title: h1;met1+/+ segregated from h1;met1+/- plant #4 (rna-seq rep3)

status: Public on Jun 30 2022

type: SRA

city: Norwich

first: Jaemyung

last: Choi

address: Norwich Research Park

department: Cell and Developmental Biology

country: United Kingdom

institute: John Innes Centre

library_source: transcriptomic

data_processing:
Illumina Hiseq basecalls were performed using 'bcl2fq' at the John Innes Centre.
For bisulfite-seq, reads were mapped with bowtie and bs-sequel pipeline (https://zilbermanlab.net/tools/) allowing up to 2 mismatches.
For RNA-seq libraries, reads were mapped to TAIR10 genome using HISAT2 (Kim et al., 2015; Pertea et al., 2016) with following  options:–max-intronlen 10000 -k 2 –-dta-cufflinks.
Genome_build: TAIR10
Supplementary_files_format_and_content: For RNA-seq, bw files contain rpkm normalized read count of 10bp windows. Bw files were generated using deepTools (bamCoverage --normalizedUsing RPKM --ignoreForNormalization ChrM ChrC; Ramirez et al., 2016). For bisufite sequencing, gff files contain the number of mapped C and T per 50bp windows at CG, CHG, and CHH contexts.

molecule: total RNA

organism: Arabidopsis thaliana

source_name: leaf tissue from 4-5 week old plants

growth_protocol: We isolated h1;met+/+ plants segregated from h1;met1+/- (Choi et al., 2020). Arabidopsis thaliana seedlings were germinated and grown for 4-5 weeks on soil at 20-25℃ in growth chamber (16 hr day/ 8 hr night) for all the experiments performed here.

extract_protocol: We extracted total RNA from rosette leaves of 4-5-week-old plants using Trizol (Invitrogen, cat. No. 15596026) according to manufacturer’s manual. To remove DNA from samples, 5 ug of RNA was treated with DNA-free DNA removal kit (Thermo, AM1907). 100-700 ng of DNA-free total RNA was subjected to RNA library construction according to manufacturer’s protocol (Illumina, 20020640 and 20019792).

tag: genotype

tag: tissue

value: leaf

tag: age

value: 4-5 week old

tag: molecule subtype

value: ribominus total RNA


title: h1;met1+/+ segregated from h1;met1+/- plant #6 (rna-seq rep3)


title: h1;met1+/+ segregated from h1;met1+/- plant #5 (rna-seq rep3)


title: h1;met1+/- (rna-seq)

extract_protocol: We extracted total RNA from rosette leaves of 4-5-week-old plants using Trizol (Invitrogen, cat. No. 15596026) according to manufacturer’s manual. To remove DNA from samples, 10 ug of RNA was treated with DNA-free DNA removal kit (Thermo, AM1907). Ribosomal RNA was depleted using the RiboMinus plant kit for RNA-seq (Invitrogen, cat. No. A1083808). 100 ng rRNA-depeleted RNA was used to construct RNA sequencing libraries with  Ovation RNA-seq systems 1-16 for model organism (Arabidopsis) (Nugen, cat. No. 0351).


title: h1;met1+/+ segregated from h1;met1+/- plant #6 (rna-seq rep2)


title: h1;met1+/+ segregated from h1;met1+/- plant #3 (rna-seq rep3)


title: h1;met1+/+ segregated from h1;met1+/- plant #5 (rna-seq rep2)


title: h1;met1+/+ segregated from h1;met1+/- plant #3 (rna-seq rep2)


title: h1;met1+/+ segregated from h1;met1+/- plant #1 (rna-seq rep2)


title: h1;met1+/+ segregated from h1;met1+/- plant #2 (rna-seq rep2)


title: h1;met1+/+ segregated from h1;met1+/- plant #4 (rna-seq rep1)


title: h1;met1+/+ segregated from h1;met1+/- plant #3 (rna-seq rep1)


title: h1;met1+/+ segregated from h1;met1+/- plant #6 (rna-seq rep1)


title: h1;met1+/+ segregated from h1;met1+/- plant #6 (bisulfite)

library_source: genomic

molecule: genomic DNA

extract_protocol: gDNA for bisulfite sequencing was extracted with Dneasy plant mini kit according to manufacturer's protocol. 500 ng total gDNA was sheared to 100-1000bp DNA using Bioruptor Pico (Diagenode), then purified with 1.2X volume of SPRI beads (Beckman Coulter, cat. No. A63881). Fragmented gDNA was ligated to NEBNext Adaptor for Illumina using NEBNext Ultra II DNA library prep kit for Illumina (New England Biolabs, ca. No. E7645). We performed bisulfite conversion twice with ligated libraries (QIAGEN, cat. No. 59104) to prevent imperfect conversion (<99% conversion) of unmethylated cytosines. Converted libraries were subjected to SPRI beads purification with 0.8X volume of beads. We amplified bisulfite-converted libraries with NEB next indexing primers (New England Biolabs Inc. cat. No. E7335S).

value: genomic DNA


title: h1;met1+/+ segregated from h1;met1+/- plant #1 (rna-seq rep1)


title: h1;met1+/+ segregated from h1;met1+/- plant #5 (rna-seq rep1)


title: h1;met1+/+ segregated from h1;met1+/- plant #2 (rna-seq rep1)


title: h1;met1+/+ segregated from h1;met1+/- plant #5 (bisulfite)


title: h1;met1+/+ segregated from h1;met1+/- plant #4 (bisulfite)


title: h1;met1+/+ segregated from h1;met1+/- plant #2 (bisulfite)


title: h1;met1+/+ segregated from h1;met1+/- plant #3 (bisulfite)


title: h1;met1+/+ segregated from h1;met1+/- plant #1 (bisulfite)


title: h1;met1+/+ segregated from h1;met1+/- plant #1 (rna-seq rep3)


title: h1;met1+/+ segregated from h1;met1+/- plant #2 (rna-seq rep3)


title: 4T1, 100ng IL-22, 24h, biol rep 3 [SK3R12_Tdil22_11m]

city: Munich

first: Daria

last: Briukhovetska

address: Lindwurmstraße 2a

department: Division of Clinical Pharmacology

country: Germany

institute: Klinikum der Universität München

data_processing:
Differential gene expression analysis was performed with the Bioconductor package metaseqR. A 3'UTR read counts table was created from the BAM files resulting the short-read mapping with the Bioconductor GenomicRanges. The Bioconductor package DESeq was used to normalize for inherent systematic or experimental biases (e.g. GC-content bias, sequencing depht, gene lenght, etc.), after removal of genes with zero counts over all samples.
Genes with any of the following features were filtered out before further analysis: i) total gene length less than 500, ii) average reads per 100 bp less than the 25th quantile of the total normalized distribution of average reads per 100 bp, iii) genes with read counts below the median read counts of the total normalized count distribution, iv) Ensembl biotype matching the following: rRNA, TR_V_pseudogene, TR_J_pseudogene, IG_C_pseudogene, IG_J_pseudogene, IG_V_pseudogene, v) genes where 50% of samples did not present more than five normalized counts across all samples.
Differential gene expression analysis for the contrast of the control versus the treated samples was performed utilizing Bioconductor packages DESeq, edgeR, limma, NBPSeq, and NOISeq.
PANDORA weighted p-value was calculated and applied to combine the statistical significance of the aforementioned algorithms.
Assembly: hg19
Supplementary files format and content: metaseqr_sig_out_Tdctrl_vs_Tdil22.txt: Tab-delimited text file containing log2 and rpgm normalized 3’UTR read counts of significantly differentially expressed genes for each sample.
Supplementary files format and content: metaseqr_all_out_Tdctrl_vs_Tdil22.txt: Tab-delimited text file containing log2 and rpgm normalized 3’UTR read counts of all differentially expressed genes for each sample.

