title: MD2

city: Yangling

first: Ming

last: Xu

state: Shaanxi

address: No. 3, Taicheng Road

department: College of Plant Protection

institute: Northwest A&F University

data_processing:
Raw data (raw reads) were first processed through custom Perl and Python scripts to obtain clean data.
Compared with mRNA (which some species may not have), RFam (containing rRNA, tRNA, snRNA, snoRNA, etc.)(http://rfam.xfam.org) and Repbase database(http://www.girinst.org/education/index.html), the filtered data is called Valid data
Based on the analysis and statistics of the raw sequencing data, we further analyzed the length distribution of the Total (Total) and the number of Unique (Unique) of the filtered Valid data
The selection of differential milRNAs mainly adopts the following algorithms:fisher's exact test( http://en.wikipedia.org/wiki/Fisher's_exact_test),Chi square(2x2) test( http://en.wikipedia.org/wiki/Chi-squared_test),Chi square(NxN) test( http://en.wikipedia.org/wiki/Chi-squared_test),T-test( http://en.wikipedia.org/wiki/Student's_t-test),ANOVA test( http://en.wikipedia.org/wiki/One-way_analysis_of_variance)
Using two software, miRanda and TargetScan to predict target genes
Genome_build: https://www.ncbi.nlm.nih.gov/genome/35576?genome_assembly_id=217638
Supplementary_files_format_and_content: MD2 is constructed using  Vm-DCL2 deletion mutanted Valsa mali

organism: Cytospora mali

source_name: hypha

growth_protocol: The wild-type 03-8 (MVm) strains were grown on the PDA plates paved with a layer of cellophane and cultured at 25℃ in dark for 3 days.

extract_protocol:
Total RNAs were extracted with Trizol TM Reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's instructions. RNA purity, concentration, and integrity were checked.
RNA of three biological replicates of MVm and MD2 were mixed, respectively. And three micrograms RNA of each sample was used to construct sRNA library construction and high-throughput sequencing in LC-BIO (Hangzhou, China).
The detailed protocol of miRNA-seq was provided by the genome sequencing company (LC-BIO Hangzhou, China) and the protocol of degradome sequnce was followed with  the published parallel analysis of RNA Ends (PARE) protocol (German et al., 2009)..

treatment_protocol: Vm-DCL2 deletion mutant (MD2) strains were grown on the PDA plates paved with a layer of cellophane and cultured at 25℃ in dark for 3 days.

value: hypha


title: D04-NIH

status: Public on Aug 07 2021

type: SRA

city: Maebashi

first: Akihiko

last: Uchiyama

state: Gunma

department: Dermatology

country: Japan

institute: Gunma university

library_source: transcriptomic

data_processing:
The quality of the libraries was assessed using with an on an Agilent Bioanalyzer using a High Sensitivity DNA chip (Agilent Technologies)
The pooled libraries of the samples were sequenced using NextSeq 500 (Illumina, Inc) in 76-base-pair (bp) single-end reads.
The QIAseq miRNA library kit adopts the Unique Molecular Indexes (UMIs) system, enabling unbiased and accurate quantification of mature miRNAs.
Original FASTQ files generated by the NextSeq were uploaded to the Qiagen GeneGlobe Data Analysis Center (https://geneglobe.qiagen.com) and aligned to the miRBase v21 (http://www.mirbase.org) and piRNABank (http://pirnabank.ibab.ac.in/).
All reads assigned to a particular miRNA or piRNA were counted and the associated UMIs were aggregated to count unique molecules. A matrix of the UMI counts of miRNA or piRNA was subjected to downstream analyses using StrandNGS 3.4 software (Agilent Technologies, Santa Clara, CA). The UMI counts were quantified using a Trimmed Mean of M-value (TMM) method <Genome Biology 11(3) (2010) R25>. miRNAs were annotated against miRbase (http://www.mirbase.org/).
Genome_build: mm10
Supplementary_files_format_and_content: Normalized data was submitted with excel file.

molecule: total RNA

organism: Mus musculus

source_name: exosomes

growth_protocol: Mesenchymal stem cells and NIH3T3 cells were incubated on uncoated plastic in αMEM medium supplemented with 5% FBS

extract_protocol:
miRNA microarray assays were performed by DNA Chip Research Inc (Tokyo, Minatoku). Exosomal RNA was isolated from cell culture supernatant using the exoRNeasy Serum/Plasma Maxi Kit (QIAGEN).
Sequencing libraries were constructed using the QIAseq™ miRNA Library Kit (Cat#331505, Qiagen) according to the manufacturer’s protocols.

treatment_protocol: Cells were inculabed for 72 hours in 37 degree

tag: cell type

value: NIH 3T3 cells

tag: strain

value: NIH Swiss


title: HCSC-0009

city: Madrid

first: Marta

last: Roche-Molina

address: C/Maiquez 7

department: Servicio de Oncologia Medica

country: Spain

institute: LAOT

description:
Spain-11-11B22197
150825_UNC15-SN850_0411_AC7E3PACXX_GGCTAC_L006

data_processing:
Read mapping performed with MapSplice v 2.2.1
Transcript cuantification was obtained with RSEM v1.3.0
Normalization was performed by upper quartile normalization (Quartile=75)
Genome_build: GRCh37
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with quantile normalized gene counts for every gene and every sample

organism: Homo sapiens

source_name: Breast tumor sample

extract_protocol:
mRNA was extracted using High Pure FFPET RNA Isolation Kit in accordance with the protocol provided by the manufacturer. Quality control was performed with Agilent Bioanalyser.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: Breast tumor sample

tag: age

tag: subtype

value: Basal


title: HCSC-0011

type: RNA

hyb_protocol: Follow protocol from Prosigna™ Breast Cancer Prognostic Gene Signature Assay (2015-01 LBL-10010-02). Use 250ng total RNA. Incubate 15h at 65ºC. After that continuue with the sample processing in the prep station (nCounter)

scan_protocol: Follow protocol from Prosigna™ Breast Cancer Prognostic Gene Signature Assay (2015-01 LBL-10010-02) and the user manual form the n Counter analysis sytem (NanoString Technologies-2015-01 MAN-10008-02).

data_processing:
Normalization was performed with Bioconductor package NanostringNorm
Quality control was performed with Bioconductor package NanostringQC
Classification was performed with bioconductor packages ctc and impute
PAM50 classification file

label_protocol: Standard Nanostring protocol

extract_protocol: On average, 5 um-thick sections were prepared for the extraction of total RNA from tumor cell-rich areas, which were identified by a surgical pathologist.

tag: treatment

value: Carboplatin and Docetaxel


title: HCSC-0027

description:
Spain-12-13B40318
150825_UNC15-SN850_0411_AC7E3PACXX_CTTGTA_L006


title: HLPR-002

description:
Spain-44-B14-01800_A2
150916_UNC17-D00216_0344_AC6P3BANXX_GTTTCG_L003


title: HCUV-0001

description:
Spain-49-HCUV-0001
151005_UNC18-D00493_0265_AC7JERANXX_GATCAG_L002


title: HCSC-0017


title: HCSC-0021


title: BL_Kyn_12h_2

city: Haifa

first: Gur

last: Sevillya

state: Israel

address: Haifa

country: Israel

institute: Technion

data_processing:
Samples were sequenced on a paired end run Illumina HiSeq 2500, to obtain 15 bp read 1 (celseq barcode) and 50 bp read 2 (the biological data).
The quality of the sequenced data (all sequenced bases in all reads) before and after trimming (using trim galore, uses cutadapt version 1.10), as well as read length distributions after trimming, were evaluated using FASTQC (FASTQC version 0.11.5).
Reads were aligned to the TAIR10 assembly of the Arabidopsis thaliana genome, using Tophat2 version 2.1.0. Transcript coordinates from the TAIR10 reference set were used to guide the alignment process.
After alignment, the numbers of reads per gene were estimated using HTseq-count version 0.6.1.  DESeq2 R package version 1.18.1 was used to normalize read counts and perform pair- wise differential expression analysis.
Gene sets were identified based on their differential expression. Significantly modulated genes were considered with a fold change of 1.5 and adjusted p-value (false discovery rate) of 0.05 or less, comparing the hormonal treatment (BL,L-Kyn or the combined BL+L-Kyn) to the control (mock) in the same treatment duration (12,24 or 48h).
Genome_build: TAIR10 reference set were used to guide the alignment process
Supplementary_files_format_and_content: Matrix table with normalized counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with final results as treatment versus control for every gene

organism: Arabidopsis thaliana

source_name: Root

extract_protocol:
Total RNA was extracted from roots (cut at about 0.2-0.5 cm from the tip) using the Spectrum plant total RNA kit (Sigma) according to the manufacturer’s instructions and treated with On-Column DNase I Digestion Set (Sigma-Aldrich).
Samples were prepared using CEL-Seq2 sample preparation protocol (Hashimshony, et al., 2016), with minor changes: Instead of single-cells as input, 2 ng purified RNA was taken as input for library preparation, and each sample was marked with a primer containing a unique barcode. In addition,  each initial RNA sample was barcoded using a pool of 3 different CEL-Seq primers, using several primers to create technical replicates for each sample reduces the possibility of technical variability caused by differences in barcode efficiency.

value: BL+Kyn

tag: time


title: BL_Kyn_12h_1


title: BL_Kyn_48h_1


title: BL_Kyn_24h_2


title: Kyn_48h_2

value: Kyn


title: HVDH-0003


title: TFE3-N-26

city: Shanghai

first: Ning

last: He

address: No. 11, Lane 100, Banxia Road, Pudong New Area, Shanghai, China

country: China

institute: GloriousMed Technology Co., Ltd.

data_processing:
The raw RNA-sequencing reads were filtered by FastQC, Reads were aligned using STAR v2.7.0f with default parameters to the Ensembl human genome assembly GRCh37.
Gene expression levels were estimated by raw count and TPM (Transcripts Per Kilobase Million).
Annotations of mRNA in the human genome were retrieved from the GENCODE (v19) database.
Paired trimmed/clipped and de-duplicated RNAseq reads were used to identify gene fusion events, and the aligned output was used as input to STAR-Fusion v1.9.1 using the developer-supplied gencode v33 CTAT library from April 6, 2020. Fusion gene supported by at least two reads was selected.
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text files include log2 transfomed raw count values by R Package DESeq2 for each Sample

source_name: Renal

extract_protocol:
Total RNA was isolated from each sample using Qiagen RNeasy formalin-fixed paraffin-embedded (FFPE) Kit (Qiagen, Hilden, Germany), following the protocol from manufacturer. Purity and quantity of total RNA were measured by Nanodrop equipment. Integrity of RNA was evaluated using the RNA Nano6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). 1μg RNA of per sample was used as input for the RNA sample preparations.
Strand-specific RNA sequencing libraries were generated using the Whole RNA-seq Lib Prep kit for Illumina (ABclonal, China). Library quality was evaluated on the Agilent Bioanalyzer 2100 system (Agilent, USA). Final libraries were sequenced at the Novogene Bioinformatics Institute (Beijing, China) on an Illumina Hiseq X10 platform by a 150bp paired-end reads.

value: Adjacent normal tissue


title: HUGM-0027


title: HUGM-0041


title: BL_Kyn_48h_2


title: Kyn_24h_1


title: Knockdown_Input_for_RiboSeq_1

city: Guangzhou

first: Haining

last: Liu

address: Zhongshan road 2

institute: The first affiliated hospital of sun yat-sen university

data_processing:
Library strategy: Ribo-seq
For RNA-Seq data analysis, after adapter trimming and low quality sequence filtering (Q30), the clean reads were mapped to human reference genome (hg38) using Tophat2. The raw counts of reads mapping to the gencode genes (v19) were computed by HTSeq with ‘union’ overlap mode. The raw counts were then normalized as Reads per kilo base per million mapped reads (RPKM) using edegR.
For Ribo-Seq data analysis, Adapter sequences were trimmed and low quality sequences (Q30) were discarded using trim_galore. The sequences with length of at least 25nt were further aligned to human rRNA and tRNA index constructed from Ensembl (Release 91) and GtRNAdb databases , respectively. The remaining reads were aligned to the UCSC canonical known gene transcripts of the human reference genome (hg38) using bowtie with a maximum one mismatch allowed.

source_name: intrahepatic cholangiocarcinoma cell line

growth_protocol: ICC cell lines were  cultrued in RMPI 1640 medium. Cells were grown in a 5% CO2 cell culture incubator at 37℃.

extract_protocol:
Total RNA samples were isolated with Trizol following the manufacturer’s instructions. small RNAs (<200nt) were first purified using the mirVana miRNA Isolation Kit (Thermo Fisher Scientific).
Libraries were prepared according to Illumina's instructions accompanying the TrueSeq Stranded mRNA library preparation kit, TruSeq Ribo Profile (Mammalian) Library Prep Kit and the NEBNext® Small RNA Library Prep Set.

