title: H-HDAC-3.A10

description: C1 CAGE


title: H-HDAC-3.A07

status: Public on Jun 30 2022

type: SRA

city: Yokohama

first: Andrew

middle: Tae-Jun

last: Kwon

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: IMS

country: Japan

institute: RIKEN

description: C1 CAGE

library_source: transcriptomic

data_processing:
Remove low quality and rDNA reads
Map to the human genome (hg38) using BWA version 0.5.9 (r16) with default parameters, except: : (1) maximum long deletion (-d) = 10 for bwa_aln and (2) maximum number of   alignments (-n) = 100 for bwa_samse
Convert mapped reads to CAGE Transcription Start Sites (CTSS) and read in using CAGEfightR package in R (4.0.3). For C1 CAGE, keep only those that are expressed in at least 3 samples. Merge reads within 20bp of one another.
Map processed reads to GENCODE v31 annotation to the nearest 1kbp up/100 bp down, and remove those overlapping known axons
Annotate enhancers using our custom enhancer set, and quantify raw expression counts by summing the overlapping reads
Assembly: hg38
Supplementary files format and content: *_CTSS.tar.gz: CAGE CTSS files (CAGE_Transcription Start Sites in BED format)
Supplementary files format and content: *_annotations.tar.gz: sample and CAGE tag cluster annotation tables
Supplementary files format and content: *_expression_tables.tar.gz: raw and normalized expression tables for CAGE tag clusters
Supplementary files format and content: gold_enhancers.bed.gz: BED file of the curated gold enhancer set

molecule: total RNA

organism: Homo sapiens

source_name: HepG2 cell line

growth_protocol: Cells were cultured in DMEM high glucose medium supplemented with 10% inactivated fetal bovine serum, 100 U/mL penicillin, 100 ug/mL streptomycin, and 1 mM sodium pyruvate.

extract_protocol:
Single cell RNA extraction and cDNA amplification were performed according to the C1 CAGE procedure deposited in Fluidigm’s Script Hub (https://www.fluidigm.com/c1openapp/scripthub/script/2015-07/c1-cage-1436761405138-3). For bulk CAGE, total RNA was extracted using RNeasy Mini Kit.
For C1 CAGE, the library was constructed following the same C1 CAGE procedure outlined in the above link. For bulk CAGE, libraries were constructed using the published nAnT-iCAGE protocol.
The prepared libraries were sequenced on Illumina HiSeq 2500 (50 nt single read).

treatment_protocol: Three treatment groups were made, with 1) untreated, 2) 1 uM TSA for 6 hours, and 3) 1 mM VPA for 6 hours.

tag: treatment

value: VPA


title: H-HDAC-3.A11

description: C1 CAGE


title: H-HDAC-3.A06

description: C1 CAGE

value: Control


title: H-HDAC-3.B06

description: C1 CAGE

value: TSA


title: H-HDAC-3.B09

description: C1 CAGE


title: H-HDAC-3.A03

description: C1 CAGE


title: H-HDAC-3.B05

description: C1 CAGE


title: H-HDAC-3.A01

description: C1 CAGE


title: H-HDAC-3.B01

description: C1 CAGE


title: H-HDAC-3.B11

description: C1 CAGE


title: H-HDAC-3.A12

description: C1 CAGE


title: H-HDAC-2.H09

description: C1 CAGE


title: H-HDAC-3.A04

description: C1 CAGE


title: H-HDAC-3.A08

description: C1 CAGE


title: H-HDAC-2.H06

description: C1 CAGE


title: H-HDAC-2.H07

description: C1 CAGE


title: H-HDAC-3.B04

description: C1 CAGE


title: H-HDAC-2.H05

description: C1 CAGE


title: H-HDAC-2.H04

description: C1 CAGE


title: H-HDAC-2.H03

description: C1 CAGE


title: H-HDAC-2.H12

description: C1 CAGE


title: H-HDAC-2.H02

description: C1 CAGE


title: H-HDAC-2.H08

description: C1 CAGE


title: H-HDAC-3.A02

description: C1 CAGE


title: H-HDAC-3.B03

description: C1 CAGE


title: H-HDAC-2.G11

description: C1 CAGE


title: H-HDAC-2.H10

description: C1 CAGE


title: H-HDAC-2.G12

description: C1 CAGE


title: US2N3_3

city: Stellenbosch

first: Anna-Maria

last: Oberholster

state: Western Cape

address: JC Smuts Building, Van der Bijl Street

department: Genetics

country: South Africa

institute: University of Stellenbosch

description: Bisulfite treated

library_source: genomic

data_processing:
Quality control with FastQC
Trimming, performed with Trimmomatic v0.39 (Bolger et al., 2014), HEADCROP:10 SLIDINGWINDOW:15:20 MINLEN:40 ILLUMINACLIP
Bismark (Krueger and Andrews, 2011) genome preparation
Bismark allignment, implementing Bowtie2 -L,-0.6,-0.8
Bismark methylation extraction, -p --no_overlap  --ignore_3prime 11 --ignore_r2 10 --no_header --cutoff 10 --gazillion
Genome_build: GCA_001186385.1
Supplementary_files_format_and_content: tab-delimited text files with 8 columns, 1:gene/intergenic, 2:gene/intergenic number, 3:contig #, 4:base position on contig, 5:total calls, 6:methylated call, 7:strandedness, 8:context

molecule: genomic DNA

organism: Diuraphis noxia

source_name: Whole organism

growth_protocol: All populations were maintained on the susceptible wheat cultivar "Byrd" prior to extraction

extract_protocol:
The QIAGEN DNeasy Blood & tissue Kit following the manufacturer’s recommended protocol for insect DNA extraction
Bisulfite conversion performed using the EZ DNA Methylation-Gold Kit (Zymo Research). The sequencing library was prepared using the Accel-NGS Methyl-Seq DNA Library Kit (Swift Biosciences)

treatment_protocol: The isolated population was established by isolating individual, neonate nymphs from their mothers before feeding occurred. These nymphs were allowed to establish new aphid colonies, free of facultative bacteria transmitted horizontally from mother to daughter during co-feeding.

tag: group

value: US2 (isolated)

tag: biotype


title: H-HDAC-2.H11

description: C1 CAGE


title: H-HDAC-3.A05

description: C1 CAGE


title: H-HDAC-2.G10

description: C1 CAGE


title: Cd_20_3

city: Guangzhou

first: fanwei

last: dai

state: Guangdong

address: The Sericulture and Agri-Food Research Institute, Guangdong Academy of Agricultural Sciences

country: China

data_processing:
For the raw data, adaptor sequences were eliminated, and distinct clean reads were identified.
Subsequently, clean reads and distinct clean reads were classified based on their copy numbers within the library, and the percentages of total clean and distinct reads were calculated.
The expression levels of each gene were estimated using the frequency of clean reads and then were normalized to reads per kilobase of exon per million reads mapped (RPKM).
Genome_build: Mulberry genome
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Morus alba var. atropurpurea

source_name: root_20mM CdCl2

growth_protocol: Seedlings of mulberry variety Yuesang10 were cultivated in soil in a greenhouse (day/night temperature, 25°C /18°C; relative air humidity, 50%–60%; natural light). After three months, mulberry seedlings were cut aerial parts to 10 cm and roots to 2 cm, and transferred to a polystyrol plate in a pot containing 10 L full-strength Hoagland solution in the greenhouse.

extract_protocol:
After plants were treated with different cadmium concentrations for 20 d, fresh roots were collected and frozened immediately in liquid nitrogen and stored at -80 oC until analysis. Total RNA in each sample was extracted using RNeasy Plant Mini kit reagents (Qiagen, Valencia, CA, USA). The concentration and quality of the resulting RNA were determined using an Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA).
RNA libraries were prepared for sequencing using standard protocols

treatment_protocol: After the plants in this solution for 3 days pretreatment, they were divided into six groups and five of these groups were stressed with different concentrations of CdCl2 (5, 10, 20mM). Full-strength Hoagland's solution without cadmium was used for treating the control plants. The nutrient solutions were aerated continuously and changed regularly at intervals of 5 d until the plants were harvested.

tag: cultivar

value: 20mM CdCl2

tag: tissue

value: root


title: US2N3_1

description: Bisulfite treated


title: H-HDAC-2.G08

description: C1 CAGE


title: Cd_20_2

department: The Sericulture and Agri-Food Research Institute

institute: Guangdong Academy of Agricultural Sciences


title: H-HDAC-2.G07

description: C1 CAGE


title: US2P2_3

description: Bisulfite treated

value: US2 (co-fed)


title: H-HDAC-2.G06

description: C1 CAGE


title: Cd_20_1


title: H-HDAC-2.H01

description: C1 CAGE


title: US2N3_2

description: Bisulfite treated


title: Cd_10_3

source_name: root_10mM CdCl2

value: 10mM CdCl2


title: US1P1_2

description: Bisulfite treated

value: US1 (co-fed)


title: US2P2_2

description: Bisulfite treated


title: US1P1_3

description: Bisulfite treated


title: Cd_5_3

source_name: root_5mM CdCl2

value: 5mM CdCl2


title: H-HDAC-2.G09

description: C1 CAGE


title: Cd_10_1


title: Cd_5_2


title: WT3-Retroperitoneal fat

city: Wen’jiang,Chengu

first: long

middle: ke

last: ren

state: Sichuan

address: Huimin road, 211#

department: 1	Institute of Animal Genetics & Breeding

institute: sichuan agriculture university

data_processing:
High-quality reads were obtained after removal of low-quality reads (with ≥ 10% unidentified nucleotides, > 10 nt aligned to the adapter with ≤ 10% mismatches, and with > 50% of bases with phred quality < 5), thereafter high-quality data were mapped to the pig reference genome (Sus Scrofa 11.1 downloaded from Ensembl) using STAR (v.2.6.0c) with parameters suggested by GENCODE. The mRN expression level (transcripts per kilobase million, TPM) of each sample was calculated with kallisto (v0.44.0); transcripts with TPM > 0.5 at least in one sample were considered to be expressed.
Genome_build: Sus Scrofa 11.1
Supplementary_files_format_and_content: Identified proteing coding transcript in each library with reads

organism: Sus scrofa

source_name: tissue

extract_protocol:
Three adult individuals for each group  were used. Animals were humanely killed to ameliorate suffering. Upon excised from the corpse, a piece of tissue fragments from five organs including liver,longissimus dorsi,psoas major,subcutaneous fat and retroperitoneal fat were placed immediately frozen in liquid nitrogen, and then stored at −80 °C until use. Total RNA were extracted using TRIZOL reagent (Life Technologies, Beijing, China),
For RNA sequencing, approximately 3 ug total RNA of each sample was used to construct transcriptome libraries following the manufacture’s standard procedures.

value: Retroperitoneal fat

tag: age

value: > 11 month

tag: genotype/variation

value: wild-type


title: WT2-Retroperitoneal fat


title: WT1-Retroperitoneal fat


title: US2P2_1

description: Bisulfite treated


title: Cd_0_2

value: non-treated


title: H-HDAC-2.G05

description: C1 CAGE


title: H-HDAC-2.G04

description: C1 CAGE


title: Cd_0_1


title: TG3-Retroperitoneal fat

value: transgenic


title: H-HDAC-2.G02

description: C1 CAGE


title: H-HDAC-2.G01

description: C1 CAGE


title: Cd_5_1


title: Cd_10_2


title: H-HDAC-2.G03

description: C1 CAGE


title: Cd_0_3


title: TG1-Retroperitoneal fat


title: H-HDAC-2.F07

description: C1 CAGE


title: H-HDAC-2.F06

description: C1 CAGE


title: H-HDAC-2.F10

description: C1 CAGE


title: TG2-Retroperitoneal fat


title: US1P1_1

description: Bisulfite treated


title: H-HDAC-3.B10

description: C1 CAGE


title: H-HDAC-2.F09

description: C1 CAGE


title: H-HDAC-2.F01

description: C1 CAGE


title: heart-OMA1_ASO2-1

type: RNA

city: Bethesda

first: Mario

middle: K.

last: Shammas

state: MD

address: 35 Convent Dr.

department: Neurogenetics Branch

country: USA

institute: National Institute of Neurological Disorders and Stroke, National Institutes of Health