organism: Mus musculus

growth_protocol: 0.3 × 10^5 4T1 cells were seeded into six-well plates and were grown in RPMI medium, supplemented with 10 % fetal bovine serum, 100 μg/ml streptomycin, 1 IU/ml penicillin, and 2 mM L-glutamine, and grown for 24 h in a humidified atmosphere at 37°C and 5% CO2.

extract_protocol:
Extraction was performed at room temperature using TRIzol reagent (Invitrogen) according to the manufacturers instructions. RNA quality was asessed using a Bioanalyzer (Agilent Technologies) with the Agilent RNA 6000 Nano Kit (Agilent Technologies) according to the manufacturers instructions.
Up to 500ng of RNA were used with the 3’ mRNA-Seq Library Prep Kit Protocol for Ion Torrent (QuantSeq-LEXOGEN™ Vienna, Austria), following the manufacturer’s instructions. Library quality and quantity was analyzed with the DNA High Sensitivity Kit (Agilent Technologies) in Bioanalyzer (Agilent Technologies). After pooling, templating and enrichment of the libraries was performed on an Ion Proton One Touch system. The pools were templated using the Ion PI™ Hi-Q™ OT2 200 Kit (ThermoFisher Scientific) and then sequenced with the Ion PI™ Hi-Q™ Sequencing 200 Kit on Ion Proton PI™ V2 chips (ThermoFisher Scientific), following commercially available protocols.

treatment_protocol: Cells were washed two times with PBS. Then 1 mL of  serum-free Opti-MEM medium with or without 100 ng/mL of IL-22 was added to each of the three biological replicates, followed by an incubation for 24 h in a humidified atmosphere at 37°C and 5% CO2.

tag: cell line

tag: cell type

value: murine breast cancer

tag: time

tag: treatment


title: h1;met1+/+ segregated from h1;met1+/- plant #4 (rna-seq rep2)


title: 4T1, serum free medium control, 24h, biol rep 3 [SK3R9_Tdctrl6]

value: serum free medium control


title: 4T1, serum free medium control, 24h, biol rep 2 [SK3R8_Tdctrl3]


title: 4T1, serum free medium control, 24h, biol rep 1 [SK3R7_Tdctrl2]


title: 4T1, 100ng IL-22, 24h, biol rep 1 [SK3R10_Tdil22_9m]


title: Myoma-3 [miRNA-seq]

city: Nagoya

first: Kosuke

last: Yoshida

state: Aichi

address: 65 Tsuruma-cho

country: Japan

institute: Nagoya University

data_processing:
CLC Genomics Workbench version 9.5.3 program
Sequence reads were trimmed and mapped to the miRbase 21 database without allowing any mismatch.
Assembly: miRbase 21
Supplementary files format and content: processed_data.txt

organism: Homo sapiens

source_name: Uterine

extract_protocol:
Total RNA was extracted using the miRNeasy Mini Kit (Qiagen, Hilden, Germany).
Small RNA libraries were prepared using the NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs, Ipswich, MA). Then, PCR products were separated by electrophoresis (120 V, 60 min), and DNA fragments corresponding to 140–160 bp (the length of small non-coding RNA plus the adaptors) were recovered.

value: Uterine

tag: Sex

value: female

tag: disease stage


title: Myoma-2 [miRNA-seq]


title: Myoma-1 [miRNA-seq]


title: Uterine Leiomyosarcoma-3 [miRNA-seq]

value: IB


title: Uterine Leiomyosarcoma-5 [miRNA-seq]


title: Uterine Leiomyosarcoma-1 [miRNA-seq]


title: Uterine Leiomyosarcoma-2 [miRNA-seq]


title: Uterine Leiomyosarcoma-6 [miRNA-seq]


title: 4T1, 100ng IL-22, 24h, biol rep 2 [SK3R11_Tdil22_10m]


title: Uterine Leiomyosarcoma-4 [miRNA-seq]

value: IIB


title: gastrocnemius muscle, RT-5

type: RNA

city: Kyoto

first: Wataru

last: Aoi

address: 1-5 Hangicho Shimogamo, Sakyo-ku

institute: Kyoto Prefectural University

hyb_protocol: 2.3ug of Fragmented and Labeled ss-cDNA were hybridized for 16 hr at 45C on GeneChip Mouse Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix).

data_processing: Signal intensity data were normalized with robust multi-array average (RMA) and expressed as log2 transformed.

label: biotin

source_name: RT, 5, muscle

label_protocol: Biotinylated ss-cDNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA.

extract_protocol: Total RNA was extracted using RNeasy Mini Kit (Qiagen, Valencia, CA) according to the manufacturer's instructions.

tag: strain

value: Tsl;ICR[GF]

value: 11 weeks

value: male

value: gastrocnemius muscle

tag: donor mice

value: training


title: gastrocnemius muscle, RT-4

source_name: RT, 4, muscle


title: gastrocnemius muscle, RT-6

source_name: RT, 6, muscle


title: gastrocnemius muscle, RT-3

source_name: RT, 3, muscle


title: gastrocnemius muscle, RT-2

source_name: RT, 2, muscle


title: gastrocnemius muscle, RS-3

source_name: RS, 3, muscle

value: sedentary


title: gastrocnemius muscle, RS-5

source_name: RS, 5, muscle


title: gastrocnemius muscle, RS-2

source_name: RS, 2, muscle


title: gastrocnemius muscle, RS-4

source_name: RS, 4, muscle


title: gastrocnemius muscle, RS-6

source_name: RS, 6, muscle


title: gastrocnemius muscle, RT-1

source_name: RT, 1, muscle


title: gastrocnemius muscle, RS-1

source_name: RS, 1, muscle


title: CK_shoot,biological rep3

city: Changchun

first: Ningning

last: Wang

address: 2888, Xinchen Street

country: China

institute: Jilin Agricultural University

description: Gene expression data from CK

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rice Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Expression Console using RMA as normalization method.

organism: Oryza sativa

source_name: CK in Rice, shoot

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Seeds of the two genotypes were thoroughly washed with distilled water and then germinated in the dark in Petri dishes containing distilled water at 28℃. After a 2-day incubation, germinated seeds were transferred to a greenhouse at 26℃ under 16 h/8 h light/dark regime about 48 hours to harvest

extract_protocol: Total RNA was isolated from the same seedlings with the Trizol Reagent (Invitrogen) according to the manufacturer’s instructions.

tag: cultivar

value: Hitomebore

value: shoot-tip


title: CK_shoot,biological rep1

description: Gene expression data from CK


title: NHEM treated with TSST-1 for 6 hours

city: Silver Spring

first: Aarti

last: Gautam

state: MD

address: 503 Robert Grant Avenue

department: Medical Readiness Systems Biology

country: USA

institute: WRAIR

hyb_protocol: cRNA was hybridized to Agilent 4 x 44k slides (Design ID: 014850, Agilent Technologies) following manufacturer's instructions

scan_protocol: Slides were scanned on Axon GenePix 4000B scanner. Features were extracted using the default setting of the Feature Extraction software (Feature Extraction software v.10.7, Agilent, CA).

data_processing: Normalization and gene expression analysis was done using custom R code and functional heatmap tool (https://bioinfo-abcc.ncifcrf.gov/Heatmap/)

source_name: Agilent's Universal Human Reference RNA composed of pooled total RNA from ten cell lines representing different human tissues

label_protocol: Total RNA (200ng) was used as starting material, which was amplified using the Quick Amp Two-Color Kit (Agilent Technologies).The labelled cRNA was purified using an RNeasy Mini Kit (Qiagen, Hilden, Germany), and eluted, labelled cRNA was quantified using a NanoDrop ND-2000 spectrophotometer (Thermo Fisher Scientific Inc, Waltham, MA, USA).

