue). The age of the embryos and larvae is indicated as hours post fertilization (hpf)

extract_protocol:
RNA was extracted from pools of 75 larvae using the RNA mini extraction kit (Qiagen, Hilden, Germany). Samples were lysed in RLT+ buffer with β-mercaptoethanol (Sigma-Aldrich, Overijse, Belgium) and homogenized 10 times with a 26-gauge needle in a 1 ml syringe. 22 ml of RNAse free water were used to resuspend total RNA. RNA extract was treated with DNAseI (Qiagen, Hilden, Germany) to avoid DNA contamination. The quantity (ng/ml) and quality of each extract was assessed by nanodrop spectrophotometer measurements (Thermofisher Scientific, Waltham, MA USA). Poor quality (260/280 < 2; 260/230 < 2) samples were subsequently purified by Lithium chloride precipitation, followed by 2 times pellet washing with 70% ethanol and resuspended in 40 µl of RNAse-free water and stored at -80°C. The integrity of total RNA extracts was assessed with BioAnalyzer analysis and provided RIN (RNA Integrity Number) scores for each sample (Agilent, Santa Clara, CA USA)
cDNA libraries were generated from 100 to 500 ng of extracted total RNA using the Illumina Truseq mRNA stranded kit (Illumina, San Diego, CA USA) according to the manufacturer's instructions.

treatment_protocol: The stock solutions for total POP mixture and six sub-mixtures were designed and prepared by the Norwegian University of Life Sciences, Oslo, Norway (Berntsen, Berg et al. 2017) . Stock solutions of POP mixtures and its sub-mixtures were prepared in DMSO and stored at -20 until the day of testing. For all treatments, we used the stock solution (1,000,000x) that was further diluted on the testing day in E3 zebrafish rising media. Next, the concentration of DMSO was corrected to achieve 0.1% in all cases, including in the control groups. Exposure tests were performed in 6 well-plates, with 25 fertilized eggs per well in 4 ml of E3 medium supplemented or not with the test compounds. For each experiment, 150 fertilized eggs were selected, 50 as controls and 100 for the specific treatment. Each treatment was repeated at least three times in independent experiments. We used a static-renewal approach were at least 90% of the media was refreshed every 24 hours. Exposure started between 0 to 6 hours post fertilization (hpf), the larvae were treated for 5 days.

value: whole larvae

value: AB


title: E3.C3


title: E3.C1


title: Liver Female WT Ctrl Diet#3


title: E3.T


title: Liver Female WT Ctrl Diet#2


title: OncoKras, 2

description: OncoKras.txt


title: Liver Female WT Ctrl Diet#1


title: Treat 125x rep 2

description: POP mix 125x


title: Treat 125x rep 3

description: POP mix 125x


title: Macrophage Male WT Ctrl Diet#1

value: Liver Resident Macrophage

value: Male


title: Liver Female OpnKI Mye NASH Diet#4

value: OpnKI Mye

value: NASH diet


title: OncoKras, 1

description: OncoKras.txt


title: OEANO1, 3

value: ANO1 overexpression


title: Treat 125x rep 1

description: POP mix 125x


title: OEANO1, 2


title: Treat 75x rep 4

description: POP mix 75x


title: OEANO1, 1


title: Liver Female OpnKI Mye NASH Diet#1

value: Total liver


title: Treat 75x rep 3

description: POP mix 75x


title: Liver Female OpnKI Mye NASH Diet#2

value: Liver tissue lysate


title: Treat 75x rep 2

description: POP mix 75x


title: WT, BxPC3, 3

description: WT_BxPC3 .txt

value: WT


title: Liver Female OpnKI Mye Ctrl Diet#4

value: Control diet

value: Female


title: OEANO1, Kras, 1

value: pancreas


title: WT, BxPC3, 2

description: WT_BxPC3 .txt

value: epithelial


title: control rep_2

value: DMSO 0.1%


title: Liver Female OpnKI Mye Ctrl Diet#3

value: 24 weeks


title: control rep_4


title: E15SCN

city: Higashiku

first: Sho

last: Okuda

state: Fukuoka

address: Maidashi 3-1-1

department: Surgery and Oncology

institute: Kyushu University

data_processing:
Raw sequencing reads were aligned to the human reference genome GRCh38 and processed to a matrix representing the UMI’s per cell barcode per gene using Cell Ranger v5.0.0 (10x Genomics)
Output files were analyzed with the R v3.6.3 package "Seurat v3.1.5".
Genome_build: GRCh38
Supplementary_files_format_and_content: To merge the data of all samples, we used the "SCTransform" package for the normalization and variance stabilization of molecular count data.

source_name: normal mucosa

extract_protocol:
Esophagus were resected, and a part of resected tissue was made into sigle cells. RNA was extracted and barcorded using Chromium Single Cell 3' Reagent Kits v3.1 (PN- 1000121).
Same as above.
single cell RNA-sequence

value: esophagus

tag: collection method

value: surgery


title: control rep_1

value: whole larvae

value: AB


title: WT, BxPC3, 1

description: WT_BxPC3 .txt


title: Liver Female OpnKI Mye Ctrl Diet#2


title: E15SCC

source_name: tumor tissue


title: Liver Female OpnKI Mye Ctrl Diet#1


title: Liver Female OpnKI Mye NASH Diet#3


title: E14SCN


title: E14SCC


title: E12SCN


title: E13SCN


title: treated rep 2

description: Plate1-6-9-2_NGS20-N768_AHNWVTDRXX_S6_L001_R1_001.fastq.gz

data_processing:
The sequencing reads were processed through the Nf-core rnaseq pipeline 3.0 (Ewels, P. A., et al.,  Nat Biotechnol 2020, 38, (3), 276-278) with default parameters and using the zebrafish reference genome (GRCz11) and the annotation set from Ensembl release 103 (www.ensembl.org).
Differential gene expression analysis was performed using DESeq2 pipeline
Assembly: zebrafish reference genome (GRCz11) and the annotation set from Ensembl release 103
Supplementary files format and content: .csv file containing: Ensembl gene ID, gene name, baseMean, log2FoldChange, lfcSE, stat, pvalue, padj, control-baseMean, Treated_baseMean

source_name: treated rep 2

growth_protocol: Zebrafish (Danio rerio) of the AB strain and the Tg(fli1:EGFP) [27] transgenic line were obtained from breeding facilities at the GIGA-Institute, Liege, Belgium. The water characteristics were as follows: pH = 7.4 and temperature = 28°C. The lighting was 14/10-h light/dark. Embryos were used and staged as described [28, 29]. Fish were mated and spawning was stimulated by the onset of light. The day before breeding, adult male and female zebrafish were set up in several breeding tanks, separated by a clear plastic wall. After the light was turned on the next morning, walls are removed, and eggs are generated by natural mating and then collected from 30 minutes to 2 hours after spawning. After sorting, fertilized clean eggs are moved to Petri dishes and incubated at 28°C in E3 medium (5 mM Na Cl, 0.17 mM KCl, 0.33 mM CaCl2, 0.33 mM MgSO4, 0.00001% Methylene Blue). The age of the embryos and larvae is indicated as hours post fertilization (hpf)

treatment_protocol: The plant extract solutions at different concentrations for toxicity tests were obtained by dilution of the stock solutions in embryo medium (E3). Treatments were administered to 2 hpf zebrafish embryos distributed in pools of 25 individuals into 6-well plates in E3 medium

tag: strain

value: Mahonia bealei ethanolic extract extract 100ug/ml


title: RNA-Seq M3cKO-LPS-1

city: Zhanjiang

first: Shuhua

last: Luo

state: guangdong

address: 2 Wenming East Roadan

institute: Guangdong Medical University

description: neutrophil, METTL3flox/flox-LyamCre, with LPS treatment

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: C57BL/6 neutrophil

extract_protocol:
RNA was harvested using TRIzol™ Plus RNA Purification Kit (Invitrogen). 10 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using U-mRNAseq Library Pre Kit following manufacturer's protocols.

treatment_protocol:
We treated C57BL/6 mice with intraperitoneal injection of LPS (20mg/kg) for endotoxemia model.
We treated C57BL/6 mice with intraperitoneal injection of salin for control group mice.