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing:
Raw data was processed with Transcriptome Analysis Console
sst-rma-gene-full analyzed with Transcriptome Analysis Console

label: biotin

organism: Mus musculus

source_name: Heart

label_protocol: Standard Affymetrix protocol

growth_protocol: Mice were maintained on a 12-hour light/dark cycle with normal chow

extract_protocol: QIAGEN RNeasy Fibrous Tissue Mini Kit

treatment_protocol: Weekly subcutaneous injections of control or OMA1 ASOs dosed at 50 mpk

tag: genotype

value: 33 weeks

value: OMA1 ASO2

value: heart


title: WT3-Subcutaneous fat

value: Subcutaneous fat


title: H-HDAC-2.F04

description: C1 CAGE

value: Control


title: H-HDAC-2.F05

description: C1 CAGE


title: H-HDAC-2.F11

description: C1 CAGE


title: heart-OMA1_ASO2-2


title: WT2-Psoas major

value: Psoas major


title: WT2-Subcutaneous fat


title: H-HDAC-2.F12

description: C1 CAGE

value: VPA


title: WT1-Subcutaneous fat


title: heart-OMA1_ASO1-5

value: OMA1 ASO1


title: heart-OMA1_ASO1-2


title: heart-OMA1_ASO2-3


title: heart-OMA1_ASO1-1


title: WT3-Psoas major


title: heart-OMA1_ASO1-4


title: TG2-Subcutaneous fat


title: H-HDAC-2.F03

description: C1 CAGE

value: TSA


title: H-HDAC-2.F08

description: C1 CAGE


title: H-HDAC-2.E10

description: C1 CAGE


title: heart-CTRL_ASO-4

value: Control ASO


title: H-HDAC-3.B08

description: C1 CAGE


title: TG3-Subcutaneous fat


title: H-HDAC-2.E12

description: C1 CAGE


title: heart-OMA1_ASO1-3


title: heart-CTRL_ASO-5


title: H-HDAC-2.F02

description: C1 CAGE


title: TG1-Subcutaneous fat


title: WT3-Longissimus dorsi

value: Longissimus dorsi


title: TG1-Psoas major


title: H-HDAC-2.E08

description: C1 CAGE


title: H-HDAC-2.E06

description: C1 CAGE


title: H-HDAC-2.E11

description: C1 CAGE


title: H-HDAC-2.E09

description: C1 CAGE


title: TG2-Psoas major


title: WT1-Psoas major


title: TG3-Psoas major


title: H-HDAC-2.E07

description: C1 CAGE


title: WT2-Longissimus dorsi


title: heart-CTRL_ASO-3


title: heart-CTRL_ASO-1


title: heart-CTRL_ASO-2


title: H-HDAC-2.E05

description: C1 CAGE


title: WT1-Longissimus dorsi


title: heart-20wkOMA1KO_C10S59L-4

extract_protocol: Direct-zol RNA Miniprep Kit

treatment_protocol: No treatments

value: 20 weeks

tag: genotype (chchd10 status)

tag: genotype (oma1 status)

value: Homozygous

tag: gender

value: Male


title: heart-20wkOMA1KO_C10S59L-2

value: Female


title: TG3-Longissimus dorsi

value: > 11 month


title: TG2-Longissimus dorsi

value: transgenic


title: TG1-Longissimus dorsi


title: heart-20wkOMA1KO_C10S59L-3


title: WT1-Liver

value: liver

value: wild-type


title: H-HDAC-2.D12

description: C1 CAGE


title: H-HDAC-2.E01

description: C1 CAGE


title: WT2-Liver


title: H-HDAC-2.E03

description: C1 CAGE


title: H-HDAC-2.E02

description: C1 CAGE


title: WT3-Liver


title: H-HDAC-2.E04

description: C1 CAGE


title: H-HDAC-2.D11

description: C1 CAGE


title: TG3-Liver


title: H-HDAC-2.D10

description: C1 CAGE


title: H-HDAC-2.D08

description: C1 CAGE


title: TG1-Liver


title: H-HDAC-2.D07

description: C1 CAGE


title: heart-20wkOMA1het_C10S59L-1

value: Heterozygous

value: heart


title: heart-20wkOMA1KO_C10S59L-1


title: heart-20wkOMA1het_C10S59L-4


title: H-HDAC-2.D06

description: C1 CAGE


title: heart-20wkOMA1het_C10S59L-2


title: heart-20wkOMA1het_C10S59L-3


title: Female EC-Myc KO HFC 413

city: Boca Raton

first: Claudia

last: Rodrigues

state: Florida

address: 777 Glades Road, BC-71, Room 224

department: Biomedical Science

institute: Florida Atlantic University

data_processing:
FASTQ files were generated from raw base calls using the Zebra Call software by BGI. FastQC was used to check the quality of raw sequencing data.
Sequenced reads were aligned to GRCm38 mouse reference genome using Elysium alignment server with default settings.
Raw counts were converted to counts per million (CPM) values using cpm function in edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene of male samples
Supplementary_files_format_and_content: Matrix table with CPM values for every gene of male samples
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene of female samples
Supplementary_files_format_and_content: Matrix table with CPM values for every gene of female samples

source_name: Liver

extract_protocol:
Livers were harvested and snap frozen in liquid nitrogen. RNA extraction and quality control were performed by BGI. Only qualified samples were used for library construction.
RNA libraries were prepared by BGI for sequencing using standard DNBSEQ protocols

tag: strain

value: Liver

value: 13 weeks

value: EC-Myc KO

value: High-fat/cholesterol diet


title: TG2-Liver


title: H-HDAC-2.D05

description: C1 CAGE

value: TSA


title: heart-20wkOMA1KO_C10WT-2

value: WT


title: Female EC-Myc KO CTD 317

value: Low fat control diet


title: H-HDAC-2.D09

description: C1 CAGE

value: VPA


title: heart-20wkOMA1KO_C10WT-3

value: 20 weeks

value: Homozygous


title: Female EC-Myc KO CTD 309

value: Female


title: Female EC-Myc KO HFC 412


title: heart-20wkOMA1KO_C10WT-1

value: Male


title: Female EC-Myc KO CTD 307


title: H-HDAC-2.D03

description: C1 CAGE

value: Control


title: H-HDAC-2.D04

description: C1 CAGE


title: H-HDAC-2.D02

description: C1 CAGE


title: heart-20wkOMA1het_C10WT-3


title: Female CT HFC 512


title: H-HDAC-2.D01

description: C1 CAGE


title: H-HDAC-2.C12

description: C1 CAGE


title: heart-20wkOMA1het_C10WT-4


title: Female CT HFC 420


title: Female CT HFC 510


title: heart-20wkOMA1het_C10WT-2


title: H-HDAC-2.C10

description: C1 CAGE


title: Female CT CTD 318


title: heart-20wkOMA1KO_C10WT-4


title: Female CT CTD 308


title: Female CT CTD 306


title: heart-14wkOMA1KO_C10G58R-2

value: 14 weeks


title: heart-14wkOMA1KO_C10G58R-1


title: heart-20wkOMA1het_C10WT-1


title: H-HDAC-2.C09

description: C1 CAGE


title: heart-14wkOMA1KO_C10G58R-3


title: heart-14wkOMA1het_C10G58R-4


title: H-HDAC-2.C07

description: C1 CAGE


title: D7-KO-2

city: Shanghai

first: Qian

last: Cai

address: No.130 Dongan road

department: Immunology

institute: Fudan University

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using SOAPnuke, then mapped to reference whole genome using bowtie.
Mapped reads were count, and Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: 2.5% DSS_d7_Colon epithelial cells

extract_protocol:
Total RNAs from IECs of DSS treated Rarres2-/- or littermate WT mice were isolated with trizol
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: Colon epithelial cells


title: heart-14wkOMA1KO_C10G58R-4


title: H-HDAC-2.C06

description: C1 CAGE


title: H-HDAC-2.C08

description: C1 CAGE


title: heart-14wkOMA1het_C10G58R-2

value: Heterozygous


title: H-HDAC-2.C05

description: C1 CAGE


title: heart-14wkOMA1het_C10G58R-3

value: heart


title: H-HDAC-2.C04

description: C1 CAGE


title: H-HDAC-2.C02

description: C1 CAGE


title: D7-WT-3


title: heart-14wkOMA1het_C10G58R-1


title: D2-KO-3

source_name: 2.5% DSS_d2_Colon epithelial cells


title: D7-WT-1


title: D7-WT-2


title: H-HDAC-2.C03

description: C1 CAGE


title: H-HDAC-2.C01

description: C1 CAGE


title: D2-KO-2


title: H-HDAC-2.C11

description: C1 CAGE


title: H-HDAC-2.B11

description: C1 CAGE


title: EPZ5676, rep2

city: Yiwu

first: keren

last: cheng

state: Zhejiang

address: 1575 chouzhou bei road

department: School of Medicine

institute: Zhejiang University

data_processing:
Basecalls were performed using bcl2fastq2 v2.20.0.422
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the UCSC mm10 genome using Rsubread. Only uniquely mapping reads with at most one mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (1X genome size) and reformatted in the bigWig file format.
Peaks were called uing MACS v3 with the significance cut-off q-value <=0.01
Assembly: bigWig files were generated using deeptools. boradPeak files were generated using MACS v3 with default settings.
Supplementary files format and content: mm10
Supplementary files format and content: bigWig, bed

source_name: Spermatogonia Stem Cells

growth_protocol: testicular cells were prepared from 7-day-old B6.129S7-Gt(ROSA)26Sor/J mice (Jackson Laboratory) that express a LacZ (β-galactosidase) reporter gene in all tissues, by enzymatic digestion using trypsin-EDTA (Thermo Fisher Scientific). Germ cells were cultured on SNL 76/7 feeders (from Allan Bradley, The Welcome Trust Sanger Institute) in a serum-free medium with 10 ng/ml GDNF (R&D Systems) and 0.5 ng/ml FGF2 (Corning) {{1994 Kubota,H. 2020;}}. After two months in culture, 1105 clump-forming cells were seeded on SNL-feeder cells in 24-well plates with 2 µM EPZ5676 (Cayman Chemical) or DMSO (Sigma-Aldrich) as a vehicle control. Medium was changed every 2—3 days, and the cells were subcultured every 7 days.

extract_protocol:
Mouse SSCs were cultured in the presence or absence of EPZ5676 for 7 days. SSCs were resuspended at 1 million per ml in PBS and crosslinked with formaldehyde (INSERT) at a final concentration of 1% for 10 min at room temperature (RT). The crosslinking reaction was stopped by adding glycine to a final concentration of 0.125 M for 5 min at RT. All following buffers were supplemented with protease inhibitors (Complete Mini, Roche or Halt, Thermo Fisher Scientific). Cells were washed twice in ice cold PBS and lysed in ChIP lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl, pH8.1).
NEBNext Ultra II DNA Library Prep kit for Illumina (E7645S, NEB) by following the manufacturer’s instructions

tag: cell line

value: Spermatogonia Stem Cells

tag: chip antibody

value: H3K79me2 antibody (ab3594, Abcam)


title: D2-KO-1


title: EPZ5676, rep1


title: heart-14wkOMA1KO_C10WT-3


title: D2-WT-3


title: Control, rep2

value: control


title: H-HDAC-2.B10

description: C1 CAGE


title: heart-14wkOMA1het_C10WT-4


title: heart-14wkOMA1het_C10WT-2


title: heart-14wkOMA1het_C10WT-3


title: heart-14wkOMA1KO_C10WT-2


title: heart-14wkOMA1KO_C10WT-1


title: H-HDAC-2.B09

description: C1 CAGE


title: EPZ5676, input, rep2


title: D2-WT-2


title: D2-WT-1


title: H-HDAC-2.B06

description: C1 CAGE


title: Control, rep1


title: D0-KO-1

source_name: untreated_d0_Colon epithelial cells

value: untreated


title: H-HDAC-2.B08

description: C1 CAGE


title: EPZ5676, input, rep1


title: D0-KO-2


title: heart-14wkOMA1het_C10WT-1


title: control, input, rep2


title: H-HDAC-2.B12

description: C1 CAGE


title: H-HDAC-2.B03

description: C1 CAGE


title: D0-KO-3


title: H-HDAC-2.B04

description: C1 CAGE

value: TSA


title: control, input, rep1


title: H-HDAC-2.B05

description: C1 CAGE


title: D0-WT-3


title: colonic IECs L_KO4

city: Worcester

first: Katherine

middle: A

last: Fitzgerald

state: Massachusetts

address: 364 Plantation Street

department: Medicine

institute: Umass Chan Medical

data_processing:
Illumina BaseSpace Dragon Analysis was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and ribosomal RNA reads were removed by Bowtie. Reads were mapped to the mouse referen genome GENCODE mm10 using STAR.
Count data was analyzed by DESeq2 (parametric, Wald) comparing WT and HNF4A IEC-KO samples in the ileum and colon respectively.
Genes with a greater than 2-fold change and a smaller than 0.01 adjusted p value were considered differentially expressed.
Assembly: mm10 (GENCODE)
Supplementary files format and content: matrix tables include MRN normalized value for each sample

source_name: Intestinal epithelial cells

growth_protocol: Animals were maintained in the specific-pathogen-free facility. Hnf4a fl/fl and Hnf4a fl/fl Villin-Cre mice were cohoused.