growth_protocol: Normal Human Epidermal Melanocytes (NHEM) and reagents required for culturing the cells were purchased from Clonetics® (Lonza, MD). Cells were maintained in Melanocyte Growth Medium (MGM) Bulletkit® media according to the supplier’s instructions (Lonza, MD). Cell cultures were established at the recommended starting cell density of 10,000 cells per cm2 and maintained in 150 cm2 flasks at 37°C and 5% CO2 in a humidified incubator.

extract_protocol: Total RNA was isolated with TRIzol reagent (Invitrogen, CA) using the manufacturer’s procedure

tag: sample type

value: reference

source_name: melanocytes

value: TSST-1 for 6 hours


title: CK_shoot,biological rep2

description: Gene expression data from CK


title: NHEM treated with TSST-1 for 30 min

value: TSST-1 for 30 min


title: Control

value: Control


title: NHEM treated with TSST-1 for 2 hours

value: TSST-1 for 2 hours


title: NHEM treated with SEB for 12 hours

value: SEB for 12 hours


title: NHEM treated with TSST-1 for 24 hours

value: TSST-1 for 24 hours


title: NHEM treated with TSST-1 for 12 hours

value: TSST-1 for 12 hours


title: NHEM treated with SEB for 24 hours

value: SEB for 24 hours


title: Col_12_B

city: Buenos Aires

first: Julieta

middle: Lisa

last: Mateos

address: Av. Patricias Argentinas 435

country: Argentina

institute: Fundacion Instituto Leloir

data_processing:
Low-quality reads in the raw data (FASTQ files) were filtered out and reads kept were then mapped to the Arabidopsis thaliana TAIR10 reference genome using TopHat with parameters : -p 8 -I 5000
Differential expression and differential splicing usage were obtained from bam files using ASpli package
Genome_build: Arabidopsis thaliana TAIR10
Supplementary_files_format_and_content: Excel files (list of differentially expressed genes for several comparisons, and list of differential bin usage for several comparisons)

molecule: polyA RNA

source_name: seedlings

growth_protocol: seedlings from Arabidopsis picln-1 mutant, prmt5-5 mutant and wt grown at 22°C for 10 days in a 12h light 12h dark photoperiod

extract_protocol:
RNeasy Plant Mini Kit (QIAGEN)
Performed at Max-Planck-Institute for Developmental Biology

treatment_protocol: 12h light - 12 h dark light regime for 9 days

tag: light regime

value: 12 h light - 12 h dark

value: WT


title: Col_12_C


title: Col_12_D


title: pICln_675_12_D


title: NHEM treated with TSST-1 for 48 hours

value: TSST-1 for 48 hours


title: pICln_675_12_A


title: pICln_675_12_C


title: NHEM treated with SEB for 2 hours

value: SEB for 2 hours


title: NHEM treated with SEA for 24 hours

value: SEA for 24 hours


title: NHEM treated with SEB for 30 min

value: SEB for 30 min


title: NHEM treated with SEA for 12 hours

value: SEA for 12 hours


title: pICln_675_12_B


title: NHEM treated with SEB for 6 hours

value: SEB for 6 hours


title: NHEM treated with SEB for 48 hours

value: reference

value: SEB for 48 hours


title: 179_12_D


title: 179_12_A


title: NHEM treated with SEA for 30 min

value: SEA for 30 min


title: MsSPC_tumor04

city: Heidelberg

first: Reka

last: Toth

address: Im Neuenheimer Feld 280

institute: DKFZ

data_processing:
Alignment: methylCtools 1.0 (BWA Version 0.7.8 -T 0  Merging Sambamba Version 0.6.5 -t 1 -l 0 --hash-table-size=2000000 --overflow-list-size=1000000 --io-buffer-size=64  Samtools Version 0.1.19)
methylation calling: MethylDackel --nOB 2,11,11,2 --nOT 8,1,2,11.
Processing: R 4.0.2, Methrix
Excluded non-covered sites,
Excluded SNP overlapping sites,
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph files: chr, start position, end position, methylation beta value

source_name: Sftpc lineage tumor

extract_protocol:
all mice were injected with tamoxifen to label the specific cell types
According to Wang et al Nat Protoc. 2013 Oct;8(10):2022-32.

treatment_protocol: DNA was extracted using the QIAamp DNA micro Kit

value: Lung

tag: group

value: tumor

tag: eml4-alk adenovirus

value: Yes

tag: gender

value: female

tag: characteristics

value: age by euthanize:28 weeks


title: Col_12_A

tag: genotype


title: MsSPC_control05

source_name: Sftpc lineage normal

tag: tissue

value: normal

value: No

value: male

value: age by euthanize:12 and 15 weeks


title: 179_12_C

value: 12 h light - 12 h dark


title: MsSPC_control06

value: mixed

value: age by euthanize:12 weeks


title: 179_12_B


title: MsSPC_tumor03

value: age by euthanize:27 weeks


title: MsSPC_tumor02

value: age by euthanize:23 and 25 weeks


title: MsHOPX_control03

source_name: Hopx lineage normal

value: age by euthanize:11 weeks


title: MsSPC_control02

value: age by euthanize:16 weeks


title: MsHOPX_control02

value: age by euthanize:14 weeks


title: MsSPC_control01

value: Lung


title: MsSPC_control03

value: age by euthanize:15 weeks


title: MsCCSP_tumor04

source_name: Scgb1a1 lineage tumor

value: tumor

value: Yes


title: MsHOPX_control04

value: female


title: MsCCSP_control03

source_name: Scgb1a1 lineage normal

value: normal

value: age by euthanize:13 and 16 weeks


title: NHEM treated with SEA for 2 hours

value: reference

value: SEA for 2 hours


title: MsSPC_tumor01

value: age by euthanize:22 and 32 weeks


title: NHEM treated with SEA for 48 hours

value: SEA for 48 hours


title: MsCCSP_control02

value: No

value: mixed


title: mTE-6

city: Los Angeles

first: Kevin

last: Huang

state: CA

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 mm10 genome 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: mm9
Supplementary_files_format_and_content: mouse_ReadCounts.txt; raw read counts
Supplementary_files_format_and_content: mouse_processed_RPKM.txt; normalized RPKM

source_name: trophectoderm

growth_protocol: Mouse zygotes were collected after timed mating and cultured in the Optimum medium to the blastocyst stages

extract_protocol:
RNA was isolated from single cells and amplified using the SMRT-seq2 protocol
Library construction was performed following Illumina manufacturer suggestions.