treatment_protocol: Mettl1 gene knockdown was mediated by short hairpin RNA.

value: Mettl1 knockdown


title: HUGM-0028


title: HCSC-0013


title: HUGM-0030


title: INEN-0007


title: BL_48h_1

value: BL


title: BL_48h_2


title: BL_12h_2


title: HUGM-0018


title: HUGM-0038


title: BL_24h_1


title: BL_Kyn_24h_1


title: HUGM-0050


title: Kyn_48h_1


title: D03-MSC

value: Mesenchymal stem cells


title: HUGM-0022


title: HUGM-0048


title: HUGM-0015


title: Kyn_12h_2


title: HCSC-0004


title: HCSC-0020


title: control_48h_1

value: Mock


title: control_24h_2


title: HUGM-0026


title: BL_24h_2


title: HUGM-0008


title: HUGM-0052


title: HUGM-0009


title: control_12h_2


title: HCSC-0014


title: Kyn_24h_2


title: BL_12h_1


title: HUGM-0019


title: flag-eIF4E Hela cells; serum starved overnight; eFT-508 pre-treat followed by PMA stimuation; biological replicate #1

city: Adelaide

first: Kirk

middle: B

last: Jensen

state: South Australia

address: North Terrace

department: Lifelong Health

country: Australia

institute: South Australian Health & Medical Research Institute

description:
4E1-eFT-01
Modified CLIP-seq (capCLIP-seq)
eIF4E protein & crosslinked RNA fragments (by anti-flag mAb immunoprecipitation)

data_processing:
raw sequencing data was adaptor trimmed and filtered for short sequences during basecalling with bcl2fastq2 (--find-adapters-with-sliding-window --adapter-stringency 0.9 --mask-short-adapter-reads 35 --minimum-trimmed-read-length 35
FASTQ files were analysed and quality checked using FastQC (www.bioinformatics.babraham.ac.uk/projects/fastqc) and Picard (broadinstitute.github.io/picard).
Filtered reads were mapped against the human reference genome (hg19) using the STAR alignment algorithm (39) (version 2.5.3a with default parameters and --chimSegmentMin 20, --quantMode GeneCounts)
UMItools was used to deduplicate reads in each sample using unique molecular identifiers (UMI’s) (default settings with --method adjacency --edit-distance-threshold
Peak calling was perfomed with MACS2 (version 2.1.1.20160309) using default parameters and reporting only peaks with an FDR cut-off (-q) < 0.05.
Differential binding analysis was performed using R (version 3.4.3) and the DiffBind package
Genome_build: hg19
Supplementary_files_format_and_content: Peak data was generated with MACS2; bed and tsv data generated from DiffBind and MACS2 peak calling data

source_name: HeLa cells

growth_protocol: flag-eIF4E Hela cells were grown to ~90% confluency in DMEM + 10% FBS in 150 mm plates

extract_protocol:
Cells were immediately harvested in 1X PXL buffer; and the lysate collected and stored @ -80 ˚C
Single read - Illumina

treatment_protocol: cells were serum-starved overnight, then either pre-treated with 100 nM eFT-508 for1 hour @ 37˚C, or with DMSO carrier (solvent) only for the same time period. All samples were then stimulated with 500 nM PMA for an additional 30 min @ 37˚C. Following treatment, all plates were placed atop an ice-water slurry and irradiated in a short-wavelength (~254 nm) Stratalinker to 350 mJ/cm2

tag: cell line

value: HeLa cells with N-terminal 3X-flag tag on endogenous eIF4E protein

tag: drug treatment

value: serum starved overnight, pre-treat with 100 nM eFT-508 in DMSO for 1 hr followed by 500 nM PMA for 30 min

tag: uv irradiation

tag: antibody

value: anti-flag mAb


title: flag-eIF4E Hela cells; serum starved overnight; PMA stimuation only; biological replicate #2

description:
4E1-PMA-01b
Modified CLIP-seq (capCLIP-seq)
eIF4E protein & crosslinked RNA fragments (by anti-flag mAb immunoprecipitation)

value: serum starved overnight, pre-treat with DMSO vehicle (control) for 1 hr followed by 500 nM PMA for 30 min


title: flag-eIF4E Hela cells; serum starved overnight; eFT-508 pre-treat followed by PMA stimuation; biological replicate #2

description:
4E1-eFT-02
Modified CLIP-seq (capCLIP-seq)
eIF4E protein & crosslinked RNA fragments (by anti-flag mAb immunoprecipitation)


title: HUGM-0037


title: INEN-0009


title: HUGM-0047


title: HUGM-0044


title: INEN-0006


title: Kyn_12h_1


title: 999-99 (SID-124)

city: Tucson

first: Dominic

last: LaRoche

state: AZ

address: 3430 E. Global Loop

country: USA

institute: HTG Molecular Diagnostics

data_processing:
Illumina bcl2fastq is used for generation of FASQ files
HTG EdgeSeq Parser software (version10196100F) is used for alignment to a priori defined target sequences.  Requirements include %Q30 >= 85%, %PF >= 75%, and 180 < CD < 290
Post-sequencing quality control using statistical process controls on negative control probes (see supplementary file for samples removed by QC).
Supplementary_files_format_and_content: Comma separated values file of raw mRNA count values with samples as columns and mRNA targets as rows.

molecule: polyA RNA

source_name: FFPE fixed biopsy of melanoma

extract_protocol:
HTG EdgeSeq Immuno-Oncology Panel (Tucson, Arizona)
Tumor samples were processed by adding HTG Lysis Buffer to lyse and/or permeabilize the RNA available to subsequently bind to corresponding target-specific Nuclease Protection Probes (NPPs). The lysed samples was transferred to a 96-well micro-titer plate. Target capture was done by adding NPPs to the lysed samples to hybridize to the target mRNA. Then S1 nuclease was added to digest non-hybridized miRNA and excess NPPs, leaving target mRNA/NPP duplexes. S1 digestion was terminated by heat denaturation of S1 enzyme. The processed samples were used as template to set up PCR reactions with primer tags. These tags share common sequences that are complementary to 5’-end and 3’-end “wing” sequences of the probes and common adaptors required for cluster generation for deep sequencing. The library was prepared using HTG EdgeSeq PCR processing. Following library preparation, it was quantified using HTG EdgeSeq KAPA Library Quantification for Illumina Sequencing. All samples and controls were quantified in triplicate.
HTG EdgeSeq KAPA Library Quantification/Calculator

tag: diagnosis

value: melanoma

value: small intestine

tag: melanoma stage, ajcc 6th edition

tag: prognosis

value: poor prognosis


title: control_48h_2


title: HCSC-0007

value: Breast tumor sample


title: HVDH-0001

value: Basal


title: 999-93 (SID-119)

value: skin/subcutaneous tissue


title: INEN-0012

value: Carboplatin and Docetaxel


title: HCSC-0023


title: INEN-0005


title: HUGM-0011


title: control_24h_1


title: HCSC-0008


title: HUGM-0001


title: 999-97 (SID-122)


title: HUGM-0042


title: 999-98 (SID-123)

value: lymph node


title: control_12h_1


title: flag-eIF4E Hela cells; serum starved overnight; PMA stimuation only; biological replicate #1

description:
4E1-PMA-01a
Modified CLIP-seq (capCLIP-seq)
eIF4E protein & crosslinked RNA fragments (by anti-flag mAb immunoprecipitation)


title: INEN-0023


title: 999-86 (SID-112)


title: INEN-0022


title: INEN-0004


title: HUGM-0051


title: 999-83 (SID-109)


title: 999-95 (SID-121)


title: 999-94 (SID-120)


title: HCSC-0003


title: HUGM-0029


title: 999-92 (SID-118)


title: HUGM-0036


title: INEN-0017


title: 999-81 (SID-107)


title: 999-91 (SID-117)


title: 999-80 (SID-106)


title: 999-89 (SID-115)


title: HVDH-0004


title: INEN-0015


title: INEN-0024


title: 999-88 (SID-114)


title: INEN-0014


title: 999-79 (SID-104)


title: INEN-0010


title: 999-9 (SID-116)


title: 999-77 (SID-102)


title: 999-87 (SID-113)


title: 999-85 (SID-111)


title: HVDH-0008


title: 999-82 (SID-108)


title: 999-73 (SID-99)


title: HVDH-0006


title: 999-8 (SID-105)


title: HVDH-0007


title: INEN-0021


title: INEN-0018


title: HUGM-0063


title: 999-78 (SID-103)


title: HUGM-0060


title: HUGM-0061


title: 999-84 (SID-110)


title: 999-67 (SID-94)


title: 999-75 (SID-101)


title: INEN-0016


title: HUGM-0058


title: HUGM-0057


title: HVDH-0011

value: Normal


title: 999-63 (SID-90)


title: 999-60 (SID-88)


title: 999-72 (SID-98)


title: INEN-0020


title: HUGM-0053


title: 999-6 (SID-87)


title: HVDH-0012


title: 999-65 (SID-92)


title: 999-59 (SID-86)


title: 999-58 (SID-85)


title: 999-74 (SID-100)


title: 999-56 (SID-83)


title: HLPR-005


title: 999-71 (SID-97)


title: 999-57 (SID-84)


title: 999-54 (SID-81)


title: 999-55 (SID-82)


title: 999-61 (SID-89)


title: HLPR-002


title: 999-69 (SID-95)


title: 999-53 (SID-80)


title: HUGM-0059


title: 999-52 (SID-79)


title: 999-64 (SID-91)


title: 999-7 (SID-96)


title: HCUV-0001


title: HUGM-0056


title: HUGM-0002


title: HUGM-0055


title: 999-48 (SID-74)


title: HSCP-0001


title: HCSC-0028


title: HLPR-003


title: HUGM-0054


title: 999-45 (SID-72)


title: HCSC-0027


title: HCSC-0032


title: 999-5 (SID-76)


title: 999-50 (SID-77)

value: peritoneum


title: 999-49 (SID-75)


title: HLPR-004


title: HUGM-0067


title: HUGM-0046


title: HSCP-0002


title: 999-41 (SID-68)


title: 999-46 (SID-73)


title: 999-51 (SID-78)


title: HCSC-0009


title: HUGM-0035


title: HCSC-0025


title: mettl16_RNA-seq_rep3

city: Xuzhou

first: Tao

state: Jiangsu

address: Shanghai Road 101

institute: Jiangsu Normal University

data_processing:
Firstly, Cutadapt and perl scripts in house were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases.
Then sequence quality was verified using fastp. We used HISAT2 to map reads to the genome of Arobidopsis thaliana (Version: TAIR 10) with default parameters.
Mapped reads of IP and input libraries were provided for R package exomePeak, which identifies m6A peaks with bed or bam format that can be adapted for visualization on the UCSC genome browser or IGV software (http://www.igv.org/).
MEME and HOMER were used for de novo and known motif finding followed by localization of the motif with respect to peak summit by perl scripts in house.
Then StringTie was used to perform expression level for all mRNAs from input libraries by calculating FPKM (FPKM=[total_exon_fragments/mapped_reads(millions)×exon_length(kB)]). The differentially expressed mRNAs were selected with log2 (fold change) >1 or log2 (fold change) <-1 and p value < 0.05 by R package edgeR.
Supplementary_files_format_and_content: Excel files include FPKM values for each Sample

source_name: Plant

growth_protocol: All plants were grown in greenhouse under a long day condition (16-h-light/8-h-dark) at 23±2°C

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quality and quantity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately more than 200 ug of total RNA was subjected to isolate Poly (A) mRNA with poly-T oligo attached magnetic beads (Invitrogen). Following purification, the poly(A) mRNA fractions is fragmented into ~100-nt-long oligonucleotides using divalent cations under elevated temperature. Then the cleaved RNA fragments were subjected to incubated for 2h at 4℃ with m6A-specific antibody (No. 202003, Synaptic Systems, Germany) in IP buffer (50 mM Tris-HCl, 750 mM NaCl and 0.5% Igepal CA-630) supplemented with BSA (0.5 μg μl−1). The mixture was then incubated with protein-A beads and eluted with elution buffer (1 × IP buffer and 6.7mM m6A). Eluted RNA was precipitated by 75% ethanol. Eluted m6A-containing fragments (IP) and untreated input control fragments are converted to final cDNA library in accordance with a strand-specific library preparation by dUTP method. The average insert size for the paired-end libraries was ~100±50 bp.
And then we performed the paired-end 2×150bp sequencing on an Illumina Novaseq™ 6000 platform at the LC-BIO Bio-tech ltd (Hangzhou, China) following the vendor's recommended protocol.