value: C57BL/6 neutrophil

value: METTL3 knockout

value: LPS treatment

value: Day 1


title: treated rep 3

description: Plate1-7-9-3_NGS20-N769_AHNWVTDRXX_S7_L001_R1_001.fastq.gz

source_name: treated rep 3


title: treated rep 1

description: Plate1-5-9-1_NGS20-N767_AHNWVTDRXX_S5_L001_R1_001.fastq.gz

source_name: treated rep 1


title: RNA-Seq M3cKO-LPS-2


title: control rep 4

description: Plate1-8-9-5_NGS20-N770_AHNWVTDRXX_S8_L001_R1_001.fastq.gz

source_name: control rep 4

value: DMSO 0.5%


title: RNA-Seq M3cKO-LPS-3


title: RNA-Seq WT-LPS-3

description: neutrophil, METTL3flox/flox, with LPS treatment

value: WT


title: E12SCC


title: RNA-Seq WT-LPS-2


title: RNA-Seq WT-LPS-1


title: E11SCN


title: control rep 2

description: Plate1-2-C2_NGS20-N764_AHNWVTDRXX_S2_L001_R1_001.fastq.gz

source_name: control rep 2


title: treated rep 4

description: Plate1-4-C5_NGS20-N766_AHNWVTDRXX_S4_L001_R1_001.fastq.gz

source_name: treated rep 4


title: RNA-Seq M3cKO-3

description: neutrophil, METTL3flox/flox-LyamCre, without LPS treatment

value: saline treatment


title: RNA-Seq M3cKO-2


title: control rep 1

description: Plate1-1-C1_NGS20-N763_AHNWVTDRXX_S1_L001_R1_001.fastq.gz

source_name: control rep 1


title: E09SCN


title: E07SCN


title: RNA-Seq WT-3

description: neutrophil, METTL3flox/flox, without LPS treatment


title: RNA-Seq M3cKO-1


title: E09SCC


title: RNA-Seq WT-2


title: E07SCC


title: RNA-Seq WT-1


title: E06SCN


title: E06SCC


title: Ribo-Seq M3cKO-1

extract_protocol:
METTL3 WT and MeETTL3 cKO  neutrophils were treated with CHX (100 ug/ml) for 1 min at 37°C. Then Cells were harvested by cell lysis buffer. After centrifugation at 4°C and 17,000× g for 10 min, the supernatant was digested with 10 μl RNaseI (Life) and 6 μl DNase I (Life) at 37°C for 45min. Nuclease digestion was stopped by adding 10µL of SUPERase·In RNase inhibitor (Ambion, Austin, TX, USA). Nuclease digestion was stopped by adding 10µL of SUPERase·In RNase inhibitor (Ambion, Austin, TX, USA). Short (50–80 bases) antisense DNA probes complementary to rRNA sequences was added to solution containing RFs, then RNase H (NEB, Ipswich, MA, USA) and DNase I (NEB, Ipswich, MA, USA) was added to digest rRNA and residual DNA probes. Finally, RFs were further purified using magnet beads (Vazyme, Nanjing, Jiangsu, China).
RNA libraries for Ribosome-seq were prepared using NEBNext® Multiple Small RNA Library following manufacturer's protocols.

treatment_protocol: We isolated neutrophil from METTL3f/f and METTL3f/f Lyzm-Cre mice by using Neutrophil Isolation Kit (Miltenyi Biotec)

value: Day 0


title: control rep 3

description: Plate1-3-C3_NGS20-N765_AHNWVTDRXX_S3_L001_R1_001.fastq.gz

source_name: control rep 3


title: MeRIP-Seq M3cKO_2_m6A_1

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the GrCM38/mm10 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01
bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate.
Assembly: mm10
Supplementary files format and content: bigWig

extract_protocol:
RNA was harvested using TRIzol™ Plus RNA Purification Kit (Invitrogen). Approximately 100 mg of total RNA for each condition was fragmented to ~100 bp in length with fragmentation buffer.Fragmented RNA was incubated with immunomagnetic beads premixed anti-m6A antibody. The mixture was then immunoprecipitated by incubation with protein-A beads. Next, purified RNA was used for the RNA-seq library for library construction by Illumina Hiseq 2500 (Illumina, CA, USA) and PE150 paired-end sequencing by InIllumina Novaseq ™ 6000.
ChIP-seq libraries were prepared using the U-mRNAseq Library Pre Kit. 10 ng of DNA was used as starting material for  m6A-seq library（IP）and RNA-seq library.


title: Ribo-Seq WT-2


title: Ribo-Seq WT-1


title: E11SCC


title: E04SCC


title: MeRIP-Seq M3cKO_1_m6A_1


title: E04SCN


title: U87-shPRMT6-3(shRNA-3)

city: suzhou

first: Ji

last: Wang

address: 1055 Sanxiang Road, Gusu District

institute: Soochow University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads were mapped to human genome assembly GRCh38 (ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz) using HISAT2 with default parameters.
HTSeq v0.13.5 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. GTF file:ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_29/gencode.v29.annotation.gtf.gz.
Assembly: GRCh38
Supplementary files format and content: File include Count and  FPKM values for each sample

source_name: human glioblastoma cell line

growth_protocol: Cells were grown in Dulbecco's Modified Eagle's Medium (DMEM) with 10% fetal bovine serum (FBS) and kept at 37°C in a humidified condition with 5% CO2.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, USA) according to the manufacturer’s instructions. The RNA purity and concentration was checked using the NanoPhotometer spectrophotometer (IMPLEN, CA, USA).
A total amount of 1.5 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: U87 cells were transfected with shRNA lentivirals by polybrene.

value: human glioblastoma cell line

value: transfected with PRMT6 shRNA


title: U87-shPRMT6-2(shRNA-2)


title: MeRIP-Seq M3cKO-2.input


title: MeRIP-Seq WT_2_m6A_1


title: ASCC3-FLAG RS input replicate 2

description: ASCC3-FLAG LSU input replicate 2

data_processing:
Library strategy: Sel-TCP-seq
Adaptor sequences were trimmed from raw reads with the use of cutadapt.
Reads of low quality were discarded with the use of fastq_quality_trimmer and fastq_quality_filter of the FASTX-Toolkit.
Ribosomal RNA reads were removed by alignment with human rRNA sequences with the use of STAR, and the remaining reads were aligned with the human transcriptome (GRCh38.p13) and human genome (hg38) also with the use of STAR.
Read counting was performed with the use of featureCounts.
Genome_build: hg38
Supplementary_files_format_and_content: Counts per transcript

source_name: HEK293T cells

extract_protocol:
Ribo-seq protocol: HEK293T cells were seeded at a density of 2.0 × 10^6 per 10-cm dish and the following analyses were performed 48 h after siRNA transfection. The medium was aspirated, and the cells were immediately placed on ice, washed once with ice-cold phosphate-buffered saline (PBS), and lysed with lysis buffer [50 mM Tris-HCl (pH 7.5), 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 1% Triton X-100, and EDTA-free protease inhibitor] supplemented with CHX (100 μg/ml). The lysates were then incubated with TURBO DNase on ice for 10 min and centrifuged at 15,000 rpm for 10 min at 4°C, and the resulting supernatants were collected carefully, assayed for RNA concentration with a Qubit RNA BR assay kit, incubated with RNase I (20 U per 10 μg of RNA, Epicentre) for 45 min at 25°C, and placed on ice before the addition of SUPERase•In RNase inhibitor (Invitrogen). The samples were then loaded on a 1 M sucrose cushion buffer [20 mM Tris-HCl (pH 7.5), 150 mM NaCl, 5 mM MgCl2, SUPERase•In (10 U/ml), 1 mM DTT, and CHX (100 μg/ml)], and the gradients were centrifuged at 100,000 rpm for 1 h at 4°C in a Beckman TLA110 rotor. The resulting pellets were suspended in ribosome splitting buffer [20 mM Tris-HCl (pH 7.5), 300 mM NaCl, 5 mM EDTA, SUPERase•In (20 U/ml), 1 mM DTT, 1% Triton X-100] and subjected to purification with the use of an Amicon Ultra filtration device (100-kDa cutoff, Millipore) to deplete rRNAs.
TCP-seq and Sel-TCP-seq protocol: Cells were seeded at a density of 8.0 × 10^6 cells per 15 cm dish, with 8 to 18 dishes per assay, and cultured for 2 days. Then, the subconfluent cells were treated for 10 min at room temperature with phosphate-buffered saline (PBS) containing 0.25% formalin, after which glycine was added to a final concentration of 125 mM and the cells were collected. The cells were washed three times with ice-cold PBS, lysed in lysis buffer [50 mM Tris-HCl (pH 7.5), 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 1% Triton X-100, cOmplete EDTA-free protease inhibitor (Roche)] supplemented with cycloheximide (CHX) (100 μg/ml), and incubated for 10 min on ice. The lysates were centrifuged at 20,380 × g for 10 min at 4°C, and the resulting supernatants were collected carefully, assayed for RNA concentration with a Qubit RNA BR assay kit, incubated with RNase I (20 U per 10 μg of RNA, Thermo Fisher Scientific) at 25°C for 45 min, and then placed on ice before the addition of 200 U SUPERase•In RNase inhibitor (Invitrogen). The samples were loaded on a 5% to 30% sucrose gradient buffer [20 mM Tris-HCl (pH 7.5), 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, CHX (100 μg/ml), SUPERase•In (10 U/ml)] and centrifuged at 38,200 rpm (180,000 × g) for 4 h at 4°C in a Himac P40ST rotor. The gradient was fractionated with the use of a TRIAX gradient-profiling system and AC-5700P microcollector. Polysome profiles were determined by measurement of absorbance at 260 nm. Dynabeads Protein G were conjugated with antibodies to FLAG by incubation overnight at 4°C in lysis buffer supplemented with 0.5% bovine serum albumin, and they were washed three times with lysis buffer before use. Small aliquots of the small ribosomal subunits (SSU) or large ribosomal subunits (LSU) fractions were stored for input or TCP-seq, and the remaining aliquots were incubated with the beads for 90 min at 4°C, and the resulting immunoprecipitates were washed four times with wash buffer [50 mM Tris-HCl (pH 7.5), 300 mM NaCl, 1 mM DTT, 0.1% Triton X-100]. For Sel-TCP-seq analysis, 250 μl of decrosslinking buffer [1% SDS, 10 mM EDTA, 10 mM Tris-HCl (pH 7.5), 10 mM glycine], 750 μl of ISOGEN LS, and 200 μl of chloroform were added to the beads, and incubated for 45 min at 65°C, and RNA was then purified by precipitation with isopropanol.
Ribo-seq protocol: The purified RNA was subjected to selection on the basis of a size range of 17 to 34 nt by electrophoresis through a 15% polyacrylamide and Tris-borate-EDTA (TBE)–urea gel (SuperSep RNA, Fujifilm). The footprint fragments were treated with T4 PNK to repair the 2x-3x cyclic phosphates, a DNA linker including barcode sequences (NI-810 to NI-817) was ligated with the use of T4 RNA Ligase 2, truncated K227Q (New England Biolabs), and the resulting products were purified on a 15% polyacrylamide and TBE-urea gel. Ribosomal RNAs were further depleted with the use of RiboZero Gold (Illumina). Reverse transcription was performed with the NI-802 primer, and the resulting products were purified on a 15% polyacrylamide and TBE-urea gel. The purified cDNAs were circularized with circLigase II (Lucigen), and index sequences were then added by amplification in a PCR reaction with the common primer (NI-798) and primers including index sequences (NI-799 and NI-822 to NI-826). Products of the desired size were purified on a 15% polyacrylamide nondenaturing gel (SuperSep DNA, Fujifilm), and the libraries were sequenced with a NovaSeq 6000 system (Illumina).
TCP-seq and Sel-TCP-seq protocol: The purified RNA was selected according to size in the range of 17 to 100 nt by electrophoresis in a 15% polyacrylamide and TBE-urea gel, and subjected to dephosphorylation, DNA linker ligation, and rRNA depletion with RiboZero Gold as described for the Ribo-seq protocol. Reverse transcription was performed with the use of the SI-019 primer, and the resulting products were purified on a 15% polyacrylamide and TBE-urea gel. The second linker (SI-018) was ligated by incubation overnight at 25°C with T4 RNA Ligase 1 (ssRNA Ligase), High Concentration (New England Biolabs). The products were then amplified in a PCR reaction with the same primers as used for the Ribo-seq protocol, and those of the desired size were purified by electrophoresis through a 15% polyacrylamide nondenaturing gel. The libraries were sequenced with a NovaSeq 6000 system.

