title: BJ_52

value: BJ Fibroblasts


title: BJ_60

status: Public on Aug 17 2020

type: SRA

city: Singapore

first: Chadi

last: El Farran

address: 61 Biopolis Drive

country: Singapore

institute: Institute of Molecular and Cell Biology

library_source: genomic

data_processing:
Library strategy: ATAC-seq
Paired-end fastq files: The high standard deviation is due to the fact that the libraries are ATAC-Seq and have nucleosomal patterns
Reads were aligned to hg19 genome assembly using STAR aligner with the option –alignIntronMatrix set to 1. Only reads that uniquely maps to hg19 and contain less than 3 mismatches were kept for further processing.
Duplicates were removed using PICARD tools
Group information was added for each library using PICARD tools
Reads in each library were ordered lexicographically using PICARD tools. ChrM and amibiguiously mapped reads were removed during this step
Coverage of each library over regions of interest was measured using GATK v3.5
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph files of merged mapped files belonging to a particular time-point generated using makeUCSCfile script of HOMER.

molecule: genomic DNA

organism: Homo sapiens

source_name: BJ Fibroblasts

growth_protocol: BJ fibroblasts were cultured in 10% Fetal Bovine Serum (Gibco) for expansion and medium was changed every two days. BJ human neonatal fibroblast was routinely tested for Mycoplasma and was negative in all instances. hES cells and iPSCs clones were maintained on irradiated murine embryonic fibroblast (MEFs, Global Stem) and cultured in 20% knockout serum replacement (KSR, Life Technologies), 200mM GlutaMAX (Life Technologies), 1 x minimal essential media (MEM) non-essential amino acids solution (Life Technologies), 8 microgram mL-1 bFGF (Life Technologies), 55 micromolar Beta-mercaptoethanol in DMEM/F12 (Life Technogies). ES and iPSCs clones was passagerd every 4-5 days using L7TM hPSC Passaging Solution (Lonza).

extract_protocol:
C1 Single-Cell Auto Prep System with its Open App™ program (Fluidigm, Inc.) is used for scATAC-seq library preparation. Briefly, cells were trypsinized into single cells. Cells at a concentration of 300-350 cells/μL were combined with C1 Cell Suspension Reagent at a ratio of 3:2.5 μL , and loaded on to the C1 Single-Cell Auto Prep IFC microfluidic chips with the “ATACseq: Cell Load and Stain (1862x)” scripts. Following experiments were performed according to the scripts, including cell viability assay, cell lysis, transposition, fragment release and quench, and fragment extension.
96 libraries were harvested from fluidigm chip and dual index were integrated by additional 14 cycle PCR. The PCR products were pooled and purified on a single MinElute PCR purification column (Qiagen). Bioanalyzer is used for library size measurement, and KAPA Library Quantification kit(Kapa Biosystems) is used for library concentration measurement.
Single-cell ATAC-Seq

tag: cell line

tag: treatment

value: WT control

tag: tra-1-60 status


title: BJ_42


title: D8_CD13_Positive_10X

library_source: transcriptomic

data_processing:
Fastq files were generated using mkfastq of cellranger v2.1.0. Gene counting was performed using ‘count’ module of cellranger (v2.1.0).
All librariers were then merged using ‘aggr’ function of cellranger without normalization.
The output of ‘aggr’ was used for further analysis with Seurat and Monocle.
Genome_build: hg19
Supplementary_files_format_and_content: Comma-delimited table containing the UMI values of the genes in each single-cell library and Tab-delimited text file containing time-point annotation of the cells.

molecule: polyA RNA

growth_protocol: Reprogramming cells were cultured with BJ medium, containing DMEM high glucose medium supplemented with 10% FBS, for the first five days post OSKM infection. From day 5 to day 8, reprogramming cells were cultured with hESC medium, containing DMEM/F12 medium supplemented with 20% KOSR.

extract_protocol:
cDNA was harvested as per the Chromium Single Cell 3’ Reagent Kits v2 user guide Rev E
Libraries were constructed as per the Chromium Single Cell 3’ Reagent Kits v2 user guide Rev E

treatment_protocol: BJ cells were infected with O2S and K2M lentivirus in the presence of 4 mg/mL polybrene. The supernatant with lentivirus was replaced with fresh medium on the following day.

value: BJ fibroblasts 8 days post induced viral expression of OSKM

tag: cd13 staining

value: Positive


title: BJ_41


title: BJ_44


title: BJ_40


title: BJ_43


title: D8 TEAD4 Input

data_processing:
The libraries were mapped using STAR aligner to hg19 genome, allowing up to 3 mismatches in each read and discarding reads that map to more than one locus. The options –alignIntronMax and –alignEndsType were set to 1 and EndToEnd respectively.
HOMER was used to create tag directory for each library.
findPeaks script of HOMER was used to detect the binding sites.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Tab-delimited tables containing information regarding the significantly detected peaks in each library.

growth_protocol: Reprogramming cells were cultured with BJ medium, containing DMEM high glucose medium supplemented with 10% FBS, for the first five days post OSKM infection. From day 5 to day 8, reprogramming cells were cultured with hESC medium, containing DMEM/F12 medium supplemented with 20% KOSR. iPSCs and hESCs were cultured with Mtesr medium.

extract_protocol:
Cells were harvested following previously published protocol (Yang et al., 2015).
ChIP-seq libraries were prepared following previously published protocol (Yang et al., 2015). Briefly, ChIP DNA was end-repaired. Then poly-A tail was added followed by ligation with adaptors. Finally, the fragments were amplified using 12 cycles of PCR. The amplified ChIP DNA was purified using Ampure beads. The concentration and size range of ChIP-seq library were measured by Agilent 2000 bioanalyzer kit.

value: BJ

tag: cell type

value: Fibroblasts

value: 8 days post induced viral expression of OSKM

tag: antibody


title: D8_CD13-_CD201+_Rep1

description:
CD13neg_CD201pos_R1_0
mRNA-seq
PolyA RNA
processed data file: D8_FPKM.txt

data_processing:
Reads were aligned to hg19 genome assembly using STAR aligner. Reads that uniquely map to hg19 and contain less than 3 mismatches were kept for further processing.
Gene quantification was performed using Cuffquant with the options -u and -b
Expression levels were then normalized using Cuffnorm using the classic-fpkm mode.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: D8_FPKM.txt: Tab-delimited text file containing the FPKM values for each gene in every sample.

molecule: total RNA

growth_protocol: BJ fibroblasts were infected with lentivirus carrying O2S and K2M polycistronic construct, and cultured in 10% Fetal Bovine Serum (Gibco) for the first 5 days. Cells were passaged at D4 and transferred onto Matrigel coated plates. From D6 till D8, reprogramming cells were cultured with hESC medium, composed of 20% knockout serum replacement (KOSR, Life Technologies), 2mM Glutamine (Life Technologies), 1x non-essential amino acids solution (NEAA, Life Technologies), 8 mg mL-1 bFGF (Life Technologies), and 55 mM Beta-mercaptoethanol in DMEM/F12 (Life Technologies).

extract_protocol:
RNA was extracted by the conventional methods using Trizol. Extracted RNA was treated with DNase I to get rid of the contaminant DNA, and purified with the RNeasy mini kit from Qiagen thereafter.
RNA-seq libraries were prepared using the TruSeq® Stranded mRNA Library Prep kit following manual guide of the kit. Briefly, mRNA was enriched by the beads conjugated with Poly-T oligo, fragmentized, and reverse transcribed to cDNA. After ligating adaptors, cDNA was further amplified by 15 cycles of PCR. The library was sequenced on HiSeq 4000 sequencer.

treatment_protocol: For sorting using surface markers, cells were trypsinized and filtered with 40um cell mesh to devoid of cell clumps. Single cells were re-suspended with 1% FBS (Sigma) at a concentration of 25 million/ml, and incubated with Anti human-CD13-FITC (Miltenyi Biotec, Cat. No.: 130-103-732) and CD201 (EPCR)-PE, human (Miltenyi Biotec, Cat. No.: 130-105-298) at a dilution of 1:11, at fridge for 15 min. Sorting was performed using MoFlo XDP Cell Sorter (Beckman Coulter).

tag: cd13 profile

value: Negative

tag: cd201 profile


title: BJ_39


title: BJ_38


title: BJ_37


title: BJ_48


title: BJ_36


title: D8_CD13_Negative_10X


title: ParE2 t600 rep2

city: Cambridge

first: Thuy-Lan

last: Lite

state: Massachusetts

address: 31 Ames Street

country: USA

institute: Massachusetts Institute of Technology

data_processing:
Library strategy: PCR amplicon sequencing
Multiplexed reads were sorted based on exact match to a six-letter barcode
Reads were filtered to remove sequences that (a) do not encode an ‘NNK’ codon in any of the 3 targeted positions, or that (b) contain any non-synonymous mutation in the remaining 91 codons.
Variants with >25 pre-selection and >0 post-selection reads were retained
Variant fitness was calculated as described in Aakre et al., 2015 and van Opijnen et al., 2009
Genome_build: Reference gene: M. opportunistum ParD3 (GenBank ID: AEH90010)
Supplementary_files_format_and_content: CSV file; first line contains column titles

organism: synthetic construct

source_name: M. opportunistum WSM2075

growth_protocol: Cells were grown in M9L medium (1x M9 salts, 2 mM MgSO4, 100 uM CaCl2, 10% v/v LB) supplemented with 0.1% casamino acids and 0.4% glycerol at 37 °C

extract_protocol:
Plasmids were extracted using the ZR Plasmid Miniprep - Classic kit (Zymogen)
The entire ParD3 gene was used as a template for PCR (12 cycles) with custom barcoded primers containing Illumina flowcell adapator sequences. To increase the diversity of the amplicon pool, the PCR also incorporated 4-6 random nucleotides to the 5' end of each ParD3 gene.

treatment_protocol: Toxin expression was induced with 0.2% arabinose and antitoxin expression was induced with 100 uM IPTG. Selection was performed by co-expressing toxin and antitoxin for 10 hours.

tag: host cells

value: Escherichia coli TOP10

tag: barcode

value: cctatgcc

tag: replicate

tag: time

tag: toxin type

tag: sequenced molecule

value: plasmid DNA


title: ParE3 t600 rep2

value: aggatcta


title: D8 FRA1

data_processing:
The libraries were mapped using STAR aligner to hg19 genome, allowing up to 3 mismatches in each read and discarding reads that map to more than one locus. The options –alignIntronMax and –alignEndsType were set to 1 and EndToEnd respectively.
HOMER was used to create tag directory for each library.
findPeaks script of HOMER was used to detect the binding sites.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *txt: Tab-delimited tables containing information regarding the significantly detected peaks in each library.

value: Anti-FRA1 antibody (Abcam, ab124722)


title: BJ_35


title: BJ_34


title: D8 Input


title: ParE2 t600 rep1

value: tcggaatg


title: ParE3 t600 rep1

value: aacttgac


title: BJ_33


title: ParE2 t0 rep2

value: catgctta


title: BJ_32


title: ParE3 t0 rep2

value: aaggatgt


title: BJ_31

value: BJ Fibroblasts


title: BJ_30

value: WT control


title: ParE3 t0 rep1

value: gcacatct


title: ParE2 t0 rep1

value: agcaattc


title: BJ_29


title: BJ_27


title: BJ_28


title: Aptamer21E-PEARL-DMSO-DMSO-None-3

city: Waltham

first: Lee

last: Vandivier

state: MA

address: 830 Winter St

institute: Arrakis Therapeutics

data_processing:
Reads were stitched with Paired-End reAd mergeR (PEAR) requiring a minimum assembled length of at least 10 nucleotides (nt)
PEARL-seq reads were trimmed with Cutadapt (at least 5-nt of overlap and a maximum of 20% mismatches), DMS-MaP and SHAPE-MaP reads were trimmed with Trimmomatic (LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:30)
Targeted experiment reads were aligned with Bowtie2. Transcriptome-wide experiments were aligned with STAR
Mutation rates (MaP) and RT stalls (PEARL-seq) were called using an in-house pipeline (https://bitbucket.org/arrakistx/pearl-seq/src/master/)
Genome_build: hg38 + Aptamer21 spikein
Supplementary_files_format_and_content: *_mut_rate.txt.gz generated with our in-house pipeline. Columns are: Sequence, Position, Base, Coverage, Sample, Mutation.Rate, Control.Mutation.Rate, Mutation.FC, Mutation.Log2FC, Reactivity
Supplementary_files_format_and_content: *_stall_rate.txt.gz generated with our in-house pipeline. Columns are: Sequence, Position, Base, Coverage, Sample, Mutation.Rate, Control.Mutation.Rate, Mutation.FC, Mutation.Log2FC
Supplementary_files_format_and_content: *_10ntBinCounts.txt (Transcriptome-wide experiments only) tabulating stalls across genomic 10nt bins. 0-count bins are not reported

organism: Synthetic plasmid

source_name: In vitro transcription

extract_protocol:
All Aptamer 21 derivatives were produced by in vitro transcription (IVT) from linearized plasmid templates, using the HiScribe IVT kit (New England Biolabs) according to the manufacturer’s standard protocol with 33.5 ng/µL template. Total RNA was extracted from 12 samples of 2x10^5 to 1.5x10^6 HepG2 cells using the ReliaPrep RNA cell miniprep system (Promega) according to the manufacturer’s standard protocol.
Libraries were produced using standard Illumina protocols.