extract_protocol:
Total RNA was extracted using QIAGEN RNeasy micro kit. RNA was assesed by Quibit fluorometer and fragment analyzer.
Library was prepared using Illumina Stranded mRNA Prep kit and resulting libraries were assesed by Qubit fluorometer and fragment analyzer.

treatment_protocol: Intestinal pieces were incubated in dissociation buffer (HBSS supplemented with 2.5 mM EDTA, 1 mM HEPES, 1 mM dithiothreitol and 5% FCS) at 37 oC, 250 rpm for 30 mins. Cells were passed through a 70 um cell strainer and further flow sorted for live EPCAM+CD45-. Sorted cells were collected directly into RLT lysis buffer.

value: Colon

value: post natal day 21

value: Hnf4a fl/fl Villin-Cre


title: colonic IECs L_KO3


title: D0-WT-2


title: D0-WT-1


title: Male EC-Myc KO HFC 539

value: Liver

value: 13 weeks

value: EC-Myc KO

value: High-fat/cholesterol diet


title: colonic IECs L_KO2


title: colonic IECs L_WT3

value: Hnf4a fl/fl


title: colonic IECs L_KO1


title: H-HDAC-2.A09

description: C1 CAGE

value: Control


title: H-HDAC-2.B01

description: C1 CAGE


title: colonic IECs L_WT4


title: Male EC-Myc KO CTD 304

value: Male

value: Low fat control diet


title: H-HDAC-2.A10

description: C1 CAGE

value: VPA


title: Male EC-Myc KO HFC 414


title: Male EC-Myc KO CTD 311


title: Male EC-Myc KO HFC 540


title: H-HDAC-2.A12

description: C1 CAGE


title: Male EC-Myc KO HFC 415


title: Male EC-Myc KO CTD 298


title: colonic IECs L_WT1


title: ileal IECs S_KO4

value: Ileum


title: H-HDAC-2.A08

description: C1 CAGE


title: H-HDAC-2.A07

description: C1 CAGE


title: Male EC-Myc KO CTD 303


title: H-HDAC-2.A06

description: C1 CAGE


title: ileal IECs S_KO3


title: ileal IECs S_KO2


title: ileal IECs S_WT4


title: colonic IECs L_WT2


title: Male CT HFC 543


title: ileal IECs S_WT3


title: ileal IECs S_WT2


title: H-HDAC-2.A11

description: C1 CAGE


title: Male CT CTD 320


title: Male CT HFC 418


title: ileal IECs S_KO1


title: Male CT HFC 416


title: Male CT HFC 417


title: H-HDAC-2.A04

description: C1 CAGE


title: H-HDAC-2.A03

description: C1 CAGE


title: cecal IECs KO1

data_processing:
Illumina BaseSpace Dragon Analysis was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and ribosomal RNA reads were removed by Bowtie. Reads were mapped to the mouse referen genome GENCODE mm10 using STAR.
Count data was analyzed by DESeq2 (parametric, Wald) comparing WT and HNF4A IEC-KO samples.
Genes with a greater than 2-fold change and a smaller than 0.01 adjusted p value were considered differentially expressed.
Assembly: mm10 (GENCODE)
Supplementary files format and content: matrix tables include MRN normalized value for each sample

growth_protocol: Animals were maintained in the specific-pathogen-free facility. Littermate Hnf4a fl/fl and Hnf4a fl/fl Villin-Cre mice were cohoused.

extract_protocol:
Total RNA was extracted using QIAGEN RNeasy micro kit. RNA was assesed by Quibit fluorometer and fragment analyzer.
Library was prepared using TruSeq Stranded Total RNA kit (Illumina) and resulting libraries were assesed by Qubit fluorometer and fragment analyzer.

treatment_protocol: Mice were orally infected with 2.60x108 CFU salmonella (SL1344, no streptomycin pretreatment) for 48 hours. Intestinal pieces were incubated in dissociation buffer (HBSS supplemented with 2.5 mM EDTA, 1 mM HEPES, 1 mM dithiothreitol and 5% FCS) at 37 oC, 250 rpm for 30 mins. Cells were passed through 70 um cell strainer and further flow sorted for live EPCAM+CD45-. Sorted cells were collected directly into RLT lysis buffer.

value: Cecum

value: 9 weeks old


title: H-HDAC-1.H10

description: C1 CAGE


title: H-HDAC-1.H11

description: C1 CAGE


title: Male CT CTD 313


title: ileal IECs S_WT1


title: D7-KO-1

value: Colon epithelial cells


title: Male CT CTD 305


title: 3264 cells,shB2M-2

city: Chapel Hill

first: Daqi

last: Li

address: 450 West Dr

institute: Univerity of North Carolina at Chapel Hill

data_processing:
RNA sequencing was performed using BGISEQ-500 platforms. FASTQ sequencing reads were trimmed using Trim Galore (RRID:SCR_011847), and transcript quantification was performed using Salmon with the quasi-mapping mode
Assembly: hg38
Supplementary files format and content: FPKM values for each Sample

source_name: glioblastoma

extract_protocol:
Total RNA was extracted with Trizol reagent (Takara) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: glioblastoma

value: glioma stem cells


title: H-HDAC-1.H12

description: C1 CAGE


title: cecal IECs KO2


title: cecal IECs WT2


title: 3264 cells,shB2M-1


title: cecal IECs KO3


title: H-HDAC-1.H09

description: C1 CAGE


title: D7-KO-3


title: cecal IECs WT1


title: H-HDAC-2.A02

description: C1 CAGE

value: TSA


title: H-HDAC-1.H08

description: C1 CAGE


title: Male CT CTD 301


title: cecal IECs WT3


title: H-HDAC-2.A05

description: C1 CAGE


title: H-HDAC-1.H06

description: C1 CAGE


title: H-HDAC-1.H07

description: C1 CAGE


title: H-HDAC-1.H04

description: C1 CAGE


title: 3264 cells,shControl-1


title: MT2_B1

city: Santa Cruz

first: Angela

middle: N

last: Brooks

state: CA

address: 1156 High Street

department: Biomolecular Engineering

institute: University California Santa Cruz

description:
RT using SmartSeq2
mut2_mt_b1

data_processing:
Albabacore version 2.1.0 was used for basecalling with the options --flowcell FLO-MIN106 and --kit SQK-LSK108.
Sequenced reads were trimmed for adaptor sequence using Porechop.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: abundance measurement; FLAIR GTF annotation file

molecule: polyA RNA

source_name: HBEC3kt MT2 cell isolate

extract_protocol:
RNA was harvested using Trizol reagent. 1ug if RNA was reverse transcribed using Smart-Seq2 approach (polyA primed), and cDNA was sequencing using Oxford Nanopore minION using 1D sequencing approach.
RNA libraries were prepared for sequencing using standard Oxford Nanopore 1D suencing approaches (SQK-LSK108)

value: human bronchial epithelial cells (HBEC)

value: U2AF1 S34F


title: MT2_B2

description:
RT using SmartSeq2
mut3_mt_b2


title: MT1_B1

description:
RT using SmartSeq2
mut1_mt_b1

source_name: HBEC3kt MT1 cell isolate


title: 4121 cells,shB2M-1


title: H-HDAC-1.H05

description: C1 CAGE


title: 4121 cells,shControl-2


title: H-HDAC-1.H03

description: C1 CAGE


title: WT2_B2

description:
RT using SmartSeq2
wt3_wt_b2

source_name: HBEC3kt WT2 cell isolate

value: wild type


title: H-HDAC-1.H02

description: C1 CAGE

source_name: HepG2 cell line


title: WT2_B1

description:
RT using SmartSeq2
wt2_wt_b1


title: WT1_B1

description:
RT using SmartSeq2
wt1_wt_b1

source_name: HBEC3kt WT1 cell isolate


title: 4121 cells,shB2M-2


title: M99.VTP

city: Milano

first: Gualtiero

middle: Ivanoe

last: Colombo

address: Via Carlo Parea, 4

country: Italy

institute: Centro Cardiologico Monzino IRCCS

data_processing:
We mapped all reads to the Human genome version HG38/GRCh38.99, downloaded from the Ensembl database, using a 2-steps approach. First, we aligned reads against the whole genome, by STAR (v.2.7.0f); then, the unmapped reads were locally mapped by Bowtie2 (version 2.3.5). We set the default parameters for both tools, except for --chimSegmentMin 18, --chimScoreMin 12 (STAR) and --local --very-sensitive-local, -q, --mm (Bowtie2).
Gene expression quantification was performed by the featuresCount tool (v. 1.6.4), taking into account genes annotated in the GRCh38.99 release.
Assembly: GRCh38.99
Supplementary files format and content: Tab-delimited text files include raw counts for each Sample. The header of the files reports gene name,  sample identifiers.

source_name: cardiospheres derived primitive cardiac stromal cells

growth_protocol: Right atrial appendage of patients undergoing aortic valve substitution and/or coronary bypass grafting was fragmented and let to attach onto the bottom of tissue culture dishes in Iscove’s modified Dulbecco’s medium (IMDM) supplemented with 20% Hyclone characterized Fetal Bovine Serum (FBS), 1% penicillin-streptomycin, 1% L-glutamine and 0.1mM 2-mercaptoethanol. Explant derived-cells were cultured onto Poly-D-Lysine coated dishes for primary cardiosphere formation in the following media: 35% IMDM/65% DMEM/F-12 Mix, 3.5% Hyclone characterized FBS, 1% penicillin streptomycin, 1% L-glutamine, 0.1mM 2-mercaptoethanol, 1 unit/ml thrombin, 1:50 B-27, 80 ng/ml bFGF, 25 ng/ml EGF, and 4 ng/ml cardiotrophin-1. Primary cardiospheres were then dissociated and cSt-Cs were plated onto Fibronectin-coated dishes and characterized with flow cytometry for antigenic expression of CD29, CD31, CD44, CD90, CD105 and CD144.

extract_protocol:
Total RNA was isolated from 6 independent cardiac stromal cells (cSt-Cs) cultured ±TGF-β ±VTP using TRIzol, and precipitated through ammonium acetate/ethanol method.
Poly(A)+ RNA enrichment followed the Dynabeads mRNA Purification Kit protocol (Thermo Fisher Scientific). Libraries were prepared and pooled together (6 samples per sequencing run) using multiplex library RNA Barcoding reagents and Total RNA-Seq Kit v2 (Thermo Fisher Scientific).

treatment_protocol: cSt-Cs were seeded on glass slides and treated with TGF-β [10 ng/mL] in presence or the absence of Verterporfin [10 μM] for 72 hours.

value: VTP

tag: cell line_id

tag: sequencing chip

tag: sequencing barcode


title: 30 dpf Octopus Hatchlings

city: Abu Dhabi

first: Kirsten

last: Sadler Edepli

state: Abu Dhabi

department: Biology

country: United Arab Emirates

institute: New York University Abu Dhabi

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads where first assessed for quality using FastQC v0.11.5. Trimmomatic v0.36 was used for quality trimming and adapter sequence removal, with the parameters (ILLUMINACLIP: trimmomatic_adapter.fa:2:30:10 TRAILING:3 LEADING:3 SLIDINGWINDOW:4:15 MINLEN:36)
The dataset from hatchling was also processed with Fastp in order to remove poly-G tails and Novaseq/Nextseq specific artifacts. Following the Fastp quality trimming, the reads were assessed again using FastQC
Quality trimmed reads were used to produce psuedoalignments using Kallisto, and quantification was assessed with the --bias flag using the reference O. bimaculoides genome (PRJNA270931) and its corresponding annotation
The resulting transcripts per kilobase per million (TPMs) from the pseudo-counts were used for further downstream analysis
Genome_build: PRJNA270931
Supplementary_files_format_and_content: .tsv file containing pseudo-counts (TPMs) for each transcript

organism: Octopus bimaculoides

source_name: 30 dpf whole body hatchling

growth_protocol: Animals were catched from wild and manteined in husbandy accordingly to the current policy for the use of cephalopods at Marine Biology Laboratories (MBL, https://www.mbl.edu/policies/files/2018/07/J1.10-CEPH-Policies-Procedures-Jan-1-31-2020-fillable-form.pdf).