value: ASCC3-FLAG KI


title: ASCC3-FLAG SSU IP replicate 1

value: FLAG


title: U87-shPRMT6-1(shRNA-1)


title: ASCC3-FLAG RS input replicate 1

description: ASCC3-FLAG LSU input replicate 1


title: MeRIP-Seq M3cKO-1.input


title: U87-NC-3(NC-3)

value: transfected with Scramble shRNA


title: U87-NC-2(NC-2)


title: Ribo-Seq M3cKO-2


title: MeRIP-Seq WT-2.input


title: ASCC3-FLAG SSU input replicate 1


title: ASCC3-FLAG SSU input replicate 2


title: ASCC3-FLAG RS IP replicate 2

description: ASCC3-FLAG LSU IP replicate 2


title: ASCC3-FLAG RS IP replicate 1

description: ASCC3-FLAG LSU IP replicate 1


title: ASCC3-FLAG SSU IP replicate 2


title: eIF4E-FLAG RS IP replicate 2

description: eIF4E-FLAG 80S IP replicate 2

value: eIF4E-FLAG KI


title: eIF4E-FLAG RS IP replicate 1

description: eIF4E-FLAG 80S IP replicate 1


title: GSC_CW468_shRNA_shSNX10.358_Replicate_2

city: San Diego

first: Jeremy

last: Rich

state: CA

address: 9500 Gilman Drive #0695

institute: University of California, San Diego

data_processing:
FASTQ sequencing reads were trimmed using Trim Galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and transcript quantification was performed using Salmon in the quasi-mapping mode. Salmon “quant” files were converted using Tximport (https://bioconductor.org/packages/release/bioc/html/ tximport.html) and differential expression analysis was performed using DESeq2. Gene set enrichment analysis was performed by selecting differentially expressed genes (FDR-corrected p-value < 0.01, Log2 fold change > 0.5 or <-0.5), generating a pre-ranked list, and inputting a pre-ranked list into the GSEA desktop application (http://software.broadinstitute. org/gsea/downloads.jsp). Pathway enrichment bubble plots were generated using the Bader Lab Enrichment Map Application and Cytoscape (http://www.cytoscape.org).
Assembly: hg38
Supplementary files format and content: Excel spreadsheet showing raw counts, transcript abundance, and differential expression analysis

source_name: Glioblastoma Stem Cell

extract_protocol:
For SNX10 knockdown experiments, Trizol reagent (Sigma Aldrich) was used to isolate total cellular RNA from cell pellets according to the manufacturer’s instructions. Three patient-derived GSCs were utilized with a non-targeting shRNA control and three independent non-overlapping shRNAs targeting SNX10 for each GSC. Biologic duplicates were utilized for each GSC. RNA was purified using an mRNAeasy kit (Qiagen) and subjected to RNA-sequencing by Novogene Corporation.
After the QC procedures, mRNA from eukaryotic organisms is enriched using oligo(dT) beads. For prokaryotic organisms or eukaryotic organisms' long-non-coding libraries, rRNA is removed using the Ribo-Zero kit that leaves the mRNA. First, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichment.

value: Glioblastoma Stem Cell

value: Patient Derived

value: SNX10 Knockdown shSNX10.358


title: GSC_CW468_shRNA_shSNX10.648_Replicate_2

value: SNX10 Knockdown shSNX10.648


title: GSC_CW468_shRNA_shSNX10.2010_Replicate_2

value: SNX10 Knockdown shSNX10.2010


title: MeRIP-Seq WT_1_m6A_1

value: C57BL/6 neutrophil


title: eIF4E-FLAG SSU IP replicate 2


title: CNS endothelial cells, PTX, 3

city: New York

first: Timothy

last: Vartanian

state: NY

address: 1300 York Avenue

department: Brain and Mind Research Institute

institute: Weill Cornell Medical College, Cornell University

data_processing:
The raw sequencing reads in BCL format were processed through bcl2fastq 2.19 (Illumina) for FASTQ conversion and demultiplexing.
The quality of the sequenced reads was assessed with FastQC and QoRTs.
Sequenced reads were aligned with default parameters to the mouse reference genome (GRCm38.p6) using STAR vv2.7.6a.
Gene expression estimates were obtained with featureCounts v2.0.1 using composite gene models from Gencode vM25.
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited text files include raw abundance values for each sample as obtained from featureCounts

source_name: Spinal cord endothelial cells

extract_protocol:
CNS tissue was enzymatically dissociated with a papain solution followed by vigorous trituration and a second dissociation with collangese and dispase solution.  Myelin was removed using Miltenyi Biotec Myelin Removal Beads II per the manufacturer’s instructions.  Isolated cells were stained with anti-CD31 clone 390, anti-CD45 clone 30-F11 (, and CD11b clone M1/70, anti-CD13 clone R3-242, anti-PDGFbeta clone APB%, and DAPI.  Viable endotheilail cells (DAPI-) positive for CD31 only (CD31+, CD45-, CD11b-, CD13-, and PDGFbeta -) were sorted via FACS using a BD Biosciences FACSAria II Cell Sorter.  RNA was extracted from sorted endothelial cells using Qiagen’s RNeasy Plus Micro Kit per the manufacturer’s instructions. cDNA was generated using Takara’s SMART-Seq v4 Ultra Low Input RNA Kit.
Total RNA integrity was checked using a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). The cDNA synthesis and amplification were performed by SMART-Seq v4 ultra low input RNA kit (Takara Bio USA, Mountain View, CA, USA) starting with less than 1 ng of total RNA from each sample.

treatment_protocol: Mice were treated with PBS, ETX (0.5 μg/kg b.w.), or PTX (5 μg/kg b.w) on two consecutive day.  16 hours after the second dose, CNS endothelial cells were isolated from spinal cords or brains with the cerebellum removed as previously described (please cite Pulido et al, 2020, Neuronal Activity Regulates Blood-Brain Barrier Efflux Transport through Endothelial Circadian Genes, Neuron. 2020 Dec 9;108(5):937-952.e7. doi: 10.1016/j.neuron.2020.09.002. Epub 2020 Sep 25).

value: Spinal cord endothelial cells

value: PTX


title: CNS endothelial cells, PTX, 2


title: eIF4E-FLAG SSU IP replicate 1


title: CNS endothelial cells, ETX, 3

value: ETX


title: GSC_CW468_shRNA_shSNX10.2010_Replicate_1


title: GSC_CW468_shRNA_shControl_Replicate_2

value: Control shRNA


title: CNS endothelial cells, ETX, 2


title: GSC_CW468_shRNA_shSNX10.358_Replicate_1


title: GSC_CW468_shRNA_shSNX10.648_Replicate_1


title: eIF4E-FLAG RS input replicate 1

description: eIF4E-FLAG LSU input replicate 1


title: eIF4E-FLAG RS input replicate 2

description: eIF4E-FLAG LSU input replicate 2


title: eIF4E-FLAG SSU input replicate 2


title: CNS endothelial cells, PBS, 2

value: PBS


title: GSC_CW468_shRNA_shControl_Replicate_1


title: CNS endothelial cells, PBS, 1


title: eIF4E-FLAG SSU input replicate 1


title: U87-NC-1(NC-1)