tag: library type

value: PEARL-seq

tag: scale

value: Targeted

tag: platform

value: MiSeq


title: D8 TEAD4

tag: cell line

value: BJ

value: Fibroblasts

value: 8 days post induced viral expression of OSKM

value: Anti-TEAD4 antibody - ChIP Grade (Abcam, ab58310)


title: BJ_25

tag: treatment


title: Aptamer21E-PEARL-DMSO-Cmpd2d-None-2


title: Aptamer21E-PEARL-DMSO-Cmpd2d-None-3


title: BJ_23

tag: tra-1-60 status


title: BJ_26


title: Aptamer21E-PEARL-DMSO-DMSO-None-2


title: Aptamer21E-PEARL-DMSO-DMSO-None-1


title: Aptamer21E-PEARL-DMSO-Cmpd2b-None-2


title: Aptamer21E-PEARL-DMSO-Cmpd2b-None-3


title: BJ_24


title: BJ_22


title: Aptamer21E-PEARL-DMSO-Cmpd2b-None-1


title: BJ_20


title: Aptamer21E-PEARL-DMSO-Cmpd2d-None-1


title: BJ_21


title: Aptamer21-PEARL-DMSO-DMSO-None-3


title: BJ_19


title: Aptamer21-PEARL-DMSO-DMSO-None-1


title: BJ_18


title: Aptamer21-PEARL-DMSO-DMSO-Enrich-3


title: BJ_15


title: Aptamer21-PEARL-DMSO-DMSO-Enrich-2


title: BJ_16


title: BJ_14


title: Aptamer21-PEARL-DMSO-Cmpd6-None-3


title: Aptamer21-PEARL-DMSO-Cmpd6-None-2


title: BJ_12


title: BJ_11


title: Aptamer21-PEARL-DMSO-Cmpd4-None-2


title: Aptamer21-PEARL-DMSO-Cmpd4-None-3


title: Aptamer21-PEARL-DMSO-Cmpd6-None-1


title: BJ_9


title: BJ_13


title: Aptamer21-PEARL-DMSO-Cmpd3-None-3


title: BJ_7


title: Aptamer21-PEARL-DMSO-DMSO-None-2


title: Aptamer21-PEARL-DMSO-Cmpd3-None-2


title: BJ_6


title: Aptamer21-PEARL-DMSO-Cmpd4-None-1


title: BJ_5


title: Aptamer21-PEARL-DMSO-Cmpd3-None-1


title: Aptamer21-PEARL-DMSO-Cmpd2d-None-3


title: BJ_4


title: BJ_3


title: BJ_17


title: Aptamer21-PEARL-DMSO-Cmpd2d-None-2


title: Aptamer21-PEARL-DMSO-DMSO-Enrich-1


title: Aptamer21-PEARL-DMSO-Cmpd2d-None-1


title: BJ_10


title: BJ_2


title: BJ_1


title: Aptamer21-PEARL-DMSO-Cmpd2d-Enrich-2


title: BJ_8


title: Aptamer21-PEARL-DMSO-Cmpd2c-None-3


title: Aptamer21-PEARL-DMSO-Cmpd2d-Enrich-1


title: Aptamer21-PEARL-DMSO-Cmpd2c-None-2


title: Aptamer21-PEARL-DMSO-Cmpd2c-None-1


title: Aptamer21-PEARL-DMSO-Cmpd2b-None-2


title: Aptamer21-PEARL-DMSO-Cmpd2b-None-3


title: Aptamer21-PEARL-DMSO-Cmpd2b-Enrich-3


title: Aptamer21-PEARL-DMSO-Cmpd2b-None-1


title: Aptamer21-PEARL-DMSO-Cmpd2b-Enrich-1


title: Aptamer21-PEARL-DMSO-Cmpd2b-Enrich-2


title: Aptamer21-PEARL-DMSO-Cmpd2a-S-None-3


title: Aptamer21-PEARL-DMSO-Cmpd2d-Enrich-3


title: Aptamer21-PEARL-DMSO-Cmpd2a-S-None-2


title: Aptamer21-PEARL-DMSO-Cmpd2a-S-None-1


title: Aptamer21-PEARL-DMSO-Cmpd2a-R-None-1


title: Aptamer21-PEARL-DMSO-Cmpd2a-R-None-2


title: Aptamer21-PEARL-DMSO-Cmpd2a-R-None-3


title: HSPCs-Electroporation-GFP-3

type: RNA

city: Lund

first: Ludwig

last: Schmiderer

address: BMC A12

department: Laboratory Medicine / Molecular Medicine and Gene Therapy

country: Sweden

institute: Lund University

hyb_protocol: 5,5 µg fragmented and labeled ss cDNA were hybridized to Affymetrix Human Gene 2.0 arrays for 16 h at 45° C and 60 rpm in a GeneChip hybridization oven 640. Hybridized arrays were washed and stained in an Affymetrix Fluidics Station FS450.

scan_protocol: The fluorescent signals were measured with an Affymetrix GeneChip Scanner 3000 7G. Fluidics and scan functions were controlled by the Affymetrix GeneChip Command Console v4.3.3 software. RNA extraction and sample processing was performed at an Affymetrix Service Provider and Core Facility, “KFB - Center of Excellence for Fluorescent Bioanalytics” (Regensburg, Germany; www.kfb-regensburg.de).

data_processing: Microarray data was normalized with the Robust Multiarray Average (rma) function of the R package oligo version 1.49.0 (24) and annotated with ENTREZIDs from the Bioconductor (25) annotation data package org.Hs.eg.db version 3.8.2, using the AnnotationDbi package version 1.47.0. Differentially expressed genes (FC > 1.5, adjusted p-value < 0.05) were detected using the limma package version 3.41.2.

label: biotin

source_name: Cord blood-derived CD34+ hematopoietic stem and progenitor cells

label_protocol: In brief, 5 ng of total RNA was used for reverse transcription to synthesize single-stranded (ss) cDNA with a T7 promoter sequence at the 5' end. Next a 3’ adaptor was added and the ss cDNA was converted to double-stranded cDNA, which acted as a template for a pre- in vitro transcription (IVT) amplification by a low-cycle PCR (6 cycles). Afterwards antisense RNA (complimentary RNA or cRNA) was synthesized and linearly amplified by an in vitro transcription (IVT) of the double-stranded cDNA template. 20 µg of cRNA was purified and reverse transcribed into sense-strand (ss) cDNA, whereat unnatural dUTP residues were incorporated at a fixed ratio relative to dTTP. Purified ss cDNA was fragmented using a combination of uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) at the dUTP residues followed by a terminal labeling with biotin.

extract_protocol: Total RNA was extracted from sorted human CD34+cells stabilized in RLT buffer according to the “Purification of total RNA from animal and human cells” protocol of the RNeasy Micro Kit (QIAGEN, Hilden, Germany). In brief, cells were stored in RLT buffer and shipped on dry ice. After thawing the samples were homogenized by using QIAshredder spin columns. Next one volume of 70 % ethanol was added and the samples were applied to RNeasy MinElute spin columns, followed by an on-column DNase digestion and several wash steps. Finally total RNA was eluted in 14 μl of nuclease free water. Purity and integrity of the RNA was assessed on the Agilent 2100 Bioanalyzer with the RNA 6000 Pico LabChip reagent set (Agilent, Palo Alto, CA, USA).

value: Electroporation-GFP


title: HSPCs-Electroporation-mock-1

value: Cord blood-derived CD34+ hematopoietic stem and progenitor cells

value: Electroporation-mock


title: HSPCs-Electroporation-mock-3


title: Aptamer21-PEARL-Cmpd7-Cmpd6-None-3


title: HSPCs-Electroporation-GFP-1


title: HSPCs-CeNT-GFP-2

value: CeNT-GFP


title: Aptamer21-PEARL-Cmpd7-Cmpd6-None-1


title: HSPCs-CeNT-GFP-3


title: Aptamer21-PEARL-Cmpd7-Cmpd6-None-2


title: HSPCs-Electroporation-GFP-2


title: ko_rep3 [RNA-seq]

city: San Joan d'Alacant

first: Jose

middle: P

last: Lopez-Atalaya

address: Av Ramon y Cajal s/n

department: Instituto Neurociencias

country: Spain

institute: CSIC-UMH

data_processing:
Reads were quality checked with FASTQC v2.6.14.RNA-Seq output reads were quality-trimmed and filtered for adapters using Trim Galore v0.6.5 and aligned to the genome assembly (GRCm38.p6) using HISAT2 (Kim et al., 2015). Gene level read counts were computed using HTSeq 0.12.4 with parameters -f bam -r pos -s reverse -m union --additional-attr=gene_name. Differentially expressed genes were identified using DESeq2 (Love et al., 2014).
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Tab-delimited text files of gene counts per sample.

organism: Mus musculus

source_name: telencephalic primordium

growth_protocol: Wild-type and Rx3-Cre mice (Swindell et al., 2006) were maintained in a CD1 background. Mice carrying floxed alleles for Dicer (Dicer1tm1Bdh/J)(Harfe et al., 2005) were maintained in C57BL/6 background. The day of vaginal plug was considered embryonic day (E) 0.5. Mice were kept at the Animal Facility of the Instituto de Neurociencias in Alicante, in accordance with institutional Spanish and European regulations.

extract_protocol:
The rostral-most region of the telencephalic primordium was dissected out from DicerF/F and RxCre-DicerF/F E11.5 embryos, and tissue pieces were immediately frozen. Tissue was then dissociated with Papain (Miltenyi Biotech, 130-092-628), RNA extracted using Quick RNA Mini Prep (Zymo Research, R1055) and 1µg of total RNA was used for library preparation and sequencing.
Libraries were prepared with NEBNext Ultra II Directional RNA Library Prep Kit and sequenced on Illumina HISeq 2500 with 100bp paired end read.

tag: tissue

value: Brain

tag: age

value: E11.5 embryos

tag: genotype

value: RxCre-Dicer F/F


title: ko_rep2 [RNA-seq]


title: WT_rep2 [miRNA-seq]

data_processing:
Reads were quality checked with FASTQC v2.6.14. SmallRNA-Seq reads were analysed using miRDeep2 (Friedlander et al., 2008) and mm10 and miRBase (v22) as reference. RNA-Seq output reads were quality-trimmed and filtered for adapters using Trim Galore v0.6.5 and aligned to the genome assembly (GRCm38.p6) using HISAT2 (Kim et al., 2015). Gene level read counts were computed using HTSeq (parameters: -m union –stranded=reverse and Ensembl gene annotations).
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files of gene counts per sample.

extract_protocol:
The rostral-most region of the telencephalic primordium was dissected out from DicerF/F and RxCre-DicerF/F E11.5 embryos, and tissue pieces were immediately frozen. Tissue was then dissociated with Papain (Miltenyi Biotech, 130-092-628) and RNA was extracted using Quick RNA Mini Prep (Zymo Research, R1055). Total RNA (1ug per sample) was used for library preparation and sequencing.
Libraries were prepared with NEB Next Small RNA Library Prep Kit (for RNA-Seq) and sequenced on Illumina HISeq 2500 with 75bp single end read.