tag: ecotype

value: 3-week-old seedling

value: The aerial part of Arobidopsis


title: HCSC-0031


title: 999-43 (SID-70)


title: HCSC-0026


title: mettl16_RNA-seq_rep1


title: 999-40 (SID-67)


title: 999-4 (SID-66)


title: 999-37 (SID-63)


title: 999-42 (SID-69)


title: HLPR-001


title: HUGM-0040


title: HUGM-0039


title: HUGM-0043


title: mettl16_RNA-seq_rep2


title: HCSC-0016


title: HCSC-0033


title: 999-39 (SID-65)


title: 999-36 (SID-62)


title: 999-44 (SID-71)


title: 999-3 (SID-55)


title: 999-34 (SID-60)


title: 999-31 (SID-57)


title: 999-38 (SID-64)


title: mettl16_m6A MeRIP-seq_rep1


title: Col-0_m6A MeRIP-seq_rep3


title: Col-0_RNA-seq_rep3


title: 999-29 (SID-54)


title: Col-0_m6A MeRIP-seq_rep1


title: 999-35 (SID-61)


title: 999-27 (SID-52)


title: Col-0_RNA-seq_rep2


title: Col-0_RNA-seq_rep1


title: mettl16_m6A MeRIP-seq_rep2


title: 999-32 (SID-58)


title: 999-33 (SID-59)


title: 999-26 (SID-51)


title: 999-2 (SID-44)


title: 999-20 (SID-45)


title: mettl16_m6A MeRIP-seq_rep3


title: Col-0_m6A MeRIP-seq_rep2


title: 999-22 (SID-47)


title: 999-21 (SID-46)


title: 999-18 (SID-42)


title: 999-30 (SID-56)


title: 999-28 (SID-53)


title: 999-24 (SID-49)


title: 999-19 (SID-43)


title: 585

city: Fukuoka

first: Kenoki

last: Ohuchida

address: 3-1-1, Maidashi, Higashi-ku

department: Surgery and Oncology

institute: Kyushu University

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Human Gene Expression Microarray 8x60K v3; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of all samples were normalized by the quantile algorithm with the Bioconductor.

source_name: PDAC organoid, Grade1

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

growth_protocol: Eight PDOs (No.497, 501, 565, 571, 573, 578, 580, and 585) from surgical specimens of PDAC patients using organoid culture methods.

extract_protocol: Total RNA was extracted from PDOs that had been passaged 4 to 6 rounds post-establishment and cultured with combined medium at day 5 post-passage using the High Pure RNA Isolation kit (11828665001; Roche, Basel, Switzerland) with DNase I (Roche).

treatment_protocol: ALL 8 PDOs were cultured in combined medium (including both organoid niche and 5% serum) at day5.

value: Pancreatic ductal adenocarcinoma

tag: tumor grade


title: 999-17 (SID-41)


title: 571


title: Lbr35-plus-MSG-2-T12

city: Madison

first: Bryan

last: Zabel

state: wi

address: 3329 Agriculture Dr

department: GEM

institute: International Flavors & Fragrances Inc

description: total RNA extracted from bacterial culture pellet

data_processing:
RTA v. 2.7.7 was used for basecalling, and bcl2fastq-v2.20.0 was used for demultiplexing
Reads were trimmed with trimgalore using default settings, and then transcripts were quantified using salmon v 1.3.0 with the respective transcriptome generated from the genome and gff file.
Transcript quantifications were read in to R using tximport v 1.14.2, and normalized with DESeq2 v 1.26.0  note: we didn't end up processing the T48 timepoint samples due to quality issues, but we included them in case others would like to have access to the data.
Genome_build: Lbr-35 = JAHERW000000000
Genome_build: Lbr-6108 = MDUA01000000
Supplementary_files_format_and_content: matrix table of normalized gene abundance for each sample and each gene

organism: Levilactobacillus brevis

source_name: bacterial pellet

growth_protocol: Overnight cultures (16-18 h) of L. brevis Lbr-6108, and Lbr-35 were inoculated in 15 mL disposable culture tubes (p/n 14-961-27; Fisher, Hanover Park, IL, USA) containing 3 mL of media to reach an optical density (OD) of approximately 0.100 measured at 600 nm using a spectrophotometer (Genesys 20; Thermo Fisher, Waltham, MA, USA). For each strain, two types of media were used; MRS broth (BD) without any other supplementation (further denoted as MRS) and MRS broth supplemented with 10,000 μg/mL (equivalent to 10 g/L) of L(+)-glutamic acid monosodium salt monohydrate (p/n 119940010; Acros Organics, Morris Plains, NJ, USA) (further denoted as MRS+MSG). The OD measurement for timepoint zero (T0) was measured shortly after inoculation of the overnight culture into disposable culture tubes containing 3 mL media. Cultures for all except ATCC 14869 were harvested at the initial timepoint (T0) and then every 3 h post-inoculation until 24 h, and then only at 48 h post-inoculation and the OD was measured just before harvesting. For ATCC 14869, the cultures were harvested after measuring the OD at 9 h, 24 h and then at 48 h post-inoculation because of its slower growth pattern. For each harvest timepoint separate sets of culture tubes were prepared, so that only the set of tubes for the designated time points were removed from the incubator for harvesting, without disturbing the culture growth. All culture tubes with strains growing in MRS or MRS+MSG were placed in the 37°C ± 1°C incubator under anaerobic conditions using anaerobic gas packsGasPak EZ container systems (p/n 260001, BD). Samples were removed from the incubator at respective timepoints and the ODs were measured at 600 nm.

extract_protocol:
Total RNA from Lbr-6018 and Lbr-35 RNA were extracted from cell pellets in RNA protect at GENEWIZ
Ribosomal RNA depletion was performed using FastSelect bacteria reagents (Qiagen, Hilden, Germany). RNA sequencing library preparation used NEBNext Ultra II RNA Library Preparation Kit for Illumina by following the manufacturer’s recommendations (NEB, Ipswich, MA, USA). Briefly, enriched RNAs are fragmented for 15 minutes at 94 °C. First strand and second strand cDNA are subsequently synthesized. cDNA fragments are end repaired and adenylated at 3’ends, and universal adapters are ligated to cDNA fragments, followed by index addition and library enrichment with limited cycle PCR.

treatment_protocol: MRS media +/- MSG

value: plus

tag: timepoint

tag: replicate


title: 999-23 (SID-48)


title: 578

source_name: PDAC organoid, Grade2


title: Lbr35-plus-MSG-2-T48

tag: strain


title: Lbr35-plus-MSG-1-T12


title: Lbr35-plus-MSG-2-T18


title: Lbr35-minus-MSG-2-T48

value: minus


title: 999-25 (SID-50)

tag: tissue


title: 999-129 (SID-35)


title: 999-15 (SID-39)


title: 999-127 (SID-33)


title: 999-130 (SID-37)


title: Lbr35-plus-MSG-1-T48


title: 999-13 (SID-36)


title: 999-16 (SID-40)


title: Lbr35-plus-MSG-1-T18


title: Lbr35-minus-MSG-1-T12


title: Lbr35-minus-MSG-1-T18


title: Lbr35-2-plus-MSG-T6


title: 999-124 (SID-30)


title: Lbr35-minus-MSG-1-T48


title: Lbr35-2-minus-MSG-T6


title: Lbr35-minus-MSG-2-T12


title: 999-123 (SID-29)


title: 999-126 (SID-32)


title: 999-121 (SID-27)


title: 999-122 (SID-28)


title: Lbr35-2-plus-MSG-T24


title: Lbr35-minus-MSG-2-T18


title: Lbr35-1-plus-MSG-T24


title: 999-120 (SID-26)


title: 999-125 (SID-31)


title: 999-12 (SID-25)


title: Lbr35-1-minus-MSG-T24


title: 999-128 (SID-34)


title: Lbr6108-plus-MSG-1-T48


title: 501

source_name: PDAC organoid, Grade3


title: Lbr6108-plus-MSG-1-T18


title: 573


title: 565


title: 580


title: 999-112 (SID-17)


title: 999-111 (SID-16)


title: 999-110 (SID-15)


title: Lbr35-1-plus-MSG-T6


title: Lbr35-1-minus-MSG-T6


title: 999-119 (SID-24)


title: Lbr6108-minus-MSG-2-T12


title: 999-114 (SID-19)


title: 999-14 (SID-38)


title: 999-118 (SID-23)


title: Lbr6108-plus-MSG-2-T18


title: 497


title: Lbr6108-plus-MSG-2-T48


title: Lbr6108-2-plus-MSG-T6


title: 999-104 (SID-9)


title: 999-105 (SID-10)


title: Lbr6108-minus-MSG-1-T12


title: Lbr6108-plus-MSG-2-T12


title: 999-109 (SID-14)


title: 999-116 (SID-21)


title: 999-113 (SID-18)


title: 999-102 (SID-7)


title: Lbr6108-2-minus-MSG-T6


title: Lbr6108-minus-MSG-1-T48


title: Lbr6108-minus-MSG-2-T18


title: 999-108 (SID-13)


title: MCFCA1

city: PITTSBURGH

first: Camille

last: Jacqueline

state: PA

address: 200 LOTHROP ST FL10, BIOMEDICAL SCIENCE TOWER, E1000-15B

institute: Univeristy of Pittsburgh

hyb_protocol: see Nanostring manufacturer's instructions

data_processing: nSolver 4.0

source_name: cell line

growth_protocol: RNA was extracted from a confluent 10cm2 plate

extract_protocol: RNA was extracted using RNAeasy mini kit from Qiagen

treatment_protocol: no treatment was applied


title: Lbr35-2-minus-MSG-T24


title: lir25 mutnat

city: Cleveland

first: Takuya

last: Sakaguchi

address: 9500 Euclid Ave.

institute: Cleveland Clinic Foundation

description: Whole body of 20 larvae at 5 dpf.

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Zv9 whole genome using bowtie
Genome_build: Zv9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for wt and lri25 mutant larvae

organism: Danio rerio

source_name: Whole body of 20 larvae at 5 dpf

extract_protocol:
Total RNA was isloated by the Rneasy Mini Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: AB/TL

value: whole body

tag: age

value: 5 dpf


title: wild type siblings

description: Whole body of 20 larvae at 5 dpf.


title: Lbr6108-minus-MSG-2-T48


title: Lbr6108-1-plus-MSG-T6


title: Lbr6108-1-plus-MSG-T24


title: Lbr6108-2-plus-MSG-T24


title: 999-103 (SID-8)

value: melanoma


title: Lbr6108-plus-MSG-1-T12


title: 999-107 (SID-12)

value: poor prognosis


title: MCFT1

scan_protocol: see Nanostring manufacturer's instructions


title: Lbr6108-1-minus-MSG-T6


title: 4 weeks post-TAM MED30-icKO rep2

city: la jolla

first: Siting

last: Zhu

state: california

address: 9500 Gilman Drive, University of California San Diego

department: Medicine

institute: UCSD

description: MED30.RNAseq.4weeks.diffOutput.summary.rpkm

data_processing:
Illumina NovaSeq 6000 platform used for seqenucing
The sequence adapters are trimmed by using cutadapt v2.6, with parameter "cutadapt -m 36 -u 5 -q 20".
The sequencing reads longer than 36nt are kept are downstream analysis.
Then, the reads were mapped to assembly of the mouse genome (mm10) using STAR (2.5.3a).
We preformed the downstream analysis by using Homer (v4.11.1) and differential expressed genes were identified by using DESeq2 (v1.12.4)
Supplementary_files_format_and_content: RPKM

source_name: Heart

extract_protocol:
E10.5 heart were removed and 4 weeks post-TAM cardiomyocytes were collected, flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent. KAPA RNA Hyper+RiboErase HMR Kit (Cat#08098131702) was used with 400 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using Roche kit protocols

tag: developmental stage

value: 3 month ages,  4 weeks post-TAM

tag: genotype


title: 4 weeks post-TAM MED30-icKO rep1


title: Lbr6108-minus-MSG-1-T18


title: MCF10A

label_protocol: see Nanostring manufacturer's instructions


title: 4 weeks post-TAM WT rep3

value: wild type


title: Knockdown_input_repeat2

data_processing:
For RNA-Seq data analysis, after adapter trimming and low quality sequence filtering (Q30), the clean reads were mapped to human reference genome (hg38) using Tophat2. The raw counts of reads mapping to the gencode genes (v19) were computed by HTSeq with ‘union’ overlap mode. The raw counts were then normalized as Reads per kilo base per million mapped reads (RPKM) using edegR.
For Ribo-Seq data analysis, Adapter sequences were trimmed and low quality sequences (Q30) were discarded using trim_galore. The sequences with length of at least 25nt were further aligned to human rRNA and tRNA index constructed from Ensembl (Release 91) and GtRNAdb databases , respectively. The remaining reads were aligned to the UCSC canonical known gene transcripts of the human reference genome (hg38) using bowtie with a maximum one mismatch allowed.