value: human glioblastoma cell line


title: GSC_3565_shRNA_shSNX10.2010_Replicate_2


title: eIF4A1-FLAG RS IP replicate 2

description: eIF4A1-FLAG LSU IP replicate 2

value: eIF4A1-FLAG KI


title: GSC_3565_shRNA_shSNX10.358_Replicate_2


title: CNS endothelial cells, PTX, 1


title: MeRIP-Seq WT-1.input

value: WT


title: eIF4A1-FLAG RS IP replicate 1

description: eIF4A1-FLAG LSU IP replicate 1

value: FLAG


title: eIF4A1-FLAG SSU IP replicate 2


title: eIF4A1-FLAG SSU IP replicate 1


title: GSC_3565_shRNA_shSNX10.648_Replicate_2


title: eIF4A1-FLAG RS input replicate 1

description: eIF4A1-FLAG LSU input replicate 1


title: eIF4A1-FLAG RS input replicate 2

description: eIF4A1-FLAG LSU input replicate 2


title: GSC_3565_shRNA_shControl_Replicate_2


title: GSC_3565_shRNA_shSNX10.358_Replicate_1


title: CNS endothelial cells, ETX, 1


title: eIF4A1-FLAG SSU input replicate 2


title: TCL1_FL3_Rep4

city: Luxembourg

first: Etienne

last: Moussay

address: 6 rue Nicolas-Ernest Barblé

department: Cancer Research

country: Luxembourg

institute: Luxembourg Institute of Health

data_processing:
After initial QCs using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and FastQ Screen (https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/), fastq files were processed using a local Snakemake workflow including the following main steps.
First, raw reads were trimmed from their UMI index, poly A and adapter sequences using a combination of dedicated scripts and cutadapt (v2.10).
Next, filtered reads were submitted for mapping (STAR v2.5.3a) on the Human Reference genome (GRCh38) or Mouse Reference Genome (GRCm38)
Collapsing of reads originating from the same fragment was achieved with umi_tools (v 1.0.0) and counting was perfomed with featureCounts (subread v2.0.0).
Assembly: GRC38
Supplementary files format and content: Table with raw gene counts for every gene and every sample

source_name: spleen

extract_protocol:
RNA was harvested and isolated using NucleoZOL reagent and columns. QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina was used with 500 ng of total RNA for the construction of sequencing libraries. UMI were added to the protocol.
QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina was used with 500 ng of total RNA for the construction of sequencing libraries. UMI were added to the protocol.
3'-RNA-Seq

value: spleen

value: CLL B cells

value: FL3 50nM


title: eIF4A1-FLAG SSU input replicate 1


title: ASCC3 KD HEK293T #1 TCP-seq replicate 2

data_processing:
Library strategy: TCP-seq
Adaptor sequences were trimmed from raw reads with the use of cutadapt.
Reads of low quality were discarded with the use of fastq_quality_trimmer and fastq_quality_filter of the FASTX-Toolkit.
Ribosomal RNA reads were removed by alignment with human rRNA sequences with the use of STAR, and the remaining reads were aligned with the human transcriptome (GRCh38.p13) and human genome (hg38) also with the use of STAR.
Read counting was performed with the use of featureCounts.
Genome_build: hg38
Supplementary_files_format_and_content: Counts per transcript

value: ASCC3 KD


title: GSC_3565_shRNA_shControl_Replicate_1

value: Glioblastoma Stem Cell

value: Patient Derived


title: TCL1_FL3_Rep2


title: eIF4A1 and eIF4A2 DKD HEK293T #2 TCP-seq replicate 2

value: eIF4A1 and eIF4A2 DKD


title: TCL1_FL3_Rep1


title: eIF4A1 and eIF4A2 DKD HEK293T #1 TCP-seq replicate 2


title: TCL1_DMSO_Rep3

value: DMSO


title: GSC_MES28_shRNA_shSNX10.2010_Replicate_1

value: SNX10 Knockdown shSNX10.2010


title: siControl HEK293T TCP-seq replicate 2

value: siControl


title: GSC_MES28_shRNA_shControl_Replicate_2


title: GSC_MES28_shRNA_shSNX10.648_Replicate_2

value: SNX10 Knockdown shSNX10.648


title: GSC_3565_shRNA_shSNX10.2010_Replicate_1


title: TCL1_DMSO_Rep2


title: ASCC3 KD HEK293T #2 TCP-seq replicate 1


title: TCL1_DMSO_Rep1


title: ASCC3 KD HEK293T #1 TCP-seq replicate 1


title: GSC_3565_shRNA_shSNX10.648_Replicate_1


title: GSC_MES28_shRNA_shSNX10.648_Replicate_1


title: GSC_MES28_shRNA_shControl_Replicate_1

value: Control shRNA


title: TCL1_FL3_Rep3


title: GSC_MES28_shRNA_shSNX10.2010_Replicate_2


title: ASCC3 KD HEK293T #2 TCP-seq replicate 2


title: eIF4A1 and eIF4A2 DKD HEK293T #2 TCP-seq replicate 1


title: NSC, H/R, rep1

city: Shenyang

first: Bo

last: Fang

state: Liaoning

address: NO.155, North Nanjing Street

department: Department of Anesthesiology

institute: The First Hospital of China Medical University

description: H/R-A

data_processing:
3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3)
For mRNA and lncRNA parts: The clean reads of all libraries were aligned to the reference genome  by Hisat2 software (v2.0.4)
For circRNA part: The high quality reads were aligned to the reference genome/transcriptome with STAR software (v2.5.1b) and circRNAs were detected and identified with DCC software (v0.4.4)
HTSeq software (v0.9.1) was used to get the gene level (mRNA) and transcript level (lncRNA) raw count as the expression profiling, and edgeR (v3.16.5) was used to perform normalization and differentially expressed RNAs were identified by p-value and fold change
Assembly: MM10
Supplementary files format and content: "Gene/LncRNA/CircRNA Expression Profiling. txt" shows the expression of mRNAs, lncRNAs and circRNAs in each sample. Additional statistical enrichment information and gene annotation information was also provided

growth_protocol: C17.2 NSCs were cultured in Dulbecco’s modified Eagle’s medium with 10% fetal bovine serum, 1% penicillin-streptomycin, and 1% glutamine. The culture medium was replaced every two days, and the cells were passaged every 4-5 days.

extract_protocol:
Total RNA was used for removing the rRNAs with GenSeq® rRNA Removal Kit
The rRNA-depleted samples were subjected to library construction with GenSeq® Low Input RNA Library Prep Kit according to the manufacturer’s instructions

treatment_protocol: To simulate ischemia-reperfusion in vitro, NSCs were placed in a humid anaerobic chamber perfused with 5% O2, 5% CO2, and 90% N2 at 37 °C for 12 h. NSCs were then moved to standard oxygen conditions and cultured for 48 h.

value: neural stem cells

value: hypoxia/reoxygenation


title: NSC, H/R, rep2

description: H/R-B


title: GSC_MES28_shRNA_shSNX10.358_Replicate_2

value: SNX10 Knockdown shSNX10.358


title: NSC, H/R, rep3

description: H/R-C

value: WT


title: siControl HEK293T TCP-seq replicate 1


title: RPE1 cells, doxorubicin 0.34 uM

city: Berlin

first: Maria

last: Valieva

address: Ihnestraße 63

country: Germany

institute: MPIMG

data_processing:
FASTQ files were mapped using STAR with parameters:--alignIntronMax 100000 --outFilterMismatchNmax 4 --alignTranscriptsPerReadNmax 10000 --outFilterMultimapNmax 500
Read counting was performed with Rsubrea (featureCounts)
Normalization of the read counts and differential expression was performed with DESeq2
Assembly: hg38 UCSC (iGenomes)
Supplementary files format and content: tab-separated file with differentially expressed genes as output of DESeq2 (p-adj<0.01)
Supplementary files format and content: tab-separated file with raw counts

growth_protocol: RPE1 cells were grown in DMEM, supplemented with 10% FCS and 1% Pen/Strep in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen), with final concentration 0.9 - 1.3 ug. Poly A-selected RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Roche's KAPA mRNA HyperPrep Kit with NextFlex UDIs.
stranded mRNA (Poly A-selection)

treatment_protocol: Cells were treated with doxorubicin, for 18h with two concentrations: either 340 uM 3 or 200 uM

value: Human retinal pigment epithelial

value: doxorubicin 0.34 uM


title: RPE1 cells, doxorubicin 02uM, rep2

value: doxorubicin 0.2 uM


title: NSC, control, rep3

description: Control-C

value: control


title: ASCC3 KD HEK293T #2 Ribo-seq replicate 2

data_processing:
Library strategy: Ribo-seq
Adaptor sequences were trimmed from raw reads with the use of cutadapt.
Reads of low quality were discarded with the use of fastq_quality_trimmer and fastq_quality_filter of the FASTX-Toolkit.
Ribosomal RNA reads were removed by alignment with human rRNA sequences with the use of STAR, and the remaining reads were aligned with the human transcriptome (GRCh38.p13) and human genome (hg38) also with the use of STAR.
Read counting was performed with the use of featureCounts.
Genome_build: hg38
Supplementary_files_format_and_content: Counts per transcript

value: ASCC3 KD


title: RPE1 cells, doxorubicin 0.2 uM


title: NSC, control, rep2

description: Control-B


title: RPE1 cells, DMSO, rep2


title: NSC, control, rep1

description: Control-A


title: GSC_MES28_shRNA_shSNX10.358_Replicate_1

value: Glioblastoma Stem Cell


title: ASCC3 KD HEK293T #2 Ribo-seq replicate 1


title: ASCC3 KD HEK293T #1 Ribo-seq replicate 2


title: ASCC3 KD HEK293T #1 Ribo-seq replicate 1


title: NSC, H/R_IP, rep3

description: treatment(H/R)

data_processing:
3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3)
Clean reads of all libraries were aligned to the reference genome  by Hisat2 software (v2.0.4)
Methylated sites on RNAs (peaks) were identified by MACS software
Assembly: MM10
Supplementary files format and content: "Methylated_RNA_sites.txt" illustrated the m6A methylation sites information, including m6A peak start site, peak stop site, peak ID, m6A peak score, peak length, generated by MACS software (see column B to column F). Additional statistical enrichment information and gene annotation information was also provided
Library strategy: MeRIP-seq

extract_protocol:
Immunoprecipitation of total RNA was completed using the GenSeq® m6A-IP Kit according to the manufacturer’s instructions.
GenSeq® Low Input Whole RNA Library Prep Kit was used to construct RNA libraries for IP and input samples according to the manufacturer’s instructions.