tag: developmental stage

value: WT


title: KO_rep2 [miRNA-seq]

value: RxCre-DicerF/F


title: HSPCs-CeNT-mock-2

tag: cell type

value: CeNT-mock


title: HSPCs-CeNT-mock-1


title: HSPCs-CeNT-mock-3


title: HSPCs-Electroporation-mock-2


title: Aptamer21-PEARL-Cmpd7-Cmpd2d-None-2

value: PEARL-seq


title: KO_rep1 [miRNA-seq]


title: HSPCs-CeNT-GFP-1


title: HSPCs-untreated-1

value: untreated


title: ko_rep1 [RNA-seq]


title: HSPCs-untreated-3


title: HSPCs-untreated-2


title: wt_rep3 [RNA-seq]


title: Aptamer21-PEARL-Cmpd7-Cmpd2b-None-3

value: Targeted

value: MiSeq


title: wt_rep2 [RNA-seq]


title: Aptamer21-PEARL-Cmpd7-Cmpd2d-None-3


title: wt_rep1 [RNA-seq]


title: Aptamer21-PEARL-Cmpd7-Cmpd2b-None-2


title: Aptamer21-PEARL-Cmpd5-Cmpd6-None-3


title: Aptamer21-PEARL-Cmpd7-Cmpd2b-None-1


title: 353W

city: Barcelona

first: Enrique

last: Blanco

address: Dr. Aiguader 88

department: Gene Regulation, Stem Cells and Cancer

institute: Center for Genomic Regulation (CRG)

description: scRNA-seq experiment

data_processing:
Quality check of the generated reads was performed with the FastQC quality control suite.
Samples that reached the quality standards were then processed to deconvolute the reads to single-cell level by de-multiplexing according to the cell and pool barcodes
Sequencing reads were mapped with the RNA pipeline of the GEMTools 1.7.0 suite using default parameters (6% of mismatches, minimum of 80% matched bases, and minimum quality threshold of 26)
The analysis of spike-in control RNA content allowed us to identify empty wells and barcodes with more than 15% of reads mapping to spike-in artificial transcripts were discarded
In addition, cells with less than 60% of reads mapping on the reference genome or more than 2 × 106 total reads were discarded
Gene quantification was performed using UMI corrected transcript information to correct for amplification biases, collapsing read counts for reads mapping on a gene with the same UMI
Only unambiguously mapped reads were considered
Genome_build: Gencode release M8, assembly GRCm38.p4
Supplementary_files_format_and_content: tab-deimited text files (.tsv) containing gene expression values as UMI counts for all protocols.
R1 = cDNA; R2 = BC (1-6), UMI (7-14)

source_name: Bone marrow

growth_protocol: Bone marrow Lin- depletion HSC CD150+ (CD48- for RNA-seq samples)  labelling. Primary cells (no growth protocol)

extract_protocol:
(RNA-seq) RNA was extracted with the RNeasy micro kit (Qiagen) following manufacturer's instruction
Sequencing librraries were prepared according to the respective single-cell RNA-seq protocols.
Library selection and sequencing was performed following recommendations of to the respective single-cell RNA-seq protocols as detailed in the Methods.

tag: protocol

value: MARS-Seq

tag: centre

value: CNAG


title: 352W

description: scRNA-seq experiment


title: Aptamer21-PEARL-Cmpd5-Cmpd6-None-2


title: 351W

description: scRNA-seq experiment


title: Aptamer21-PEARL-Cmpd5-Cmpd2d-None-2


title: Aptamer21-PEARL-Cmpd5-Cmpd2d-None-1


title: adult murine lung GLI1+ stromal cells treated with bleomycin

city: San Francisco

first: Peng

last: Tien

state: CA

address: 513 Parnassus Ave, Health Sciences East 1350

department: Department of Pulmonary Medicine

institute: University of California San Francisco

description: single cell RNA sequencing of adult murine lung GLI1+ stromal cells with bleomycin injury

data_processing:
Data were processed according to the 10x Cellranger pipeline.
BAM files were generated with v2.1.1 10X Genomics Cellranger software using default parameters.
Gene-barcode matrices were generated from Cellranger v2.1.1 using default parameteres.
Genome_build: mm10
Supplementary_files_format_and_content: Cellranger outputs a .mtx file with the gene-barcode matrix. This matrix contains the counts of molecules per cell (UMI/cell) as determined after filtering and counting by Cellranger. The matrix is in market exchange format while the row (gene names) and columns (cell barcodes) are provided as TSV files. File formats are documented in Cellranger software manual.

source_name: adult murine lung GLI1+ stromal cells

extract_protocol:
Whole lung was dissected from the adult mouse and tracheally perfused with a digestion cocktail of Collagenase Type I (225 U/ml, Thermo Fisher), Dispase (15 U/ml, Thermo Fisher) and Dnase (50 U/ml, Sigma) and removed from the chest. The lung was further diced with razor blades and the mixture was incubated for 45 mins at 37 °C and vortexed continuously. The mixture was then washed with sorting buffer (2% FBS, 1% Pen-Strep in DMEM). The mixture was passed through a 70 µm cell strainer and resuspended in RBC lysis buffer, before passing through a 40 µm cell strainer. Cell suspensions were resuspended in sorting buffer. DAPI (0.2 µg/ml) was used to exclude dead cells. Doublets and dead cells were excluded based on forward and side scatter and DAPI fluorescence respectively. Cells were sorted into sorting buffer. FACS analysis was performed by FACSDiva. This preparation was performed separately for each sample.
cDNA libraries were prepared for sequencing using standard protocol for the 10x Single Cell instrument. The libraries for the two samples were prepared and sequenced separately.
Droplet-based single cell RNA-Seq

treatment_protocol: Two adult Gli1-CreERT2/R26R-YFP mice were injected with 0.2 mg/g tamoxifen on five consecutive days. One week later, one animal was intranasally treated with 1 unit/kg bleomycin every seven days for four weeks. The other animal was treated with PBS at the same timepoints.

value: GLI1+ stromal cells

value: lung

value: adult

value: Repetitive bleomycin (lung fibrosis)


title: Aptamer21-PEARL-Cmpd5-Cmpd2d-None-3


title: Aptamer21-PEARL-Cmpd7-Cmpd2d-None-1


title: ATACseq_Control_1

city: Cincinnati

first: Richard

last: Lu

state: OH

address: 3333 Burnet Ave

department: CBDI

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence.
Reads mapped to mm10 whole genome by Bowtie2 with default options
Peak calling was performed using MACS1.4 with a default p value cut off.
Genome_build: mm10
Supplementary_files_format_and_content: wig files were generated by MACS1.4
Supplementary_files_format_and_content: bed files

source_name: mouse OPC

extract_protocol: ATAC-seq: ATAC-seq assays were performed as previously described (Buenrostro et al., 2013). Briefly, we isolated nuclei of 50,000 sorted cells from the mouse cortex in a cold lysis buffer. Immediately after the nuclei preparation, we performed the transposase reaction for 30 min at 37 °C. The samples were purified using a Qiagen MinElute kit. Following purification, we amplified library fragments using 1× NEBnext PCR master mix.

treatment_protocol: ATAC-seq: For mouse OPC panning, single cell suspension was prepared from control and Eed cKO mouse cortices with papain dissociation, and cell suspension was transferred into O4 positive selection dish to pull down OPCs.

tag: sample type

value: Control

tag: genotype/variation

value: Eed c/+, Olig1 cre

value: Immunopanning for O4+ OPCs


title: adult murine lung GLI1+ stromal cells treated with PBS

description: single cell RNA sequencing of adult murine lung GLI1+ stromal cells

value: PBS (control)


title: ATACseq_EedcKO_1

value: EedcKO

value: Eed c/c, Olig1 cre


title: Aptamer21-PEARL-Cmpd5-Cmpd6-None-1


title: Aptamer21-PEARL-Cmpd5-Cmpd2b-None-1


title: Aptamer21-PEARL-Cmpd5-Cmpd2b-None-3


title: Aptamer21-PEARL-Cmpd1-Cmpd6-None-3


title: Aptamer21-PEARL-Cmpd5-Cmpd2b-None-2


title: wt_376_2_5_m

city: Rehovot

first: Mike

last: Fainzilber

address: 234 Herzl Street

department: Department of Biomolecular Sciences

country: Israel

institute: Weizmann Institute of Science

description:
processed1_raw_counts.xlsx
processed2_normalized_counts.xlsx

data_processing:
fastq files were generated by the usage bcl2fastq-v2.17.1.14 (basecalling)
Reads were trimmed using cutadapt
Reads were aligned to the mouse genome build GRCm38 using, STAR (2.4.2a0).
Counting reads on reference genome GRCm38, Ensembl realese 92, was done with HTSeq-count (version 0.6.1p1)
Differential analysis was carried out using DESeq2 (1.10.1)
Genome_build: GRCm38
Supplementary_files_format_and_content: processed1_raw_counts.xlsx
Supplementary_files_format_and_content: processed2_normalized_counts.xlsx

source_name: Dorsal root ganglia

extract_protocol:
RNAqueous-Micro Kit Ambion
Inhouse polyA based RNA seq

tag: spared nerve inury samples

value: 2.5 months

value: wild type


title: ko_367_2_5_m

value: imp{alpha}3 knockout mice


title: ko_378_2_5_m


title: Aptamer21-PEARL-Cmpd1-Cmpd6-None-2

value: PEARL-seq

value: Targeted


title: Aptamer21-PEARL-Cmpd1-Cmpd6-None-1

value: MiSeq


title: wt_416_7d

value: 7 days


title: wt_410_7d


title: Aptamer21-PEARL-Cmpd1-Cmpd2d-None-3


title: Aptamer21-PEARL-Cmpd1-Cmpd2d-None-2


title: wt_409_7d


title: 350W

description: scRNA-seq experiment

value: MARS-Seq

value: CNAG


title: ko_426_7d


title: ko_422_7d


title: ko_420__7d


title: Aptamer21-PEARL-Cmpd1-Cmpd2b-None-2


title: wt_67

value: naïve


title: Aptamer21-PEARL-Cmpd1-Cmpd2b-None-3


title: wt_28


title: Aptamer21-NAI-probe-3

value: NAI-MaP


title: wt_44


title: wt_48


title: ko_95


title: Aptamer21-NAI-probePlusCmpd1-3


title: Aptamer21-NAI-probePlusCmpd1-1


title: ko_39


title: ko_40


title: ko_362_2_5_m


title: Aptamer21-PEARL-Cmpd1-Cmpd2b-None-1


title: Aptamer21-NAI-control-2


title: Aptamer21-NAI-control-1


title: RNAseq_EedcKO2

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence.
Reads mapped to mm10 whole genome by Tophat with default options
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cufflinks with default options. Outputs from Cufflinks are provided as supplementary files as a tab-delimited text file.
format:fpkm_traking ; Contain the estimated expression values produced by Cufflinks.
Genome_build: mm10

extract_protocol:
RNA-seq: Total RNA from control and Eed KO OPC was extracted using Trizol (Life Technologies) protocol followed by purification using an RNeasy Micro Kit (Qiagen).
RNA-seq: RNA-seq libraries from control and Eed mutant OPCs were prepared using Illumina RNA-Seq Preparation Kit.

treatment_protocol: RNA-seq: For mouse OPC panning, single cell suspension was prepared from control and Eed cKO mouse cortices with papain dissociation, and cell suspension was transferred into O4 positive selection dish to pull down OPCs.


title: Aptamer21-PEARL-Cmpd1-Cmpd2d-None-1


title: Aptamer21-NAI-probe-2


title: Aptamer21-NAI-probe-1


title: ATACseq_Control

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence.
Reads mapped to mm10 whole genome by Bowtie2 with default options
Peak calling was performed using MACS1.4 with a default p value cut off.
Genome_build: mm10
wig files were generated by MACS1.4

value: Control


title: ATACseq_EedcKO


title: Aptamer21-DMS-probePlusCmpd1-3

value: DMS-MaP


title: Aptamer21-DMS-probePlusCmpd1-1


title: Aptamer21-NAI-probePlusCmpd1-2


title: RNAseq_Control2

value: Eed c/+, Olig1 cre

value: Immunopanning for O4+ OPCs


title: Aptamer21-DMS-control-3


title: RNAseq_Control1


title: Aptamer21-DMS-probe-3


title: Aptamer21-DMS-probe-1


title: Aptamer21-DMS-probe-2


title: Aptamer21-DMS-control-2


title: Aptamer21-NAI-control-3


title: S7

city: Bar Harbor

first: Catherine

middle: C

last: Kaczorowski

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

description:
genesTPM_Rd2_GEO_Ntg.csv
genesERC_Rd2_GEO_Ntg.csv
genesTPM_allDataComBatCorrected_final.csv

data_processing:
Bowtie 1.1.2 alignment (bowtie -q -p 8 -a --best --strata --sam -v 3)
EMASE 0.10.16 for abundance measurements
TPM data was combined with GSE101144 and Ntg littermates from 3rd GEO accession (total n = 290) and batch corrected using ComBat. Samples S3 and S285 were excluded as outliers from final analysis (S3 prior to clusters, S285 post-clustering).
Genome_build: mm10
Supplementary_files_format_and_content: genesTPM_round2_includedSamples_noReps.csv; direct TPM output from EMASE quantification
Supplementary_files_format_and_content: genesERC_round2_includedSamples_noReps.csv; direct expected read count from EMASE quantification

source_name: Hippocampus

growth_protocol: Animals were fear conditioning at either 6 or 14 months. Immediately following contextual fear memory testing, mice were euthanized by isoflurane, decaptitated, and brains were immediately harvested. Hippocampus was freshly dissected, snap frozen in liquid nitrogen, and stored at -80 until RNA extraction

extract_protocol:
RNEasy mini kit (QIAGEN) on QIACUBE (QIAGEN)
RNA was isolated on a Qiacube using the RNeasy mini kit (Qiagen) and treated with Dnase to remove contaminating DNA. RNA quality was confirmed using a BioAnalyzer (Agilent Technologies). All samples had RNA Integrity Numbers (RIN values) > 8.0. Sequencing libraries were prepared from 1 µg RNA with the Truseq Stranded mRNA Sample Preparation Kit (Illumina Inc) following the manufacturer’s protocol. Final PCR-enriched fragments were validated on a 2200 Tapestation Instrument using the D1000 ScreenTape (Agilent Technologies) and quantified by qPCR using a Universal Library Quantification Kit (Kapa Biosystems) on the QuantStudio 6 Flex (ThermoFisher Scientific). Final library pools were sequenced by 75bp paired-end sequencing on a HiSeq2500 (Illumina Inc).