extract_protocol:
For each sample, tissues stored at -80°C were ground in liquid nitrogen using a mortar placed in dry ice. Resulting powder was aliquoted and 15 mg of this powder was used to extract  RNA. RNA was extracted using Trizol (Invitrogen) following the manufacturer’s instructions with some modifications. Briefly, during precipitation in isopropanol, 10 µg of Glycoblue (Thermo Fisher Scientific) was added and precipitation was performed overnight at -20°C followed by 1 hour centrifuge at 12000g at 4°C. RNA was resuspended in water . RNA was treated by DNAse I for 30 minutes at 37 °C followed by RNA purification (RapidOut DNA Removal Kit – Thermo Fisher Scientific).
RiboZero was used to remove ribosomal RNA and the remaining sample was used for library preparation according to manufacturer’s instructions (Illumina) from 250 ng of RNA. Libraries were sequenced on NextSeq550 (Illumina) to obtain 150 bp paired end reads.

treatment_protocol: Animals were euthanized by overdose of ethanol and tissues were immediately collected, flash frozen in liquid nitrogen, and stored at -80°C.

tag: Sex

tag: developmental stage

value: 30 dpf


title: M99.TGFb

value: cardiospheres derived primitive cardiac stromal cells

tag: treatment

value: TGFb


title: Octopus Adult Arm Left 1 Proximal

source_name: Transverse section of adult arm, collected 5.5  cm from the arm tip

value: Male

value: Adult


title: H-HDAC-1.G10

description: C1 CAGE


title: H-HDAC-1.G11

description: C1 CAGE

value: Control


title: M99.CTRL

value: CRTL


title: M89.VTP


title: M89.TGFb_VTP

value: TGFB+VTP


title: H-HDAC-1.H01

description: C1 CAGE


title: M99.TGFb_VTP


title: H-HDAC-1.G08

description: C1 CAGE


title: H-HDAC-1.G06

description: C1 CAGE


title: M81.VTP


title: 4121 cells,shControl-1

tag: tissue


title: H-HDAC-1.G09

description: C1 CAGE


title: heart-14wkOMA1KO_C10WT-4

tag: age

value: 14 weeks

value: WT

value: Homozygous

value: Female

value: heart


title: M81.TGFb_VTP


title: H-HDAC-1.G12

description: C1 CAGE

value: VPA


title: M89.CTRL


title: M89.TGFb


title: H-HDAC-1.G07

description: C1 CAGE


title: H-HDAC-1.G05

description: C1 CAGE


title: L1 Volcano + Acanthamoeba Rep4

city: Christchurch

first: Heather

last: Hendrickson

department: Biological Sciences

country: New Zealand

institute: University of Cantebury

data_processing:
reads were aligned to the Acanthamoeba reference genome (Acanthamoeba castellanii strain NEFF GCA_000313135.1) using HiSat2
unused reads were then aligned to the bacterial reference genome (Pseudomonas fluorescens SBW25 GCA_000009225.1) using Bowtie2
Sequence reads were assigned to genomic features using featureCounts
Differential expression using GLM and count normalisation was calculated with edgeR, Counts were normalised by library size (counts per million, CPM) with log2 transformation.
Assembly: GCA_000313135.1, GCA_000009225.1
Supplementary files format and content: tab-delimited text files include CPM values per sample

organism:
Pseudomonas fluorescens
Acanthamoeba sp.

source_name: Bacteria and Acanthamoeba

growth_protocol: Individual colonies of bacterial strains pre-cultured on LB agar were homogenised in LB broth and spread in single lines across PM agar plates using a 1ul transfer loop. Plates were allowed to dry before applying 2 ul of suspension containing ~103 Acanthamoeba cysts µl-1 at one end of the bacterial line. Plates were incubated at 28˚C for up to 1 week and the interaction zone was collected once the amoeba had formed a visible clearing. Pseudomonas fluorescens SBW25 strains were collected with Acanthamoeba from the bacteria-protozoa interaction zone and alone from the opposite end of the culture line with a transfer loop and immediately homogenised in RNA shield (n=4

extract_protocol:
Total RNA was extracted from bacterial and amoebae cells using the Quick-RNA MiniPrep Kit (Zymo Research, USA)
Preparations were dried in GenTegra RNA tubes according to manufacturer’s instructions (Gentegra, USA) and sent to the Microbial Genome Sequencing (MiGS, USA) Center for Illumina Stranded RNA library preparation with RiboZero Plus rRNA depletion and sequencing on the NextSeq 550 platform.

value: SBW25 L1VOL + Acanthamoeba Sp


title: H-HDAC-1.G02

description: C1 CAGE


title: M81.TGFb


title: Leg, 0month, uninjured

city: Lyon

first: Mathilde

last: PARIS

address: 32-34 Av. Tony Garnier

country: France

institute: CNRS

description: 10x genomics

library_source: transcriptomic single cell

data_processing:
Reads were mapped to the P. hawaiensis genome version Phaw_5.0 using the Cell Ranger Software Suite 6.0.1 (10x Genomics; (Zheng et al., 2017)). Cell Ranger output included lists of features, barcodes and matrices for intronic genomic features (corresponding to putative genes, cells and read counts, respectively). Subsequent analyses were performed using the R package Seurat v4 (Hao et al., 2021).
Assembly: Phaw_5.0
Supplementary files format and content: All files named “*_matrix.mtx.gz”: tab-delimited value file of the count matrix for each gene and each barcode.
Supplementary files format and content: All files named “*cell_containing_barcodes.txt.gz”: tab-delimited value file listing the barcodes that have  been filtered a posteriori to contain cells.
Supplementary files format and content: All files named “*_barcodes.tsv.gz”: tab-delimited value file listing the barcodes.
Supplementary files format and content: Phaw_exon_annotation.gtf.gz : tab-delimited value file listing the gene structures mapped on the Phaw_5.0 genome assembly.
Supplementary files format and content: Phaw_intron_annotation.gtf.gz : tab-delimited value file listing the genome-wide intron coordinates extrapolated from the file Phaw_exon_annotation.gtf.gz and used for the mapping of reads to the genome. The introns are called “exons” so that they are taken into account by CellRanger for building the count matrix.

molecule: nuclear RNA

organism: Parhyale hawaiensis

source_name: leg

extract_protocol:
For each snRNAseq dataset we collected a pool of 12-16 thoracic T4 and T5 legs from large adult males. The smallest specimens had a body length of ~9 mm (estimated age >12 months) and the average had a body length of ~11 mm (estimated age >18 months). The legs were amputated at the proximal end of the basis (excluding the gills and the coxal plates) using a microsurgical knife (Electron Microscopy Sciences, #72047-30) under anaesthesia in 0.02% clove oil. To compare regenerated and intact legs, T4 and T5 thoracic legs from one side of the animal were ampu- tated and allowed to regenerate and to grow until ~2 months (8 weeks) after amputation in one pool of individuals, or ~6 months (24 weeks) after amputa- tion in a separate pool. The contralateral legs were left intact and used as controls. We then collected the sets of regenerated and control T4 and T5 legs by cutting them off at the basis, and dissected them (cut the podomeres lengthwise) in a chilled hypotonic buffer containing 250 mM sucrose, 25 mM KCl, 5 mM MgCl2, 10 mM Tris buffer pH 8.0 and 1 μM DTT and supplemented with 1x protease inhibitor (Sigma, #11873580001), 0.4 U/μl RNasein (Invitrogen, #AM2682), 0.2 U/μl SUPERase-In RNase inhibitor (Invitrogen, #AM2694), 1 mM spermine and 0.1 M spermidine (modified from (Krishnaswami et al., 2016)). The tissue was extruded from the cuticle by gently scraping and peeling using a microsurgical blade and fine forceps (Fine Science Tools, #10316-14 and #11251-20) under a dissecting stereoscope. Triton X-100 was then added to a final concentration of 0.3 % and the tissues were mechan- ically disrupted by gently pipetting 25 times through a 200 μl filter tip with a cut tip. These steps were carried out in 300 μl of buffer, in the lid of a 5 ml DNA LoBind tube (Eppendorf, #0030108302) kept cold on the surface of a frozen metal plate. The disrupted tissue samples were then transferred to a 1.5 ml DNA LoBind Eppendorf tube (Ependorf, #0030108051), and large pieces of cuticle were let to settle down. The supernatant containing dissociated nuclei was transferred to a new LoBind tube, in which 600 μl fresh hypotonic buffer were added. The nuclei were collected by centrifugation at 500 rcf at 4 ̊C for 6 minutes on a 5424 R Eppendorf microcentrifuge. Centrifugation was kept to a minimum, which result- ed in a loose pellet, because longer or faster centrifu- gations result in lower quality nuclei. The supernatant was discarded and the pellet was washed with 600 μ l 1x Dulbecco's phosphate-buffered saline (DPBS) supplemented with 2% bovine serum albumin (BSA). After a second centrifugation, all the supernatant except 25 μL was removed and an equal volume of 3x DPBS with 2% BSA was added to reach a final concentration of 2x DPBS (we observed that nuclei are better preserved but they are more difficult to pellet in 2x DPBS). To remove aggregates, the sam- ples were filtered through 10 μm cell strainer (PluriSelect Mini strainer) to generate single-nucleus suspensions. All the steps were performed in the cold and samples were kept on ice until nucleus capture. The quality of the nuclei was assessed by staining with trypan blue and nuclei counts were made using a Malassez haemocytometer.
Single nucleus RNA sequencing was performed using the 10x Genomics single-cell capturing system. Nuclei suspensions, including 20,000 to 25,000 nuclei, were loaded on the 10x Genomics Chromium Controller following the manu- facturer's instructions, within 1 hour of preparation. Single nucleus cDNA libraries were prepared using the Chromium Single Cell 3' Reagent Kit according to the manufacturer’s instructions (chemistries v3 and v3.1). Libraries were sequenced on an Illumina NextSeq500 (28 bp for R1 and 122 bp for R2) and 248 to 315 million reads were obtained per library.

value: leg

tag: batch

tag: time point

value: 0 Months post amputation

value: Chicago-F

value: uninjured


title: H-HDAC-2.B02

description: C1 CAGE

extract_protocol:
Single cell RNA extraction and cDNA amplification were performed according to the C1 CAGE procedure deposited in Fluidigm’s Script Hub (https://www.fluidigm.com/c1openapp/scripthub/script/2015-07/c1-cage-1436761405138-3). For bulk CAGE, total RNA was extracted using RNeasy Mini Kit.
For C1 CAGE, the library was constructed following the same C1 CAGE procedure outlined in the above link. For bulk CAGE, libraries were constructed using the published nAnT-iCAGE protocol.
The prepared libraries were sequenced on Illumina HiSeq 2500 (50 nt single read).


title: Leg, 6months, regenerated

description: 10x genomics

value: 6 Months post amputation

tag: genotype

value: regenerated


title: L1 Volcano + Acanthamoeba Rep3


title: Leg, 6months, uninjured

description: 10x genomics


title: Leg, 2months, uninjured

description: 10x genomics

value: 2 Months post amputation


title: H-HDAC-1.G04

description: C1 CAGE


title: Octopus Adult Arm Left 1 Medial

source_name: Transverse section of adult arm, collected 3.5  cm from the arm tip

value: Male

value: Adult


title: H-HDAC-1.F12

description: C1 CAGE

value: Control


title: L1 Volcano + Acanthamoeba Rep2


title: H-HDAC-1.G03

description: C1 CAGE


title: Octopus Adult Arm Left 1 Distal

source_name: Transverse section of adult arm, collected 1.5  cm from the arm tip


title: WT + Acanthamoeba Rep4

value: SBW25 + Acanthamoeba Sp


title: M78.CTRL

value: cardiospheres derived primitive cardiac stromal cells

value: CRTL


title: H-HDAC-1.F10

description: C1 CAGE

value: TSA


title: M78.TGFb

value: TGFb


title: WT + Acanthamoeba Rep2


title: M81.CTRL


title: H-HDAC-1.F09

description: C1 CAGE


title: M77.VTP

value: VTP


title: H-HDAC-1.G01

description: C1 CAGE

value: VPA


title: M78.VTP


title: H-HDAC-1.F08

description: C1 CAGE


title: Female EC-Myc KO HFC 419

source_name: Liver

value: Female

value: Liver

value: 13 weeks

value: EC-Myc KO

value: High-fat/cholesterol diet


title: M78.TGFb_VTP

value: TGFB+VTP


title: WT + Acanthamoeba Rep1


title: H-HDAC-1.F07

description: C1 CAGE


title: L2 Mountain + Acanthamoeba Rep4

value: SBW25 L2MNT + Acanthamoeba Sp


title: L1 Volcano + Acanthamoeba Rep1

value: SBW25 L1VOL + Acanthamoeba Sp


title: H-HDAC-1.F11

description: C1 CAGE


title: Leg, 2months, regenerated

description: 10x genomics

value: leg

value: 2 Months post amputation

value: Chicago-F

value: regenerated


title: L2 Mountain + Acanthamoeba Rep3


title: M77.TGFb_VTP

value: cardiospheres derived primitive cardiac stromal cells


title: H-HDAC-1.F06

description: C1 CAGE


title: H-HDAC-1.F05

description: C1 CAGE

value: Control


title: H-HDAC-1.F04

description: C1 CAGE


title: M04.VTP


title: L2 Mountain + Acanthamoeba Rep1


title: H-HDAC-1.F02

description: C1 CAGE


title: OCI-YTHDF2 kockdown(KD) cells

city: Nanjing

first: Zhen

last: Hua

state: Jiangsu

address: 138 Xianlin Avenue, Xianlin University Town, Nanjing

institute: Nanjing University of Chinese Medicine

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 mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) 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.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Genome_build: Beta_vulgaris.GCF_000511025.2_RefBeet-1.2.2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Multiple Myeloma cells