title: eIF4A1 and eIF4A2 DKD HEK293T #1 TCP-seq replicate 1


title: eIF4A1 and eIF4A2 DKD HEK293T #2 Ribo-seq replicate 2


title: NSC, H/R_IP, rep2

description: treatment(H/R)


title: eIF4A1 and eIF4A2 DKD HEK293T #2 Ribo-seq replicate 1


title: eIF4A1 and eIF4A2 DKD HEK293T #1 Ribo-seq replicate 2


title: NSC, H/R_input, rep2

description: treatment(H/R)


title: input-RPE-DOX034_R1

data_processing:
Single-end reads from ChIP-seq experiments were mapped with bowtie (v2.2.6) to the reference genome hg19.
Mapped reads were filtered for mapping quality MAPQ ≥10, and duplicates were removed using samtools (v1.8).
Reads were extended to 200bp and scaled by the total number of unique reads (total count of reads/106) to produce coverage tracks that could be visualized in UCSC. Tracks were reformatted in the bigWig file
Assembly: hg19
Supplementary files format and content: bigWig (except for Input sample)

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a Bioruptor
For the ChIP-seq library preparation we have followed Illumina's TruSeq Chip Sample Preparation Guide including NextFlex UDIs.  have followed Illumina's TruSeq Chip Sample Preparation Guide including NextFlex UDIs.

treatment_protocol: Cells were treated with 1) DMSO for 18h 2) doxorubicin, for 18h with two final concentrations: either 340 uM 3 or 200 uM 3) ICRF193 for 18h with a final concentration 5uM

tag: chip antibody


title: input-RPE-DOX02_R1


title: eIF4A1 and eIF4A2 DKD HEK293T #1 Ribo-seq replicate 1


title: NSC, control_IP, rep2

description: control


title: input-RPE-DMSO_R1


title: input-RPE-ICRF193_R1


title: siControl HEK293T Ribo-seq replicate 2


title: NSC, H/R_input, rep3

description: treatment(H/R)


title: NSC, H/R_input, rep1

description: treatment(H/R)


title: ASCC3 KD HEK293T #2 RNA-seq replicate 2

data_processing:
Adaptor sequences were trimmed from raw reads with the use of cutadapt.
Reads of low quality were discarded with the use of fastq_quality_trimmer and fastq_quality_filter of the FASTX-Toolkit.
Ribosomal RNA reads were removed by alignment with human rRNA sequences with the use of STAR, and the remaining reads were aligned with the human transcriptome (GRCh38.p13) and human genome (hg38) also with the use of STAR.
Read counting was performed with the use of featureCounts.
Genome_build: hg38
Supplementary_files_format_and_content: Counts per transcript


title: RPE1 cells, DMSO


title: NSC, control_IP, rep3

description: control


title: ASCC3 KD HEK293T #2 RNA-seq replicate 1


title: siControl HEK293T Ribo-seq replicate 1


title: NSC, control_input, rep3

description: control


title: NSC, control_input, rep1

description: control


title: ASCC3 KD HEK293T #1 RNA-seq replicate 2


title: NSC, H/R_IP, rep1

description: treatment(H/R)


title: ASCC3 KD HEK293T #1 RNA-seq replicate 1


title: eIF4A1 and eIF4A2 DKD HEK293T #2 RNA-seq replicate 2


title: eIF4A1 and eIF4A2 DKD HEK293T #2 RNA-seq replicate 1


title: eIF4A1 and eIF4A2 DKD HEK293T #1 RNA-seq replicate 2


title: eIF4A1 and eIF4A2 DKD HEK293T #1 RNA-seq replicate 1


title: siControl HEK293T RNA-seq replicate 2


title: NSC, control_IP, rep1

description: control


title: FB, d10, Replicate 3

city: Munich

first: Dongsheng

last: Jiang

address: Max-Lebsche-Platz 31

department: Institute of Regenerative Biology and Medicine

institute: Helmholtz Zentrum München

data_processing:
RNA-Seq raw reads were mapped to the mouse genome build mm10 using the STAR in nf-core/rnasea. The mapped reads were then counted using salmon.
Raw counts were applyed differential gene expression analysis (DEG) using DEseq2 (version 1.34.0 with R version 4.1.2).
Normalized counts were scaled for Pearson’s correlation matrices and plotting feature genes expression in heat map.
Gene ontology (GO) enrichment of DEGs was done using clusterProfiler (version 4.2.2) and viewed by ggplot2 (Version 3.3.6)
Assembly: mm10
Supplementary files format and content: tsv files include raw coults for each Sample

molecule: polyA RNA

source_name: Skin

extract_protocol:
Sorted GFP+ cells were lysed and cDNA synthesis and expansion were performed using the Smart-Seq® v4 Ultra® Low Input RNA Kit for Sequencing (Takara #634889), according to manufacturer’s instructions. The amplified cDNA was purified with NucleoMag NGS Clean-up and Size Select beads (Takara 7449705).
The library preparation were performed by Biomarker Technologies (BMKGene) GmbH (Münster, Germany). Double-stranded cDNA were ligated with adaptors, enriched by Agencourt AMPure XP beads (Beckman Coulter, Inc) and amplified by PCR.

treatment_protocol: 5-mm full-thickness excisional wounds were made on the back of AdipoqCre;R26mTmG and En1Cre;R26mTmG mice. Wounds were harvested at 10 days and 21 days after wounding. Adipocytes were FACS sorted as GFP+ cells from AdipoqCre;R26mTmG wounds, and fibroblasts were FACS sorted from En1Cre;R26mTmG wounds.

value: Skin

value: Fibroblast

value: Excisional wound at day 10


title: FB, d21, Replicate 1

value: Excisional wound at day 21


title: FB, d10, Replicate 2


title: FB, d21, Replicate 3


title: FB, d21, Replicate 2


title: FB, NS, Replicate 3

value: None (normal skin)


title: FB, NS, Replicate 2


title: FB, d10, Replicate 1


title: FB, NS, Replicate 1


title: AD, d21, Replicate 2

value: Adipocytes

value: AdipoqCre+


title: AD, d21, Replicate 1


title: NSC, control_input, rep2

description: control

value: neural stem cells


title: MiaPaCa2, injected Part4, Leader, rep3 [s_Part4Lead3]

first: Bic

last: MSKCC

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

data_processing:
CutAdapt version cutadapt-1.6 was used to trim and filter reads. Adapters were trimmed with minimum overlap of 10 bases and reads of less than half original read length were filtered out.
STAR version STAR-STAR_2.5.0a was run using the 2-pass method. First pass was run with the following parameters: --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMattributes All --outSAMunmapped Within. Genome database was then generated using the minimum read length of half desired read length and second pass was run against the new genome file with the same parameters as pass 1.
Expression count matrix was computed using HTSeq version HTSeq-0.5.3. Parameters set were: -m intersection-strict -s no -t exon
Raw count matrix was processed using the R/Bioconductor package DESeq, version 1.22.1, which is used to both normalize the full dataset and analyze differential expression between sample groups.
Assembly: hybrid
Supplementary files format and content: tab-delimited file containing normalized counts

extract_protocol:
RNA was extracted using the RNeasy Micro Kit (Qiagen #74004). After RiboGreen quantification and quality control by Agilent BioAnalyzer, 2 ng total RNA with RNA integrity numbers ranging from 9.5 to 10 underwent amplification using the SMART-Seq v4 Ultra Low Input RNA Kit (Clonetech catalog # 63488), with 12 cycles of amplification.
Subsequently, 10 ng of amplified cDNA was used to prepare libraries with the KAPA Hyper Prep Kit (Kapa Biosystems KK8504) using 8 cycles of PCR. Samples were barcoded and run on a HiSeq 4000 in a PE50 run, using the HiSeq 3000/4000 SBS Kit (Illumina).  An average of 34 million paired reads was generated per sample and the percent of mRNA bases per sample ranged from 63% to 83%.

value: pancreatic cancer cells

value: In vivo Passage4


title: AD, d10, Replicate 3


title: MiaPaCa2, injected Part4, Leader, rep2 [s_Part4Lead2]

value: WT


title: AD, d10, Replicate 2


title: AD, d10, Replicate 1


title: MiaPaCa2, injected Part3, Leader, rep3 [s_Part3Lead3]

value: In vivo Passage3


title: AD, NS, Replicate 3


title: MiaPaCa2, injected Part4, Leader, rep1 [s_Part4Lead1]


title: siControl HEK293T RNA-seq replicate 1

value: siControl


title: MiaPaCa2, injected Part3, Leader, rep2 [s_Part3Lead2]


title: B6

first: Jingwen

last: Shi

address: 36 Sanhao Street, Heping District, Shenyang City

institute: Shengjing hospital of China medical university

data_processing:
The information for the reference genome used in this project is as follows: Version 104, Ensembl database, genome Homo_sapiens GRCh38. DNA. Primary_assembly. Fa
RNA was extracted by TRIzol, total amount and purity were controlled by NanoDrop ND-1000, and mRNA with PolyA was purified by oligo(dT) magnetic beads and captured specifically. The segmentation was carried out using the NEBNext Magnesium RNA Fragmentation Module.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using TruSeq Stranded mRNA Library Prep Kits were used for PolyA capture, junction and labeling. (parameter- Quality limit: 0.05)
Plane raw data format for fastq, use the fastp (https://github.com/OpenGene/fastp) software to offload raw data for quality control, including removal of joint, repeat sequence, and low quality parameters as the default.
Read count extraction and normalization were performed.
Supplementary files format and content: fpkm.txt

organism: Homo

source_name: ectopic endometrium

extract_protocol:
RNA was extracted by TRIzol, total amount and purity were controlled by NanoDrop ND-1000, and mRNA with PolyA was purified by oligo(dT) magnetic beads and captured specifically. The segmentation was carried out using the NEBNext Magnesium RNA Fragmentation Module.
Illumina Novaseq 6000 sequencing platform was used and the sequencing mode was PE150.