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

value: trophectoderm


title: mTE-5


title: MsSPC_control04

value: male

value: age by euthanize:17 weeks


title: mTE-3


title: MsHOPX_tumor01

source_name: Hopx lineage tumor

value: age by euthanize:26 weeks


title: MsHOPX_control05

value: Lung

value: age by euthanize:11 weeks


title: MsCCSP_control07

value: age by euthanize:10 weeks


title: MsCCSP_tumor02

value: tumor

value: Yes

value: age by euthanize:31, 36 and 36 weeks


title: MsCCSP_tumor03

value: female

value: age by euthanize:37 weeks


title: mICM-4

source_name: inner cell mass

value: inner cell mass


title: mICM-2


title: MsCCSP_tumor01

value: age by euthanize:17 and 22 weeks


title: MsCCSP_control04

value: normal

value: age by euthanize:25 weeks


title: mTE-7 (multiple)


title: mTE-2


title: mTE-4


title: MsHOPX_tumor02

value: mixed

value: age by euthanize:24 weeks


title: mTE-1

value: trophectoderm


title: mICM-6


title: mICM-7


title: NHEM treated with SEA for 6 hours

value: reference

value: SEA for 6 hours


title: MsCCSP_control06

value: Lung

value: No


title: mICM-5


title: mICM-3 (multiple)


title: SK-LMS-1_miR-10b-5p_rep1

data_processing:
Single-end sequenced reads were checked by FastQC.
Estimation of transcripts was performed using Kallisto.
The expression matrix was constructed and normlized by Tximport in R
Assembly: hg19
Supplementary files format and content: tab-delimited text files include scaledTPM values for each Sample

growth_protocol: The cells were maintained in MEM (Nacalai Tesque, Kyoto, Japan) containing 10% fetal bovine serum, 1 mM sodium pyruvate (Thermo Fisher Scientific), and antibiotics.

extract_protocol:
Total RNA was extracted using the miRNeasy Mini Kit (Qiagen, Hilden, Germany).
cDNA libraries for RNA sequencing were prepared by Azenta (South Plainfield, NJ).

treatment_protocol: mirVana miRNA mimic for miR-10b-5p (MC11108) and Negative Control #1  were used (Thermo Fisher Scientific). Cells were transfected with 20 nM miRNA mimic using Lipofectamine RNAi Max (Thermo Fisher Scientific).

tag: cell line

value: sarcoma cells


title: SK-LMS-1_miR-10b-5p_rep2

tag: cell type


title: SK-UT-1_NC_rep2

value: 20 nM Negative control


title: C24C: MCF7_control_24h_rep3

city: Lund

first: Christer

last: Larsson

address: Medicon Village, Bldg 404:C3

department: Laboratory Medicine

country: Sweden

institute: Lund university

hyb_protocol: Standard Illumina iScan N240 scanning protocol

scan_protocol: Direct Hyb

data_processing: The data were normalised using quantile normalisation with BASE

source_name: MCF-7  cells

extract_protocol: Illumina®Totalprep-96RNA Amplification kit 4397949 RevD, (Modification of Amplification kit v 2.2)


title: C963A: MCF7_control_96h3d_rep1


title: LT24A: MCF7_LCLTRAIL_24h_rep1


title: LT24C: MCF7_LCLTRAIL_24h_rep3


title: C963C: MCF7_control_96h3d_rep3


title: C963B: MCF7_control_96h3d_rep2


title: LT963C: MCF7_LCLTRAIL_96h3d_rep3


title: C24B: MCF7_control_24h_rep2


title: LT963B: MCF7_LCLTRAIL_96h3d_rep2


title: SK-LMS-1_NC_rep2


title: SK-UT-1_miR-10b-5p_rep1


title: SK-UT-1_miR-10b-5p_rep2


title: Myoma_2

data_processing:
Single-end sequenced reads were checked by FastQC.
Estimation of transcripts was performed using Kallisto.
The expression matrix was constructed and normlized by Tximport in R
Genome_build: hg19
Supplementary_files_format_and_content: counts

source_name: Uterus

extract_protocol:
Total RNA was extracted using QIAzol (Qiagen, Hilden, Germany) according to manufacturer’s protocols. RNA quantity and quality were evaluated with a Nanodrop ND-1000 spectrophotometer (Thermo Fisher Scientific) and an Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA)
cDNA libraries for RNA sequencing were established from total RNA using NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs) for selecting poly-A mRNA followed by strand-specific library preparation using MGIEasy RNA Directional Library Prep Set V2.0 (MGI tech). The resulting double-stranded library fragments were further processed into single-stranded circular DNA (sscDNA), which is the final form of MGI library. The sscDNA libraries were quantified by Qubit ssDNA Assay Kit and used for generating DNA nanoballs (DNBs) by rolling circle replication reaction. DNBs were then loaded into a flow cell for sequencing on DNBSEQ-G400 platform (MGI tech), according to the manufacturer’s instructions.

value: Uterus

tag: disease

value: myoma


title: mICM-1


title: SK-UT-1_NC_rep1

tag: treatment


title: Myoma_1


title: SK-LMS-1_NC_rep1


title: Leiomyosarcoma_5

value: leiomyosarcoma


title: Leiomyosarcoma_3


title: LT963A: MCF7_LCLTRAIL_96h3d_rep1


title: Leiomyosarcoma_6


title: Leiomyosarcoma_1


title: C24A: MCF7_control_24h_rep1


title: Myoma_3


title: Leiomyosarcoma_2


title: L1 Volcano 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

source_name: Bacteria

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


title: L2 Mountain Rep4

value: SBW25 L2MNT


title: L1 Volcano Rep1


title: Leiomyosarcoma_4


title: HBECs, CBSoe

city: LEXINGTON

first: Aria

last: Byrd

state: Kentucky

address: 2865 Middlesex Way

institute: University of Kentucky

data_processing:
Sequencing and base-calling were performed by BGI (Beijing Genomics Institute).
Sequencing reads were trimmed and filtered using Trimmomatic (V0.39) to remove adapters and low quality reads. Reads were mapped to Ensembl GRCh38 transcripts annotation (release 98), using RSEM (v1.3.2) and STAR (2.6.1d) with default settings.
Genome_build: GRCh38 release 98
Supplementary_files_format_and_content: tab-delimited text files including TPM and expected_count for each gene

source_name: Human Bronchial Epithelial Cells

growth_protocol: HBECs were cultured on gelatin-coated 2D plates and maintained in pneumocult EX media for 4-5 days

extract_protocol:
Human Bronchiolar Epithelial Cell RNA was extracted using the Absolutely RNA Prep kit.
Library preparation and sequencing were sent to and performed by the Beijing Genomics Institute using the DNBseq platform.

treatment_protocol: HBECs were transduced with either pLenti6-hCBS or pLenti6 virus for 4-8 hours. Fully transduced HBECs were selected for with blastocidin at 10µg/mL.

value: Human Bronchial Epithelial Cells

value: Cystathionine beta synthase (CBS) Over expression


title: HBECs, pLenti6EV

value: control


title: WT Rep2


title: L2 Mountain Rep3


title: L1 Volcano Rep3


title: Tobacco leaf tissue - G70×GDH11_rep3

city: Guiyang

first: kai

last: pi

state: Guizhou

department: Key Laboratory for Tobacco Quality Research Guizhou Province

institute: Guizhou University

description:
hybrid G70×GDH11
S21

data_processing:
The raw paired end reads were trimmed and quality controlled by SeqPrep(https://github.com/jstjohn/SeqPrep) and Sickle (https://github.com/najoshi/sickle) with default parameters.
Then clean reads were separately aligned to reference genome(https://solgenomics.net/organism/Nicotiana_tabacum/genome) with orientation mode using HISAT2 (http://ccb.jhu.edu/software/hisat2/index.shtml) software.
The mapped reads of each sample were assembled by StringTie(https://ccb.jhu.edu/software/stringtie/index.shtml?t=example) in a reference-based approach
The software RSEM was used to quantitatively analyze the expression levels of genes and transcripts
Assembly: https://solgenomics.net/organism/Nicotiana_tabacum/genome
Supplementary files format and content: tab-delimited text files include FPKM values for 18 Samples

organism: Nicotiana tabacum

source_name: Tobacco leaf tissue

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent (Plant RNA Purification Reagent for plant tissue) according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara). Then RNA quality was determined by 2100 Bioanalyser (Agilent) andquantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample(OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >1μg) was used to construct sequencing library.
RNA-seq transcriptome librariy was prepared following TruSeqTM RNA sample preparation Kit from Illumina (San Diego, CA) using 1μg of total RNA. After quantified by TBS380, paired-end RNA-seq   sequencing library was sequenced with the Illumina HiSeq xten/NovaSeq 6000 sequencer (2 ×   150bp read length)