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: knockdown


title: M77.TGFb

value: TGFb


title: M04.TGFb

source_name: cardiospheres-derived primitive cardiac stromal cells


title: M04.CTRL

value: cardiospheres-derived primitive cardiac stromal cells

value: CRTL


title: M04.TGFb_VTP


title: H-HDAC-1.F03

description: C1 CAGE

data_processing:
Remove low quality and rDNA reads
Map to the human genome (hg38) using BWA version 0.5.9 (r16) with default parameters, except: : (1) maximum long deletion (-d) = 10 for bwa_aln and (2) maximum number of   alignments (-n) = 100 for bwa_samse
Convert mapped reads to CAGE Transcription Start Sites (CTSS) and read in using CAGEfightR package in R (4.0.3). For C1 CAGE, keep only those that are expressed in at least 3 samples. Merge reads within 20bp of one another.
Map processed reads to GENCODE v31 annotation to the nearest 1kbp up/100 bp down, and remove those overlapping known axons
Annotate enhancers using our custom enhancer set, and quantify raw expression counts by summing the overlapping reads
Assembly: hg38
Supplementary files format and content: *_CTSS.tar.gz: CAGE CTSS files (CAGE_Transcription Start Sites in BED format)
Supplementary files format and content: *_annotations.tar.gz: sample and CAGE tag cluster annotation tables
Supplementary files format and content: *_expression_tables.tar.gz: raw and normalized expression tables for CAGE tag clusters
Supplementary files format and content: gold_enhancers.bed.gz: BED file of the curated gold enhancer set

value: VPA


title: OCI-wildtype(WT) cells

description: OCI-WT

value: wildtype


title: H-HDAC-1.F01

description: C1 CAGE


title: H-HDAC-1.E12

description: C1 CAGE


title: ARP1-wildtype(WT) cells


title: L2 Mountain + Acanthamoeba Rep2


title: H-HDAC-1.E11

description: C1 CAGE


title: H-HDAC-1.E10

description: C1 CAGE

value: TSA


title: HEK293T_PRMT7-sh3

city: ShangHai

first: Zefeng

last: Wang

address: 320 YueYang Road

department: CAG-MPG Partner Institution for Computational Biology

institute: Chinese Academy of Sciences

data_processing:
Illumina Casava1.7 software used for basecalling
The sequencing adapters were trimmed by Cutadapt (v1.18)
the RNA-seq reads were mapped onto the human genome reference (Ensembl GRCh37) using HISAT with default parameters
The PSI (Percent-Spliced-In) values were estimated by MISO and rMATs for each annotated splicing event
For significant change of splicing were filtered using FDR cutoff of 0.01, we also required the ΔPSI cutoff at 0.1 with minimal read count at 50
Genome_build: Ensembl GRCh37

source_name: HEK293T cell line

growth_protocol: HEK293T cells were cultured according to ATCC

extract_protocol:
cells were harvested in Trizol reagent (Ambion) and total RNAs were extracted according to the manufacturer’s protocol.
Poly(A)+ RNA-seq libraries were prepared by using Illumina TruSeq Stranded mRNA LT Sample Prep Kit (Illumina) and subjected to deep sequencing with Illumina Hiseq X10 under PE150 sequencing model.

treatment_protocol: HEK293T cells were stably transfected with scramble shRNA or shRNAs against PRMT using letivirus knockdown system

value: PRMT7 knockdown


title: ARP1-YTHDF2 kockdown(KD) cells


title: HEK293T_PRMT6-sh3

value: PRMT6 knockdown


title: H-HDAC-1.E09

city: Yokohama

first: Andrew

last: Kwon

institute: RIKEN

description: C1 CAGE


title: Patient 03 N11

city: São Luís

first: Silma

middle: Regina

last: Pereira

state: Maranhão

address: Av. dos Portugueses, 1966, Bacanga

department: Department of Biology

country: Brazil

institute: Federal University of Maranhão

hyb_protocol: Expression of miRNAs was determined using the nCounter® Human v.3 miRNA expression platform (Nanostring Technologies™, Seattle, Wa, USA), which contains human probes from miRBase v.22, targeting 827 human miRNAs, six positive controls, eight negative controls, three positive binding controls, three negative binding controls, five internal reference genes (ACTB, B2M, GAPDH, RPL19, and RPL0) and five miRNA controls (ath-miR- 159a, cel-miR-248, cel-miR-254, osa-miR-414, and osa-miR-442).

data_processing: The raw data were normalized and analyzed using the ROSALIND® Nanostring platform. Non-tumor tissues for the primary tumor were used as control. Read distribution percentages and sample MDS plots were generated as part of the QC step. The normalization was conducted following the background subtraction based on POS_A probes correction factors (positive control normalization and codeset normalization). For both steps, the geometric mean of each probeset was used to create a normalization factor. The fold changes and p-values for comparisons were calculated using the t-test method (p≤0.05). P-value adjustment was performed using the Benjamini-Hochberg (p≤0.01) method to estimate false discovery rates (FDR).

source_name: Non-tumor tissue of the penis

extract_protocol: Total RNA from tumors and adjacent non-tumor tissues was isolated using the TRIzol protocol (Invitrogen Carlsbad, CA, USA). RNA concentration and quality were tested by measuring the 260/280 and 260/230 ratios using the Nanodrop 2001 spectrophotometer (Willington, DE, USA).

value: 81 years

tag: smoking

value: yes

tag: alcoholism

tag: hpv infection

tag: histological subtype

value: normal tissue

tag: predominant lesion

tag: tumor size

tag: tumor grade

tag: tumor stage

tag: lymphatic invasion

tag: perineural invasion

tag: lymph node invasion

tag: metastasis


title: Patient 18 N50

value: 32 years


title: HEK293T_PRMT5-sh2

tag: cell line

tag: treatment

value: PRMT5 knockdown


title: HEK293T_PRMT5-sh1


title: Patient 21 N55

tag: age

value: 73 years

value: smoker former

value: no


title: Patient 08 N20

value: 78 years


title: HEK293T_PRMT4-sh3

value: PRMT4 knockdown


title: H-HDAC-1.E08

description: C1 CAGE

value: Control


title: H-HDAC-1.E06

description: C1 CAGE


title: H-HDAC-1.E05

description: C1 CAGE


title: HEK293T_PRMT7-sh2


title: Patient 22 CP60

source_name: Squamous cell carcinoma of the penis

value: 59 years

value: positive

value: verrucous

value: II

value: pNx

value: pMx


title: H-HDAC-2.A01

description: C1 CAGE

value: TSA


title: HEK293T_PRMT3-sh2

value: PRMT3 knockdown


title: Patient 13 N29

value: 40 years

value: normal tissue


title: H-HDAC-1.E03

description: C1 CAGE

value: VPA


title: H-HDAC-1.E04

description: C1 CAGE


title: H-HDAC-2.B07

description: C1 CAGE


title: Patient 18 CP50

value: 32 years

value: yes

value: HPV16, HPV44, HPV74

value: usual and condilomatous

value: ulcer-vegetative


title: Patient 21 CP55

value: 73 years

value: smoker former

value: no

value: usual

value: ulcerated


title: Patient 19 CP53

value: 71 years

value: III

value: pNx


title: HEK293T_PRMT3-sh1

value: PRMT3 knockdown


title: H-HDAC-1.E07

description: C1 CAGE


title: HEK293T_PRMT1-sh1

value: PRMT1 knockdown


title: Patient 20 CP54

value: 69 years

value: condilomatous

value: vegetative

value: I

value: pMx


title: H-HDAC-1.E01

description: C1 CAGE

value: Control


title: HEK293T_PRMT-shScramble

value: Scramble shRNA control


title: H-HDAC-1.D12

description: C1 CAGE


title: H-HDAC-1.D11

description: C1 CAGE

value: TSA


title: HEK293T_PRMT1-sh3


title: HEK293T_PRMT4-sh1

value: PRMT4 knockdown


title: Patient 17 CP48

value: 74 years

value: yes

value: no

value: positive

value: II


title: Patient 16 CP44

value: 51 years

value: usual

value: ulcero-vegetante

value: 3 cm

value: pNx


title: PRMT4_inhibitor_Ribo

description: Ribosome protected RNA

data_processing:
Library strategy: Ribo-seq
Illumina Casava1.7 software used for basecalling
Adapters were removed by Cutadapt (v1.18) and reads aligning to rRNA sequences were removed using Bowtie (v1.1.2).
Unaligned Ribo-seq reads and RNA-seq reads were aligned to Gencode annotation release 27lift37 (GRCh37.p13) for human using STAR (v2.4.2a) allowing a maximum of 2 mismatches and multimapping of to up to eight different positions.
The translation efficiency of each gene was estimated by dividing the TPM of ribosome-protected mRNA with the relative transcript abundance from RSEM (v1.2.22).
For coverage plot, we used best aligned reads to estimate the coverage of protein coding genes at each position and scaled each transcript to 20, 100, and 50 windows on 5’ UTR, CDS, and 3’ UTR regions, respectively.
The Ribo-footprint coverage in each window was normalized to mean coverage of the entire transcript.
To assess the statistical changes of translation efficiency, Ribo-seq signals and RNA-seq signals were analyzed using Xtail pipeline
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text file includes translation efficiency values for each Sample

extract_protocol:
Cleared cell lysates from polysome profiling procedure were treated with RNase I to obtain ribosome-protected mRNA fragments (RPF). Subsequently, lysates were loaded onto 10-50% sucrose gradients, ultracentrifuged and fractionated as described above. Fractions containing monoribosome particles were combined and undergone RNA clean-up by TriZol reagent.
The RNA sequencing library was prepared according to Ingolia et al. with some modifications.
The RPF library was prepared as described in Illumina Small RNA Library Prep Reference Guide. RNA samples were reverse-transcribed and cDNA libraries were gel purified and amplified by limited-cycle PCR with index primers.

value: treated with PRMT4 inhibitor

tag: fraction

value: ribosome


title: PRMT4_inhibitor_input

description: Ribosome protected RNA

value: input


title: H-HDAC-1.D10

description: C1 CAGE

value: Control


title: Patient 14 CP31

value: 68 years

value: condilomatous

value: verrucosa

value: I

value: pMx


title: H-HDAC-1.D09

description: C1 CAGE

value: TSA


title: Patient 15 CP39

value: 65 years

value: vegetative

value: no


title: PRMT1_inhibitor_Ribo

description: Ribosome protected RNA

value: treated with PRMT1 inhibitor


title: Patient 13 CP29

value: 40 years

value: HPV59, HPV66

value: ulcer-vegetative

value: II

value: pNX


title: Patient 12 CP26

value: 83 years

value: smoker former

value: alcoholic former

value: usual

value: ulcerated

value: III

value: yes

value: MX


title: H-HDAC-1.D07

description: C1 CAGE

value: TSA


title: Patient 11 CP25

value: 85 years

value: condilomatous

value: nodular ulcerated

value: 4 cm

value: pNx

value: pMx


title: 3264 cells,shControl-2

source_name: glioblastoma

tag: tissue

value: glioblastoma

tag: cell type

value: glioma stem cells


title: PRMT1_inhibitor_input

description: Ribosome protected RNA

value: treated with PRMT1 inhibitor

value: input


title: DMSO_Ribo

description: Ribosome protected RNA

value: treated with DMSO

value: ribosome


title: DMSO_input

description: Ribosome protected RNA


title: Patient 09 CP22

value: 44 years

tag: smoking

value: no

tag: alcoholism

value: usual

value: ulcerated

value: II


title: Hereward_Ptr_inoculated_96h rep1

city: Aberystwyth

first: Luis

middle: A J

last: Mur

address: Penglais Road

department: IBERS

country: United Kingdom

institute: Aberystwyth University

data_processing:
The original raw data from Illumina platform were transformed to sequenced reads, known as Raw Data, by base calling.
Removed sequenced reads containing adapters, N >10 %  (N represents the base cannot be determined), and low quality (Qscore<= 5) base which is over 50% of the total base.
Filtered reads were mapped to the wheat reference genome IWGSC RefSeq v1.0 using Salmon v. 1.3.0 with default parameters.
Fragments per kilobase per million mapped reads (FPKM) and the normalised counts were obtained using the R packages tximport and DESeq2.
Assembly: IWGSC RefSeq v1.0 (GCA_900519105.1)
Supplementary files format and content: tab-delimited text files include FPKM values for every gene and every sample
Supplementary files format and content: Matrix table with normalized counts for every gene and every sample

organism: Triticum aestivum

source_name: leaf

growth_protocol: Seeds of the wheat lines were sown into commercial compost John Innes no.2 and mixed with sand (4:1) and incubated in environmentally controlled growth rooms at 21 ºC under 16 hours of light, and at 18 ºC in the dark. Seedlings were thinned down to three plants per pot - with each pot being treated as a single replicate. Each treatments had three replicates that were randomly distributed within the growth room.