value: ectopic endometrium

tag: patient diagnosis

value: adenomyosis


title: B2


title: B7


title: B1


title: AD, NS, Replicate 2


title: MiaPaCa2, injected Part2, Leader, rep1 [s_Part2Lead1]

value: In vivo Passage2


title: MiaPaCa2, injected Part1, Leader, rep3 [s_Part1Lead3]

value: In vivo Passage1


title: MiaPaCa2, injected Part2, Leader, rep3 [s_Part2Lead3]


title: A6

source_name: control

value: eutopic endometrium


title: MiaPaCa2, injected Part3, Leader, rep1 [s_Part3Lead1]


title: MiaPaCa2, injected Part2, Leader, rep2 [s_Part2Lead2]


title: A7


title: MiaPaCa2, injected Part1, Leader, rep2 [s_Part1Lead2]


title: AD, NS, Replicate 1

value: Skin


title: MiaPaCa2, injected Part1, Leader, rep1 [s_Part1Lead1]


title: A4


title: Donor_3_Macula

type: RNA

city: Tokyo

first: Taku

last: Tanaka

address: 2-10-1 Okura, Setagaya

department: Ophthalmology

institute: National Center for Child Health and Development

hyb_protocol: 0.6 µg of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Sureprint G3 Human Gene Expression Microarrays 8 × 60 K v2 (Agilent Technologies) for 17 hours at 65°C in a hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with Gene Expression Wash Buffer 1 (Agilent Technologies) and 1 minute at 37°C with Gene Expression Wash Buffer 2 (Agilent Technologies), then air-dried immediately.

scan_protocol: Slides were scanned on an Agilent G2505C microarray scanner at 100% PMT and 3 um resolution.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent Technologies) using default parameters (protocol GE1_107_Sep09 and Grid: 039494_D_F_20120411) to obtain background subtracted and spatially detrended Processed Signal intensities. Normalized signal intensity (75th percentile shift normalized) calculated from the processed signal after Feature Extraction using the GeneSpring software version 12.1 (Agilent).

source_name: donor3, retina, macula region

label_protocol: Total RNAs (50 ng) extracted from the macular and peripheral regions of retina were used to prepare Cy3-labelled target cRNA using the Low Input Quick Amp Labeling Kit (Agilent Technologies) followed by RNeasy column purification (QIAGEN).

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (QIAGEN, Hilden, Germany) in accordance with the manufacturer’s instructions. The concentration and purity of the isolated RNA was evaluated using a NanoDrop LITE (Thermo Fisher Scientific, Waltham, MA, USA). The integrity of the RNA samples was analyzed on the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: Donor eyes were obtained from 3 patients (age 4-17 months) with retinoblastoma after enucleation. The tumor-free neural retina was immediately dissociated from the eye with forceps and surgical scissors. The macula region and peripheral retina were dissected from the neural retina using forceps and scissors and directly transferred to a tube containing RNA extraction solution.

tag: disease

value: retinoblastoma

value: retina

value: female

tag: age in month


title: Donor_3_Periphery

source_name: donor3, retina, peripheral region

tag: tissue


title: Donor_2_Macula

source_name: donor2, retina, macula region

value: male


title: Donor_1_Periphery

source_name: donor1, retina, peripheral region


title: MiaPaCa2, injected Part1, Lagger, rep3 [s_Part1Lag3]

tag: genotype

tag: treatment


title: A2


title: Donor_2_Periphery

source_name: donor2, retina, peripheral region


title: MiaPaCa2, injected Part1, Lagger, rep1 [s_Part1Lag1]

tag: cell type


title: B4


title: MiaPaCa2, non-injected, rep1 [s_MiaFRFP1]

value: In vitro


title: Donor_1_Macula

source_name: donor1, retina, macula region

tag: gender


title: MiaPaCa2, non-injected, rep2 [s_MiaFRFP2]


title: Liver Male OpnKI Mye NASH Diet#4

first: Hui

last: HAN

address: 909 S Wolcott Ave

institute: University of Illinois at Chicago

data_processing:
Data were aligned using RNA-Seq Alignment v.2.0.1 in basespce
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw count for each sample

source_name: Total liver

extract_protocol:
Total liver RNA was isolated with illustra™ RNAspin Mini RNA Isolation Kit; macrophage RNA was isolated with Qiagen miRNeasy micro kit.
RNA libraries for RNA-seq were prepared using Illumina TruSeq Stranded mRNA library prep

value: Total liver

value: Liver tissue lysate

value: OpnKI Mye

tag: time

value: 24 weeks

value: NASH diet

value: Male


title: AKO9

city: Beijing

first: ye

last: Liu

address: You'anmenwai

institute: Capital Medical University

description: agedPparaSMC_vs_youngPparaSMC differ gene expression.xlsx

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw data(raw reads) of fastq format were firstly processed through in-houseperl scripts.In this step,clean data(clean reads) were obtained by removing reads containing adapter,reads containing ploy-N and low quality reads from raw data.
Reference genome and gene model annotation files were downloaded from genome website directly.Index of the reference genome was built using Hisat 2v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat 2v2.0.5.
Feature Counts 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 readscount mapped to this gene.
Differential expression analysis of two conditions/groups was performed using the DESeq R package (1.8.3).
Genome_build: Mus_musculus.GRCm38
Supplementary_files_format_and_content: tab_delimited text files include count values for each Sample

source_name: aorta

extract_protocol:
The harvested aortas are quickly put into liquid nitrogen and stored at low temperature. TRIzol (Invitrogen, Waltham, Massachusetts, USA) was used to isolate total RNA from islets according to the manufacturer's protocol. The amount of total RNA was measured with Nanodrop 2000 (Thermo Scientific, Waltham, Massachusetts, USA), and the quality was evaluated by 1% agarose gel electrophoresis, and stained with 4S Red Plus nucleic acid stain (Sango, Shanghai, China).
RNA-seq libraries were prepared using the KAPA Stranded RNA-Seq Library Preparation Kit.

value: aorta

tag: age

value: 28 mionths old


title: AKO8


title: AKO7


title: Pilo3

city: Singapore

first: Jessica

middle: R

last: Gaunt

address: 11 Mandalay Road

department: LKC Medicine

country: Singapore

institute: Nanyang Technological University

description: Scopolamine + pilocarpine

data_processing:
Sequenced reads were pre-processed using Trimmomatic (v0.39) {Bolger, 2014 #3951} to remove adapter sequences and low-quality or short-length reads and then aligned to the mouse genome (GENCODE M24) using STAR (v2.7.1a) {Dobin, 2013 #3378}. Reads aligned to exons were counted using HTseq (v0.11.2) {Anders, 2015 #3950} using the GENCODE primary assembly annotation. These steps were performed on the Gekko high-performance computing cluster.
Gene count matrices were analysed using R 4.1.1. First, genes with < 1 log2 counts per million (CPM) in more than 4 samples were removed, retaining N=14,115 expressed genes, and then trimmed mean of M values (TMM) normalisation was applied. Differential expression between Mock and Seizure conditions was analysed using edgeR quasi-likelihood F-test with robust dispersion estimation (Robinson et al, 2010; Zhou et al, 2014; Lun et al, 2016). Thresholds of false discovery rate (FDR) < 1% and log2 fold change (LFC) > ±1 were used to identify differentially expressed genes (DEGs).
Gene set enrichment analyses (GSEA) were conducted on expressed genes or proteins ranked by LFC between conditions using the fgsea R package (Korotkevich et al, 2021) using Gene Ontology, PFAM, ReactomeDB and KEGG pathway gene sets. Terms with <5 or >800 annotated genes were excluded.
Aligned reads were requantified using the INSPEcT R package (de Pretis et al, 2015) with UCSC mm10 knownGene annotation and ‘prioritizeExons’ set to false. Data were filtered to retain protein-coding genes with reads in both exon and intron regions and differential expression analyses were conducted on exons and introns separately as described above. Exon-intron split analysis (EISA) was then performed using default parameters to determine differential expression between exon and intron levels (Gaidatzis et al, 2015). Data were again filtered to retain genes with average log2 CPM > 1 and DEGs were determined using thresholds of LFC > ±0.5 and FDR < .01 for each test.
Assembly: Gencode M24
Supplementary files format and content: Raw count matrices for every gene and sample for exons only and for exons and introns of protein-coding genes

source_name: Forebrain excitatory neuronal nuclei

extract_protocol:
INTACT protocol was modified from Mo et al (2015). Briefly, mice were euthanised by cervical dislocation and the brains were harvested and placed in ice-cold homogenisation buffer (HB; 0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM tricine, pH 7.8) supplemented with cOmplete™, EDTA-free protease inhibitor cocktail (Roche). Forebrains were isolated and homogenised in a 5 mL Potter-Elvehjem tissue grinder with 10 strokes of the pestle (Corning). 0.3% IGEPAL®-CA 630 (Sigma) in PBS was then added to the homogenate and further homogenised with another 5 strokes of the pestle. Homogenates were then filtered through a 40 µm cell strainer (Falcon) and mixed 1:1 with 50% OptiPrep™ Density Gradient Medium in dilution buffer (DB, 150 mM KCl, 30 mM MgCl2, 120 mM tricine, pH 7.8) before being layered over an iodixanol gradient composed of 30% and 40% OptiPrep™ in HB. Samples were centrifuged at 10,000 g for 18 min with SW28 swinging bucket rotor at a deceleration setting of 5 (Beckman Coulter). After centrifugation, nuclei were extracted from the interface between 30% and 40% of the OptiPrep™ gradient. To immunoprecipitate SUN1-sfGFP positive nuclei by INTACT, immunoprecipitation buffer (IPB, 0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM tricine, 0.4% IGEPAL®-CA 630, pH 7.8) was added to nuclear extracts (approximately 4-5 million nuclei) with 3 µg of anti-IgG or anti-GFP antibodies used for each reaction and incubated for 30 min at 4°C. Pre-washed Dynabeads™ Protein G (Invitrogen) were added for another 40 min before nuclei were isolated with extensive and repeated binding steps to enhance binding efficiency. Dynabeads™-bound nuclei were pelleted and washed with IPB, then lysed in 1 mL of TRIzol™ Reagent (Invitrogen) and stored at -80°C until RNA extraction. Total RNA was extracted then column-purified with PicoPure™ RNA isolation kit (Applied Biosystems™) according to manufacturer’s instructions.
Directional poly(A) mRNA libraries were prepared for RNAseq by NovogeneAIT Genomics (Singapore) and 45 M 150 bp paired-end reads per sample were generated by sequencing on the Illumina Novaseq 6000 platform.