tag: developmental stage

value: growing for 70 days

value: Middle leaf


title: Tobacco leaf tissue - G70×GDH11_rep2

description:
hybrid G70×GDH11
S20


title: WT Rep4


title: Tobacco leaf tissue - GDH11 of hybrid G70×GDH11_rep1

description:
male parent GDH11 of hybrid G70×GDH11
S22


title: WT Rep3


title: L2 Mountain Rep2


title: WT Rep1


title: Tobacco leaf tissue - G70_rep2

description:
Female parent G70 of hybrid G70×GDH11
S17


title: Tobacco leaf tissue - GDH11 of hybrid G70×GDH11_rep2

description:
male parent GDH11 of hybrid G70×GDH11
S23


title: L2 Mountain Rep1


title: Tobacco leaf tissue - G70_rep1

description:
Female parent G70 of hybrid G70×GDH11
S16


title: Tobacco leaf tissue - GDH11 of hybrid K326×GDH11_rep1

description:
male parent GDH11 of hybrid K326×GDH11
S7


title: LT24B: MCF7_LCLTRAIL_24h_rep2


title: Tobacco leaf tissue - GDH11 of hybrid K326×GDH11_rep3

description:
male parent GDH11 of hybrid K326×GDH11
S9


title: Tobacco leaf tissue - K326×GDH11_rep3

description:
hybrid K326×GDH11
S6


title: Tobacco leaf tissue - GDH11 of hybrid G70×GDH11_rep3

description:
male parent GDH11 of hybrid G70×GDH11
S24


title: L1 Volcano Rep2


title: Tobacco leaf tissue - K326×GDH11_rep2

description:
hybrid K326×GDH11
S5


title: Tobacco leaf tissue - GDH11 of hybrid K326×GDH11_rep2

description:
male parent GDH11 of hybrid K326×GDH11
S8


title: Tobacco leaf tissue - G70×GDH11_rep1

description:
hybrid G70×GDH11
S19


title: Tobacco leaf tissue - K326_rep2

description:
Female parent K326 of hybrid K326×GDH11
S2


title: Tobacco leaf tissue - K326×GDH11_rep1

description:
hybrid K326×GDH11
S4


title: Tobacco leaf tissue - K326_rep3

description:
Female parent K326 of hybrid K326×GDH11
S3


title: t0

city: Peoria

first: Aide

last: Macias-Khan

state: Arizona

address: 9565 W Patrick Ln

institute: UC Irvine

data_processing:
demultiplex with ddSeeker
read mappiing with kallisto v. 0.46.1

organism: Hydra vulgaris

source_name: 0hr regeneration

extract_protocol:
Pronase E was used to dissociaate tissue, Cells were washed through a 70 um then 40um cell strainer and resuspended in 1X PBS with BSA.
single cell RNA-Seq libraries were constructed by following the Illumina Bio-Rad SureCell WTA 3' Library Prep Guide
Libraries were multiplexed and sequenced as 43 bp paired end reads on a NextSeq 500 sequencer

value: regenerating hypostome

tag: time point


title: Tobacco leaf tissue - G70_rep3

description:
Female parent G70 of hybrid G70×GDH11
S18


title: t4

source_name: 4hr regeneration

tag: strain


title: hypostome 1

source_name: hypostome

value: hypostome


title: Tobacco leaf tissue - K326_rep1

description:
Female parent K326 of hybrid K326×GDH11
S1


title: mixed tissue sample of Eriocheir sinensis

city: Tianjin

first: Tong

last: Hao

state: China

department: College of Life Sciences

institute: College of Life Sciences, Tianjin Normal University

data_processing:
The original image data is transferred into sequence data by base calling, which is defined as raw reads. Raw reads were processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Then the transcriptome de novo assembly was carried out with the short reads assembling program-Trinity to generate transcripts. The longest transcript generated with Trinity for a gene was identified as a unigene.
The sequenced unigenes were subsequently aligned against the NR and Nt databases using BLAST searching with E-value < 1*E-5 and PFAM database using HUMMER package with E-value < 0.01.
GO annotation of unigenes was obtained by the Blast2GO program based on NR and PFAM annotations with an E-value cut-off at 1*E−6.KO and pathway annotation was obtained by KAAS (KEGG Automatic Annotation Server) with an E-value cut-off at 1*E−10.
Genome_build: Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Bowtie v2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12.Differential expression analysis use transcriptome data as reference genome.
Supplementary_files_format_and_content: Read_count      FPKM

organism: Eriocheir sinensis

source_name: mixed 1

growth_protocol: The healthy river crabs obtained from aquatic farm were cultured in a plastic incubator (70×40×50 cm) at 20±1◦C with natural light.

extract_protocol:
The total RNA was extracted using the TRIzol method (Invitrogen) for transcriptome analysis.
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer's recommendations.The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer's instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq 2500 platform.

treatment_protocol: During collection of the samples, crabs with average weight of 8.41±1.47 g were put on the ice plate for low-temperature anesthesia. Five tissues of each crab, including gill, muscle, haemocyte, intestine and hepatopancreas, were quickly collected and put in liquid nitrogen immediately, and then transferred to −80◦C refrigerator for preservation.

tag: weight

value: untreated


title: hypostome 2


title: t12

source_name: 12hr regeneration


title: DES3

first: Mi

last: Zhou

address: Anshan street 168th

institute: Tianjin Medical University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. And then by removing sequence-dependent bias and amplification noise using UMI-tools.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Supplementary files format and content: fpkm and count

organism: Rattus norvegicus

source_name: Cortical neuron, direct current stimulation,3μA 20hz 20min,7days

growth_protocol: Primary cortical neuron cultures were generated from embryonic day 16-18 Wistar rat embryos, neurons  were plated at a density of 105 neurons/cm² on a 9.6 cm² six-well plates precoated with Poly-L-Lysine (Sigma–Aldrich, USA). Cultures were maintained in 2% B27-A, and 1% GlutaMAX (Gibco) supplemented with Neurobasal media (Invitrogen) until 14 d in vitro (DIV).

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters, which including custom Unique Molecular Identifiers for minimizing sequence-dependent bias and amplification noise according to (Shiroguchi et al. 2012). Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.

value: embryo DIV 7d

value: primary cell

value: cortical neuron

value: WT

value: direct current stimulation,3μA 20hz 20min，7days


title: ACS3

source_name: Cortical neuron, alternative current stimulation,3μA 20hz 20min, 7days

value: alternative current stimulation,3μA 20hz 20min，7days


title: Control3

source_name: Cortical neuron, control group

value: control group


title: DES1


title: ACS1


title: DES2


title: ACS2


title: Control2


title: Pheripheral blood cells, healthy control, CITE- seq

city: Sendai

first: Tomonori

last: Kaifu

state: Miyagi

address: 1-15-1 Fukumuro Miyagino ku

department: Faculty of Medicine

institute: Tohoku Medicine and Pharmaceutical University

description: 10x Genomics

library_source: other

data_processing: The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.0. (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)

molecule: protein

source_name: peripheral blood

extract_protocol:
Peripheral white blood cells (pWBCs) were gathered as below. Blood samples were collected in heparin blood collection tubes, and red blodd cells were removed usinig Hetasep (STEMCELL Technologies).pWBCs were enriched by density gradient centrifugation at 90 x g for 4 minutes at room temperature.
pWBCs were labeled by TotalSeq-B Human TBNK Cocktail (BioLegend).Library was performed according to the manufacter’s instructions (Chromium Single Cell 3' Reagent Kits v3.1, 10x Genomics) for scRNA-seq and CITE-seq. Briefly, pWBC were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRI select reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: peripheral blood