treatment_protocol: Hippocampus was dissected from fresh tissue, snap frozen in liquid nitrogen, and stored at -80 until RNA extraction

tag: Sex

value: Male

tag: strain

value: Ntg


title: Mm_esc_ncorko.rp3

city: Shenzhen

first: Andrew

last: Hutchins

address: 1088 Xueyuan Rd

department: Bioinformatics

country: China

institute: Southern University of Science and Technology

description:
esc_ncorko.3
Mouse ESC Ncor2-flox, Knockout, repeat 3

data_processing:
STAR was used to align the reads to the gencode transcriptome (mm10, m21), mouse genome and the repeatmasker transposable element (TE) database.
Reads mapping to genes or TEs were counted using te_counter (https://github.com/oaxiom/te_counter).
Genes with more than 100 sequence tags in 2 or more timepoints were kept for further analysis.
Mapped tag counts were GC normalised using EDASeq v2.0.0.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: genes_ntc_expression.tsv: TSV containing a table of expression data, columns are samples, rows are genes or transposable elements.
Supplementary_files_format_and_content: genes_ntc_expression_escs.tsv: TSV containing a table of expression data, columns are samples, rows are genes or transposable elements, for the ESC samples.

source_name: ESC cell culture

growth_protocol: EpiLCs (epiblast-like cells) were differentiated according to the protocol described in Hayashi et al., 2011. Briefly, 1.0x10e5 ESCs were plated onto a well of a 6-well plate coated with human plasma fibronectin (20ug/ml) in 2iLif medium (DMEM/F12 (HyClone) and Neurobasal (Gibco) medium mixed 1:1, supplemented with N2 (Gibco), B27 (Gibco), non-essential amino acids (Gibco), GlutaMAX (Gibco), sodium pyruvate (Cellgro), penicillin/streptomycin (HyClone), 0.1 mM β-mercaptoethanol (Gibco), 1,000 U per ml leukemia inhibitory factor (LIF; Millipore), CHIR99021 (3 μM; Selleck) and PD0325901 (1 μM; Selleck)), after a 12 hour incubation, the cells would attach to the plate. We take this time point as 0h. We then changed the medium to N2B27 medium containing activin A (20ng/ml; Peprotech), bFGF (12ng/ml; Peprotech) and Knockout Serum Replacement (1%; Gibco). The medium was changed every day. We collected cells every 12h and extracted total RNA for sequencing.

extract_protocol:
Extracted using TRIzol using the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: At hour 0, we then changed the medium to N2B27 medium containing activin A (20ng/ml; Peprotech), bFGF (12ng/ml; Peprotech) and Knockout Serum Replacement (1%; Gibco). The medium was changed every day. We collected cells every 12h and extracted total RNA for sequencing. For Ncor wildtype and knockout ESCs, Ncor2 exon ast (mm10:chr5:125,116,000-125,179,053) was floxed, and in the knockout cells was removed by transfection of Cre. Single cells were propagated and cloned, and the knockout was confirmed by qRT-PCR, genomic PCR.

value: ESC

tag: time


title: S304

value: Female


title: Aptamer21-DMS-control-1

tag: library type

tag: scale

tag: platform


title: S301


title: S302


title: S30


title: S285

description:
sample excluded as outlier after batch correction, not in processed file combat_2016reps_4batchRun_nonpara_genesTPM_final.csv
genesTPM_Rd2_GEO_Ntg.csv
genesERC_Rd2_GEO_Ntg.csv


title: Mm_esc_ncorko.rp2

description:
esc_ncorko.2
Mouse ESC Ncor2-flox, Knockout, repeat 2


title: Mm_esc_ncorko.rp1

description:
esc_ncorko.1
Mouse ESC Ncor2-flox, Knockout, repeat 1


title: S299


title: Aptamer21-DMS-probePlusCmpd1-2


title: Mm_esc_ncorwt.rp3

description:
esc_ncorwt.3
Mouse ESC Ncor2-flox, Wildtype, repeat 3

value: Wildtype


title: RNAseq_EedcKO1

value: EedcKO

value: Eed c/c, Olig1 cre


title: S294


title: Mm_esc_ncorwt.rp2

description:
esc_ncorwt.2
Mouse ESC Ncor2-flox, Wildtype, repeat 2


title: Mm_esc_ncorwt.rp1

description:
esc_ncorwt.1
Mouse ESC Ncor2flox, Wildtype, repeat 1


title: S297


title: S29


title: S291


title: S287


title: S281


title: S278


title: IL-2/12 vehicle biological replicate 2

city: Frederick

first: Jessica

last: Walls

state: MD

address: Bulding 560, Rm 31-45

institute: National Cancer Institute

description: sample/E

data_processing:
BAM files were converted to fastq, followed by Fast QC
Align fastq files to Genecode mouse reference using STAR (with soft trimming)
Post-alignment quality control with RNASeqQC
Subreads counting on aligned BAM files (using RefSeq gtf file)
Genome_build: mm10

source_name: IL-2/12 Stimulated NK cells 18 hours

growth_protocol: Splenocytes were expanded for 6 days in murine IL-15 (10ng/mL, Peprotech) and then NK cells were MACS purified (miltenyi, NK cell isolation kit II). Cells were then stimulated with IL-2/12 (330U/10ng/mL) with or without treatment. Cells were lysed and RNA was purified.

extract_protocol:
Total RNA was isolated using the GeneJet RNA purification kit (Thermofisher), as per manufacturer's instructions (with the addition that 2-mercaptoethanol (1%v/v) was added to the lysis buffer.
TruSeq Stranded RNA-Seq with poly (A) selection

treatment_protocol: Cells were treated with IL-2/12 +/- vehicle or TEPP-46 in replete RPMI for 18 hours. Cells were then lysed using GeneJet RNA purification kit lysis buffer

value: WT

value: 6 day IL-15 expanded splenic NK cells

tag: treatment


title: IL-2/12 TEPP  biological replicate 3

description: sample/I


title: S273


title: IL-2/12 TEPP biological replicate 2

description: sample/F


title: IL-2/12 TEPP biological replicate 1

description: sample/C


title: IL-2/12 vehicle biological replicate 1

description: sample/B


title: S266


title: KO IL-2/12 18hr biological replicate 3

value: NCR1Cre het  PKM2fl/fl


title: KO IL-2/12 18hr biological replicate 1


title: Phco_ENV_F3

city: Auzeville Tolosane

first: Sylvain

last: MERLOT

address: 24, chemin de Borde Rouge

department: Biological Sciences

country: France

institute: CNRS

description:
Phco_transcriptome_v1.fasta
BYI_AAAFOSRB_6_1_CBA4RACXX.IND12_noribo

data_processing:
Illumina HiSeq 2000 100bp paired-end mode
Adaptors and low quality pair-end sequences were removed from the raw reads and the ribosomal RNA was filtered using the SortMeRNA algorithm (Kopylova, E., Noé, L. & Touzet, H. SortMeRNA: Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data. Bioinformatics 28, 3211–3217 (2012).
To generate transcriptome sequences, paired-end reads originating from one individual plant of Phyllanthus luciliae (Phlu) or Phyllanthus conjugatus (Phco) were assembled de novo using CLC Genomic Workbench 9 with Lenght fraction:0.75; Similarity fraction: 0.95; word size: 30 (Phlu), 24 (Phco). Contig sequences were annotated using Blast2GO using BlastX with E-value≤10-6.
Paired-end reads of all independant samples were mapped to the Phlu_transcriptome_v1 using CLC Genomic Workbench 9 with Lenght fraction 0.5 and Similarity fraction 0.875. Read counts are used for abundance measurements.
Genome_build: Phlu_transcriptome_v1.fasta
Supplementary_files_format_and_content: abundance measurements

organism: [Phyllanthus] conjugatus var. ducosensis

source_name: Leaf_environmental sample

growth_protocol: Plant samples were collected in their natural environment

extract_protocol:
Total RNA were extracted from frozen leaves of one individual plant using a CTAB-PVP/LiAc method (Protocol#3, Johnson et al. 2012, PLoS ONE 7(11): e50226. doi:10.1371), and treated with DNAseI. RNA were stabilized with GenTegra-RNA for shipping
Libraries were constructed using 1 µg total RNA with Illumina TruSeq Stranded mRNA kit by the POPS transcriptomic plateform (IPS2, Orsay, France) following Illumina kit recommendations.

treatment_protocol: Samples were rapidly frozen in liquid nitrogen upon collection and stored at -80°C before RNA extraction

tag: collection site

value: Kamere, Noumea, New Caledonia

tag: gps location

tag: collection date


title: WT IL-2/12 18hr biological replicate 3

tag: genotype

value: NCR1Cre het


title: S272

tag: age


title: Phco_ENV_F2

description:
Phco_transcriptome_v1.fasta
BYI_AAAEOSRB_6_1_CBA4RACXX.IND7_noribo


title: S270


title: KO IL-2/12 18hr biological replicate 2

tag: cell type


title: S265


title: Phlu_ENV_F3

description:
Phlu_transcriptome_v1.fasta
BYI_AAACOSRB_6_1_CBA4RACXX.IND5_noribo

organism: Phyllanthus luciliae

value: Houaïlou, New Caledonia


title: S268


title: WT IL-2/12 18hr biological replicate 1


title: Phlu_ENV_F2

description:
Phlu_transcriptome_v1.fasta
BYI_AAABOSRB_6_1_CBA4RACXX.IND4_noribo


title: IL-2/12  vehicle biological replicate 3

description: sample/H


title: S264


title: Phlu_ENV_F1

description:
Phlu_transcriptome_v1.fasta
BYI_AAAAOSRB_6_1_CBA4RACXX.IND2_noribo


title: S258


title: S254


title: B16_anti-PD-L1 + Swainsonine_3 [41]

city: Shanghai

first: jun

last: ge

address: 1239 Siping Road

department: School of Life Sciences and Technology

institute: Tongji University

data_processing:
fastq files were aligned to  of mouse reference genome mm10 vM16 using STAR.
RSEM was used to map aligned reads and to generate a gene count matrix.
Genome_build: Mouse reference genome mm10
Supplementary_files_format_and_content: tab-delimited text files include raw count and Transcripts Per Kilobase Million (TPM) values for each Sample ...

source_name: B16_anti-PD-L1 + Swainsonine

extract_protocol:
RNA was extracted using TRIzol reagent (Invitrogen Life Technologies, Gaithersburg, MD, USA) according to the manufacturer’s instructions.
Purified mRNA was fragmented into short fragments with fragment buffer and cDNAs were synthesized using the RNA fragments as templates for random primer, followed by end reparation and ligation to adapters.

treatment_protocol: B16F10 treated with IgG isotype control or anti-PD-L1 or swainsonine or the combination of anti-PD-L1 and swainsonine in C57BL/6 mouse.

tag: cell line

tag: background strain

value: wild-type


title: B16_anti-PD-L1 + Swainsonine_2 [39]


title: B16_anti-PD-L1 + Swainsonine_1 [38]


title: B16_Swainsonine_3 [36]

value: Swainsonine +IgG


title: HUVEC_LNA4_HT_2

city: La Jolla

first: Sheng

last: Zhong

address: 9500 Gilman Dr

department: Bioengineering

institute: University of California San Diego

description: polyA-RNA enriched

data_processing:
Illumina bcl2fastq version 2.18 used for base calling
Reads were aligned to the hg38 genome assembly using STAR (2.5.4b) with parameter '--sjdbGTFfile'
featureCounts from Subread package (2.0.0) was used to count the number of uniquely mapped reads over exons (-t) per each gene. Strand specific parameter (-s) set to 2
Genome_build: hg38
Supplementary_files_format_and_content: The processed counts.txt file is a tab-delimited table which includes annotation columns (‘Geneid’, ‘Chr’, ‘Start’, ‘End’, ‘Strand’ and ‘Length’) and data columns (eg. read counts for genes for each library).

source_name: Human Umbilical Vein Endothelial Cells under treatment combining transfection with LNA-2 targeting LINC00607, high glucose (HG, to mimic hyperglycemia) and TNFα (to mimic inflammation) for 3 days (replicate 2).

growth_protocol: HUVECs were grown following the manufacturer's protocol

extract_protocol:
Approximately 1 million cells were used for total RNA extraction and construction of strand-specific mRNA-seq library
The libraries were constructed using the KAPA mRNA stranded Hyper kit following the user manual

treatment_protocol: HUVECs were transfected with either scramble LNA or two different LNAs targeting LINC00607; and treated with 25mM Mannitol in the control group; Cells in the H_T groups were treated with 25mM D-Glucose and 5ng/mL TNFalpha for 3 days

value: HUVEC


title: HUVEC_LNA1_HT_2

description: polyA-RNA enriched

source_name: Human Umbilical Vein Endothelial Cells under treatment combining transfection with LNA-1 targeting LINC00607, high glucose (HG, to mimic hyperglycemia) and TNFα (to mimic inflammation) for 3 days (replicate 2).