treatment_protocol: Mice received intraperitoneal injections of scopolamine methyl nitrate (1 mg/kg; Sigma-Aldrich), followed by pilocarpine hydrochloride (340 mg/kg; Sigma-Adrich) or equivalent volume of diluent (0.9% NaCl; B. Braun) 30 min later. Pilocarpine-injected mice were allowed to develop acute seizures for 100 min. Mice with seizure behaviours which fell within the range of 3-5 on the Racine scale were used for downstream experiments (Racine, 1972).

tag: Sex

value: 6-8 weeks


title: Mock4

description: Scopolamine + saline


title: Mock3

description: Scopolamine + saline


title: Pilo2

description: Scopolamine + pilocarpine


title: Pilo1

description: Scopolamine + pilocarpine


title: AKO1


title: Liver Male OpnKI Mye Ctrl Diet#4

city: Chicago

value: Control diet


title: Pilo4

description: Scopolamine + pilocarpine


title: Liver Male OpnKI Mye NASH Diet#1


title: Liver Male OpnKI Mye NASH Diet#3


title: Mock2

description: Scopolamine + saline


title: A6

description: agedPparaSMC_vs_agedPparafl differ gene expression.xlsx

value: Pparafl/fl


title: Liver Male OpnKI Mye NASH Diet#2


title: Liver Male OpnKI Mye Ctrl Diet#3


title: A12


title: A11


title: Mock1

description: Scopolamine + saline


title: Liver Male OpnKI Mye Ctrl Diet#2


title: Liver Male OpnKI Mye Ctrl Diet#1


title: A4


title: MiaPaCa2, injected Part1, Lagger, rep2 [s_Part1Lag2]

value: pancreatic cancer cells

value: WT

value: In vivo Passage1


title: A1

value: eutopic endometrium

value: adenomyosis


title: 2321YKO

description: youngPparaSMC_vs_youngPparafl differ gene expression.xlsx

value: 2 months old


title: 2115YKO


title: Liver Male NASH Diet#3

value: Total liver


title: MiaPaCa2, non-injected, rep3 [s_MiaFRFP3]

value: In vitro


title: Liver Male NASH Diet#2

value: Liver tissue lysate


title: 2112YKO


title: 2114YKO


title: Liver Male NASH Diet#1

value: 24 weeks


title: 2111YKO


title: Liver Male WT Ctrl Diet#4


title: 2326Y

description: agedPparafl_vs_youngPparafl diff gene expression.xlsx


title: Liver Male WT Ctrl Diet#2


title: 2348Y


title: 2324Y


title: Liver Male WT Ctrl Diet#3


title: 2323Y


title: Liver Male WT Ctrl Diet#1


title: preDC WT3

city: London

first: Carlos

last: Minutti

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Institute

data_processing:
The RSEM package (version 1.3.0) (Li and Dewey, 2011) was used in conjunction with the STAR alignment algorithm (version 2.5.2a) (Dobin et al., 2013) for the mapping and subsequent gene-level counting of the sequenced reads with respect to Ensembl mouse GRCm38 release 89  transcriptome
Normalisation of raw count data and differential expression analysis was performed with the DESeq2 package (version 1.16.1)  within the R programming environment (version 3.3.1)
Genome_build: GRCm38 release 86
Supplementary_files_format_and_content: VST log2 normalised expression values. Rows = genes; Columns = samples.

source_name: pre-cDCs from mouse BM

extract_protocol:
pre-cDCs were extracted from mouse bones by flushing the marrow cells. Subsequently, pre-cDCs were enriched using MACS columns and FACS-sorted to obtain a pure population.
Nugen Ovation® RNA‑Seq System V2 kit (part No. 7102)

value: pre-cDCs from mouse BM

value: PBS-injected


title: preDC WT2


title: preDC WT4


title: preDC WT1


title: CD1 Limb 5

city: Cincinnati

first: Samantha

last: Brugmann

state: OH

address: Department of Developmental Biology, DK 1 BLDG R, 240 Albert Sabin Way

institute: Cincinnati Children's Hospital Medical Center

data_processing:
For analysis with Strand, BAM files were loaded into Strand NGS. Mm10 build was used as the reference genome for the alignment. Samples passing Q30 quality were used for gene expression studies. Detection of novel genes and exons was allowed, and partial reads were also included. DESeq2 was used for normalization of expression data. Differential gene expression between any two tissues was defined with a threshold of fold change of at least 2 and a 5% false discovery rate
For analysis with CSBB, Q30 quality trimmed reads were mapped onto mm10 build of the mouse genome. Reads passing quality control were mapped onto the genome using Bowtie 2 with default thresholds. Differential expression analysis was carried out with RUVSeq normalization with a fold change of at least 2 and false discovery rate of 5%.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include transcript counts for each sample

source_name: limb

growth_protocol: Timed matings were recorded and embryonic day 0.5 was counted to be noon of the day on which a copulation plug was discovered.

extract_protocol:
Mice were euthanized according to established protocols. The embryos were harvested and washed extensively with ice cold Depc treated PBS. Maxillary prominence, Mandibular prominence, Frontonasal prominence, limb, dorsal brain and ventral brain were dissected from the embryos and samples from multiple embryos were pooled for each tissue. The isolated tissue samples were homogenized using a tissue homogenizer and total RNA was extracted using Trizol (Fisher Scientific) following manufacturer’s instructions. After quality control validation, samples were submitted for NGS sequencing. Six independent biological replicates were used for each tissue
Paired end sequencing was performed for each sample with a minimum of 20 million reads per library with a 75bp read length. All library preparation and sequencing were performed at the DNA sequencing core at CCHMC using standard illumina sequencing protocols.

value: limb

value: embryonic day 11.5

value: Wild Type


title: CD1 Limb 4


title: CD1 Limb 6


title: CD1 Limb 3


title: CD1 Limb 2


title: MES-Asxl2KO-rep3

city: Tianjin

first: Rui

last: Li

state: Tianjin

address: Qixiangtai Road No.22

department: Department of Cell Biology, School of Basic Medical Sciences

institute: Tianjin Medical University

data_processing:
RNA-seq datasets were performed using the TOPMed RNA-seq pipeline.
Differentially expressed genes were identified using DESeq2 according to default parameters. To generate more accurate fold change estimates, lfcShrink function of DESeq2 was used to correct the fold change of lowly expressed genes.
Genome_build: mm10

source_name: MES

growth_protocol: Mouse ESC culture and the generation of Asxl2KO ESCs through CRISPR/Cas9 technique were performed as previously described. Briefly, proper amounts of ESCs were seeded on 0.1% gelatin-coated plates in GMEM medium (Gibco) supplemented with 15% FBS, 2 mM L-glutamine, 1×Penicillin/Streptomycin, 1×non-essential amino acids, 0.5 mM β-mercaptoethanol, and 100 U/ml leukemia inhibitory factor. To delete Asxl2, the specific sgRNA was designed to target Exon 5 of mouse Asxl2 and cloned into pX458 vector (Addgene #48138).

extract_protocol:
Total RNA was extracted with TRIZOL
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For MES differentiation, the EBs harvested from dish covers were dissociated after trypsinization. Around 5×105 cells were seeded on 0.2% gelatin-coated 10 cm plates with cultured with differentiation medium containing 10 ng/ml vEGF,20 ng/ml a-Activin A, 5 ng/ml BMP4 for another 3 days. Then cells were harvested for RNA extraction or chromatin preparation.