tag: disease state

value: healthy control

value: white blood cells

value: no treatment


title: INC_J002_D5

city: Msida

first: Brendon

last: Scicluna

address: Msida campus

country: Malta

institute: University of Malta

data_processing:
Read alignment done by HISAT2 version 2.1.0.
Reads were trimmed using Trimmomatic version 0.36.
Count data were generated by means of the HTSeq method.
Genome_build: GRCh38
Supplementary_files_format_and_content: counts

source_name: whole blood

growth_protocol: Sampling was performed on days 1 and 5, for all consenting patients, using PAXgene blood RNA tubes (BD Biosciences). A separate optional informed consent form for Belgium. As described in the Statistical Analysis Plan (Online Supplement 1), only patients with extreme phenotypes (i.e. the upper quartile of SOFA score distribution) were included in the current analysis. Samples from 7 age,- sex- and Charlson comorbidity index-matched control subjects without sepsis, enrolled within the prospective registry of the Hellenic Sepsis Study Group (55 study sites across Greece under the respective Ethics Committee approval) were used to assess differential gene expression with INCLASS patients

extract_protocol:
Total RNA was isolated from PAXgene blood tubes using PaxGene Blood miRNA kits according to the manufacturer’s instructions (Qiagen). RNA quality was assessed by bioanalysis (Agilent), with all samples having RNA integrity numbers > 6.0. Total RNA concentrations were determined by Qubit® 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA).
Libraries were prepared from 200ng total RNA using KAPA RNA Hyperprep with RiboErase (Roche) kits.

value: whole blood

tag: individual

tag: condition

value: sepsis

tag: class

value: Clarithromycin

tag: time

value: treatment day 5

tag: age

tag: Sex

value: male


title: Pheripheral blood cells, patient with prostate cancer, CITE-RNA seq

description: 10x Genomics

value: prostate cancer

value: Androgen deprivation therapy


title: INC_H006_D5


title: Pheripheral blood cells, patient with prostate cancer, scRNA seq

description: 10x Genomics

library_source: transcriptomic single cell


title: INC_J002_D1

value: treatment day 1


title: INC_G006_D1

value: female


title: INC_H006_D1


title: Control1

value: embryo DIV 7d

value: primary cell

value: cortical neuron

tag: genotype

value: WT


title: INC_F005_D1

tag: tissue

value: Placebo


title: INC_F002_D5


title: INC_G004_D5


title: INC_G006_D5


title: INC_G004_D1


title: INC_E009_D1


title: INC_E009_D5


title: INC_G001_D1


title: INC_F002_D1


title: INC_F005_D5


title: INC_E006_D5


title: INC_F006_D1


title: Pheripheral blood cells, healthy control, scRNA seq

description: 10x Genomics

value: peripheral blood

value: healthy control


title: INC_E005_D1


title: INC_E005_D5


title: INC_B023_D5


title: INC_B015_D5


title: INC_B023_D1


title: INC_B015_D1


title: INC_B010_D5


title: INC_B031_D1


title: INC_B008_D1


title: INC_A009_D5


title: INC_A004_D1


title: INC_B010_D1


title: INC_A003_D5


title: INC_A009_D1


title: INC_A003_D1


title: HVI_009_S26

value: control

value: healthy


title: HVI_007_S24

value: whole blood


title: HVI_008_S25


title: HVI_006_S23


title: HVI_004_S21


title: HVI_005_S22


title: HVI_003_S20


title: CID005506

city: Amsterdam

first: Leandro

last: Moreno

address: Meibergdreef 9

country: Netherlands

institute: AmsterdamUMC

data_processing:
Single cell sequencing data were aligned to the human reference genome (GRCh38) and processed using the CellRanger 2.1.0 software from 10x Genomics to generate unique molecular identifier (UMI) counts.
Genome_build: GRCh38
Supplementary_files_format_and_content: Raw counts table

source_name: patient with peritoneal metastasis

extract_protocol: Samples were dissociated as nuclei and sequenced with 10x Genomics 5’ chemistry. 10.000 nuclei persample were loaded on the 10x 5’ Genomics chip

value: peritoneal metastasis


title: CID005504


title: CID005505


title: CID005499


title: CID005503


title: CID005502


title: MYC med 24h T4

city: London

first: Dinis

middle: Pedro

last: Calado

address: Midland Road

institute: The Francis Crick Institute

description:
MYC_medium_treated
LUE735A48

data_processing:
The RSEM package (version 1.2.31) (Li and Dewey, 2011) was used in conjunction with the STAR alignment algorithm (version 2.5.2a) (Dobin et al., 2013) for the mapping and subsequent gene-level counting of the sequenced reads with respect to Ensembl human GRCh38 release 86  transcriptome
Normalisation of raw count data and differential expression analysis was performed with the DESeq2 package (version 1.16.1)  within the R programming environment (version 3.4.1)
Genome_build: GRCh38 release 86
Supplementary_files_format_and_content: VST log2 normalised expression values. Rows = genes; Columns = samples.

source_name: P493-6 (MYC medium)

growth_protocol: The P493-6 was grown in DMEM with 10% FBS.

extract_protocol:
Cell lysis and extraction of the RNA was conducted with the QIAGEN miRNeasy kit according to manufacturer's instructions.
Samples were prepared with Nugen cDNA kit and sequenced using Illumina HiSeq system

treatment_protocol: The different MYC levels were induced 24 hours prior adding the NMT inhibitor IMP1088 (MYC high: NA; MYC medium: DMEM with 0.1 ug/mL doxycycline and 1 uM of beta-estradiol). Subsequently 100 nM of the NMT inhibitor or a corresponding DMSO control was added.

tag: cell line

value: Immortalised cell line P493-6

tag: myc level

value: medium

value: NMT inhibitor IMP1088


title: MYC med 24h T2

description:
MYC_medium_treated
LUE735A46


title: MYC high 24h T4

description:
MYC_high_treated
LUE735A32

source_name: P493-6 (MYC high)

value: high


title: MYC med 24h T3

description:
MYC_medium_treated
LUE735A47


title: MYC med 24h C3

description:
MYC_medium_control
LUE735A43

value: DMSO


title: INC_A004_D5

value: sepsis

value: treatment day 5

value: male


title: MYC med 24h T1

description:
MYC_medium_treated
LUE735A45


title: MYC med 24h C4

description:
MYC_medium_control
LUE735A44


title: MYC high 24h C4

description:
MYC_high_control
LUE735A28


title: MYC high 24h T2

description:
MYC_high_treated
LUE735A30


title: MYC high 24h T1

description:
MYC_high_treated
LUE735A29


title: MYC high 24h C2

description:
MYC_high_control
LUE735A26


title: MYC high 24h C3

description:
MYC_high_control
LUE735A27


title: MYC high 24h C1

description:
MYC_high_control
LUE735A25


title: T cell [T3]

city: Guangzhou

first: Dongming

last: Kuang

address: No. 135, Xingang Xi Road

institute: Sun Yat-sen University

description:
T3
T cells cultured in medium.