tag: cell type

value: Mettl1 knockdown


title: 999-10 (SID-4)

value: skin/subcutaneous tissue


title: 4 weeks post-TAM MED30-icKO rep3


title: 999-100 (SID-5)


title: 999-101 (SID-6)

value: small intestine


title: 4 weeks post-TAM WT rep2


title: Lbr6108-2-minus-MSG-T24


title: 999-096A (SID-1)


title: Knockdown_input_repeat1


title: 999-1 (SID-3)

value: lymph node


title: Knockdown_Alkb_and_NaBH4_Treated_TRAC-Seq Repeat2

data_processing:
Library strategy: TRAC-Seq
For TRAC-Seq, after adaptor trimming and quality filtering, the clean sequencing data were first mapped to the tRNA sequences using Bowtie2. Then read count for each tRNA was calculated using the method in (Cozen et al., 2015). The read counts of tRNA are normalized as reads per million (RPM) by the total number of small RNA reads that are matched to tRNAs in each sample.

value: intrahepatic cholangiocarcinoma cell line

tag: sample type

value: small RNA-TRAC-Seq


title: WT_input_repeat2


title: MCFNeoT

tag: cell line

value: MCFNeoT


title: 999-096B (SID-2)


title: Knockdown_Alkb_and_NaBH4_Treated_TRAC-Seq Repeat1


title: Lbr6108-1-minus-MSG-T24


title: WT_input_repeat1


title: FhiPS_shCt_3_N6B

city: Nantes

first: Antoine

last: Rimbert

address: 8 quai moncousu

country: France

institute: Institut du thorax inserm-U1087

hyb_protocol: 0.3 ug of Cy3-labelled cRNA (specific activity > 8 pmol Cy3/ug cRNA) pooled with 0.3 µg of Cy5-labelled cRNA (specific activity > 8 pmol Cy5/ug cRNA) were fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent GEx hybridization buffer Hi-RPM was added to the fragmentation mixture and hybridized to Agilent Sure Print G3  Human   8x 60K Microarrays (G4851A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent), 1 minute with 37°C GE Wash buffer 2 (Agilent), 10 seconds with Acetonitrile anhydrous 99.8% at room temperature and 1 minute with Stabilization and Drying solution (Agilent) at room temperature. Then, Microarrays were dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using two colors scan setting for 8x60k array slides (Scan Area HD 61x21.6 mm, Scan resolution 3 µm, Dye channels are set to Green and Red) and PMT is setup on autoscale.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters (protocol GE2_107_Sep09 and Grid: 028004_D_F_20110819) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Induced pluripotent stem cells

label_protocol: Cyanine-3 (Cy3) labeled cRNA and Cyanine-5 (Cy5) labeled cRNA were prepared from 0.1 ug RNA using the Low Input QuickAmp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (Qiagen). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: HiPSC were cultured on plates coated with Matrigel (Corning; 0.05 mg/ml) in StemMACS iPS-Brew medium (Miltenyi) and passages were performed using the Gentle Cell Dissociation Buffer (Stem Cell Technologies).

extract_protocol: RNA was prepared using thethe RNeasy Mini Kit (Qiagen) following the manufacturer's recommendations. RNA was quantified using a NanoDrop ND-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent).

tag: shRNA

value: shCt


title: 4 weeks post-TAM WT rep1


title: WT_Alkb_and_NaBH4_Treated_TRAC-Seq Repeat1

value: wild type


title: Knockdown_rnc_repeat2


title: FhiPS_shCt_2_N5B


title: FhiPS_sh4_3_N12D


title: E10.5 MED30-cKO rep1

description: MED30.RNAseq.E105.diffOutput.summary.rpkm

value: embryonic E10.5


title: E10.5 MED30-cKO rep2


title: Nasal Organoids - SARS-Cov-2 Infection_Mock

city: Shenzhen

first: Liang

last: Yang

address: No. 1088 Xueyuan Avenue, Nanshan District

institute: SUStech

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 (v2.1.0) .
Htseq-count software is used to obtain the number of reads on each gene in each sample.  The FPKM(Fragments Per Kilobase per Million) value of gene is calculated by clifflinks software.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: Nasal Organoids

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

value: Nasal Organoids

tag: treatment

value: untreated

tag: time


title: Knockdown_Alkb_Treated_Input_for_TRAC-Seq Repeat2

value: small RNA-Seq


title: WT_Alkb_and_NaBH4_Treated_TRAC-Seq Repeat2


title: E10.5 MED30-cKO rep3


title: FhiPS_sh4_1_N10D


title: Nasal Organoids - SARS-Cov-2 Infection_24h_replicate2

value: SARS-Cov-2 Infection


title: FhiPS_shCt_1_N4B


title: Knockdown_rnc_repeat1


title: E10.5 WT rep3


title: WT_rnc_repeat2


title: FhiPS_sh4_2_N11D


title: Knockdown_Alkb_Treated_Input_for_TRAC-Seq Repeat1


title: Nasal Organoids - SARS-Cov-2 Infection_24h_replicate1


title: WT_Alkb_Treated_Input_for_TRAC-Seq Repeat2


title: E10.5 WT rep2


title: Nasal Organoids - SARS-Cov-2 Infection_48h_replicate1


title: WT_Alkb_Treated_Input_for_TRAC-Seq Repeat1


title: E10.5 WT rep1


title: Nasal Organoids - SARS-Cov-2 Infection_48h_replicate2


title: Kidney, M5

status: Public on Aug 06 2021

city: Tianjin

first: Hangxing

last: Yu

address: No.88 Changling Road, Xiqing District

institute: First Teaching Hospital of Tianjin University of Traditional Chinese Medicine

description: UUO

data_processing:
Illumina bcl2fastq software used for basecalling.
The clean reads were then aligned to the reference genome using HISAT2 (v2.1.0) with default parameters
The gene expression analyses were performed with StringTie (v1.3.3b).
DESeq(v1.28.0) was used to analyze the DEGs between samples.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Rattus norvegicus

source_name: Kidney

extract_protocol:
Kidneys were removed, flash frozen on dry ice. Total RNA was extracted with Trizol (Invitrogen) and assessed with Agilent 2100 BioAnalyzer (Agilent Technologies, Santa Clara, CA, USA) and Qubit Fluorometer (Invitrogen).
The NEB Next Ultra RNA Library Prep Kit for Illumina (NEB) was used to construct the libraries for sequencing. NEB Next Poly(A) mRNA Magnetic Isolation Module (NEB) kit was used to enrich the poly(A) tailed mRNA molecules from 1 μg total RNA. The mRNA was fragmented into ~200 base pair pieces. The first-strand cDNA was synthesized from the mRNA fragments reverse transcriptase and random hexamer primers, and then the second-strand cDNA was synthesized using DNA polymerase I and RNaseH. The end of the cDNA fragment was subjected to an end repair process that included the addition of a single “A” base, followed by ligation of the adapters. Products were purified and enriched by polymerase chain reaction (PCR) to amplify the library DNA.

value: Kidney

value: SD

value: 6 weeks

tag: uuo status

value: yes

value: Sanitary saline


title: Kidney, S3

description: UUO hirudin-treated

value: wild type

value: Hirudin


title: Kidney, J3

description: UUO curcumin-treated

value: Curcumin


title: Kidney, K5

description: sham

value: no


title: WT_rnc_repeat1


title: Kidney, M2

description: UUO


title: MEKi_#10

city: Essen

first: Laura

last: Godfrey

address: Hufelandstraße 55

country: Germany

institute: DKTK Partner Site Essen/Düsseldorf

data_processing:
Demultiplexing of the sequencing reads with Illumina CASAVA v. 2.17
Adapter trimming using Skewer v. 0.1.116
Quasi-mapping with salmon v. 0.12
Converting transcript-level counts to gene-level counts and performing of differentially gene expression analysis using DESeq2 v.1.18
Genome_build: mm10
Supplementary_files_format_and_content: csv files of normalized read counts

source_name: Primary cell lines derived from pancreatic cancer of a genetically engineered mouse model

growth_protocol: DMEM high-glucose medium containing 10% fetal bovine serum, 1% penicillin/streptomycin and 1% non-essential amino acids

extract_protocol:
RNA was isolated using the Maxwell® RSC simplyRNA Cells Kit (Promega) according to manufacturer’s instruction.
TruSeq Stranded mRNA Kit (Illumina) with 100 ng input RNA

treatment_protocol: MEKi samples were treated with their IC50 of trametinib for 48 h

value: Pancreas

tag: mouse model

value: 48 h MEKi treatment


title: Kidney, G2

description: UUO BHF-treated

value: BHF


title: MEKi_#5


title: Kidney, K6

description: sham


title: DMSO_#5

value: DMSO treated control


title: Kidney, G1

description: UUO BHF-treated


title: Kidney, J2

description: UUO curcumin-treated


title: Kidney, S1

description: UUO hirudin-treated


title: Kidney, S2

description: UUO hirudin-treated


title: DMSO_#1


title: Kidney, M4

description: UUO


title: Kidney, K4

description: sham


title: Kidney, J1

description: UUO curcumin-treated


title: DMSO_#10


title: Pt_19ML0096

type: genomic

city: Yongin-si

first: Chang Ahn

last: Seol

state: Gyeonggi-do

address: 107, Ihyeon-ro 30beon-gil, Giheung-gu

department: Genome Research Center

country: South Korea

institute: GC Genome

description: Hybridized to CytoScan 750K

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to the array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using GeneChip Fulidics Station 450, and scanned using the Gene Chip Scanner 3000.

data_processing: The CEL file was analysed using Chromosome Analysis Suite (Thermo Fisher Scientific) and converted to a CYCHP file to visualize the status of genomic copy number and absence of heterozygosity.

label: biotin

molecule: genomic DNA

label_protocol: As per manufacturer (CytoScan)

extract_protocol: The genomic DNA (250 ng) extracted from peripheral blood using chemagic MSM I.

value: peripheral blood leukocyte

tag: diagnosis

value: ataxia


title: Kidney, G3

description: UUO BHF-treated


title: DMSO_#3


title: 60minATAC_PV_UF_SAL_rep4

city: Durham

first: David

last: Gallegos

state: North Carolina

address: 311 Research Dr

department: Neurobiology

institute: Duke University

description:
ATAC-seq from Nac Unbound Fraction 60 min following Saline or AMPH administration
PVATACrawcounts.xlsx

library_source: genomic

data_processing:
Illumina Hi-seq 4000 and Illumina Novaseq 6000 were used for sequencing using 50-base pair single end, and paired end S-Prime protocols respectively
The quality of the raw reads was determined using FastQC v0.11.2. All adaptors and reads with quality < 30 were trimmed using cutadapt v1.8.3. The reads were then aligned using bowtie2 v2.3.4.3 against the Gencode annotation GRCm38v72 reference genome with no more than 1 mismatch. The aligned reads were sorted and we filtered out unmapped reads using bedtools v2.25.0. Samples with a fraction of reads in peaks (FRIP) <0.125 or with mapped reads <4X the mean mapped reads were excluded.
Peaks were called by converting to a bed file using bedtools, filtering duplicates, and calling broad and narrow peaks using MACS2 v 2.1.2 (parameters: --nomodel --shift 37 --ext 73) as suggested for ATAC peaks. The overhanging peak ends were clipped off the ends of chromosomes using KentUtils bedClipv302.The peaks for all samples in each comparison were merged (# peaks) to create a master peak file for a basis of comparison.
Further analysis was carried out in R 3.4.4. A peak count matrix was creating using Rsubreadv1.28.1 to read in the ATAC counts from the merged peak regions. Prior to differential expression analysis, peaks with a CPM<1 in fewer than 3 samples were filtered out. DESeq2 v1.18.1 was then used to perform the differential peak analysis using an adjusted p-value threshold of p<0.05 for significance.
For visualization these peaks were converted into bigwigs using deepTools bamCoverage at 10bpresolution (parameters: -- normalizeUsing RPKM).
Genome_build: mm10
Supplementary_files_format_and_content: Excel spreadsheet of raw counts for MACS2 called peaks
Supplementary_files_format_and_content: BigWig fiiles for track visualization

source_name: Fresh Dissected Nucleus Accumbens

growth_protocol: Adult Rosa-LSL-Sun1-GFP x Pvalb-IRES-CRE mice or Rosa-LSL-Sun1-GFP x Sst-IRES-CRE