value: Mesodermal cell


title: CD1 Limb 1


title: MES-Asxl2KO-rep2


title: MES-Asxl2KO-rep1


title: MES-WT-rep3


title: 2319Y

value: aorta

value: Pparafl/fl


title: MES-WT-rep2

value: WT


title: CD1 vNT 6

source_name: ventral neural tube

value: ventral neural tube


title: CD1 vNT 5


title: CD1 vNT 4


title: CD1 vNT 3


title: CD1 vNT 1


title: CD1 vNT 2


title: MES-WT-rep1


title: ESC-WT-rep2

source_name: mESC

value: mouse embryonic stem cells


title: ESC-Asxl2KO-rep2


title: ESC-WT-rep1


title: ESC-Asxl2KO-rep1


title: CD1 dNT 5

source_name: dorsal neural tube

value: dorsal neural tube


title: CD1 dNT 4


title: CD1 dNT 3


title: CD1 dNT 1


title: CD1 FNP 4

source_name: frontonasal promnences

value: frontonasal promnences


title: CD1 FNP 5


title: CD1 FNP 3


title: CD1 dNT 6


title: CD1 dNT 2


title: CD1 FNP 2


title: CD1 FNP 1


title: LoNA KD 2C-like mESC rep3

city: Hefei

first: Ding

middle: feng

address: Huang shan road 443

institute: USTC

description:
LoNA KD 2C-like mESC rep3
LoNA KD 2C like  mESC normalized control 2C like mESC

data_processing:
Illumina Casava1.7 software used for basecalling.
Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0
Reads Count for each gene in each sample was counted by HTSeq v0.6.0
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited txt files include normalized gene expression for each group

growth_protocol: Standard protocol for embryos and mESC culture for RNA-seq

extract_protocol:
Total RNA was extracted by Trizol.Total amount of 2 ¦Ìg RNA per sample was used as input material for the RNA
RNA libraries were prepared for sequencing using standard Illumina protocols

value: mESC

value: LoNA KD 2C-like mESC


title: CD1 MXP 3

source_name: maxillary prominences

value: maxillary prominences


title: LoNA KD 2C-like mESC rep2

description:
LoNA KD 2C-like mESC rep2
LoNA KD 2C like  mESC normalized control 2C like mESC


title: CD1 MXP 2


title: CD1 MXP 5


title: LoNA KD 2C-like mESC rep1

description:
LoNA KD 2C-like mESC rep1
LoNA KD 2C like  mESC normalized control 2C like mESC


title: Control 2C-like mESC rep3

description:
Control 2C-like mESC rep3
LoNA KD 2C like  mESC normalized control 2C like mESC

value: Control 2C-like mESC


title: CD1 MNP 6

source_name: mandibular prominence

value: mandibular prominence


title: CD1 MXP 1


title: CD1 FNP 6


title: CD1 MXP 6


title: CD1 MNP 4


title: Control 2C-like mESC rep2

description:
Control 2C-like mESC rep2
LoNA KD 2C like  mESC normalized control 2C like mESC


title: Control 2C-like mESC rep1

description:
Control 2C-like mESC rep1
LoNA KD 2C like  mESC normalized control 2C like mESC


title: CD1 MNP 3


title: CD1 MNP 2


title: LoNA KO 24h embryos rep4

description:
LoNA KO 24h 2-cell embryos rep4
24h LoNA KO embryos normalized control 24h embryos .txt

source_name: embryos

value: embryos

value: LoNA KO

tag: time point


title: LoNA KO 24h embryos rep2

description:
LoNA KO 24h 2-cell embryos rep2
24h LoNA KO embryos normalized control 24h embryos .txt


title: CD1 MNP 1

value: embryonic day 11.5


title: LoNA KO 24h embryos rep3

description:
LoNA KO 24h 2-cell embryos rep3
24h LoNA KO embryos normalized control 24h embryos .txt


title: LoNA KO 24h embryos rep1

description:
LoNA KO 24h 2-cell embryos rep1
24h LoNA KO embryos normalized control 24h embryos .txt


title: CD1 MNP 5

value: Wild Type


title: LoNA KO 22h embryos rep3

description:
LoNA KO 22h 2-cell embryos rep3
22h LoNA KO embryos normalized control 22h embryos .txt


title: LoNA KO 22h embryos rep1

description:
LoNA KO 22h 2-cell embryos rep1
22h LoNA KO embryos normalized control 22h embryos .txt


title: LoNA KO 22h embryos rep2

description:
LoNA KO 22h 2-cell embryos rep2
22h LoNA KO embryos normalized control 22h embryos .txt


title: LoNA KO 22h embryos rep4

description:
LoNA KO 22h 2-cell embryos rep4
22h LoNA KO embryos normalized control 22h embryos .txt


title: LoNA KO 20h embryos rep4

description:
LoNA KO 20h 2-cell embryos rep4
20h LoNA KO embryos normalized control 20h embryos .txt


title: LoNA KO 20h embryos rep3

description:
LoNA KO 20h 2-cell embryos rep3
20h LoNA KO embryos normalized control 20h embryos .txt


title: LoNA KO 20h embryos rep2

description:
LoNA KO 20h 2-cell embryos rep2
20h LoNA KO embryos normalized control 20h embryos .txt


title: liver 758

type: genomic

city: Minneapolis

last: Razzoli

state: Minnesota

department: Integrative Biology and Physiology

institute: University of Minnesota

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Mouse Methylation Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BeadStudio software

label: biotin

source_name: liver

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from liver samples using Qiagen DNeasy Kit according to standard instructions

value: Male

tag: sample type

value: frozen liver

tag: disease state

value: normal


title: liver 764


title: liver 742_2


title: liver 754


title: LoNA KO 18h embryos rep4

description:
LoNA KO 18h 2-cell embryos rep4
18h LoNA KO embryos normalized control 18h embryos .txt


title: liver 757


title: LoNA KO 18h embryos rep3

description:
LoNA KO 18h 2-cell embryos rep3
18h LoNA KO embryos normalized control 18h embryos .txt


title: liver 742_1


title: LoNA KO 20h embryos rep1

description:
LoNA KO 20h 2-cell embryos rep1
20h LoNA KO embryos normalized control 20h embryos .txt


title: LoNA KO 18h embryos rep2

description:
LoNA KO 18h 2-cell embryos rep2
18h LoNA KO embryos normalized control 18h embryos .txt


title: liver 753


title: Liver Male NASH Diet#4

value: Total liver

value: Liver tissue lysate

value: 24 weeks

value: NASH diet


title: LoNA KO 18h embryos rep1

description:
LoNA KO 18h 2-cell embryos rep1
18h LoNA KO embryos normalized control 18h embryos .txt


title: A3

description: agedPparaSMC_vs_agedPparafl differ gene expression.xlsx

value: aorta

value: 28 mionths old

value: Pparafl/fl


title: liver 744


title: control 24h embryos rep4

description:
control 24h 2-cell embryos rep4
24h LoNA KO embryos normalized control 24h embryos .txt

value: control


title: control 24h embryos rep3

description:
control 24h 2-cell embryos rep3
24h LoNA KO embryos normalized control 24h embryos .txt


title: control 24h embryos rep2

description:
control 24h 2-cell embryos rep2
24h LoNA KO embryos normalized control 24h embryos .txt


title: liver 704


title: liver 724


title: liver 730


title: liver 708


title: liver 697


title: liver 741


title: liver 707


title: control 24h embryos rep1

description:
control 24h 2-cell embryos rep1
24h LoNA KO embryos normalized control 24h embryos .txt


title: control 22h embryos rep3

description:
control 22h 2-cell embryos rep3
22h LoNA KO embryos normalized control 22h embryos .txt


title: liver 699


title: liver 736


title: control 22h embryos rep4

description:
control 22h 2-cell embryos rep4
22h LoNA KO embryos normalized control 22h embryos .txt


title: liver 695


title: liver 691


title: control 22h embryos rep2

description:
control 22h 2-cell embryos rep2
22h LoNA KO embryos normalized control 22h embryos .txt


title: control 22h embryos rep1

description:
control 22h 2-cell embryos rep1
22h LoNA KO embryos normalized control 22h embryos .txt


title: liver 706


title: liver 685


title: AKO13

description: agedPparaSMC_vs_youngPparaSMC differ gene expression.xlsx


title: control 20h embryos rep2

description:
control 20h 2-cell embryos rep2
20h LoNA KO embryos normalized control 20h embryos .txt


title: control 20h embryos rep3

description:
control 20h 2-cell embryos rep3
20h LoNA KO embryos normalized control 20h embryos .txt


title: control 20h embryos rep1

description:
control 20h 2-cell embryos rep1
20h LoNA KO embryos normalized control 20h embryos .txt


title: control 18h embryos rep4

description:
control 18h 2-cell embryos rep4
18h LoNA KO embryos normalized control 18h embryos .txt


title: control 18h embryos rep3

description:
control 18h 2-cell embryos rep3
18h LoNA KO embryos normalized control 18h embryos .txt


title: control 20h embryos rep4

description:
control 20h 2-cell embryos rep4
20h LoNA KO embryos normalized control 20h embryos .txt


title: control 18h embryos rep2

description:
control 18h 2-cell embryos rep2
18h LoNA KO embryos normalized control 18h embryos .txt


title: liver 692


title: liver 677


title: liver 675


title: liver 679


title: liver 673


title: control 18h embryos rep1

description:
control 18h 2-cell embryos rep1
18h LoNA KO embryos normalized control 18h embryos .txt


title: liver 680


title: liver 688


title: WT+3w DOX

city: Nanjing

first: Qi

last: Chen

state: Jiangsu Province

address: 101 Longmian Avenue

department: Department of Pathophysiology

institute: Nanjing Medical University

description: 5 samples mixed for RNA extraction and RNA-seq

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using STAR v.2.6.1b
All downstream statistical analyses were performed using R (v3.5.1). After RNA-seq data was aligned to the transcriptome, counts were transformed to TPM (transcript per million).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM/FPKM values for each Sample …

source_name: Heart

extract_protocol:
Hearts were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.  Sequencing libraries were generated using the TruSeq RNA Sample Preparation Kit (Illumina, San Diego, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: heart

value: post natal week 12

tag: duration of drug treatment

value: DOX injection for 3 weeks


title: WT+2w DOX

tag: strain

value: DOX injection for 2 weeks


title: WT+4w DOX

value: DOX injection for 4 weeks


title: liver 669


title: WT+1w DOX

value: DOX injection for 1 week


title: liver 671

value: Male


title: WT

value: DOX injection for 0 week


title: liver 668

value: frozen liver

value: normal