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing poly-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Bowtie v2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12. We selected TopHat as the mapping tool for that TopHat can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. Then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Genome_build: ftp://ftp.ensembl.org/pub/release-77/fasta/homo_sapiens/dna/
Supplementary_files_format_and_content: *fpkm.txt: Tab-delimited text files include FPKM values.

extract_protocol:
Trizol reagent (Invitrogen) was used to isolate total RNA of T from an in vitro culture system. A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: T cells, cultured in medium or with B cells for 7 days in the presence of CD3-cross-linking Abs, were sorted for RNA-sequencing.

tag: cell type

value: T cells

tag: culture condition

value: Medium

tag: donor


title: T cell [T_2]

description:
T_2
T cells cultured in medium.


title: T cell [T1]

description:
T1
T cells cultured in medium.


title: B-cell-treated T cell [T_4]

description:
T_4
T cells cultured with B cells.

value: B cells


title: Microglia, STAT1-KO, 12DPI, replicate 3

city: Charlottesville

first: Tajie

last: Harris

state: VA

address: 200 Jeanette Lancaster Way

department: Neuroscience

institute: University of Virginia

description:
matrix column 8
stat1_mg_rlog_counts.csv
stat1_mg_deseq2_results.csv

data_processing:
fastq files were processed with Trimmomatic (v0.39, paired-end mode)  to trim adapters and filter reads with a minimum quality score of 15, leading and trailing quality scores of 3, and a minimum fragment length of 36.
FastQC (v0.11.9) was used to assess quality of trimmed and filtered reads
Salmon (v0.8.2) was used to align reads to the mm10 reference genome
Tximport (v1.24.0) and DESeq2 (v1.36.0) were used in R to import abundance files, consolidate transcripts, and conduct differential gene expression analysis.
Assembly: GENCODE M13
Supplementary files format and content: .csv file containing DESeq2 rlog-transformed count matrix
Supplementary files format and content: .csv file containing DESeq2 output (differential gene expression analysis)

source_name: brain

growth_protocol: Mice were age- and sex-matched for all experiments. T. gondii was passaged through chronicallly-infected CBA/J mice. Infected CBA/J brains were homogenized, and T. gondii was isolated for use in experimental infections.

extract_protocol:
RNA was extracted using Rneasy Plus Mini Kit (Qiagen). RNA was quantified using Qubit Fluorometer (Life Technologies) and integrity was checked with TapeStation (Agilent Technologies)
Illumina Nextera XT library was used for sequencing library construction, according to manufacturer's instructions.

treatment_protocol: Mice received five consecutive doses of tamoxifen (4 mg per 20g body weight) at 4 weeks of age. Following a four week rest period, they were intraperitoneally infected with 10 cysts of the Me49 strain of Toxoplasma gondii and brains were analyzed at 12 days post-infection. All procedures followed the regulations of the University of Virginia Institutional Animal Care and Use Committee.

value: brain

value: Microglia

value: Male

tag: infection

value: T. gondii

value: 12 days post-infection


title: Microglia, STAT1-KO, 12DPI, replicate 2

description:
matrix column 7
stat1_mg_rlog_counts.csv
stat1_mg_deseq2_results.csv


title: Microglia, STAT1-KO, 12DPI, replicate 1

description:
matrix column 6
stat1_mg_rlog_counts.csv
stat1_mg_deseq2_results.csv


title: MYC med 24h C2

description:
MYC_medium_control
LUE735A42

tag: treatment


title: Microglia, control, 12DPI, replicate 3

description:
matrix column 3
stat1_mg_rlog_counts.csv
stat1_mg_deseq2_results.csv

value: CX3CR1creERT2/+ :ROSA26ZsGreen/ZsGreen


title: Microglia, control, 12DPI, replicate 1

description:
matrix column 1
stat1_mg_rlog_counts.csv
stat1_mg_deseq2_results.csv


title: MYC high 24h T3

description:
MYC_high_treated
LUE735A31

value: Immortalised cell line P493-6


title: MYC med 24h C1

description:
MYC_medium_control
LUE735A41

value: medium


title: CD133+ DNGR-1 traced cells

first: Bruno

last: Frederico

address: 1 Midland Road

institute: Francis Crick Institute

data_processing:
10X’s Cell Ranger software was used to de-multiplex Illumina BCL output, create fastq files and generate single cell feature counts.
Raw reads were initially processed by the Cell Ranger v.3.0.2 pipeline, which deconvolved reads to their cell of origin using the UMI tags, aligned these to the mm10 transcriptome using STAR (v.2.5.1b) and reported cell-specific gene expression count estimates.
All subsequent analyses were performed in R v.3.6.0 using the Seurat (v3) package. Genes were considered to be ‘expressed’ if the estimated (log10) count was at least 0.1. Primary filtering was then performed by removing from consideration: cells expressing fewer than 50 genes and cells for which mitochondrial genes made up greater than 10% of all expressed genes.
Assembly: mm10
Supplementary files format and content: *txt: Tab-delimited texts contain raw counts.

source_name: Spinal cord

growth_protocol: No growth protocol was used. Cells were dissected from spinal cord tissue.

extract_protocol:
Cell lysis and RT reaction occur in droplets containing uniquely barcoded beads (GEMs (Gel Bead-In EMulsion).
Library generation for 10x Genomics analysis were performed following the Chromium Single Cell 3′ Reagents Kits (10x Genomics) and sequenced on an Hiseq4000 (Illumina), to achieve an average of ~280,000 reads per cell.

treatment_protocol: Clec9acre/creR26LSLtdTomato/LSLtdTomato mice were sacrificed with i.p. injection of pentobarbital, perfused with 20ml of sterile PBS, spinal cords dissected and digested into a single-cell suspension using Neural Tissue Dissociation Kit (P) (Miltenyi Biotec) following manufacturer instructions. Sample was enriched for ependymal cells by further processing with myelin removal magnetic beads II (Mltenyi Biotec) to remove myelinated cells by passage through a MACS column (Miltenyi Biotec). Cells were then stained with AF488-conjugated anti-CD133 (clone 13A4), AD647-conjugated anti-CD45 (clone 30-F11) and LIVE/DEAD blue viability dye. LIVE/DEAD- CD45- CDF133+ DNGR-1 traced or LIVE/DEAD- CD45- CDF133+ non-traced cells were FACS sorted into two different tubes on an Aria Fusion (BD) with a 100um nozzle.

value: Spinal cord

value: CD133+ DNGR-1 traced cells

value: Adult (10-12 weeks-old)

tag: strain


title: CD133+ non-traced cells

value: CD133+ non-traced cells


title: CONTROL #2

city: New Haven

first: Leyuan

last: Xu

state: CT

address: 300 Cedar Street, Ste S255B

department: Internal Medicine/Section of Nephrology

institute: Yale University

description: Single cell RNA

data_processing:
Cell Ranger version 5.0.1 was used to process Chromium single cell 3’ RNA-seq output and align the Read to the mouse reference transcriptome (mm10-2020-A).
A downstream data analysis was performed using Seurat v4.0 R package.
Cells with transcriptome < 200 (likely cell fragments) or > 3,500 (potentially cell duplets) and cells with mitochondrial gene percentage > 50% were excluded.
Genome_build: mm10-2020-A
Supplementary_files_format_and_content: Tab-delimited text files include gene counts, data, and scaled data for each cell and each sample.
Supplementary_files_format_and_content: *_counts.txt: Counts
Supplementary_files_format_and_content: *_data.txt: Normalized data
Supplementary_files_format_and_content: *__metadata.txt: Metadata
Supplementary_files_format_and_content: *_scale_data.txt: Scaled data

source_name: Kidney

extract_protocol:
Injured kidneys were harvested, minced into approximately 1 mm3 cubes, and digested using Liberase™ (100 µg/mL) and DNase I (10 µg/mL) (Roche Diagnostics) for 25 min at 37 °C. Reaction was deactivated by adding chilled DMEM with 10% FBS. The solution was then passed through a 40-µm cell strainer. After centrifugation at 300 g for 5 min at 4 °C, the cell pellet was resuspended in chilled DMEM with 10% FBS and passed through another 40-µm cell strainer. The dead cells were removed using Dead Cell Removal Kit (Miltenyi Biotec). Cell number and viability were analyzed using trypan blue staining (Invitrogen). This method generated single cell suspensions with greater than 80% viability.
The scRNA-seq library and sequencing were performed at the Yale Center for Genome Analysis (YCGA).