title: WT IL-2/12 18hr biological replicate 2


title: Phco_ENV_F1

description:
Phco_transcriptome_v1.fasta
BYI_AAADOSRB_6_1_CBA4RACXX.IND6_noribo


title: S251


title: S247


title: HUVEC_Scr_HT_2

description: polyA-RNA enriched

source_name: Human Umbilical Vein Endothelial Cells under treatment combining transfection with scramble LNA, high glucose (HG, to mimic hyperglycemia) and TNFα (to mimic inflammation) for 3 days (replicate 2).


title: B16_Swainsonine_1 [30]


title: B16_Swainsonine_2 [34]


title: B16_anti-PD-L1_3 [23]


title: S261


title: HUVEC_Scr_NG_2

description: polyA-RNA enriched

source_name: Human Umbilical Vein Endothelial Cells cultured under osmotic control (25 mM mannitol) combined with transfection with scramble LNA (replicate 2).


title: S246


title: B16_IgG + PBS_3 [11]

source_name: B16_IgG + PBS

value: IgG +PBS


title: HUVEC_LNA4_HT_1

description: polyA-RNA enriched

source_name: Human Umbilical Vein Endothelial Cells under treatment combining transfection with LNA-2 targeting LINC00607, high glucose (HG, to mimic hyperglycemia) and TNFα (to mimic inflammation) for 3 days (replicate 1).


title: B16_anti-PD-L1_1 [19]


title: B16_IgG + PBS_2 [9]


title: HUVEC_LNA1_HT_1

description: polyA-RNA enriched

source_name: Human Umbilical Vein Endothelial Cells under treatment combining transfection with LNA-1 targeting LINC00607, high glucose (HG, to mimic hyperglycemia) and TNFα (to mimic inflammation) for 3 days (replicate 1).


title: S243


title: B16_IgG + PBS_1 [7]


title: S239


title: B16_sgMan2a1_anti-PD-L1_3 [89]

value: Man2a1 Knockout


title: S237

value: Ntg


title: B16_sgMan2a1_anti-PD-L1_2 [87]


title: HUVEC_Scr_HT_1

description: polyA-RNA enriched

source_name: Human Umbilical Vein Endothelial Cells under treatment combining transfection with scramble LNA, high glucose (HG, to mimic hyperglycemia) and TNFα (to mimic inflammation) for 3 days (replicate 1).


title: B16_sgMan2a1_anti-PD-L1_1 [72]


title: HUVEC_Scr_NG_1

description: polyA-RNA enriched

source_name: Human Umbilical Vein Endothelial Cells cultured under osmotic control (25 mM mannitol) combined with transfection with scramble LNA (replicate 1).


title: S236

value: Male


title: B16_sgMan2a1_IgG_3 [83]

value: IgG


title: WT_rep1 [miRNA-seq]

source_name: telencephalic primordium

tag: tissue

value: Brain

tag: developmental stage

value: E11.5 embryos


title: B16_sgMan2a1_IgG_2 [82]


title: B16_anti-PD-L1_2 [22]


title: B16_sgRosa26_anti-PD-L1_3 [51]

value: Ctrl


title: B16_sgMan2a1_IgG_1 [81]


title: S234

tag: Sex

value: Female


title: B16_sgRosa26_anti-PD-L1_2 [49]


title: B16_sgRosa26_anti-PD-L1_1 [47]


title: Viral_NCs_B

city: Bethesda

first: Markus

last: Hafner

address: 50 South Drive

department: NIAMS

institute: NIH

data_processing:
library strategy: PAR-CLIP
conversion of base call (BCL) files into FASTQ files using bcl2fastq (bcl2fastq/2.20.0)
demultiplexing FASTQ files using cutadapt (cutadapt 2.4 with python/3.3.4)
adapter trimming using cutadapt (cutadapt 2.4 with python/3.3.4)
alignment to SFV genome with bowtie/1.1.1
coverage using bedtools2/2.27.1  (bedtools genomecov)
Genome_build: Semliki Forest Virus genome (https://www.ncbi.nlm.nih.gov/nuccore/KT009012.1 with the following SNPs: 59G>C, 1627T>C, 4236C>A, 7488T>C, 7609G>A, 7677A>C, 8530A>G, 8732C>A, 8905G>A, 10155C>T)
Supplementary_files_format_and_content: per base coverage of aligned sequences and TtoC mutations

organism: Semliki Forest virus

growth_protocol: Vero cells were cultured in DMEM containing 4 mM L-glutamine, 100 UI/mL penicillin, 100 ug/mL streptomycin, and 10% FBS at 37oC.

extract_protocol:
Cp-mAVI-biotin was retrieved form Total cellular lysates, purified Cellular NCs and from purified viral NCs with Streptavidin beads
Crosslinked RNAs where further processed using the standard PAR-CLIP protocol (Benhalevy et al., 2017b; Danan et al., 2016; Hafner et al., 2010b; Yamaji et al., 2017)
Illumina TruSeq Small RNA library adapters and primers

treatment_protocol: The cells were infected with SFV mAVI at an MOI=10 for 1.5 h, washed three times, and then placed into media supplemented with 50 µM biotin and 100 µM 4-thiouridine. At 7 hpi, the cells were UV-irradiated with 368 nm light at 0.15 J/cm2

value: Vero-BirA cells

value: infected with SFV-Cp-mAVI for 1.5 h

value: treated with biotin and photoactivatable ribonucleoside 4-thiouridine (4SU)

tag: molecule subtype

value: alphavirus capsid protein; Cp-mAVI-biotin

tag: molecule source

value: purified Viral Nucleocapsids (NC)


title: Viral_NCs_A


title: B16_sgRosa26_IgG_3 [42]


title: ko_35

tag: spared nerve inury samples

value: naïve

value: imp{alpha}3 knockout mice


title: S229

tag: strain


title: Cellular_NC_B

value: purified Cellular Nucleocapsids (NC)


title: Cellular_NC_A


title: S228


title: 29_AML_Pt12_34_pos_38_pos_Rl_LSC

city: Aurora

first: Brett

last: Stevens

state: CO

institute: University of Colorado

description:
relapse LSC
29_AML_Pt12_34_pos_38_pos_Rl_LSC

data_processing:
Raw reads generated from the Illumina HiSeq2500 sequencer were demultiplexed using bcl2fastq version 2.19.0.
Quality filtering and adapter removal are performed using Trimmomatic-0.36 with the following parameters: "TRAILING:13 LEADING:13 ILLUMINACLIP:adapters.fasta:2:30:10 SLIDINGWINDOW:4:20 MINLEN:35".
Processed/cleaned reads were then mapped to the Homo sapiens reference sequence (GRCh38, hg38) with STAR-2.6.0c given the following parameters: "--twopassMode Basic --runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical".
The subread-1.6.1 package (featureCounts) was used to derive gene counts given the following parameters: “-s 2 -t exon -g gene_name”.
Differential expression analysis and data normalization was performed using DESeq2-1.16.1 with an adjusted p-value threshold of 0.05 within an R-3.4.1 environment. A batch factor was given to the differential expression model in order to control for batch differences.
Genome_build: GRCh38, hg38
Supplementary_files_format_and_content: raw counts produced by deSeq2 analysis provided in txt file

source_name: AML Bone marrow Pt Sample

growth_protocol: Freshly thawed and sorted, no growth involved

extract_protocol:
QIAGEN RNeasy Plus Kit
The TruSeq Stranded mRNA Sample Preparation Kit (Illumina, San Diego, CA) was used for next generation sequencing library construction per manufacturer’s protocols.
Briefly, mRNA was purified from 200ng total RNA with oligo-dT magnetic beads and fragmented. First-strand cDNA synthesis was performed with random hexamer priming followed by second-strand cDNA synthesis using dUTP incorporation for strand marking. End repair and 3` adenylation was then performed on the double stranded cDNA. Illumina adaptors were ligated to both ends of the cDNA, purified by gel electrophoresis and amplified with PCR primers specific to the adaptor sequences to generate cDNA amplicons of approximately 200-500bp in size. The amplified libraries were hybridized to the Illumina single end flow cell and amplified using the cBot (Illumina, San Diego, CA). Single end reads of 100nt were generated for each sample on the Illumina HiSeq2500 platform.

treatment_protocol: Freshly thawed and sorted, no treatment involved

value: Primary human AML patient specimen

tag: sub-fraction

value: LSCs


title: 30_AML_Pt12_34_pos_38_neg_Rl_LSC

description:
relapse LSC
30_AML_Pt12_34_pos_38_neg_Rl_LSC


title: 25_AML_Pt07_34_neg_38_neg_Rl_LSC

description:
relapse LSC
25_AML_Pt07_34_neg_38_neg_Rl_LSC


title: 26_AML_Pt07_34_neg_38_pos_Rl_LSC

description:
relapse LSC
26_AML_Pt07_34_neg_38_pos_Rl_LSC


title: 22_AML_Pt02_34_neg_38_pos_Rl_LSC

description:
relapse LSC
22_AML_Pt02_34_neg_38_pos_Rl_LSC


title: Total_cellular_Cp_A

tag: treatment

value: Total cellular lysates


title: 21_AML_Pt02_34_neg_38_neg_Rl_LSC

description:
relapse LSC
21_AML_Pt02_34_neg_38_neg_Rl_LSC


title: B16_sgRosa26_IgG_2 [40]


title: S226

description:
genesTPM_Rd2_GEO_Ntg.csv
genesERC_Rd2_GEO_Ntg.csv
genesTPM_allDataComBatCorrected_final.csv

value: Ntg


title: 20_AML_Pt02_34_pos_38_pos_Rl_LSC

description:
relapse LSC
20_AML_Pt02_34_pos_38_pos_Rl_LSC


title: S233


title: 16_AML_Pt88_32_neg_38_pos_Rl_LSC

description:
relapse LSC
16_AML_Pt88_32_neg_38_pos_Rl_LSC


title: S220


title: S219


title: S232


title: 14_AML_Pt04_32_pos_38_pos_Rl_LSC

description:
relapse LSC
14_AML_Pt04_32_pos_38_pos_Rl_LSC


title: B16_sgRosa26_IgG_1 [37]

value: IgG


title: B16_sgRosa26_2 [B16-48]

value: No


title: B16_sgRosa26_1 [B16-46]


title: B16_sgMan2a1_2 [B16-43]

value: Man2a1 Knockout


title: B16_sgMan2a1_1 [B16-42]


title: S215

value: Male


title: Mcat, Day 1, replicate D

city: Salt Lake City

first: Jeff

last: Morgan

state: UT

address: 15 N Medical Drive East

department: Biochemistry

institute: University of Utah

data_processing:
Reads were trimmed of adaptor sequence using cutadapt (v.2.8) with the parameters '-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -m 15'. Trimmed reads were aligned to the mouse genome (mm10) using STAR (v.2.5) with the parameters ‘--outFilterMismatchNoverLmax 0.2 --sjdbOverhang 49 --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts’ and with ‘–sjdbGTFfile’ supplied with transcript annotations from Ensembl (Mus_musculus.GRCm38.99.chr_patch_hapl_scaff.gtf).
Three samples were censored from further analyses (one replicate each of GFP day −1, Mcat day 0, and Oxsm day 1) due to outlier status relative to all remaining samples.
Transcripts were given a pseudocount. Differential expression across the remaining 44 samples was determined using DESeq2 (v.1.26.0). For plotting and analysis, count data were shrunk using the ‘apeglm’ option of the DESeq2 function ‘lfcShrink’.
Genome_build: mm10 (Mus_musculus.GRCm38.99.chr_patch_hapl_scaff.gtf)
Supplementary_files_format_and_content: Normalized abundance measurements, which were shrunk using the ‘apeglm’ option of the DESeq2 function ‘lfcShrink’.

source_name: immortalized skeletal myoblasts

growth_protocol: MtFAS mutants and GFP controls were seeded in 10 cm plates and grown in DMEM (Corning, 10-013-CV) supplemented with 10% FBS (Sigma, F0926) to 70% confluency (Day −1). The next day at 95% confluency cells were switched to DMEM supplemented with 2% horse serum (Thermo, 16050122) (Day 0). Media was changed and replaced with fresh DMEM + 2% horse serum every 24 hours (Day 1).

extract_protocol:
Total RNA was extracted from one confluent 10 cm dish per replicate using TRI Reagent (Zymo Research, R2050-1-200) according to the manufacturer’s protocol. Poly(A) RNA was purified from total RNA samples (100-500 ng) with oligo(dT) magnetic beads.
Stranded mRNA sequencing libraries were prepared as described using the Illumina TruSeq Stranded mRNA Library Prep kit (20020595) and TruSeq RNA UD Indexes (20022371). Librarieswere sequenced on an Illumina NovaSeq instrument using 2 x 51 cycle paired end sequencing.