extract_protocol:
Total RNA was extracted using the RNeasy Plant Mini Kit (Qiagen), with in-column DNase digestion RNeasy Plant Mini Kit (QIAGEN)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Seedlings were inoculated with Pyrenophora tritici-repentis (toxA positive) or mock-inoculated (controls) at growth stage GS13 (three-leaf seedlings). Leaves were sampled from the four sets of plants (Hereward Ptr_inoculated, Hereward Mock_inoculated, Robigus Ptr_inoculated, Robigus Mock_inoculated) before treatment (0h), and at 48 and 96 hours post inoculation.

value: leaf

value: wheat seedling leaf

tag: cultivar

value: Hereward

tag: time point


title: H-HDAC-1.D03

address: 1-7-22 Suehiro-cho, Tsurumi-ku

description: C1 CAGE

source_name: HepG2 cell line

value: Control


title: Robigus_Ptr_inoculated_96h rep3

value: Robigus


title: H-HDAC-1.D02

description: C1 CAGE

value: VPA


title: Patient 06 CP15

value: 54 years

value: yes

tag: hpv infection

value: positive

tag: histological subtype

tag: predominant lesion

value: vegetative

tag: tumor size

value: pMx


title: Robigus_Mock_inoculated_96h rep3


title: H-HDAC-1.D04

description: C1 CAGE


title: Patient 08 CP20

value: 78 years

value: HPV16, HPV06

value: usual and basaloid

value: 4 cm

tag: tumor grade

value: III

tag: tumor stage

tag: lymphatic invasion

tag: perineural invasion

value: pNx


title: M77.CTRL

value: cardiospheres derived primitive cardiac stromal cells

tag: treatment

value: CRTL

tag: cell line_id

tag: sequencing chip

tag: sequencing barcode


title: Hereward_Mock_inoculated_96h rep2

tag: tissue

value: leaf

tag: cell type

value: wheat seedling leaf

value: Hereward


title: H-HDAC-1.D01

description: C1 CAGE

value: VPA


title: Patient 05 CP14

tag: age

value: 76 years

tag: smoking

value: no

tag: alcoholism

value: condilomatous

value: ulcerated

value: 3 cm

value: I

tag: lymph node invasion

tag: metastasis


title: H-HDAC-1.C12

description: C1 CAGE

value: TSA


title: Patient 04 CP13

value: 37 years

value: yes

tag: hpv infection

value: positive

tag: histological subtype

value: usual

tag: predominant lesion

value: nodular ulcerated

value: 5 cm

value: pMx


title: Patient 03 CP11

value: 81 years

value: HPV18, HPV53

tag: tumor size

tag: tumor grade

value: II

tag: tumor stage

value: pNx


title: H-HDAC-1.D06

description: C1 CAGE

tag: treatment


title: H-HDAC-1.C11

description: C1 CAGE

value: Control


title: H-HDAC-1.D05

description: C1 CAGE


title: H-HDAC-1.D08

description: C1 CAGE


title: Robigus_Ptr_inoculated_96h rep1

value: leaf

value: wheat seedling leaf

tag: cultivar

value: Robigus

tag: time point


title: Patient 07 CP16

value: 74 years

value: no

value: usual and basaloid

value: verrucosa

value: I

tag: lymphatic invasion

tag: perineural invasion


title: Patient 01 CP06

value: 62 years

value: usual

value: ulcerated

value: yes


title: Fig6b_RTprimer24

first: Tianmin

address: Huaxia Middle Road, 393

department: School of Life Science and Technology

institute: ShanghaiTech University

description: E. coli K12 BW25113

data_processing:
quality trimming step using cutadapt (v2.10) command with a quality threshold of 20
the pooled sample was demultiplexed according to the anchored barcode of the first seven nucleotides at the 5’-end from the first read
internal adaptor sequence embedding in some second reads with too short insert was also trimmed
a minimum length threshold of 20 bp for both the first and second reads was used to filter out those pair-end reads with too short insert
bowtie2 (v2.4.1) to align the second read to a reference genome (NC000913.3) (default setting)
Feature counting was carried out using R method summarizeOverlaps from GenomicAlignments package (v1.26.0) in a strand-specific manner, giving rise to a read count table for each gene.
Genome_build: NC000913.3
Supplementary_files_format_and_content: gene raw count data, comma-delimited matrix table

organism: Escherichia coli BW25113

source_name: RNA-seq data in Fig. 6b, , using miniBac-seq method to generate RNA-seq data with RT primer 24

growth_protocol: Single colony was picked up from a stock LB agar plate and was grown aerobically with shaking at 220 rpm in LB medium overnight (typically 12 hours) as the seed culture. A subculture was established by firstly washing the bacteria once using M63B1 medium (centrifuge by 7000 g, 3 minutes) and resuspension; and then cultivating the seed culture into fresh M63B1 medium (4% volume) and grown for 10 hours with shaking at 220 rpm to reach exponential stage (OD600 ~ 0.6).

extract_protocol:
Bacterial RNA was obtained utilizing the RNAClean XP beads (Beckman, A63987). Lysate was prepared using lysozyme and proteinase K
miniBac-seq, a customized bacterial RNA-seq library construction method, see description of our paper for details

tag: strain


title: Fig6b_RTprimer23

description: E. coli K12 BW25113

source_name: RNA-seq data in Fig. 6b, , using miniBac-seq method to generate RNA-seq data with RT primer 23


title: H-HDAC-1.C10

description: C1 CAGE

value: TSA


title: H-HDAC-1.C09

description: C1 CAGE


title: Robigus_Ptr_inoculated_96h rep2

tag: tissue

tag: cell type


title: Hereward_Ptr_inoculated_96h rep3

value: Hereward


title: H-HDAC-1.C06

description: C1 CAGE


title: Robigus_Mock_inoculated_96h rep2


title: Fig6b_RTprimer22

description: E. coli K12 BW25113

source_name: RNA-seq data in Fig. 6b, , using miniBac-seq method to generate RNA-seq data with RT primer 22


title: Hereward_Mock_inoculated_96h rep3


title: Robigus_Mock_inoculated_96h rep1


title: Fig6b_RTprimer19

description: E. coli K12 BW25113

source_name: RNA-seq data in Fig. 6b, , using miniBac-seq method to generate RNA-seq data with RT primer 19


title: H-HDAC-1.C07

description: C1 CAGE


title: H-HDAC-1.E02

description: C1 CAGE

value: VPA


title: Patient 02 CP08

tag: age

value: 80 years

tag: smoking

value: smoker former

tag: alcoholism

value: condilomatous

value: 10 cm

value: II

value: pNx

value: pMx


title: H-HDAC-1.C08

description: C1 CAGE

value: Control


title: Robigus_Mock_inoculated_48h rep3

value: leaf

value: wheat seedling leaf

value: Robigus


title: Fig6b_RTprimer20

description: E. coli K12 BW25113

source_name: RNA-seq data in Fig. 6b, , using miniBac-seq method to generate RNA-seq data with RT primer 20


title: Fig6b_RTprimer18

description: E. coli K12 BW25113

source_name: RNA-seq data in Fig. 6b, , using miniBac-seq method to generate RNA-seq data with RT primer 18


title: H-HDAC-1.C05

description: C1 CAGE


title: Robigus_Mock_inoculated_48h rep2


title: Fig6b_RTprimer17

description: E. coli K12 BW25113

source_name: RNA-seq data in Fig. 6b, , using miniBac-seq method to generate RNA-seq data with RT primer 17


title: Hereward_Ptr_inoculated_96h rep2


title: Robigus_Mock_inoculated_48h rep1


title: Fig6b_RTprimer21

description: E. coli K12 BW25113

source_name: RNA-seq data in Fig. 6b, , using miniBac-seq method to generate RNA-seq data with RT primer 21


title: H-HDAC-1.C03

description: C1 CAGE


title: H-HDAC-1.C02

description: C1 CAGE


title: Hereward_Mock_inoculated_48h rep2


title: Hereward_Mock_inoculated_96h rep1


title: H-HDAC-1.B12

description: C1 CAGE


title: Hereward_Mock_inoculated_48h rep1


title: H-HDAC-1.C01

description: C1 CAGE


title: Hereward_Mock_inoculated_48h rep3


title: Fig6b_RTprimer16

description: E. coli K12 BW25113

source_name: RNA-seq data in Fig. 6b, , using miniBac-seq method to generate RNA-seq data with RT primer 16


title: Fig6b_RTprimer12

description: E. coli K12 BW25113

source_name: RNA-seq data in Fig. 6b, , using miniBac-seq method to generate RNA-seq data with RT primer 12


title: Fig6b_RTprimer11

description: E. coli K12 BW25113

source_name: RNA-seq data in Fig. 6b, , using miniBac-seq method to generate RNA-seq data with RT primer 11


title: Fig6b_RTprimer15

description: E. coli K12 BW25113

source_name: RNA-seq data in Fig. 6b, , using miniBac-seq method to generate RNA-seq data with RT primer 15


title: Fig6b_RTprimer13

description: E. coli K12 BW25113

source_name: RNA-seq data in Fig. 6b, , using miniBac-seq method to generate RNA-seq data with RT primer 13


title: Robigus_Ptr_inoculated_48h rep3


title: Robigus_Ptr_inoculated_48h rep1


title: H-HDAC-1.C04

description: C1 CAGE


title: H-HDAC-1.B09

description: C1 CAGE


title: Fig6b_RTprimer10

description: E. coli K12 BW25113

source_name: RNA-seq data in Fig. 6b, , using miniBac-seq method to generate RNA-seq data with RT primer 10


title: H-HDAC-1.B10

description: C1 CAGE


title: H-HDAC-1.B07

description: C1 CAGE


title: H-HDAC-1.B08

description: C1 CAGE


title: Fig6b_RTprimer9

description: E. coli K12 BW25113

source_name: RNA-seq data in Fig. 6b, , using miniBac-seq method to generate RNA-seq data with RT primer 9


title: Robigus_Ptr_inoculated_48h rep2

source_name: leaf


title: Hereward_Ptr_inoculated_48h rep3


title: Hereward_Ptr_inoculated_48h rep2


title: H-HDAC-1.B11

description: C1 CAGE

source_name: HepG2 cell line


title: Hereward_Ptr_inoculated_48h rep1


title: H-HDAC-1.B06

description: C1 CAGE


title: Fig6b_RTprimer8

description: E. coli K12 BW25113

source_name: RNA-seq data in Fig. 6b, , using miniBac-seq method to generate RNA-seq data with RT primer 8


title: WT + Acanthamoeba Rep3

source_name: Bacteria and Acanthamoeba

value: SBW25 + Acanthamoeba Sp


title: Fig6b_RTprimer7

description: E. coli K12 BW25113

source_name: RNA-seq data in Fig. 6b, , using miniBac-seq method to generate RNA-seq data with RT primer 7


title: H-HDAC-1.B04

description: C1 CAGE


title: Robigus_Mock_inoculated_0h rep3

value: Untreated


title: Fig6b_RTprimer6

description: E. coli K12 BW25113

source_name: RNA-seq data in Fig. 6b, , using miniBac-seq method to generate RNA-seq data with RT primer 6


title: H-HDAC-1.B05

description: C1 CAGE


title: Fig6b_RTprimer5

description: E. coli K12 BW25113

source_name: RNA-seq data in Fig. 6b, , using miniBac-seq method to generate RNA-seq data with RT primer 5