extract_protocol:
For each experiment, the two NAc samples from each single mouse were immeditaly placed in ice-cold homogenization buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 20mM Tricine-KOH) after dissection. The tissue was minced with a razor blade and dounce homogenized using a loose pestle in 1.5mL of homogenization buffer supplemented with 1mM DTT, 0.15mM spermine, 0.5mM spermidine, 172g/L kynurenic acid, and EDTA-free protease inhibitor. A 5% IGEPAL-630 solution was added to bring the homogenate to 0.3% IGEPAL-630, and the homogenate was further dounced with eight strokes of the tight pestle. When purifying RNA, RNaseOUT was added to all buffers at 60U/mL. When isolating nuclei for ATAC-seq, sodium butyrate was added to all buffers at a final concentration of 5mM. The sample was filtered through a 40μm strainer, mixed with 1.5mL of Working Solution (1:5 150mM KCl, 30mM MgCl2, 120mM Tricine-KOH, pH 7.8 Diluent and Optiprep Density Gradient Medium), underlaid with a gradient of 30% and 40% iodixanol, and centrifuged at 10,000xg for 18min on an Sw41Ti rotor in a swinging bucket centrifuge at 4°C. Nuclei were collected at the 30%-40% interface and pre-cleared by incubating with 20μL of protein G magnetic Dynabeads for 10min. After removing the beads with a magnet, the mixture was diluted with wash buffer (homogenization buffer plus 0.4% IGEPAL-630) and incubated with 10μL of 0.2mg/mL rabbit monoclonal anti-GFP antibody (Thermo Fisher Scientific Cat# G10362, RRID:AB_2536526) for 30min. 60μL of Dynabeads were added, and the mixture was incubated for an additional 25 minutes. To increase yield, the bead-nuclei mixture was placed on a magnet for 30sec to 1min, completely resuspended by inversion, and placed back on the magnet. This was repeated 5-7 times. Samples were then re-placed on the magnet for 5min. 1mL of supernatant was removed as the Unbound Nuclear Fraction (UF) and placed on ice. The remaining beads were washed 3 times in 1mL of wash buffer followed by one wash in 6mL wash buffer. The 6mL was then sequentially applied to the magnet until all beads had been isolated. The final bead mixture was resuspended in 100µL wash buffer for downstream applications. All steps were performed on ice or in the cold room, and all incubations were carried out using an end-to-end rotator. 10µL of suspended UF nuclei were counted on a hemocytometer and 5000 UF nuclei were removed for use in downstream applications as an approximate reference sample to the number of PV+ nuclei harvested per mouse (calculated range 3000-5000/mouse).
Omni-ATAC-seq was done as previously described in Corces MR, et al. (Nat Methods 14, 959–962 (2017))  with the sole modification of an adjusted Tn5 volume (0.5µL/sample) to avoid over transposition in a low number of input nuclei. Briefly, 5000 UF nuclei or the entirety of the bead-bound immunoprecipitated fraction nuclei (IP) were resuspended in cold RSB buffer prior to the beginning of the Omni-ATAC procedure. Libraries were made as described with the added inclusion of a 1:1 volume library cleanup with Ampure XP beads

treatment_protocol: On day one, after habituation, mice received a mock injection and were returned to the open field. Locomotor activity was monitored as horizontal distance traveled (cm). To study acute responses to AMPH, on day 2, either saline (as a vehicle control) or 3mg/kg AMPH was administered (i.p.) and mice were returned immediately to the open field for 60min before sacrifice and harvest

value: Brain/ Nucleus Accumbens

value: Pvalb-IRES-Cre x INTACT Compound HET

value: Saline 60 min

value: PV- UF


title: ATAC_SST_UF_SAL_rep2

description:
ATAC-seq from SST-Cre Nac Unbound Fraction
SSTATACrawcounts.xlsx

value: Sst-IRES-Cre x INTACT Compound HET

value: Saline

value: SST- UF


title: ATAC_SST_UF_SAL_rep3


title: MEKi_#3


title: 60minATAC_PV_UF_AMPH_rep4

value: 3mg/kg Amph 60 min


title: 60minATAC_PV_UF_AMPH_rep2


title: 60minATAC_PV_UF_AMPH_rep3


title: ATAC_SST_IP_SAL_rep1

description:
ATAC-Seq from Saline-treated SST+ Interneurons
SSTATACrawcounts.xlsx

value: SST+


title: 60minATAC_PV_IP_SAL_rep5

description:
ATAC-Seq from Immunoprecipitated PV+ Interneurons 60 min following Saline or AMPH administration
PVATACrawcounts.xlsx

value: PV+


title: 60minATAC_PV_IP_SAL_rep2


title: 60minATAC_PV_IP_AMPH_rep2


title: 60minATAC_PV_UF_SAL_rep1


title: 60minATAC_PV_IP_SAL_rep1


title: ATAC_SST_IP_SAL_rep2


title: 60minATAC_PV_IP_AMPH_rep4


title: MEKi_#1


title: 60minATAC_PV_IP_AMPH_rep1


title: 60minATAC_PV_UF_AMPH_rep1


title: ATAC_SST_UF_SAL_rep1


title: 3HrPV_UF_AMPH_Isolation4_Sample1

description:
Total Nuclear RNA from Nac Unbound Fraction 3Hr following Saline or AMPH administration
PV3HrGEOraw_counts_filt.csv

data_processing:
Illumina Hi-seq 4000 and Illumina Novaseq 6000 were used for sequencing using 50-base pair single end, and paired end S-Prime protocols respectively. Illumina Hiseq 2500 was used for Ribo-Tag Cytoplasmic RNA samples
FASTQ-formatted data files were processed using the Trimmomatic toolkit v0.38 to trim low-quality bases and Illumina sequencing adapters from the 3′ end of the reads. Only reads that were 32nt or longer after trimming were kept for further analysis. Reads were mapped to the Gencode annotation GRCm38v72 version of the mouse genome and transcriptome using the STAR RNA-seq alignment tool. Gene counts were compiled using the HTSeq tool. For this analysis, we used the standard method of only counting reads that mapped to known exons and reads with mapq > 30 were used for the differential expression analysis. Prior to differential expression analysis, genes with a counts per million (CPM) <1 for any sample were excluded.
[Total RNA]  Normalization and differential expression analyses were carried out using the DESeq2 Bioconductor package with the R statistical programming environment while accounting for batch, treatment, and PCR-bottlenecking effects. The false discovery rate was calculated to control for multiple hypothesis testing. In the case of cell-type specific genes, genes with FDR<0.05 were considered significantly differentially expressed. For cell-type specific stimulus-regulated genes, an FDR<0.1 was used.
[Cytoplasmic/Ribo-Tag RNA]  Aligned and sorted by coordinate  bam files were used as the input for CuffLinks CuffDiff v2.2.1 analysis using the using the Gencode vM21 transcript annotation gtf and following syntax: fdiff -L WT_IP,WT_INPUT,KO_IP,KO_INPUT -p 8 -o (Output Directory) -dispersion-method pooled -library-type fr-firststrand (Annotation gtf path)
Genome_build: mm10
Supplementary_files_format_and_content: BigWig fiiles for track visualization
Supplementary_files_format_and_content: csv files include raw counts for multiple samples as labeled in Title
Supplementary_files_format_and_content: Xlsx file includes processed output from Cuffdiff of all aligned Ribo-Tag samples

source_name: Dissected Nucleus Accumbens

growth_protocol: Adult Rosa-LSL-Sun1-GFP x Pvalb-IRES-CRE mice, Rosa-LSL-Sun1-GFP x Sst-IRES-CRE,  Pvalb-2A-Cre x MeCP2 Ser421Ala KI, or hemizygous WT male littermates

extract_protocol:
[Total RNA]  For each experiment, the two NAc samples from each single mouse were thawed in ice-cold homogenization buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 20mM Tricine-KOH). The tissue was minced with a razor blade and dounce homogenized using a loose pestle in 1.5mL of homogenization buffer supplemented with 1mM DTT, 0.15mM spermine, 0.5mM spermidine, 172g/L kynurenic acid, and EDTA-free protease inhibitor. A 5% IGEPAL-630 solution was added to bring the homogenate to 0.3% IGEPAL-630, and the homogenate was further dounced with eight strokes of the tight pestle. When purifying RNA, RNaseOUT was added to all buffers at 60U/mL. When isolating nuclei for ATAC-seq, sodium butyrate was added to all buffers at a final concentration of 5mM. The sample was filtered through a 40μm strainer, mixed with 1.5mL of Working Solution (1:5 150mM KCl, 30mM MgCl2, 120mM Tricine-KOH, pH 7.8 Diluent and Optiprep Density Gradient Medium), underlaid with a gradient of 30% and 40% iodixanol, and centrifuged at 10,000xg for 18min on an Sw41Ti rotor in a swinging bucket centrifuge at 4°C. Nuclei were collected at the 30%-40% interface and pre-cleared by incubating with 20μL of protein G magnetic Dynabeads for 10min. After removing the beads with a magnet, the mixture was diluted with wash buffer (homogenization buffer plus 0.4% IGEPAL-630) and incubated with 10μL of 0.2mg/mL rabbit monoclonal anti-GFP antibody (Thermo Fisher Scientific Cat# G10362, RRID:AB_2536526) for 30min. 60μL of Dynabeads were added, and the mixture was incubated for an additional 25 minutes. To increase yield, the bead-nuclei mixture was placed on a magnet for 30sec to 1min, completely resuspended by inversion, and placed back on the magnet. This was repeated 5-7 times. Samples were then re-placed on the magnet for 5min. 1mL of supernatant was removed as the Unbound Nuclear Fraction (UF) and placed on ice. The remaining beads were washed 3 times in 1mL of wash buffer followed by one wash in 6mL wash buffer. The 6mL was then sequentially applied to the magnet until all beads had been isolated. The final bead mixture was resuspended in 100µL wash buffer for downstream applications. All steps were performed on ice or in the cold room, and all incubations were carried out using an end-to-end rotator. 10µL of suspended UF nuclei were counted on a hemocytometer and 5000 UF nuclei were removed for use in downstream applications as an approximate reference sample to the number of PV+ nuclei harvested per mouse (calculated range 3000-5000/mouse). RNA isolation was performed using the RNaqeuous Micro kit (Thermo Fisher) according to the manufacturer’s instructions, excepting that DNase digestion was not performed at this step, as the downstream library preparation included a DNase step. RNA was eluted in 15µL elution buffer from which 4µL was used for qRT-PCR gene enrichment validation.
[RiboTag/Cytoplasmic RNA]  NAc tissue was rapidly dissected and Dounce homogenized in a tissue weight to buffer volume ratio of 5% (0.6-1mL) of homogenization buffer (HB-S, 50mM Tris, 100mM KCl, 12mM MgCl2, 1% NP-40) supplemented with 200U/mL RNAaseOUT, 1X Protease inhibitor, 1mM DTT, 100ug/mL Cyclohexamide, and 1mg/mL Heparin. Homogenate was spun down at 10,000 RPM and the supernatant was moved to the immunoprecipitation step after removal of 80µL for input vs IP comparisons. To prepare the antibody-bead mixture, Dynabeads were first washed in 1X PBS before 10µL Rabbit α-HA tag antibody (Abcam, #9110, RRID:AB_307019) was added to 300µL PBS+60µL Dynabeads and rotated at 4ºC for 4hr.  For immunoprecipitation, the remaining supernatant was subsequently combined with α-HA antibody-bead mixture and rotated overnight at 4ºC. Beads were isolated, washed 3 times in high-salt buffer, and lysed in Qiagen lysis buffer RLT for elution. RNA was subsequently extracted using the Qiagen RNeasy Mini Kit.  SMART-Seq™ v4 Ultra™ Low Input RNA Kit (Takara Bio #634888) was used to convert RNA to cDNA, which was then amplified and sequenced using an Illumina Hiseq 2500.
[Total RNA]  Nugen Ovation Solo
[RiboTag/Cytoplasmic RNA]  SMART-Seq™ v4 Ultra™ Low Input RNA Kit
Total RNA-seq
Ribo-Tag

value: 3mg/kg Amph 3 Hr


title: 60minATAC_PV_IP_AMPH_rep3


title: ATAC_SST_IP_SAL_rep3


title: 3HrPV_UF_AMPH_Isolation3_Sample1


title: 60minATAC_PV_UF_SAL_rep5


title: 60minATAC_PV_IP_SAL_rep4


title: 3HrPV_UF_SAL_Isolation2_Sample1

value: Saline 3 Hr


title: 3HrPV_IP_SAL_Isolation3_Sample1

description:
Total Nuclear RNA from Immunoprecipitated PV+ Interneurons 3Hr following Saline or AMPH administration
PV3HrGEOraw_counts_filt.csv


title: 3HrPV_UF_SAL_Isolation3_Sample1


title: 3HrPV_IP_AMPH_Isolation4_Sample1


title: 3HrPV_IP_SAL_Isolation4_Sample1


title: 3HrPV_UF_AMPH_Isolation1_Sample1


title: 60minATAC_PV_UF_SAL_rep2


title: 3HrPV_IP_SAL_Isolation1_Sample1


title: 3HrPV_UF_SAL_Isolation1_Sample1


title: 3HrPV_UF_AMPH_Isolation2_Sample1


title: 3HrPV_IP_SAL_Isolation2_Sample1


title: 3HrPV_UF_SAL_Isolation4_Sample1


title: 35minSST_IP_SAL_Isolation3_Sample1

description:
Total Nuclear RNA from Immunoprecipitated SST+ Interneurons 35 min following Saline or AMPH administration
SST35minGEOraw_counts_filt.csv