value: C2C12 immortalized mouse skeletal myoblasts (ATCC CRL-1772)

value: Mcat hypomorph


title: S213

source_name: Hippocampus


title: 13_AML_Pt04_32_pos_38_neg_Rl_LSC

description:
relapse LSC
13_AML_Pt04_32_pos_38_neg_Rl_LSC


title: Total_cellular_Cp_B

value: Vero-BirA cells

value: infected with SFV-Cp-mAVI for 1.5 h


title: Mcat, Day 1, replicate C


title: Mcat, Day 1, replicate B


title: Mecr, Day 1, replicate D

value: Mecr hypomorph


title: S210


title: Mcat, Day 1, replicate A


title: S212


title: Mecr, Day 1, replicate B


title: 11_AML_Pt04_32_neg_38_neg_Rl_LSC

description:
relapse LSC
11_AML_Pt04_32_neg_38_neg_Rl_LSC


title: 12_AML_Pt04_32_neg_38_pos_Rl_LSC

description:
relapse LSC
12_AML_Pt04_32_neg_38_pos_Rl_LSC


title: Mecr, Day 1, replicate A


title: 36_AML_Pt35_34_neg_38_neg_Rl_LSC

description:
relapse LSC
36_AML_Pt35_34_neg_38_neg_Rl_LSC


title: GFP, Day 1, replicate D

value: Wild type


title: S207

value: Female


title: GFP, Day 1, replicate C


title: GFP, Day 1, replicate B


title: 35_AML_Pt35_34_pos_38_pos_Rl_LSC

description:
relapse LSC
35_AML_Pt35_34_pos_38_pos_Rl_LSC


title: 34_AML_Pt35_34_pos_38_neg_Rl_LSC

description:
relapse LSC
34_AML_Pt35_34_pos_38_neg_Rl_LSC


title: S206


title: GFP, Day 1, replicate A


title: S202


title: Oxsm, Day 1, replicate D

value: Oxsm hypomorph


title: 32_AML_Pt35_34_pos_38_pos_Dx_LSC

description:
diagnosis LSC
32_AML_Pt35_34_pos_38_pos_Dx_LSC


title: Mecr, Day 1, replicate C


title: S201


title: Oxsm, Day 1, replicate C


title: 31_AML_Pt35_34_pos_38_neg_Dx_LSC

description:
diagnosis LSC
31_AML_Pt35_34_pos_38_neg_Dx_LSC


title: 27_AML_Pt12_34_pos_38_pos_Dx_LSC

description:
diagnosis LSC
27_AML_Pt12_34_pos_38_pos_Dx_LSC


title: S195


title: S194


title: 24_AML_Pt07_34_neg_38_pos_Dx_LSC

description:
diagnosis LSC
24_AML_Pt07_34_neg_38_pos_Dx_LSC


title: S208


title: 23_AML_Pt07_34_neg_38_neg_Dx_LSC

description:
diagnosis LSC
23_AML_Pt07_34_neg_38_neg_Dx_LSC


title: Oxsm, Day 1, replicate B


title: S193


title: 17_AML_Pt02_34_pos_38_pos_Dx_LSC

description:
diagnosis LSC
17_AML_Pt02_34_pos_38_pos_Dx_LSC


title: 15_AML_Pt88_32_neg_38_pos_Dx_LSC

description:
diagnosis LSC
15_AML_Pt88_32_neg_38_pos_Dx_LSC


title: S191

description:
genesTPM_Rd2_GEO_Ntg.csv
genesERC_Rd2_GEO_Ntg.csv
genesTPM_allDataComBatCorrected_final.csv


title: Mcat, Day 0, replicate D


title: Mcat, Day 0, replicate C


title: Mcat, Day 0, replicate B


title: S188


title: Mecr, Day 0, replicate D


title: 9255013094_I: CD57hiPD1dim

city: Cleveland

first: Rafick

last: Pierre-Sekaly

address: 2103 Cornell Avenue

department: Pathology

institute: Case Western Reserve University

description: Healthy

hyb_protocol: Microarray analysis was conducted using 750ng of biotinylated cRNA hybridized to Human RefSeq-12 V4 BeadChips (Illumina) at 58°C for 20 hours, according to Illumina's direct hybridization protocol by the Genomics core at Collaborative Genomics Center (CGC).

scan_protocol: The arrays were scanned using an Illumina iScan scanner and quantified using GenomeStudio software (Illumina).

data_processing: Analysis of the GenomeStudio output data was conducted using the R statistical language and various software packages from Bioconductor by the Bioinformatics core at the Collaborative Genomics Center. Missing values were imputed using the KNN algorithm from the impute R package. Quantile normalization was applied, followed by a log2 transformation.

label: Biotin

label_protocol: The hybridized BeadChips were washed, blocked, stained and scanned according to the Illumina's direct hybridization protocol.

growth_protocol: Upon receipt, tonsils were washed with ice-cold medium R-10 (RPMI 1640 supplemented with 10% fetal bovine serum, 2 mM L-glutamine, 100 U/mL penicillin and 100 μg/mL streptomycin (Invitrogen), surrounding fatty tissue was removed and tissues were cut into small pieces. Tonsillar cells were isolated from the remaining specimen by mechanical disruption, followed by Ficoll-Paque density gradient centrifugation. Cells were stored in liquid nitrogen until further use

extract_protocol: CD4 T cell subsets were sorted in 2x buffer for RNA extraction. Reverse transcription reactions were performed to obtain cDNAs which were hybridized to the Illumina Human HT-12 version 4 Expression BeadChip according to the manufacturer’s instruction, and quantified using an Illumina iScan System. The data were collected with Illumina GenomeStudio software. Analysis of the genome array output data was conducted using the R statistical language and the Limma statistical package from Bioconductor.

treatment_protocol: Sorting of tonsillar CD4 T cells was performed without any prior treatment.

tag: subject

tag: cell population

value: tonsil Tfh


title: 9255013094_L: CD57hiPD1hi

description: Healthy


title: 9255013094_K: CD57hiPD1hi

description: Healthy


title: 9255013094_F: CD57loPD1dim

description: Healthy


title: 9255013094_E: CD57loPD1hi

description: Healthy


title: 9255013094_D: CD57loPD1hi

description: Healthy


title: 9255013094_C: CD57loPD1dim

description: Healthy


title: Mecr, Day 0, replicate B


title: S185


title: S187


title: 07_AML_Pt04_32_neg_38_neg_Dx_LSC

description:
diagnosis LSC
07_AML_Pt04_32_neg_38_neg_Dx_LSC

value: Primary human AML patient specimen


title: WT RNAseq rep3

first: Wee Siong Sho

last: Goh

state: Guangdong

address: Shenzhen Bay Laboratory, No. 5, Kelian Road, Goh Lab, A1819, Guangming District

department: Institute of Molecular Physiology

institute: Shenzhen Bay Laboratory

data_processing:
m6ACE-seq analysis  Fastq sequences were first filtered for a quality score of 20, then trimmed of 5’ and 3’ adapter sequences and poly(A) tails using Cutadapt. The 8-mer UMI located at the first 8 nucleotides of read 1 was registered and trimmed. Any complementary UMI sequence in read 2 was also trimmed. Reads were mapped to the methylated spike-in (Table 1) using Bowtie2, or to the hg38 assembly transcriptome (Gencode v28 comprehensive gene annotations) using STAR. Aligned pairs that had the same mapping coordinates and UMIs were filtered out as PCR duplicates. Read-start coordinates in hg38-mapped reads that began with an adenosine nucleotide, and had a minimum mean read count of 1 across the triplicate samples were collated. m6A or m6Am sites were identified as read starts that were at least 2-fold enriched in m6ACE libraries than in the corresponding input libraries. This enrichment was calculated using DESeq2 performed on A-only sites across triplicate pairs of m6ACE and corresponding input libraries (FDR<0.1, padj<0.05). Identified sites that were 1-4 nucleotides upstream of another identified significant Rm6AC site or sites found within clustered read-starts were filtered out.   To calculate the RML of each site in each sample: The read-start counts at positions -4 to 0 of each site in the m6ACE library were summed and divided by the read-start counts at positions -51 to 0 of the same site in the input library to give ‘X’. Similarly, the read-start counts at positions -4 to 0 of the spike-in m6A site in the m6ACE library were summed and divided by the read-start counts at positions -21 to 0 of the same spike-in m6A site in the input library to give ‘Y’. X was normalized to Y to give RML. RML values of each site was averaged across triplicates for each sample condition. A site was denoted as differentially methylated between METTL4WT-rescue and METTL4CD-rescue if the average RML differs between sample conditions with a log2fold-change cutoff of 2.0, as well as a one-tailed Student’s T-test p-value cutoff of <0.041 (false discovery rate, FDR < 0.1). Consensus motif analysis was performed using Meme-chip. Metagene analysis was performed using MetaPlotR.   RNAseq  10µg of RNA was treated with RQ1 RNase-Free DNase (Promega M6101) as per manufacturer’s protocol. 5µg of samples were then depleted of rRNA using the ribozero kit (Illumina MRZH11124). 50ng of each rRNA-depleted samples were then used for construct RNA-seq libraries using the ScriptSeq v2 RNASeq Library Preparation Kit (Illumina SSV21124). Libraries were sequenced on an Illumina PE151 platform.  RNAseq Splicing Analysis  WT and Mettl4-KO HEK293T RNAseq libraries were first processed using CutAdapt to remove adaptors and to trim all reads to a uniform length of 101bp for compatibility with downstream analysis steps. Read alignment to the genome was then performed using STAR (2.7.0a) in two-pass mode using the hg38 genome assembly and GENCODE v28 gene annotations.   Alternative splicing differences were analysed by an in-house pipeline using replicate MATS (rMATS 3.2.5) and filtered based on cut-offs of FDR ≤ 0.05, an absolute change in percent spliced in (|ΔPSI|) ≥ 0.1. In addition, events with mean sample junction counts (IC_Sample + SC_Sample) < 20 were filtered out to reduce false positives arising from transcript dropout in low abundance isoforms. The validation of several differential alternative splicing events were performed using an RT-PCR assay.  Additional exon-level features were added to the data using databases constructed from the UCSC Table Browser, as well as in-house R scripts. Splice-site strengths were calculated using MaxEntScan. Comparisons were made between the exon features of the differentially spliced cassette exons and a transcriptome-wide background based on all known human internal exons. Cut-offs of 500nt and 30,000nt were applied on the exon and intron length datasets respectively to reduce data skewing caused by extreme outliers. Splice site strength values below 0 were also discarded from the analysis for similar reasons. The statistical significance of feature differences were calculated using Welch’s t-test and p-values were adjusted using Bonferroni correction when necessary.   The Jensen-Shannon Divergences of splice site sequence subsets and associated tests for statistical significance were calculated using DiffLogo. All other sequence logos were generated using ggseqlogo. The cassette exon sequences, as well as up to 200nt stretches up- and downstream of the exon (excluding the splice sites), were scanned for strand-specific 6-10nt motifs using MEME. The sequences generated by MEME were then fed into TOMTOM to search for RNA binding proteins with similar binding motifs. Functional annotation of the genes containing differentially spliced cassette exons was performed using DAVID.
RNAseq Analysis - WT and Mettl4-KO HEK293T RNAseq libraries were first processed using CutAdapt to remove adaptors and to trim all reads to a uniform length of 101bp for compatibility with downstream analysis steps. Read alignment to the genome was then performed using STAR (2.7.0a) in two-pass mode using the hg38 genome assembly and GENCODE v28 gene annotations (33).
Genome_build: hg38
Supplementary_files_format_and_content: Bedgraph files of first nucleotide coordinates of forward reads. Bed files of RNAseq reads

source_name: Human embryonic kidney cells

growth_protocol: ATCC HEK293T CRL-3216 cells were cultivated in a sterile 5% CO2 incubator at 37oC, and in DMEM supplemented with 10% FBS and 1% penicillin/streptomycin, and used within passage number 3-20.