title: Robigus_Mock_inoculated_0h rep2


title: Hereward_Ptr_inoculated_0h rep3


title: Fig6b_RTprimer4

description: E. coli K12 BW25113

source_name: RNA-seq data in Fig. 6b, , using miniBac-seq method to generate RNA-seq data with RT primer 4


title: Fig6b_RTprimer14

description: E. coli K12 BW25113

source_name: RNA-seq data in Fig. 6b, , using miniBac-seq method to generate RNA-seq data with RT primer 14


title: Robigus_Mock_inoculated_0h rep1


title: H-HDAC-1.B03

description: C1 CAGE


title: H-HDAC-1.B01

description: C1 CAGE


title: Hereward_Mock_inoculated_0h rep3


title: Fig6b_RTprimer2

description: E. coli K12 BW25113

source_name: RNA-seq data in Fig. 6b, , using miniBac-seq method to generate RNA-seq data with RT primer 2


title: H-HDAC-1.A12

description: C1 CAGE


title: H-HDAC-1.B02

description: C1 CAGE


title: Robigus_Ptr_inoculated_0h rep1


title: H-HDAC-1.A10

description: C1 CAGE


title: Fig6b_RTprimer3

description: E. coli K12 BW25113

source_name: RNA-seq data in Fig. 6b, , using miniBac-seq method to generate RNA-seq data with RT primer 3


title: Fig5ab_100fg_replicate2

description: E. coli K12 BW25113

source_name: RNA-seq data in Fig. 5a, b, , using miniBac-seq method to generate RNA-seq data from 100 fg total RNA, replicate 2


title: H-HDAC-1.A11

description: C1 CAGE


title: Robigus_Ptr_inoculated_0h rep2


title: Patient 10 CP23

source_name: Squamous cell carcinoma of the penis

value: 57 years

value: no

value: yes

tag: hpv infection

value: usual and condilomatous

value: nodular ulcerated

value: 3 cm

value: III

tag: lymph node invasion

tag: metastasis


title: Fig6b_RTprimer1

description: E. coli K12 BW25113

source_name: RNA-seq data in Fig. 6b, , using miniBac-seq method to generate RNA-seq data with RT primer 1


title: Robigus_Ptr_inoculated_0h rep3


title: Fig5ab_100fg_replicate1

description: E. coli K12 BW25113

source_name: RNA-seq data in Fig. 5a, b, , using miniBac-seq method to generate RNA-seq data from 100 fg total RNA, replicate 1


title: H-HDAC-1.A09

description: C1 CAGE

value: VPA


title: Hereward_Ptr_inoculated_0h rep2

value: Hereward


title: Hereward_Mock_inoculated_0h rep2


title: H-HDAC-1.A08

description: C1 CAGE


title: Hereward_Mock_inoculated_0h rep1

value: wheat leaf


title: Fig5ab_1pg_replicate2

description: E. coli K12 BW25113

source_name: RNA-seq data in Fig. 5a, b, , using miniBac-seq method to generate RNA-seq data from 1 pg total RNA, replicate 2


title: Fig5ab_10pg_replicate2

description: E. coli K12 BW25113

source_name: RNA-seq data in Fig. 5a, b, , using miniBac-seq method to generate RNA-seq data from 10 pg total RNA, replicate 2


title: H-HDAC-1.A06

description: C1 CAGE


title: H-HDAC-1.A07

description: C1 CAGE

value: TSA


title: H-HDAC-1.A05

description: C1 CAGE


title: Hereward_Ptr_inoculated_0h rep1

source_name: leaf


title: TAC 3

city: Baltimore

first: Samarjit

last: Das

address: 720 Rutland Avenue

department: Anesthesiology and Critical Care Medicine

institute: Johns Hopkins School of Medicine

data_processing:
Each library was indexed in order to multiplex six samples per sequencing run on the Illumina NextSeq platform.
Primary analysis was performed using QIAseq miRNA Quantification (Qiagen software). All sample with more than 500.000 miRNA reads were analyzed.
Secundary analysis was performed using QIAseq miRNA Quantification (Qiagen software)
geNorm was used as normalization method. Fold-Change is the normalized miRNA expression in each Sample divided the normalized miRNA expression in the Control Sample.
Fold-change values less than one indicate a down-regulation, and the fold-regulation is the negative inverse of the fold-change.
For the geNorm normalization methods, the p values are calculated based on a Student's t-test of the replicate normalized miRNA expression values for each miRNA in the control group and treatment groups.
Assembly: GRCm38
Supplementary files format and content: primary analysis contains miRNA information (.xlsx)

source_name: skeletal muscle

growth_protocol: Normal mouse chow

extract_protocol:
RNA was isolated using miRNeasy mini kit (Qiagen Cat# 217004). 100 ng of total RNA was used for the construction of sequencing libraries.
Small RNA libraries for RNA-seq were prepared using QIAseq miRNA Library Kit (Qiagen Cat# 331505) following manufacturer's protocols.

treatment_protocol: Transverse aortic constriction (TAC) was conducted on mice to induce pressure overload for cardiac hypertrophy and eventual heart failure. At 8-10 weeks post-TAC, skeletal muscle was harvest.

value: skeletal muscle

tag: genotype

tag: Sex

value: male

value: 16 weeks

value: Transverse aortic constriction

tag: treatment time

value: 8 weeks


title: H-HDAC-1.A04

department: IMS

description: C1 CAGE

source_name: HepG2 cell line

tag: treatment


title: H-HDAC-1.A03

description: C1 CAGE


title: Fig5ab_100pg_replicate2

description: E. coli K12 BW25113

source_name: RNA-seq data in Fig. 5a, b, , using miniBac-seq method to generate RNA-seq data from 100 pg total RNA, replicate 2


title: TAC 2


title: Fig5ab_100pg_replicate1

description: E. coli K12 BW25113

source_name: RNA-seq data in Fig. 5a, b, , using miniBac-seq method to generate RNA-seq data from 100 pg total RNA, replicate 1


title: Sham 3

value: Control


title: H-HDAC-1.A02

description: C1 CAGE


title: Fig5ab_1ng_replicate1

description: E. coli K12 BW25113

source_name: RNA-seq data in Fig. 5a, b, , using miniBac-seq method to generate RNA-seq data from 1 ng total RNA, replicate 1


title: Fig5ab_1ng_replicate2

description: E. coli K12 BW25113

source_name: RNA-seq data in Fig. 5a, b, , using miniBac-seq method to generate RNA-seq data from 1 ng total RNA, replicate 2


title: H-HDAC-1.A01

description: C1 CAGE


title: Fig5ab_1pg_replicate1

description: E. coli K12 BW25113

source_name: RNA-seq data in Fig. 5a, b, , using miniBac-seq method to generate RNA-seq data from 1 pg total RNA, replicate 1


title: F-HDAC-4.H12

description: C1 CAGE

source_name: Dermal fibroblasts, neonatal


title: Fig4b_ourmethod

description: E. coli K12 BW25113

source_name: RNA-seq data in Fig. 4b, using miniBac-seq method to generate RNA-seq data


title: Sham 2


title: Sham 1


title: TAC 1


title: F-HDAC-4.H11

description: C1 CAGE


title: F-HDAC-4.H10

description: C1 CAGE


title: Fig5ab_10pg_replicate1

description: E. coli K12 BW25113

source_name: RNA-seq data in Fig. 5a, b, , using miniBac-seq method to generate RNA-seq data from 10 pg total RNA, replicate 1


title: F-HDAC-4.H08

description: C1 CAGE


title: F-HDAC-4.H09

description: C1 CAGE


title: F-HDAC-4.H07

description: C1 CAGE


title: Fig4b_TruSeq

description: E. coli K12 BW25113

source_name: RNA-seq data in Fig. 4b, using TruSeq kit to generate RNA-seq data


title: Fig4a_replicate2_5ab_5ng

description: E. coli K12 BW25113

source_name: RNA-seq data in Fig. 4a, using miniBac-seq method to generate RNA-seq data from 5 ng total RNA, replicate 2


title: F-HDAC-4.H03

description: C1 CAGE


title: BMM, DI treated rep2

city: PALO ALTO

first: yuting

last: wang

state: California

address: 265 campus drive, lokey stem cell research building, RM-G3105-SIM1

institute: Stanford University

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

source_name: BMM

growth_protocol: BMMs isolated from 8-week-old male C57BL/6 mice were cultured with a-MEM in the absence of FBS for 12 h, then changed to complete media supplied with RANKL (100 ng/mL)

extract_protocol:
Cells for RNA-sequencing were lysed with Trizol Reagent and submitted to Shanghai Biotechnology Corporation for the following process. Briefly, total RNA was extracted and checked for aand checked for a  RIN number to inspect RNA integrity. Qualified total RNA was  further purified by RNAClean XP and RNase-Free DNase Set.  RIN number to inspect RNA integrity. Qualified total RNA was  further purified by RNAClean XP and RNase-Free DNase Set.
The libraries were prepared with VAHTS mRNA-seq v2 Library Prep Kit for Illumina

value: BMM

value: Primary bone marrow derived Monocyte/Macrophage

value: wt

value: RANKL (100 ng/mL) and DI (20mM) for 24hours


title: MLKLko.HFD4

city: Oklahoma City

first: Jonathan

last: Wren

state: OK

address: 825 N.E. 13th Street

department: Genes & Human Disease Research Program

institute: OMRF

data_processing:
Raw sequencing reads (in a FASTQ format) were trimmed of residual adaptor sequences using Scythe software. Low quality bases at the beginning or the end of sequencing reads were removed using sickle then the quality of remaining reads was confirmed with FastQC.
Reads were aligned to the Mus musculus genome reference (GRCm39/mm39) using STAR and per transcript reads were counted with HTSeq.
Differentiall expression analyses was performed using edgeR package in the context of limma/voom workflow.
Assembly: GRCm39/mm39
Supplementary files format and content: tab-delimited text file includes ENSEMBL id and raw read counts for each transcript, in each sample

source_name: liver

extract_protocol:
Total RNA was isolated for approximately 25 mg of liver tissue using RNeasy Mini kit (Cat# 74106) from Qiagen (Valencia, CA, USA) . RNA was quantified using Qubit RNA BR Assay kit (Cat# Q10211,ThermoScientific, Waltham, MA) in a Qubit3.0 fluorometer.
Library preparation was done using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA) as per the manufacturers instructions. The library preparation and sequencing were performed by the Clinical Genomics Core at the Oklahoma Medical Research Foundation

treatment_protocol: Wild type (WT), MLKL knockout (MLKL KO or Mlkl-/-)  and Ripk3 knockout (Ripk3KO or Ripk3-/-) at 2 months of age were fed with normal chow (control diet) , CD-LFD or CD-HFD  diet for 6 months.  Liver was dissected out, RNA isolated using Qiagen RNeasy mini kit. 500 ng of RNA was used for RNA sequencing.

value: Mlkl-/-

tag: diet

value: CD-HFD

value: liver


title: WT-3.

city: Shanghai

first: Deming

last: Jiang

address: No. 500, Dongchuan Road, Minhang District, Shanghai

institute: East China Normal University

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  Agrobacterium fabrum str. c58 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
HTSeq software used for calculating RPKM
Genome_build: Agrobacterium fabrum str. c58
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample …

organism: Agrobacterium sp. CGMCC 11546

source_name: Agrobacterium  sp. CGMCC 11546 after 24 h of curdlan fermentation

extract_protocol:
bacterial cells were flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 5 ug of total RNA for the construction of sequencing libraries.
RNA labrarys were prepared for sequencing using standard Illumina protocols

value: WT


title: phbC 3

value: phbC deletion


title: WT-2.