value: Saline 35 min


title: 35minSST_UF_AMPH_Isolation2_Sample1

description:
Total Nuclear RNA from Nac Unbound Fraction 35 min following Saline or AMPH administration
SST35minGEOraw_counts_filt.csv

value: 3mg/kg Amph 35 min


title: 35minSST_UF_SAL_Isolation1_Sample1


title: 35minSST_UF_SAL_Isolation3_Sample1


title: 3HrPV_IP_AMPH_Isolation3_Sample1


title: 35minSST_IP_AMPH_Isolation3_Sample1


title: 3HrPV_IP_AMPH_Isolation2_Sample1


title: 35minSST_UF_AMPH_Isolation3_Sample1


title: 35minSST_UF_AMPH_Isolation1_Sample1


title: 35minPV_UF_AMPH_Isolation4_Sample1

description:
Total Nuclear RNA from Nac Unbound Fraction 35 min following Saline or AMPH administration
PV35minGEOraw_counts_filt.csv


title: 35minSST_IP_AMPH_Isolation2_Sample1


title: 35minSST_UF_SAL_Isolation2_Sample1


title: 35minPV_UF_AMPH_Isolation5_Sample1


title: 35minSST_IP_SAL_Isolation1_Sample1


title: 35minSST_IP_SAL_Isolation2_Sample1


title: 35minSST_IP_AMPH_Isolation1_Sample1


title: 3HrPV_IP_AMPH_Isolation1_Sample1


title: 35minPV_UF_SAL_Isolation4_Sample1


title: 35minPV_IP_AMPH_Isolation5_Sample1

description:
Total Nuclear RNA from Immunoprecipitated PV+ Interneurons 35 min following Saline or AMPH administration
PV35minGEOraw_counts_filt.csv


title: 35minPV_IP_SAL_Isolation5_Sample1


title: 35minPV_IP_SAL_Isolation4_Sample1


title: 35minPV_IP_AMPH_Isolation4_Sample1


title: 35minPV_UF_SAL_Isolation5_Sample1


title: 35minPV_UF_SAL_Isolation1_Sample1


title: 35minPV_UF_SAL_Isolation2_Sample1


title: 35minPV_UF_AMPH_Isolation2_Sample1


title: 35minPV_UF_SAL_Isolation3_Sample1


title: 35minPV_UF_AMPH_Isolation3_Sample1


title: 35minPV_IP_SAL_Isolation1_Sample1


title: 35minPV_UF_AMPH_Isolation1_Sample1


title: 35minPV_IP_SAL_Isolation2_Sample1


title: 35minPV_IP_SAL_Isolation3_Sample1


title: Ov_RNA_PB3

city: Rennes

first: Fatima

last: SMAGULOVA

address: 9 av. Prof. Léon Bernard

institute: Irset - U1085

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Reads were mapped onto mm10 assembly of mouse genome using Hisat2 (v2.1.0).
For each biological replicate, a transcriptome was generated using Stringtie (v1.3.5). Individual transcriptomes were then merged using Stringtie merge.
Genes and transcripts were then quantified and prepDE.py script provided by Stringtie developers was used to prepare input matrix for DESeq2 R package.
Differential expression analysis (Control vs Panobinostat) was performed using R package DESeq2 (v1.30.0).
Genome_build: mm10
Supplementary_files_format_and_content: bam files and corresponding indexes, tsv file containing transcript counts,tsv file containing differential expression analysis (from DESeq2).

source_name: embryonic ovary

extract_protocol:
Total RNA was extracted using the RNeasy plus mini kit (Qiagen) according to the manufacturer’s instructions. To generate each biological replicate, RNAs were extracted from a pool of 4 embryonic ovaries.
The libraries were prepared using the NEBNEXT® Ultra II Directional RNA Library kit for Illumina® (NEB E7760S) using 1µg of total RNA according to the manufacturer’s instructions.

treatment_protocol: Pregnant mice (F0) were treated during development (E6.5-E15.5) at dose 5mg/kg/day with Panobinostat. The mice were sacrificied at E15.5 and embryonic ovary were collected.

tag: strian

value: E15.5 ovary

value: 5 mg/kg/day of panobinostat


title: Ov_RNA_PB1


title: 35minPV_IP_AMPH_Isolation3_Sample1


title: 35minPV_IP_AMPH_Isolation1_Sample1


title: 35minPV_IP_AMPH_Isolation2_Sample1


title: Ov_RNA_Con2

value: control


title: Ov_RNA_Con3


title: Ov_RNA_Con1


title: PyMT_iEOS_3

city: ROSH HAAYIN

first: Shai

last: Dulberg

address: Maayan 5, apt 47

department: Department of Pathology

institute: Tel Aviv University

data_processing:
RNA libraries were generated using Cell-seq Library protocol, and sequenced on Illumina HiSeq2500, 50 single-end run.
The reads  were mapped to the Mus musculus, GRCm38 genome using Tophat2 version 2.1.0.
Only uniquely mapped reads were counted to genes, using 'HTSeq- count' package version 0.6.1 with ‘union’ mode.
Normalization was conducted using DESeq2 R package version 1.10.0.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Eosinophils

extract_protocol:
Eosinophils were directly sorted (>98% purity validated using Cytospin) into TRIzol (19367501, Ambion) supplemented with RNasin ribonuclease inhibitor (N2111, Promega), samples were then pooled from 3-4 mice. RNA was extracted by the addition of chloroform followed by centrifugation and addition of absolute ethanol to the top layer. Thereafter, the fluid was transferred to PureLink RNA mini kit (Invitrogen) and processed according to manufacturer’s instructions.The RNA integrity number (RIN) was analyzed   using Bioanalyzer and only samples of RIN>6.3 were used.
RNA libraries were prepared for sequencing using Cell-seq protocols

treatment_protocol: PyMT tumor cells were grown in DMEM with 10% FCS. Tumor cells were detached using 0.25% Trypsin- 0.05% EDTA (Biological Industries) and washed twice in PBS before injection. For experimental lung metastasis, 1 × 105 PyMT cells were resuspended in saline (200 µl) and used for tail vein injections, saline only was used as control.

value: Metastatic Lung Siglec-F high Eosinophils

value: PyMT cells


title: PyMT_rEOS_2

value: Metastatic Lung Siglec-F int Eosinophils


title: PyMT_rEOS_1


title: Naive_3

value: Lung Eosinophils


title: PyMT_iEOS_2


title: Naive_2


title: Naive_1


title: PyMT_iEOS_1


title: MeCP2_S421A_KO-INPUTall

description:
Total Input RNA from S421A Nac
CuffdiffGeneExpOutputMeCP2WTvKI.xlsx

molecule: cytoplasmic RNA

value: Brain/ Nucleus Accumbens

value: Pvalb-2A-Cre x MeCP2 Ser421Ala KI

value: Drug-Naïve

value: NAc Input All Cell Types

tag: antibody


title: MeCP2_S421A_WT1-IPall

description:
Ribo-Tag Pulldown from WT PV+ Neurons
CuffdiffGeneExpOutputMeCP2WTvKI.xlsx

value: Pvalb-2A-Cre x MeCP2 Ser421Ala WT

value: α-HA antibody


title: MeCP2_S421A_WT-INPUTall

description:
Total Input RNA from WT Nac
CuffdiffGeneExpOutputMeCP2WTvKI.xlsx


title: Ov_RNA_PB2


title: MeCP2_S421A_KO1-IPall

description:
Ribo-Tag Pulldown from S421A PV+ Neurons
CuffdiffGeneExpOutputMeCP2WTvKI.xlsx

value: PV+


title: Sample 5_Resident cardiac macrophages_Day 4 AngII_Expt 2

city: Toronto

first: Slava

last: Epelman

state: Ontario

address: 101 College St.

country: Canada

institute: University Health Network

data_processing:
Cell Ranger Single Cell Software Suite (10x Genomics) was used to pre-process sequenced cells, and to generate the expression matrices.
Raw base call (BCL) files from HiSeq2500 sequencer were demultiplexed into FASTQ files.
Sequencing reads were aligned to the mouse or human transcriptome using STAR aligner.
Cell barcodes and UMIs underwent filtering and correction, followed by barcode and UMI counting to generate the feature-barcode matrices.
Genome_build: mm10 (Samples 1-5); hg19 (Samples 6-7)
Supplementary_files_format_and_content: Cell barcodes: TSV, Genes: TSV, Counts: expression matricies, MTX

source_name: Heart macrophages

extract_protocol:
(Samples 1-5, mouse):
Hearts were perfused with 20 ml of cold PBS. Hearts were chopped finely and digested, while being shaken, at 37 °C in DMEM containing collagenase I (450 U ml–1), DNase I (60 U ml–1) and hyaluronidase (60 U ml–1) enzymes and 1mM Flavopiridol. Digestions were stopped after 30 min and cells were processed into a single-cell suspension on ice. Cells were labeled with CD45 magnetic beads (Miltenyi Biotec) and subsequently fluorescently tagged antibodies to CD45, CD64, CD11b, B220, CD3, Ly6G, NK1.1, Ly6C and MHC-II. Hematopoietic cells were positively enriched using the AutoMACS instrument (Miltenyi Biotec). Live resident macrophages (DAPI-CD45+CD64+CD11b+Td+) and monocytes (DAPI-CD11b+Ly6C+) were sorted on the Aria Fusion (BD Bioscience) under low pressure into DMEM containing 50% bovine serum for 10x Genomics single-cell RNA sequencing. Monocytes and macrophages were mixed in a 1:100 ratio and sequenced together.
(Samples 6-7, human):
Resected tissue was immediately placed into sterile, cold DMEM media supplemented with 50% fetal bovine serum. Human cardiac tissue was processed similar to mouse tissue and stained with anti-CD45 antibody. Cell sorting was performed using Aria II instrumentation (BD Bioscience). Total live immune cells were sorted by gating on DAPI-CD45+ cells. Samples were sorted directly into DMEM + 50% bovine serum for single-cell RNA sequencing submission.
(Samples 1-5, 7):
Libraries were prepared as outlined by the Chromium Single Cell 3’ Reagent Kits v3 user guide with appropriate modifications to the PCR cycles based on the calculated cDNA concentration (as recommended by 10X Genomics).
(Sample 6):
Libraries were prepared as outlined by the Chromium Single Cell 3’ Reagent Kits v2 user guide with appropriate modifications to the PCR cycles based on the calculated cDNA concentration (as recommended by 10X Genomics).

value: Heart

value: Heart macrophages

tag: cell subtype/info

value: Td+ macrophages

value: Day 4 AngII

value: 10-12 weeks


title: MeCP2_S421A_WT2-IPall

tag: strain


title: Sample 2_Resident cardiac macrophages_Day 4 AngII_Expt 1

tag: tissue


title: Sample 1_Resident cardiac macrophages_Sham_Expt 1

value: Sham

tag: age


title: Sample 3_Resident cardiac macrophages_Day 28 AngII_Expt 1

value: Day 28 AngII


title: Neural crest specific Angpt1 knockout mouse iridocorneal angle and limbal region ko1

city: Chicago

first: Benjamin

middle: R

last: Thomson

state: IL

address: 303 E Superior St. SQ8-500

department: Feinberg Cardiovascular and Renal Research Institute

data_processing:
Sequencing data was demultiplexed using Cell Ranger mkfastq version 2.1.1
FASTQ files were aligned and counted to mm10 (10X Genomics transcript version 1.2.0) using Cell Ranger count version 2.1.1
Matrix files were analyzed using Seurat 3.1.3.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited matrix output files from Cell Ranger count
Supplementary_files_format_and_content: cloupe files from Cell Ranger output
Supplementary_files_format_and_content: web summary html files from Cell Ranger output
Supplementary_files_format_and_content: Filtered and compiled datasets after Seurat 3.1.3 analysis

source_name: Iridocorneal angle / limbus

extract_protocol:
To avoid melanin aggregation during tissue dissociation and sample preparation, Angpt1ΔNC mice were crossed for 2 generations onto WT ICR mice to obtain litters of albino control and mutant animals. Animals were then aged to 6 weeks and groups of 2-3 Angpt1ΔNC and control mice were euthanized for pooled tissue collection. Male and female animals were pooled for analysis, resulting in two pooled control samples and a single pooled Angpt1ΔNC sample. 4-6 enucleated eyes were immediately dissected in ice-cold HBSS (Gibco-Life Technologies, Carlsbad CA) to obtain the isolated limbal-iridocorneal angle region. First, eyes were bisected on the saggital plane before the lens and retina were removed. The sclera was then removed by cutting immediately posterior to the ciliary body. Finally, the cornea was separated by cutting just anterior to the limbus, avoiding the TM. The majority of the iris was then removed, taking care to leave the ciliary body and TM intact. Limbal regions were then transferred to ice-cold DMEM containing 10% FBS and minced using fine scissors. After mincing, 1mg/ml Collagenase A (Worthington, Lakewood NJ) and 10μM Y27362 were added and tissues were transferred to a tissue culture incubator for 2 hours at 37°/5% CO2. After incubation, tissues were washed 1x in PBS before incubation in 0.25% Trypsin solution (Gibco) containing 100 units/ml DNAse 1 (Roche, Basel, Switzerland) 10μM Y27362 for 25 minutes at 37° with shaking and trituration. Dissociated cells were then washed 2x in DMEM and passed through a 40μm cell strainer before resuspension in ice-cold HBSS containing 1% BSA at a concentration of 1000 cells/μl. Cells were then filtered a second time and immediately used for library preparation.
Library preparation by the NuSeq core at the Northwestern University Feinberg School of Medicine using the 10x Genomics Chromium platform. Libraries were then sequenced using a HiSeq4000 instrument at a depth of 50,000 reads per cell.
single cell RNA-Seq

value: Iridocorneal angle / limbus

value: Mixed

value: Angpt1 flox/flox;Wnt1Cre+

value: 6 weeks-old


title: KO no RUN rep 2

city: Udine

first: Simone

last: Scalabrin

state: UD

address: via Jacopo Linussio 51

country: Italy

institute: IGA Technology Services

description:
909_570_18
mRNA
KO_NO-RUN_vs_KO_RUN.gene_exp.uniq.diff
WT_NO-RUN_vs_KO_NO-RUN.gene_exp_uniq.diff
WT_RUN_vs_KO_NO-RUN.gene_exp_uniq.diff