extract_protocol:
Total RNA was isolated using Trizol-LS.
Poly(A) RNA was purified using Poly(A)Purist Mag kit (Thermofisher AM1922) according to manufacturer’s instructions. Poly(A) RNA was fragmented using RNA fragmentation buffer (Ambion AM8740) and dephosphorylated at its 3’ end with T4 PNK (NEB M0201) for 30min at 37oC. 5’ phosphorylation was then initiated by adding 1mM ATP and incubating for 30min at 37oC. 3’ ligation was then performed as previously described 2, where 5’-adenylated,3-dideoxyC DNA adapters were ligated with truncated T4 RNA ligase 2 (NEB M0242) in 1X ATP-free T4 RNA ligase buffer [50mM Tris pH 7.5, 60µg/ml BSA, 10mM MgCl2, 10mM DTT, 12.5% PEG8000] for 2hr at 25oC. 3’-ligated methylated RNA spike-in (Table S1) was added to ligated Poly(A) RNA and the mixture was denatured for 5min at 65oC before incubating for 2min on ice. This denatured RNA mixture was incubated overnight at 4oC with anti-m6A antibody (Synaptic Systems 202003) in 1X IP buffer [150mM NaCl, 10mM Tris pH 7.4, 0.1% IGEPAL CA-630 (Sigma I8896)] supplemented with RNasin Plus (Promega N2611). In parallel, Protein-A-dynabeads (Life Technologies 10002D) was blocked overnight at 4oC in 1X IP buffer supplemented with 0.5mg/ml BSA (Sigma A7906). The iced antibody-RNA mixture was crosslinked with 0.15J/cm2 254nm UV radiation six times. 1% of the antibody-RNA mixture was set aside as “input” and the rest (designated as “m6ACE”) was mixed with decanted BSA-blocked Protein-A-dynabeads for 1.5hr at 4oC. Beads bound with crosslinked RNA were then washed with the following cold buffers in this order: Wash buffer 1 [1M NaCl, 50mM HEPES-KOH pH 7.4, 1% Triton X-100, 0.1% Sodium Deoxycholate, 2mM EDTA], Wash buffer 2 [0.5M NaCl, 50mM HEPES-KOH pH 7.4, 1% IGEPAL, 0.1% Sodium Deoxycholate, 2mM EDTA], Wash buffer 3 [1% Sodium Deoxycholate, 25mM LiCl, 10mM Tris pH 8, 1% Triton X-100, 2mM EDTA], TE [10mM Tris pH 8, 1mM EDTA] and finally 10mM Tris pH 8. m6ACE RNA was subjected to 5’ to 3’ exonuclease treatment with XRN-1 (NEB M0338) for 1hr at 37oC. The m6ACE RNA-bead mixture was then washed with Wash buffer 1, Wash buffer 2, Wash buffer 3, TE and 10mM Tris pH 8. Both input and m6ACE RNAs were reverse crosslinked in elution buffer [1%SDS, 200mM NaCl, 25mM Tris pH 8, 2mM EDTA, 1mg/ml Proteinase K (Thermo Scientific EO0491)] for 1.5hr at 50oC. RNAs were ethanol-precipitated and ligated to 5’adapters (Table S1) with T4 RNA ligase (Ambion AM2140) for 16hr at 16oC. Reverse transcription primer (Table S1) was annealed (72oC 2min, ice 2min) and reverse transcription was performed with SuperscriptIII (Invitrogen 18080) for 1hr at 50oC, with the reaction stopped by incubating for 15min at 70oC. The cDNA was used for PCR amplification with Phusion High-fidelity PCR mastermix (NEB M0530) and Truseq PCR primers. Finally, primer-dimer and adapter-dimers were removed with AMpure XP beads before undergoing PE75 sequencing on the Illumina Nextseq platforms.

tag: m6a antibody

tag: passage number

value: WT


title: S184

tag: age

tag: genotype


title: Mecr, Day 0, replicate C

tag: cell line


title: S182


title: WT RNAseq rep1


title: Mettl4-KO RNAseq rep3


title: WT RNAseq rep2


title: GFP, Day 0, replicate C


title: GFP, Day 0, replicate B


title: 08_AML_Pt04_32_neg_38_pos_Dx_LSC

description:
diagnosis LSC
08_AML_Pt04_32_neg_38_pos_Dx_LSC

tag: cell type

value: LSCs


title: 9255013094_G: CD57hiPD1dim

description: Healthy


title: 9255013094_B: CD57hiPD1hi

description: Healthy


title: S175

value: Ntg


title: Mecr, Day 0, replicate A


title: 9255013094_A: CD57hiPD1hi

description: Healthy


title: GFP, Day 0, replicate A


title: S173


title: Oxsm, Day 0, replicate D


title: S178


title: ATACseq_KO_Replicate1

data_processing:
ChIP-seq analysis: Alignment: Sequence reads of the first replicate were mapped to the mouse genome (mm9) using BOWTIE (PubMed ID 19261174) with the option -m 1. Sequence of the reads of the second replicate were mapped to a synthetic genome containing the mouse and the fruit fly chromosomes (mm9+dm3).
ChIP-seq analysis: Peak detection was performed with MACS (PubMed ID: 18798982). Peaks were reported in BED format. ChIP-seq genome-wide profiles of the first replicate were normalized by the total number of reads of each sample. ChIP-seq genome-wide profiles of the second replicate were normalized by the total number of fly reads of each sample.
RNA-seq analysis: Alignment: Sequence reads were mapped against the mm9 mouse genome assembly using TopHat (PubMed ID 22383036) with the option ‐g 1.
ATAC-seq analysis: Alignment: Sequence reads were mapped to the mouse genome (mm9) using BOWTIE (PubMed ID 19261174) with the option -m 1.
Genome_build: mm9
Supplementary_files_format_and_content: Files *.bdg.gz (BedGraph, genome-wide ChIP-seq/RNA-seq/ATAC-seq)
Supplementary_files_format_and_content: ChIPseq_H3K27me3_FF_Replicate1.bedgraph.gz
Supplementary_files_format_and_content: ChIPseq_H3K27me3_KO_Replicate1.bedgraph.gz
Supplementary_files_format_and_content: ChIPseq_H3K27me3_FF_Replicate2.bedgraph.gz
Supplementary_files_format_and_content: ChIPseq_H3K27me3_KO_Replicate2.bedgraph.gz
Supplementary_files_format_and_content: RNAseq_FF_Replicate1.bedgraph.gz
Supplementary_files_format_and_content: RNAseq_KO_Replicate1.bedgraph.gz
Supplementary_files_format_and_content: RNAseq_FF_Replicate2.bedgraph.gz
Supplementary_files_format_and_content: RNAseq_KO_Replicate2.bedgraph.gz
Supplementary_files_format_and_content: ATACseq_FF_Replicate1.bedgraph.gz
Supplementary_files_format_and_content: ATACseq_KO_Replicate1.bedgraph.gz
Supplementary_files_format_and_content: Files .bed (BED, ChIP-seq signal enriched regions)
Supplementary_files_format_and_content: ChIPseq_H3K27me3_FF_Replicate1.bed.gz
Supplementary_files_format_and_content: ChIPseq_H3K27me3_KO_Replicate1.bed.gz
Supplementary_files_format_and_content: ChIPseq_H3K27me3_FF_Replicate2.bed.gz
Supplementary_files_format_and_content: ChIPseq_H3K27me3_KO_Replicate2.bed.gz

source_name: Bone marrow

extract_protocol:
(ATAC-seq) Omni-ATAC protocol from  PubMedID  28846090 was followed
Libraries were prepared according to Illumina instructions.

tag: genotype/variation

value: PHF19 KO


title: 9231092100_J: CD57hiPD1dim

description: Healthy


title: 9231092100_L: CD57loPD1dim

description: Healthy


title: Oxsm, Day 0, replicate C


title: Mettl4-KO RNAseq rep1


title: S159


title: Oxsm, Day 0, replicate B


title: 9231092100_K: CD57loPD1hi

description: Healthy


title: SW480

first: Lorinc

last: Pongor

address: 37 Convent Dr,

department: DTB

data_processing:
Reads were trimmed with Trimmomatic software
Trimmed reads were aligned to the hg19 human genome using STAR aligner and Gencode v19 annotation
Aligned reads were indexed with samtools
Sequencing coverage track was created with BAMscale in RNA-mode.
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig coverage track files for visualization were created with BAMscale

source_name: Colon

growth_protocol: All cell lines were maintained in Dulbecco's modified Eagle's (DMEM) (Thermo Fisher Scientific, Invitrogen) medium containing 10% (v/v) fetal bovine serum (Thermo Fisher Scientific) and 1% penicillin-streptomycin

extract_protocol:
RNA extractions was performed with RNeasy plus mini kit (QIAGEN, Cat# 74134). Samples were subjected to ribosomal RNA depletion by using the RiboMinus Transcriptome Isolation Kit
RNA integrity for each sample was confirmed with the Agilent 2100 Bioanalyzer (Agilent Technologies).  TruSeq PolyA kit (Illumina) library preparation was used, sequencing was performed on a HiSeq 2500 system with paired-end read

treatment_protocol: untreated cells

value: colon epithelial


title: 9231092100_I: CD57loPD1hi

description: Healthy


title: C80


title: S150


title: 9231092100_H: CD57loPD1dim

description: Healthy


title: Mettl4-KO RNAseq rep2


title: RNAseq_FF_Replicate2

extract_protocol:
(RNA-seq) RNA was extracted with the RNeasy micro kit (Qiagen) following manufacturer's instruction
Libraries were prepared according to Illumina instructions.

value: Floxed-condition (Control)


title: Oxsm, Day 0, replicate A


title: SW1222


title: Mcat, Day −1, replicate D


title: RNAseq_KO_Replicate1


title: S141

value: Male


title: S135


title: Mcat, Day −1, replicate C

value: C2C12 immortalized mouse skeletal myoblasts (ATCC CRL-1772)


title: RNAseq_FF_Replicate1


title: S170


title: S131


title: Mcat, Day −1, replicate B

value: Mcat hypomorph


title: S121


title: ChIPseq_H3K27me3_KO_Replicate2

extract_protocol:
(ChIP-seq) The low cell Input ChIP Active Motif Kit was employed in this step
Libraries were prepared according to Illumina instructions.

tag: chip antibody

value: H3K27me3 Active Motif 39155 Rab pAb


title: Mcat, Day −1, replicate A


title: S119

tag: Sex


title: ChIPseq_H3K27me3_FF_Replicate2


title: RNAseq_KO_Replicate2


title: ChIPseq_H3K27me3_FF_Replicate1


title: Mecr, Day −1, replicate C


title: S116


title: S115


title: Mecr, Day −1, replicate A


title: ChIPseq_H3K27me3_KO_Replicate1


title: LS180


title: Mecr, Day −1, replicate B


title: METTL4_CD_rescue rep3 m6ACE

data_processing:
m6ACE-seq analysis  Fastq sequences were first filtered for a quality score of 20, then trimmed of 5’ and 3’ adapter sequences and poly(A) tails using Cutadapt. The 8-mer UMI located at the first 8 nucleotides of read 1 was registered and trimmed. Any complementary UMI sequence in read 2 was also trimmed. Reads were mapped to the methylated spike-in (Table 1) using Bowtie2, or to the hg38 assembly transcriptome (Gencode v28 comprehensive gene annotations) using STAR. Aligned pairs that had the same mapping coordinates and UMIs were filtered out as PCR duplicates. Read-start coordinates in hg38-mapped reads that began with an adenosine nucleotide, and had a minimum mean read count of 1 across the triplicate samples were collated. m6A or m6Am sites were identified as read starts that were at least 2-fold enriched in m6ACE libraries than in the corresponding input libraries. This enrichment was calculated using DESeq2 performed on A-only sites across triplicate pairs of m6ACE and corresponding input libraries (FDR<0.1, padj<0.05). Identified sites that were 1-4 nucleotides upstream of another identified significant Rm6AC site or sites found within clustered read-starts were filtered out.   To calculate the RML of each site in each sample: The read-start counts at positions -4 to 0 of each site in the m6ACE library were summed and divided by the read-start counts at positions -51 to 0 of the same site in the input library to give ‘X’. Similarly, the read-start counts at positions -4 to 0 of the spike-in m6A site in the m6ACE library were summed and divided by the read-start counts at positions -21 to 0 of the same spike-in m6A site in the input library to give ‘Y’. X was normalized to Y to give RML. RML values of each site was averaged across triplicates for each sample condition. A site was denoted as differentially methylated between METTL4WT-rescue and METTL4CD-rescue if the average RML differs between sample conditions with a log2fold-change cutoff of 2.0, as well as a one-tailed Student’s T-test p-value cutoff of <0.041 (false discovery rate, FDR < 0.1). Consensus motif analysis was performed using Meme-chip. Metagene analysis was performed using MetaPlotR.   RNAseq  10µg of RNA was treated with RQ1 RNase-Free DNase (Promega M6101) as per manufacturer’s protocol. 5µg of samples were then depleted of rRNA using the ribozero kit (Illumina MRZH11124). 50ng of each rRNA-depleted samples were then used for construct RNA-seq libraries using the ScriptSeq v2 RNASeq Library Preparation Kit (Illumina SSV21124). Libraries were sequenced on an Illumina PE151 platform.  RNAseq Splicing Analysis  WT and Mettl4-KO HEK293T RNAseq libraries were first processed using CutAdapt to remove adaptors and to trim all reads to a uniform length of 101bp for compatibility with downstream analysis steps. Read alignment to the genome was then performed using STAR (2.7.0a) in two-pass mode using the hg38 genome assembly and GENCODE v28 gene annotations.   Alternative splicing differences were analysed by an in-house pipeline using replicate MATS (rMATS 3.2.5) and filtered based on cut-offs of FDR ≤ 0.05, an absolute change in percent spliced in (|ΔPSI|) ≥ 0.1. In addition, events with mean sample junction counts (IC_Sample + SC_Sample) < 20 were filtered out to reduce false positives arising from transcript dropout in low abundance isoforms. The validation of several differential alternative splicing events were performed using an RT-PCR assay.  Additional exon-level features were added to the data using databases constructed from the UCSC Table Browser, as well as in-house R scripts. Splice-site strengths were calculated using MaxEntScan. Comparisons were made between the exon features of the differentially spliced cassette exons and a transcriptome-wide background based on all known human internal exons. Cut-offs of 500nt and 30,000nt were applied on the exon and intron length datasets respectively to reduce data skewing caused by extreme outliers. Splice site strength values below 0 were also discarded from the analysis for similar reasons. The statistical significance of feature differences were calculated using Welch’s t-test and p-values were adjusted using Bonferroni correction when necessary.   The Jensen-Shannon Divergences of splice site sequence subsets and associated tests for statistical significance were calculated using DiffLogo. All other sequence logos were generated using ggseqlogo. The cassette exon sequences, as well as up to 200nt stretches up- and downstream of the exon (excluding the splice sites), were scanned for strand-specific 6-10nt motifs using MEME. The sequences generated by MEME were then fed into TOMTOM to search for RNA binding proteins with similar binding motifs. Functional annotation of the genes containing differentially spliced cassette exons was performed using DAVID.
RNAseq Analysis - WT and Mettl4-KO HEK293T RNAseq libraries were first processed using CutAdapt to remove adaptors and to trim all reads to a uniform length of 101bp for compatibility with downstream analysis steps. Read alignment to the genome was then performed using STAR (2.7.0a) in two-pass mode using the hg38 genome assembly and GENCODE v28 gene annotations (33).
Genome_build: hg38
Supplementary_files_format_and_content: Bedgraph files of first nucleotide coordinates of forward reads (m6ACE) or bedgraph files of transcript reads (RNA-seq).