title: glnA-1

value: glnA deletion


title: BMM, DMSO treated rep1

description: The libraries were prepared with VAHTS mRNA-seq v2 Library Prep Kit for Illumina

value: RANKL (100 ng/mL) and DMSO for 24hours


title: F-HDAC-4.H06

description: C1 CAGE


title: F-HDAC-4.H05

description: C1 CAGE


title: F-HDAC-4.H01

description: C1 CAGE

value: VPA


title: F-HDAC-4.H04

description: C1 CAGE


title: Fig2bc_Commercial

description: E. coli K12 BW25113

source_name: RNA-seq data in Fig. 2b, c, using commercial rRNA depletion method


title: MLKLko.HFD1


title: BMM, DI treated rep1


title: MLKLko.HFD2


title: WT 3


title: F-HDAC-4.H02

description: C1 CAGE


title: F-HDAC-4.G11

description: C1 CAGE


title: WT 1


title: WT 2


title: F-HDAC-4.G09

description: C1 CAGE


title: Fig4a_replicate1_5ab_5ng

description: E. coli K12 BW25113

source_name: RNA-seq data in Fig. 4a, using miniBac-seq method to generate RNA-seq data from 5 ng total RNA, replicate 1


title: phbC 1


title: F-HDAC-4.G08

description: C1 CAGE


title: glnA-3


title: F-HDAC-4.G07

description: C1 CAGE


title: MLKLko.C5

value: control diet


title: BMM, DMSO treated rep2


title: phbC 2


title: F-HDAC-4.G05

description: C1 CAGE

value: TSA


title: MYCN-overexpressing cell line in long-term culture replicate 2 [MYCN.2826]

city: Uppsala

first: Finn

last: Hallböök

address: Dag Hammarskjölds v 20

department: Dept Immunology, Genetics and Pathology

country: Sweden

institute: Uppsala University

data_processing:
Quality check and alignment of the data was done with nf-core/rnaseq pipeline (version 3.4) by adjusting the alignment parameter (--alignEndsProtrude 100 ConcordantPair).
The first 10bp was clipped to avoid biased base composition.
To extract fragment counts, featurecounts (version 2.0.0) (Liao, Smyth, and Shi 2014) was used with minimum mapping quality of 20, and requiring both pairs to be properly aligned on the same chromosome.
Differential expression analysis was done by edgeR (Robinson, McCarthy, and Smyth 2009). Significant differential expressed genes were selected by 1) FDR by the Benjamini and Hochberg method <= 0.05 and 2) |log2 fold-change| >= 1.
For GO/Pathway enrichment analysis, clusterProfiler (version 4.0.6) (Yu et al. 2012) was used. GO gene set enrichment analysis was done by gseGO and at least 10 genes were required to be included in the GO term to be visualized. KEGG gene set enrichment analysis was done by gseKEGG.
Assembly: Galgal6, added transgenes "human MYCN" (Ensembl ID: ENST00000281043.4), "eGFP"
Supplementary files format and content: The file is .txt format and contains normalized gene counts using TMM values with every gene and every sample

organism: Gallus gallus

source_name: Retina

growth_protocol: For MYCN-overexpressing cell lines, the cells were kept in suspension in RPMI 1640 medium supplemented with 10%FBS, 1% MEM-NEAA and 1% Pen/Strep. The medium was changed twice a week.

extract_protocol:
The central region of E14 chicken retina was dissected and dissociated with 1X Trypsin EDTA. The total RNA was extracted with Qiagen Rneasy Micro Kit (Qiagen, #74004). The RIN value and RNA concentration was measured by TapeStation and 1µg of total RNA was sent for library construction.
MYCN-overexpressing cells were taken and dissociated by vibration and pipetting. The total RNA was extracted with Qiagen Rneasy Micro Kit (Qiagen, #74004). The RIN value and RNA concentration was measured by TapeStation and 1µg of total RNA was sent for library construction.
The library was prepared using the TruSeq stranded mRNA library preparation kit with polyA selection (Illumina Inc.).

value: White Leghorn

value: MYCN overexpression

tag: in ovo mycn electroporation

value: At E3.5

value: E14 dissection


title: Fig2bc_Customized

description: E. coli K12 BW25113

source_name: RNA-seq data in Fig. 2b, c, using our customized rRNA depletion method


title: F-HDAC-4.G04

description: C1 CAGE


title: MLKLko.LFD3

value: CD-LFD


title: F-HDAC-4.G10

description: C1 CAGE


title: MLKLko.LFD4


title: MYCN-overexpressing cell line in long-term culture replicate 1 [MYCN.2825]


title: MLKLko.LFD2


title: Control E14 chicken retina sample replicate 3 [E14.Retina.Rpt3]

value: control

value: No

tag: culture condition

value: Suspension in RPMI medium with FBS

value: > 4 weeks in culture


title: MLKLko.C1

value: Mlkl-/-

value: liver


title: Control E14 chicken retina sample replicate 2 [E14.Retina.Rpt2]


title: Ripk3ko.HFD5

value: CD-HFD


title: F-HDAC-4.G01

description: C1 CAGE


title: MLKLko.LFD1


title: MLKLko.C2


title: Ripk3ko.HFD3


title: F-HDAC-4.F12

description: C1 CAGE

value: Control


title: MLKLko.C6


title: WT-1.

value: WT


title: F-HDAC-4.G06

description: C1 CAGE

value: VPA


title: Ripk3ko.HFD2


title: Ripk3ko.HFD1


title: F-HDAC-4.F10

description: C1 CAGE


title: Ripk3ko.LFD2


title: glnA-2

value: glnA deletion


title: MYCN-overexpressing cell line in long-term culture replicate 3 [MYCN.2828]


title: MLKLko.C4

value: control diet


title: F-HDAC-4.F08

description: C1 CAGE


title: F-HDAC-4.F07

description: C1 CAGE


title: F-HDAC-4.F06

description: C1 CAGE


title: SiHa cells 24h post DMSO rep2

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

description: miRNA expression at 24h post DMSO (Control)

hyb_protocol: The dried sample was resuspended in nuclease free water and mixed with Hybridization Mix containing blocking solution (Agilent Technologies, Part Number: 5190-0456) and Hi-RPM Hybridization Buffer (Agilent Technologies, Part Number: 5190-0456) and incubated at 100oC for 5 minutes followed by snap chill on ice for 5 minutes.  The samples were hybridized on the Human miRNA 8x60K Arrays. The hybridization was carried out at 55°C for 20 hours. After hybridization, the slides were washed using Gene Expression Wash Buffer1 (Agilent Technologies, Part Number 5188-5325) at room temperature for 5 minutes and Gene Expression Wash Buffer 2 (Agilent Technologies, Part Number 5188-5326) at 37oC for 5 minutes.

scan_protocol: The microarray slide was scanned on a G2600D scanner (Agilent Technologies)

data_processing: Images were quantified using Feature Extraction Software ( Agilent). Feature extracted raw data was analyzed using GeneSpring GX software from Agilent. Normalization of the data was done in GeneSpring GX using the 90th percentile shift miRNA based.

label_protocol: The miRNA labeling was performed using miRNA Complete Labeling and Hyb Kit (Agilent Technologies, Part Number: 5190-0456).The total RNA sample was diluted to 100ng/ul in nuclease free water. About 200ng of total RNA was dephosphorylated using Calf Intestinal Alkaline Phosphatase (CIP) master mix (Agilent Technologies, Part Number: 5190-0456) by incubating at 37oC for 30 minutes. The dephosphorylated miRNA sample was denatured by adding Dimethyl Sulfoxide (DMSO) and heating at 100 oC for 10 minutes and transferred to ice-water bath. The Ligation master mix (Agilent Technologies, Part Number: 5190-0456) containing Cyanine 3-pCp was added to the denatured miRNA sample and incubated at 16oC for 2 hours. The Cyanine 3-pCp labeled miRNA sample was dried completely in the vacuum concentrator (Eppendorf, Concentrator Plus, Catalog Number 5305000) at 45oC for 2 hour.

extract_protocol: RNA Extraction was perforemd using TRIZOL as per the manufacturer's recommendations.

tag: cell line

value: SiHa

value: Cervical cancer cell line

value: 24h post DMSO (Control)


title: SiHa cells 24h post DMSO rep1

source_name: miRNA expression at 24h post DMSO (Control)


title: Ripk3ko.C4


title: SiHa cells 24h post curcumin, rep1

description: miRNA expression at 24h post curcumin

source_name: SiHa Cell line_curcumin

tag: hpv status

value: HPV 16+


title: F-HDAC-4.F03

description: C1 CAGE


title: SiHa cells 24h post curcumin, rep2

description: miRNA expression at 24h post curcumin


title: F-HDAC-4.G12

description: C1 CAGE


title: SiHa cells 24h post DMSO, rep3

source_name: SiHa Cell line_DMSO


title: F-HDAC-4.F09

description: C1 CAGE


title: F-HDAC-4.F11

description: C1 CAGE

value: TSA


title: WT.HFD6

tag: tissue


title: F-HDAC-4.G02

description: C1 CAGE


title: F-HDAC-4.G03

description: C1 CAGE


title: SiHa cells 24h post emodin rep2

description: miRNA expression at 24h post emodin

source_name: miRNA expression at 24h post emodin

tag: cell type

value: 24h post emodin


title: WT.HFD5


title: F-HDAC-4.E12

description: C1 CAGE


title: F-HDAC-4.E11

description: C1 CAGE


title: SiHa cells 24h post DMSO rep3


title: Control E14 chicken retina sample replicate 1 [E14.Retina.Rpt1]

tag: strain

value: White Leghorn

value: control

value: No

tag: age


title: SiHa cells 24h post emodin rep1

description: miRNA expression at 24h post emodin


title: cyno early blastocyst 4-7

city: Los Angeles

first: Kevin

last: Huang

address: Gonda BLDG Rm. 6554, P.O.Box 957088

department: Human Genetics

institute: UCLA

data_processing:
Raw reads from the Illumina HiSeq2000 were mapped to the cynomolgus genome (GCA_000364345.1 Macaca_fascicularis_5.0) using default parameters in BWA
Mapped transcripts reads were transformed using the reads per kilobase per million (RPKM) metric
Genes with low expression were filtered out, followed by quantile normalization.
Genome_build: GCA_000364345.1 (GenBank assembly accession)
Supplementary_files_format_and_content: monkey_processed_RPKM.txt: matrix listing normalized RPKM

organism: Macaca fascicularis

source_name: early blastocyst

growth_protocol: Single blastomeres were isolated by removing the zona pellucida using acidic tyrode solution (Sigma, cat. no. T1788), then separated by gentle mouth pipetting in a calcium-free medium.

extract_protocol:
RNA was isolated from single cells or single morula embryos and amplified as previously described
Library construction was performed following Illumina manufacturer suggestions.

treatment_protocol: Single cells were washed twice with 1x PBS containing 0.1% BSA before placing in lysis buffer.

tag: sample type

value: early blastocyst


title: MLKLko.C3

value: Mlkl-/-

value: liver


title: Ripk3ko.LFD1

value: CD-LFD


title: WT.HFD4

value: WT

value: CD-HFD


title: Ripk3ko.LFD3


title: Ripk3ko.C5


title: F-HDAC-4.E09

description: C1 CAGE

source_name: Dermal fibroblasts, neonatal

growth_protocol: Cells were cultured in DMEM high glucose medium supplemented with 10% inactivated fetal bovine serum, 100 U/mL penicillin, 100 ug/mL streptomycin, and 1 mM sodium pyruvate.

value: VPA


title: cyno early blastocyst 4-6


title: cyno early blastocyst 4-5


title: F-HDAC-4.E10

description: C1 CAGE

value: Control


title: F-HDAC-4.F04

description: C1 CAGE


title: WT.HFD2


title: F-HDAC-4.E08

description: C1 CAGE


title: F-HDAC-4.F05

description: C1 CAGE


title: Ripk3ko.C6

value: control diet


title: Ripk3ko.C3


title: SiHa cells 24h post curcumin, rep3

description: miRNA expression at 24h post curcumin

value: Cervical cancer cell line

value: SiHa


title: F-HDAC-4.E06

description: C1 CAGE


title: cyno early blastocyst 4-9


title: cyno early blastocyst 4-2


title: WT.LFD5


title: F-HDAC-4.F02

description: C1 CAGE


title: Ripk3ko.C1


title: SiHa cells 24h post DMSO, rep2

value: HPV 16+


title: Ripk3ko.C2


title: WT.LFD4


title: cyno early blastocyst 4-4


title: F-HDAC-4.F01

description: C1 CAGE

value: TSA


title: cyno early blastocyst 3-4


title: WT.LFD2


title: WT.HFD3


title: cyno early blastocyst 4-8


title: SiHa cells 24h post DMSO, rep1


title: WT.LFD1


title: cyno early blastocyst 4-1


title: WT.C6


title: cyno early blastocyst 3-1


title: cyno early blastocyst 2-3


title: F-HDAC-4.D12

description: C1 CAGE


title: WT.C5


title: F-HDAC-4.E07

description: C1 CAGE


title: WT.C3


title: cyno early blastocyst 3-5


title: F-HDAC-4.D09

description: C1 CAGE


title: WT.LFD6


title: WT.HFD1


title: F-HDAC-4.E05

description: C1 CAGE


title: F-HDAC-4.E03

description: C1 CAGE


title: F-HDAC-4.E02

description: C1 CAGE


title: WT.C1


title: F-HDAC-4.D11

description: C1 CAGE


title: F-HDAC-4.D07

description: C1 CAGE


title: cyno late blastocyst 4-31

source_name: late blastocyst

value: late blastocyst