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using TopHat with default parameters.
Cufflinks was then used to assemble transcripts and quantify their expression.
Cuffdiff was used to compare expression levels of genes and find significant changes in expression between different conditions (http://cole-trapnell-lab.github.io/cufflinks/cuffdiff/).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.diff: Tab-delimited text files include gene-level differential expression. Tests differences in the summed FPKM of transcripts sharing each gene_id.

source_name: isolated dentate gyrus

growth_protocol: Mice were maintained under standard specific-pathogen-free conditions and were housed in standard cages until P60.

extract_protocol:
RNA was extracted by using Trizol. Extracted RNA was quantified and assessed for purity using a NanoDrop ND-1000 Spectrophotometer (Thermo Fisher Scientific, Wilmington, DE, USA) and an Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara CA). RNAs were subsequently employed for transcriptome sequencing and/or for real-time PCR experiments. The identity of the dissected dentate gyri was checked by comparing the relative expression of specific markers, i.e., Tdo2, Dsp, Meis2, Tyro3, as indicated in Hagihara et al. (2009) (data not shown).
RNA libraries were prepared for sequencing using standard Illumina protocol TruSeq RNA Library Prep Kit.

treatment_protocol: At P60 mice were randomly assigned to running wheel or standard cages for 12 days.

value: Btg1 knockout

value: Dentate gyrus

value: Control (sedentary)

value: Adult


title: KO RUN rep 2

description:
911_570_20
mRNA
KO_NO-RUN_vs_KO_RUN.gene_exp.uniq.diff
WT_NO-RUN_vs_KO_RUN.gene_exp_uniq.diff
WT_RUN_vs_KO_RUN.gene_exp_uniq.diff

value: Voluntary running (12 days)


title: PyMT_rEOS_3

value: Metastatic Lung Siglec-F int Eosinophils

value: PyMT cells


title: WT RUN rep 2

description:
906_590_15A
mRNA
WT_NO-RUN_vs_WT_RUN.gene_exp_uniq.diff
WT_RUN_vs_KO_NO-RUN.gene_exp_uniq.diff
WT_RUN_vs_KO_RUN.gene_exp_uniq.diff

value: Btg1 wild-type


title: WT no RUN rep 2

description:
905_570_14
mRNA
WT_NO-RUN_vs_KO_NO-RUN.gene_exp_uniq.diff
WT_NO-RUN_vs_KO_RUN.gene_exp_uniq.diff
WT_NO-RUN_vs_WT_RUN.gene_exp_uniq.diff


title: WT RUN rep3

description:
907_570_16
mRNA
WT_NO-RUN_vs_WT_RUN.gene_exp_uniq.diff
WT_RUN_vs_KO_NO-RUN.gene_exp_uniq.diff
WT_RUN_vs_KO_RUN.gene_exp_uniq.diff


title: KO RUN rep 1

description:
910_570_19
mRNA
KO_NO-RUN_vs_KO_RUN.gene_exp.uniq.diff
WT_NO-RUN_vs_KO_RUN.gene_exp_uniq.diff
WT_RUN_vs_KO_RUN.gene_exp_uniq.diff


title: UMG12 mTOR KD Replicate 3

city: LOS ANGELES

first: Bassem

last: Ben Cheikh

state: CA

address: 8723 Alden Drive, Suite 100

department: Biomedical Sciences

institute: CEDARS SINAI MEDICAL CENTER

description:
Mtor_3
Sequencing instrument Illumina HiSeq model number not provided by sequencing company; Illumina HiSeq 4000 used a default model.

data_processing:
STAR alignment software, version 2.5.1b, command options: --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000
featureCounts software, command options: -t exon -g gene_id, -a gencode.v26.annotation.gtf
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: UMUC3 bladder cancer cell line

growth_protocol: Cells were cultured in MEM media supplemented with 10% FBS and 1X Sodium pyruvate.

extract_protocol:
Qiagen RNAeasy plus kit
Done by Novogene Inc

treatment_protocol: Transfected with Smartpool siRNAs for each gene separately using RNAiMax tranfection reagent and recommended protocol.

value: GFP tagged to hTERT mutant promoter allele

tag: knockdown treatment

value: mTOR Knockdown


title: UMG12 mTOR KD Replicate 2

description:
Mtor_2
Sequencing instrument Illumina HiSeq model number not provided by sequencing company; Illumina HiSeq 4000 used a default model.

tag: genotype


title: UMG12 TRIM24 KD Replicate 3

description:
T24_3
Sequencing instrument Illumina HiSeq model number not provided by sequencing company; Illumina HiSeq 4000 used a default model.

value: TRIM24 Knockdown


title: UMG12 TRIM28 KD Replicate 3

description:
T28_3
Sequencing instrument Illumina HiSeq model number not provided by sequencing company; Illumina HiSeq 4000 used a default model.

value: TRIM28 Knockdown


title: WT no RUN rep 1

description:
904_570_13
mRNA
WT_NO-RUN_vs_KO_NO-RUN.gene_exp_uniq.diff
WT_NO-RUN_vs_KO_RUN.gene_exp_uniq.diff
WT_NO-RUN_vs_WT_RUN.gene_exp_uniq.diff


title: UMG12 TRIM24 KD Replicate 1

description:
T24_1
Sequencing instrument Illumina HiSeq model number not provided by sequencing company; Illumina HiSeq 4000 used a default model.


title: UMG12 mTOR KD Replicate 1

description:
Mtor_1
Sequencing instrument Illumina HiSeq model number not provided by sequencing company; Illumina HiSeq 4000 used a default model.


title: MeCP2_S421A_KO2-IPall

value: Brain/ Nucleus Accumbens

value: Pvalb-2A-Cre x MeCP2 Ser421Ala KI

value: Drug-Naïve

tag: cell type

value: PV+

value: α-HA antibody


title: UMG12 TRIM28 KD Replicate 2

description:
T28_2
Sequencing instrument Illumina HiSeq model number not provided by sequencing company; Illumina HiSeq 4000 used a default model.


title: KO no RUN rep 1

description:
908_570_17
mRNA
KO_NO-RUN_vs_KO_RUN.gene_exp.uniq.diff
WT_NO-RUN_vs_KO_NO-RUN.gene_exp_uniq.diff
WT_RUN_vs_KO_NO-RUN.gene_exp_uniq.diff

value: Btg1 knockout


title: WT mouse iridocorneal angle and limbal region wt185

institute: Northwestern University Feinberg School of Medicine

value: Iridocorneal angle / limbus

value: Mixed

value: Angpt1 flox/flox

value: 6 weeks-old


title: cDMD-ES_2

city: New York

first: Zhaoning

last: Wang

state: New York

address: 701 West 168th Street Hammer 14 - 1410

department: Genetics and Development

institute: Columbia University

description: biological replicate 2

data_processing:
Quality control of RNA-Seq data was performed using FastQC Tool (Version 0.11.4).
Sequencing reads were aligned to mouse GRCh38 (hg38) reference genome using HiSTAT2 (Version 2.0.4) with default settings and --rna-strandness F.
Aligned reads were counted using featurecount (Version 1.6.0) per gene ID.
Differential gene expression analysis was performed with the R package edgeR (Version 3.30.1) using the GLM approach. For each comparison, genes with more than 1 CPM (Count Per Million) in at least three samples were considered as expressed and were used for calculating normalization factor. Cutoff values of absolute fold change greater than 2.0 and false discovery rate less than 0.01 were used to select differentially expressed genes between sample group comparisons. Normalized gene CPM values were used to calculate RPKM (Reads Per Kilobase per Million mapped reads) values, which were then used for heatmap plotting.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files including raw count values and RPKM values for each sample, and excel spreadsheet files for differential expression analysis results from edgeR.

source_name: iPSC-derived cardiomyocytes

extract_protocol:
RNA was extracted using TRIzol according to the manufacturer's protocol.
Stranded mRNA-Seq libraries were generated using the KAPA mRNA HyperPrep Kit (Roche, KK8580) following manufacturer’s protocol.

tag: disease state

value: Duchenne Muscular Dystrophy

value: Delta 44-exon skipping

value: iPSC-derived cardiomyocytes


title: cDMD-RF_3

description: biological replicate 3

value: Delta 44-reframing


title: UMG12 Mock Replicate 2

description:
M_2
Sequencing instrument Illumina HiSeq model number not provided by sequencing company; Illumina HiSeq 4000 used a default model.

tag: cell line

value: GFP tagged to hTERT mutant promoter allele

value: Control


title: UMG12 TERT KD Replicate 2

description:
Tert_2
Sequencing instrument Illumina HiSeq model number not provided by sequencing company; Illumina HiSeq 4000 used a default model.

value: TERT Knockdown


title: WT mouse iridocorneal angle and limbal region wt285


title: UMG12 Mock Replicate 1

description:
M_1
Sequencing instrument Illumina HiSeq model number not provided by sequencing company; Illumina HiSeq 4000 used a default model.


title: cDMD-ES_3

description: biological replicate 3


title: Sample 4_Resident cardiac macrophages_Sham_Expt 2

value: Heart

value: Heart macrophages

value: Td+ macrophages

value: Sham

value: 10-12 weeks


title: cDMD-RF_1

description: biological replicate 1


title: cDMD-ES_1

description: biological replicate 1


title: MDA-MB-231 TMEM33 OE clone1 rep2

city: Madison

first: Wei

last: Xu

state: WI

address: 7459 WIMR II 1111 Highland Ave.

institute: UW-Madison

description: biological repeat 2

data_processing:
Each library was sequenced in single read mode, 1 x 50 bp, using the HiSeq4000 platform.
Sequencing reads were aligned to human genome (hg38) by STAR (version 2.5.2b)
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for Parental and PKM2 KO samples, and normalized differential expression levels of genes.

source_name: Breast cancer cell line

extract_protocol:
Fresh RNA was harvested using E.Z.N.A.® HP Total RNA Kit (#101414-852). TruSeq RNA Library Prep Kit v2 (#RS-122-2001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Breast

value: TMEM33 overexpression

value: MDA-MB-231 cells

value: lenti TMEM33 virus infection


title: MDA-MB-231 TMEM33 OE clone8 rep1

description: biological repeat 1


title: MDA-MB-231 TMEM33 OE clone1 rep3

description: biological repeat 3


title: cDMD-RF_2

description: biological replicate 2


title: UMG12 TERT KD Replicate 3

description:
Tert_3
Sequencing instrument Illumina HiSeq model number not provided by sequencing company; Illumina HiSeq 4000 used a default model.


title: MDA-MB-231 control rep3

description: biological repeat 3

value: TMEM33 WT

value: lenti vectrol virus infection


title: MDA-MB-231 TMEM33 OE clone8 rep3

description: biological repeat 3


title: UMG12 TRIM28 KD Replicate 1

description:
T28_1
Sequencing instrument Illumina HiSeq model number not provided by sequencing company; Illumina HiSeq 4000 used a default model.

value: TRIM28 Knockdown


title: DMD_1

description: biological replicate 1

value: Duchenne Muscular Dystrophy

value: Delta 44

value: iPSC-derived cardiomyocytes


title: MDA-MB-231 control rep1

description: biological repeat 1


title: MDA-MB-231 TMEM33 OE clone8 rep2

description: biological repeat 2


title: DMD_3

description: biological replicate 3


title: UMG12 TRIM24 KD Replicate 2

description:
T24_2
Sequencing instrument Illumina HiSeq model number not provided by sequencing company; Illumina HiSeq 4000 used a default model.