value: Synaptic Systems 202003

value: Mettl4-KO +METTL4_CD


title: 344SQR_anti-PD1rep1

city: Dallas

first: Maria

middle: A

last: Freitas-Cortez

state: Texas

address: 6000 Harry Hines Blvd

institute: UT Southwestern

data_processing:
Basecalling was done by Illumina HiSeq Control Software (version 3.3.76).
The adapters were removed from the 3’ends of the reads by Trim Galore! (version 0.4.1) and cutadapt (version 1.9.1).
Then the reads were mapped to mouse genome mm10 by the bisulfite converted read mapper Bismark (version v0.16.1) and Bowtie (version 1.1.2).
The methylation percentages for the CpG sites were calculated by the bismark_methylation_extractor script from Bismark and an in-house Perl script.
Genome_build: mm10
Supplementary_files_format_and_content: Methylation calling for each CpG site with at least 1x coverage. The file is in methylkit input format: chrBase, chr, base, strand, coverage, freqC, freqT.

source_name: mouse tumor

extract_protocol:
DNA was isolated from 344SQP and 344SQR tumors treated with anti-PD1.
A KAPA Library Quantification Kit (KAPA Biosystems) was utilized to quantify RRBS libraries for pooling, and a final concentration of 1.5 nM was loaded onto an Illumina cBOT for cluster generation before sequencing on an Illumina HiSeq3000 using a Single Read 50 bp run. The libraries were sequenced using 50 bases single-read protocol on Illumina HiSeq 3000 instrument. 49-85 million reads were generated per sample.

treatment_protocol: Primary tumors were established by subcutaneous injection of 344SQP or 344SQR cells (0.5 × 106 in 100 μL of sterile phosphate buffered saline [PBS]) into the leg of syngeneic 129Sv/Ev mice (female, 12–16 weeks old). Mice were then given intraperitoneal injections of anti-PD1 or control IgG antibodies (10 mg/kg), starting on day 4 after tumor cell inoculation and continuing twice per week for a total of 4 doses. At 24 hours after the last anti-PD1 treatment, tumor tissues were collected for DNA isolation for RRBS analysis

value: lung adenocarcinoma


title: 344SQR_anti-PD1rep2


title: 344SQP+anti-PD1rep2


title: GFP, Day −1, replicate D

value: Wild type


title: METTL4_CD_rescue rep2 m6ACE


title: GFP, Day −1, replicate B


title: GFP, Day −1, replicate A


title: 344SQP+anti-PD1rep1


title: Mecr, Day −1, replicate D

value: Mecr hypomorph


title: S117

value: Female


title: T3

city: Hangzhou

first: Jianning

last: Liu

address: 866 Yuhangtang Road

institute: Zhejiang University

data_processing:
Quality trimmed raw reads from samples were aligned to the reference genome sequence (NCBI Aradu1.0 and Araip1.0 assembly) separately using HISAT (v 2.0.5, Kim et al, 2015) with NCBI Aradu1.0 and Araip1.0 junctions as a guided reference annotation. All programs were performed with default setting (unless otherwise specified).
The aligned reads for each sample were assembled into transcripts using Stringtie (v 1.3.1, Pertea et al, 2015) and compared with NCBI Aradu1.0 and Araip1.0 reference annotation. Separate GTF files were generated for each of the sixteen samples. The assembled transcripts abundance was estimated and annotated with FPKM (fragments per kilobase of exon per million mapped fragments) using the R package Ballgown (Frazee et al, 2015).
Genome_build: NCBI Aradu1.0 and Araip1.0
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Arachis hypogaea

source_name: the seed coat samples infected with A. flavus

growth_protocol: Seeds of peanut cultivars J11 were cultivated in the test field of Shandong Peanut Research Institute, China. Previous experiments showed that J11 was resistant to A. flavus invasion and aflatoxin production (Li et al, 2013). Aspergillus flavus isolate NRRL3357, a wide-type strain was provided by ARS Culture Collection. NRRL3357 were taken from the stored sample and cultured on Czapek–Dox Medium at 27 ± 1 °C for 7 days. Conidia were then collected and suspended in sterile water containing 0.05 % Tween-80.Twenty-five days before harvest, peanuts were infected with A. flavus. A. flavus artificial inoculation was completed by the method of Li et al. (2013) and Wang et al. (2010). Infected plants were sampled at 3, 5, 7 and 10 days after inoculation. Seed coats were taken from infected peanut and kept at -80°C as samples.

extract_protocol:
Total RNA was extracted by using the RNesasy mini kit (QIAGEN) with DNase treatment according to the manufacturer’s instructions. The RNA quantity was obtained using NanoDrop 2000 (Thermo Fisher Scientific Inc, USA) and Qubit 2.0 RNA Broad Range Assay (Invitrogen, USA). The quality of RNA was examined using Agilent Bioanalyzer RNA Nano chip Bioanalyzer (Agilent Technologies) to obtain RNA Integrity number (RIN) of over 7.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: seed coat

tag: infection

value: A. flavus


title: Oxsm, Day −1, replicate D

value: Oxsm hypomorph


title: T2


title: METTL4_WT_rescue rep2 m6ACE

value: Mettl4-KO +METTL4_WT


title: Oxsm, Day −1, replicate C


title: METTL4_WT_rescue rep3 m6ACE


title: T1


title: ATACseq_FF_Replicate1

first: Enrique

last: Blanco

address: Dr. Aiguader 88

institute: Center for Genomic Regulation (CRG)


title: 7-ca: patient 7 cancer

city: Jinan

first: Jinghui

last: Liang

address: Wenhuaxi street

institute: Shandong University

description: Gene expression from lung adenocarcinoma

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, genes that at least 6 out of 14 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis. Differentially expressed genes with statistical significance between the two groups were identified through Volcano Plot filtering. Differentially expressed genes between the two samples were identified through Fold Change filtering. Hierarchical Clustering was performed using the R scripts. GO analysis and Pathway analysis were performed in the standard enrichment computation method.

source_name: fresh lung

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the Trizol following the manufacturer's recommendations.  RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis

tag: gender

value: male


title: 7-n: patient 7 normal

description: Gene expression from normal tissues

value: lung  normal tissue


title: CK3

source_name: the seed coat samples without infected with A. flavus

value: control


title: Oxsm, Day −1, replicate B


title: Mettl4-KO rep3 m6ACE


title: METTL4_WT_rescue rep1 m6ACE


title: CK2


title: Oxsm, Day −1, replicate A


title: 6-ca: patient 6 cancer


title: METTL4_CD_rescue rep1 m6ACE


title: 6-n: patient 6 normal

description: Gene expression from normal tissues


title: CK1


title: Mettl4-KO rep2 m6ACE


title: Mettl4-KO rep1 m6ACE


title: 5-n: patient 5 normal

description: Gene expression from normal tissues


title: 5-ca: patient 5 cancer


title: 4-n: patient 4 normal

description: Gene expression from normal tissues

value: female


title: METTL4_CD_rescue rep3 input


title: 4-ca: patient 4 cancer


title: METTL4_CD_rescue rep2 input


title: METTL4_CD_rescue rep1 input


title: METTL4_WT_rescue rep3 input


title: METTL4_WT_rescue rep2 input


title: Diurnal_ZT12_repl_B

city: Liverpool

first: Mirko

last: Pegoraro

state: Liverpool

address: Byrom Street

department: School of Natural Science and Psychology

country: United Kingdom

institute: Liverpool John Moores University

description:
cuffdiff output ZT12
RLD12B

data_processing:
The data were then processed using trimmomatic (version 0.32) to remove the adapters.
The library were quality checked using fastQC (version 0.11.2).
The RNA-seq was aligned to the Drosophila melanogaster transcriptome (NCBI_build5.41) using TopHat (version 2.1.0) with these options: -i 50 -I 5000 --transcriptome-index NCBI_genes --coverage-search -p 8 Bowtie2Index/genome -G genes.gtf (from NCBI_build5.41) as genome annotation reference.
Cufflinks and cuffmerge (version 2.2.1) were used to quantify the expression of the transcripts isoforms of the TopHat aligned RNA with the following options: –u multi-reads correction, -g genes.gtf (from NCBI_build5.41) as gene annotation reference –b genome.fa (from NCBI_build5.41/Bowtie2Index) as reference genome –M Mask_sequences.fa (including mitochondrial and ribosomal RNA as well polyA, polyC sequences).
To calculate difference of expressions between samples we used cuffdiff. As for cuffmerge we used –b genome.fa –M Mask_sequences.fa. In addition we used -u multi-read correction, merged.gtf (the transcript annotation file produced by cuffmerge) and a geometric method for library normalization
Genome_build: Drosophila melanogaster transcriptome (NCBI_build5.41)
Supplementary_files_format_and_content: the process data are the output of cuffdiff analysis. We ran the analysis for ZT0 and ZT12 separetelly.

organism: Drosophila melanogaster

growth_protocol: 12 hour of dark:12 hours of darknes, 25C, standart yeast rich drosophila food.

extract_protocol:
Flies (3-4 days old) were entrained for 3 days in LD12:12 at 25°C and then male heads were collected in liquid nitrogen at ZT0 and 12. RNA was extracted using the Maxwell®16 MDx Research Instrument (Promega) combine with the Maxwell®16 Tissue Total RNA pufication kit (AS1220, Promega).
The RNAseq library preparation and sequencing was carried by Glasgow Polyomics using an IlluminaNextseq500 platform.Two independent libraries paired-end were generated per time point per line

treatment_protocol: Samples where keep at 12:12LD and 25C until the collection time. Lines were generated from selected lines for nocturnal/diurnal behavior, via crossing with balancers lines.

tag: line/diurnal preference

value: Diurnal (RLD)

tag: dev stage

value: Adults

tag: time point

value: Heads


title: Mettl4-KO rep3 input

value: Synaptic Systems 202003


title: METTL4_WT_rescue rep1 input


title: Diurnal_ZT0_repl_B

description:
cuffdiff output ZT0
RLD0B


title: Diurnal_ZT12_repl_A

description:
cuffdiff output ZT12
RLD12A


title: Diurnal_ZT0_repl_A

description:
cuffdiff output ZT0
RLD0A


title: 3-n: patient 3 normal

description: Gene expression from normal tissues


title: 3-ca: patient 3 cancer


title: Mettl4-KO rep1 input


title: Control_ZT12_repl_B

description:
cuffdiff output ZT12
PJN12B

value: control intermidiate (PJN)


title: LS180_genomic_rep2

data_processing:
Reads were trimmed with Trimmomatic software
Trimmed reads were aligned to the hg19 human genome using the bwa mem aligner.
Aligned reads were indexed with samtools
Sequencing coverage track was created with BAMscale.
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig coverage track files for visualization were created with BAMscale

extract_protocol: Chromatin immunoprecipitation (ChIP) was performed using the Active Motif ChIP kit (Active Motif, Carlsbad, CA, USA) According the instruction by the manufacturer. Briefly, 5 × 107 LS180 cells grown in 15-cm plates were cross-linked with 1% formaldehyde, and cells were lysed and sonicated. Protein–DNA complexes were immunoprecipitated with control IgG (Santa cruz, Cat#2028) or anti-FOXA1 (Santa Cruz, Cat# sc-6553) antibody. The IP material was washed and heated at 65°C overnight to reverse crosslinks.

value: colon epithelial

tag: antibody


title: 2-ca: patient 2 cancer

value: lung adenocarcinoma


title: 2-n: patient 2 normal

description: Gene expression from normal tissues