value: GFP tagged to hTERT mutant promoter allele

value: TRIM24 Knockdown


title: UMG12 TERT KD Replicate 1

description:
Tert_1
Sequencing instrument Illumina HiSeq model number not provided by sequencing company; Illumina HiSeq 4000 used a default model.

value: TERT Knockdown


title: UMG12 Mock Replicate 3

description:
M_3
Sequencing instrument Illumina HiSeq model number not provided by sequencing company; Illumina HiSeq 4000 used a default model.

value: Control


title: MDA-MB-231 PKM2KO rep2

description: biological repeat 2

value: PKM2 knockout


title: MDA-MB-231 PKM2KO rep3

description: biological repeat 3


title: MZ_12182_early [DJ-76]

city: Winston Salem

first: Ming

last: Leung

state: NC

address: 1 Medical Center Blvd

department: Comprehensive Cancer Center

institute: Atrium Health Wake Forest

data_processing:
library strategy: hMe-Seal
Processed leucocyte composition of MZ twin samples was obtained from HudsonAlpha Institue for Biotechnology (Illumina HumanMethylation 450K BeadChip)
hydroxymethylation reads were aligned to the hg19 using Bowtie2
Differentially hydroxymethylated regions of the monozygotic twin hydroxymethylation samples were identified, quantified, and compared using Methylaction (Bhasin et. Al. Nucleic Acids Res. 2016). Three comparisons using different combinations of covariates were made: 1. no covariates 2. All blood leucocytes excluding granulocytes 3. All blood leucocytes excluding granulocytes and age
A subset of the regions identified in the previous step was used by Methylaction to quantify the dizygotic twin hydroxymethylation samples.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with normalized hydroxymethylation levels of each region and differential significance when comparing discordant deaths.
Supplementary_files_format_and_content: Estimated relative proportion of leukocyte cell types within a sample.

source_name: monozygotic_twin_early death

growth_protocol: Whole blood was drawn from the antecubital vein into EDTA tubes after an overnight fast and immediately placed on ice. Buffy coats were obtained and used to extract DNA

extract_protocol:
Genomic DNA was isolated in digestion buffer (100 mM Tris-HCl, pH 8.5, 5 mM EDTA, 0.2% SDS, 200 mM NaCl), Proteinase K (Thermo Fisher cat# EO0491) treatment at 55 °C for overnight. The second day, phenol:chloroform:isoamyl alcohol (25:24:1 Saturated with 10 mM Tris, pH 8.0, 1 mM EDTA) (Sigma-Aldrich, cat# P-3803) was added to samples, mixed completely, and centrifuged for 10 min at 12,000 rpm. The aqueous layer solution was transferred into a new Eppen- dorf tube and precipitated with 600 mL isopropanol. The pellet was washed with 75% ethanol, air-dried, and eluted with Nuclease-Free Water (Ambion).
hMe-Seal assay (NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina + single end 50bp Hiseq 2000 Illumina sequencing)

tag: twin type

tag: twin pair

tag: discordant death (when compared their corresponding twin)

value: early death

tag: tissue/molecule

value: Buffy coat DNA samples extracted from whole blood

tag: molecule subtype

value: DNA hydroxymethylation


title: MZ_12182_late [DJ-75]

source_name: monozygotic_twin_late death

value: late death


title: DMD_2

description: biological replicate 2


title: MCF7 PKM2KO rep3

description: biological repeat 3

value: Breast

value: MCF7 cells

tag: treatment


title: MDA-MB-231 TMEM33 OE clone1 rep1

description: biological repeat 1

value: TMEM33 overexpression

value: MDA-MB-231 cells

value: lenti TMEM33 virus infection


title: MDA-MB-231 PKM2KO rep1

description: biological repeat 1


title: DZ_12189_early [DJ-77]

source_name: dizygotic_twin_early death


title: MCF7 PKM2KO rep1

description: biological repeat 1


title: DZ_12170_early [DJ-71]


title: DZ_12162_early [DJ-69]


title: MDA-MB-231 parental rep3

description: biological repeat 3

value: PKM2 WT

value: No treatment


title: MZ_12158_late [DJ-67]


title: MZ_12191_late [DJ-80]


title: MZ_12171_early [DJ-74]


title: MZ_12191_early [DJ-79]


title: Stiff1

city: Chongqing

first: chuanchuan

last: lin

state: China

address: Shayang Road, Shapingba distract,

institute: Chongqing University

description: Cells cultured in 18 kPa hydrogel for 48 h.

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v0.12.9.
Reads Per Kilobase of exon per Megabase of library size (RPKM) was performed with Cufflinks v2.1.1, aligned reads were counted with HTSeq.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: gene_fpkm.txt: Tab-delimited text file includes FPKM values for each Sample.

source_name: Bone Marrow

growth_protocol: Cells were cultured in Low glucose DMED medium which contained 10% (v/v) FBS and 1% (v/v) penicillin/ streptomycin.

extract_protocol: MSCs were isolated from hydrogel and the mRNA library constructed using QIAseq FX Single Cell RNA Library Kit (QIAGEN) according to the manufacturer.

treatment_protocol: MSCs cultured in soft (2 kPa) and stiff (18 kPa) SA hydrogel for 48 h.

value: Mesenchymal stem cells (MSCs)

value: 18 kPa hydrogel for 48 h

tag: intervention

value: Stiff


title: Stiff2


title: MCF7 parental rep3

description: biological repeat 3


title: DZ_12155_late [DJ-64]

source_name: dizygotic_twin_late death


title: DZ_12170_late [DJ-72]


title: MCF7 PKM2KO rep2

description: biological repeat 2


title: MCF7 parental rep2

description: biological repeat 2


title: MDA-MB-231 parental rep1

description: biological repeat 1


title: MZ_12171_late [DJ-73]


title: MDA-MB-231 control rep2

description: biological repeat 2

value: TMEM33 WT

value: lenti vectrol virus infection


title: DZ_12162_late [DJ-70]


title: DZ_12155_early [DJ-63]


title: MZ_12152_late [DJ-61]


title: Stiff3


title: DZ_12189_late [DJ-78]


title: Sample 6_Human cardiac immune cells

source_name: Heart immune cells

value: Heart

value: Heart immune cells

value: 46 years old

tag: subject status

value: Hypertrophic cardiomyopathy

tag: subject gender

value: male


title: MDA-MB-231 parental rep2

description: biological repeat 2

value: Breast


title: DZ_12157_early [DJ-66]

value: early death

value: Buffy coat DNA samples extracted from whole blood

value: DNA hydroxymethylation


title: DZ_12148_early [DJ-60]


title: MCF7 parental rep1

description: biological repeat 1

value: MCF7 cells


title: DZ_12148_late [DJ-59]

value: late death


title: MZ_12158_early [DJ-68]


title: siZ6_rep1_r1

city: Exeter

first: Steven

last: West

state: Devon

address: Stocker Rd

department: Living Systems Institute

country: United Kingdom

institute: University of Exeter

description:
single nucleotide bigwig coverage files were generated for total reads and separate stranded reads
siZ6_POOL_antisense.bigwig
siZ6_POOL_sense.bigwig

data_processing:
RNA-seq: Adapters were removed from nuclear RNA-seq reads using Trim Galore! v0.4.4 (wrapper tool for Cutadapt v1.15).
RNA-seq: Alignment of nuclear RNA-Seq reads with Hisat2 v2.1.0 to ensembl GRCh38.
RNA-seq: Properly mapped single-end reads were extracted and indexed using samtools v1.4.1.
RNA-seq: For stranded coverage analysis, sense and antisense reads were seperated from merged BAMs using samtools v1.4.1
RNA-seq: Bigwig files of nuclear RNA-seq reads were generated from BAM files using the bamCoverage of Deeptools v3.0.2
RNA-seq: Log2 files were created using BigWig compare (deepTools v3.5)
Supplementary_files_format_and_content: Bigwig files of nuclear RNA-seq reads represent normalised read coverage (RPKM) at a single nucleotide resolution across the genome.
ChIP-seq: Adapters were removed from nuclear RNA-seq reads using Trim Galore! V.0.6.5 (wrapper tool for Cutadapt v2.9).
ChIP-seq: Alignment of ChIP-Seq reads using BWA to ensembl GRCh38.
ChIP-seq: PCR duplicates were removed
ChIP-seq: Replicates were merged using bamtools v2.4.0.
ChIP-seq: Bigwig files of ChIP-Seq reads were generated from BAM files using the bamCoverage of Deeptools v3.4.2
ChIP-seq: Log2 files were created using Bam compare (deepTools v3.5)
Genome_build: GRCh38
Supplementary_files_format_and_content: Bigwig files of ChIP-Seq reads represent normalised read coverage (CPM) at a single nucleotide nucleotide across the genome.

molecule: nuclear RNA

growth_protocol: HCT116 cell lines were maintianed in DMEM with 10% fetal bovine serum, pen/strep at 37 °C and 5% CO2.

extract_protocol: Nuclear RNA was depleted of ribosomal RNA using Illumina Ribo-Zero Gold (Illumina #MRZE706). Library was constructed using Illumina TruSeq® Stranded Total RNA (Illumina #20020596)

treatment_protocol: The sample was transfected with a silencer select ZC3H6 siRNA 72h prior to collection in media without any pen/strep using Lipofectamine RNAiMAX (Life Technologies)

tag: genotype/variation

value: No variation

value: siZ6 treatment, nuclear RNA

value: Nuclear RNA


title: siZ4_Z6_rep2_r1

description:
single nucleotide bigwig coverage files were generated for total reads and separate stranded reads
none

treatment_protocol: The sample was transfected with a silencer select ZC3H4 and ZC3H6 siRNA 72h prior to collection in media without any pen/strep using Lipofectamine RNAiMAX (Life Technologies)

value: siZ4/Z6 treatment, nuclear RNA


title: Soft3

description: Cells cultured in 2 kPa hydrogel for 48 h.

value: Mesenchymal stem cells (MSCs)

value: 2 kPa hydrogel for 48 h

value: Soft


title: Soft2


title: Soft1


title: DZ_12157_late [DJ-65]


title: MZ_12152_early [DJ-62]


title: Sample 7_Human cardiac immune cells

tag: tissue

value: Heart

value: Heart immune cells

value: 5 months old

value: Congenital cardiomyopathy


title: siZ4_rep1_r1

description:
single nucleotide bigwig coverage files were generated for total reads and separate stranded reads
siZ4_POOL_antisense.bigwig
siZ4_POOL_sense.bigwig
RNAseq_Log2_siZ4_Vs_siCONT.bigwig

treatment_protocol: The sample was transfected with a silencer select ZC3H4 siRNA 72h prior to collection in media without any pen/strep using Lipofectamine RNAiMAX (Life Technologies)

value: siZ4 treatment, nuclear RNA


title: MZ_12136_early [DJ-55]

value: early death


title: siZ6_rep2_r1


title: DZ_12101_late [DJ-52]

value: Buffy coat DNA samples extracted from whole blood


title: siZ4_Z6_rep1_r1


title: DZ_12128_late [DJ-54]

value: DNA hydroxymethylation


title: siCONT_rep1_r1

description:
single nucleotide bigwig coverage files were generated for total reads and separate stranded reads
siCONT_POOL_antisense.bigwig
siCONT_POOL_sense.bigwig

treatment_protocol: The sample was transfected with a silencer select negative control siRNA 72h prior to collection in media without any pen/strep using Lipofectamine RNAiMAX (Life Technologies)

value: siCONT treatment, nuclear RNA


title: MZ_12136_late [DJ-56]

value: late death


title: DZ_12097_late [DJ-49]


title: DZ_12097_early [DJ-50]


title: CPSF30_R2_r1

description: single nucleotide bigwig coverage files were generated for total reads and separate stranded reads

treatment_protocol: Control: Treated for 3 h with ethanol (absolute 1ul/ml media).

value: CPSF30-mAID_P2A_[HygromycinR/NeomycinR]_SV40-pA; sleeping_beauty(TIR1; blasticidn).  Note that mAID-tagging CPSF30 is not expected to alter the behaviour of the cell line unless auxin treated

value: Control - mock treated (ethanol), nuclear RNA


title: siCONT_2_r1

value: No variation

value: Nuclear RNA


title: CPSF30_R2_IAA_r1

treatment_protocol: Auxin was added to cell media at a final concentration of 500 µM  3 h  prior to collection.

value: 3 Hr Auxin treatment, nuclear RNA


title: DZ_12101_early [DJ-51]


title: MZ_12095_late [DJ-48]


title: MZ_12095_early [DJ-47]


title: DZ_12073_late [DJ-46]


title: CPSF30_R1_IAA_r1