value: Kidney

value: 9 weeks

value: Wild-type

value: Healthy control


title: B-cell-treated T cell [T2]

description:
T2
T cells cultured with B cells.

value: T cells

value: B cells


title: B-cell-treated T cell [T4]

description:
T4
T cells cultured with B cells.


title: U-IRI D7 #2

description: Single cell RNA

value: Unilateral IRI with contralateral kidney intact

tag: time point

value: 7 days after IRI


title: IRI/CL-NX D7 #2

description: Single cell RNA

value: Unilateral IRI with contralateral nephrectomy


title: IRI/CL-NX D7 #1

description: Single cell RNA


title: U-IRI D7 #1

description: Single cell RNA


title: IRI/CL-NX D14 #1

description: Single cell RNA

value: 14 days after IRI


title: U-IRI D14 #2

description: Single cell RNA


title: Microglia, control, 12DPI, replicate 5

description:
matrix column 5
stat1_mg_rlog_counts.csv
stat1_mg_deseq2_results.csv

value: brain

value: Microglia

value: CX3CR1creERT2/+ :ROSA26ZsGreen/ZsGreen

value: Male

value: T. gondii

value: 12 days post-infection


title: Microglia, control, 12DPI, replicate 4

description:
matrix column 4
stat1_mg_rlog_counts.csv
stat1_mg_deseq2_results.csv


title: IRI/CL-NX D30 #2

description: Single cell RNA

value: 30 days after IRI


title: Microglia, control, 12DPI, replicate 2

description:
matrix column 2
stat1_mg_rlog_counts.csv
stat1_mg_deseq2_results.csv


title: HICA_A3

data_processing:
Trimmomatic v0.36 was used to remove the adapters and filter raw reads below 36 bases long. The filtered reads were aligned to the Mus musculus genome Ensembl GRCm38 (release 86) using RSEM v1.3.0  and STAR v2.5.2 with the “--forward-prob” parameter was set to “0.5” and all other parameters were kept as default.
Raw counts were processed using the bioconductor package DESeq2 v1.18.1 in R v3.4.3, and normalized using the DESeq method to remove the library-specific artefacts. Variance stabilizing transformation was applied to obtain normalized log2 gene expression values.
Genome_build: Ensembl GRCm38 (release 86)
Supplementary_files_format_and_content: VST log2 normalised expression values. Rows = genes; Columns = samples.

source_name: Hippocampus

growth_protocol: Growth and maintenance of adherent NSCs: Tissue culture (T25) were pre-coated for at least 1 hour with DMEM:F12 supplemented with N-2Max supplement, bFGF (20ng/ml), EGF (20ng/ml), Heparin (5ug/ml), Laminin (2ug/ml) antibiotics and glutamine. NSCs were further cultured with this media for 4 days.

extract_protocol:
NSCs were collected after 4 days and astrocytes were collected after 6 days of culture. Cells were lysed in RLT buffer supplemented with 2-mercaptoethanol. Cell lysates were stored at -80C before RNA extraction.Total RNA was extracted with RNeasy Mini kit (Qiagen) following manufacturer protocol.
RNA (200 ng) was used to prepare cDNA libraries using the TruSeq Stranded mRNA HT Library Preparation Kit (Illumina). Libraries were normalized, pooled and then clustered using the HiSeq® 3000/4000 PE Cluster Kit (Illumina). The libraries were imaged and sequenced on an Illumina HiSeq 4000 sequencer using the HiSeq® 3000/4000 SBS kit (Illumina) at a minimum of 25 million single-end reads (76 bp) per sample.

treatment_protocol: Astrocyte differentiation: NSCs were cultured under adherent conditions for 24 hours had their NSC media removed and replaced with DMEM:F12 supplemented with BMP4 (20ng/ml). After 3 days media was replaced with fresh media containing BMP4 (20ng/ml).

value: Astrocyte


title: DNGR-1 lineage traced ependymal cells

data_processing:
10X’s Cell Ranger software was used to de-multiplex Illumina BCL output, create fastq files and generate single cell feature counts
Raw reads were initially processed by the Cell Ranger v.3.0.2 pipeline, which deconvolved reads to their cell of origin using the UMI tags, aligned these to the mm10 transcriptome using STAR (v.2.5.1b) and reported cell-specific gene expression count estimates.
All subsequent analyses were performed in R v.3.6.0 using the Seurat (v3) package.  Genes were considered to be ‘expressed’ if the estimated (log10) count was at least 0.1. Primary filtering was then performed by removing from consideration: cells expressing fewer than 50 genes and cells for which mitochondrial genes made up greater than 10% of all expressed genes.
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited text containing raw counts

growth_protocol: No growth protocol was used. Cells were dissected from spinal cord tissue

extract_protocol:
Cell lysis and RT reaction occur in droplets containing uniquely barcoded beads (GEMs (Gel Bead-In EMulsion)
Library generation for 10x Genomics analysis were performed following the Chromium Single Cell 3′ Reagents Kits (10x Genomics) and sequenced on an Hiseq4000 (Illumina), to achieve an average of ~280,000 reads per cell.

treatment_protocol: Clec9a+/creR26LSLtdTomato/LSLtdTomato mice were sacrified with i.p. injection of pentobarbital, perfused with 20ml of sterile PBS, spinal cords dissected and digested into a single-cell suspension using Neural Tissue Dissociation Kit (P) (Miltenyi Biotec) following manufacture instructions. Sample was enriched for ependymal cells by further processing withmyelin removal magnetic beads II (Mltenyi Biotec) to remove myelinated cells by passage through a MACS column (Miltenyi Biotec). Cells were then stained with FITC-conjugated anti-CD45 (clone 104), incubated with anti-FITC magnetic Microbeads and put through another MACS column to remove CD45+ cells. Cells were finally stained with APC-conjugated CD45 (clone 30-F11) and DAPI (to exclude dead cells and single DNGR-1-traced (tdTomato+) CD45- DAPI- cells were FACS sorted on an Aria Fusion (BD) with a 100um nozzle.

value: Spinal cord

tag: Stage

value: Adult animals (10-14 weeks-old)

value: DNGR-1 lineage traced ependymal cells


title: CRDT_A3

source_name: Spinal Cord - DNGR-1 lineage traced (EYFP)

value: DNGR-1 +/- EYFP+/-


title: HICA_A2


title: U-IRI D30 #1

description: Single cell RNA

value: Kidney

value: 9 weeks

value: Wild-type


title: CRDU_A3

source_name: Spinal Cord - DNGR-1 lineage traced (tdTomato)


title: CONTROL #1

description: Single cell RNA

value: Healthy control


title: CRDT_A2


title: IRI/CL-NX D30 #1

description: Single cell RNA

value: Unilateral IRI with contralateral nephrectomy


title: CRDU_A1


title: HICA_S3

value: Stem Cell


title: CRDU_A2


title: IRI/CL-NX D14 #2

description: Single cell RNA

value: 14 days after IRI


title: CRDT_S1


title: HICA_S1


title: U-IRI D14 #1

description: Single cell RNA

value: Unilateral IRI with contralateral kidney intact


title: CRDU_S1


title: CRDT_A1


title: CRDT_S2


title: HICA_A1


title: CRDT_S3


title: ATAC-seq_IR_WT

city: TianJin

first: Xiao Tong

last: Ma

state: TianJin

address: Blood hospital, 288 Nanjing Road

department: Institute of Hematology & Blood Diseases Hospital

institute: Chinese Academy of Medical Sciences

data_processing:
RNA-seq: Illumina Casava1.7 software used for basecalling.
RNA-seq: Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence,then use BWA (Li, H. and Durbin, R., 2009) to map clean reads to genome reference and use Bowtie (Langmead B, et al., 2009) to gene reference.
ATAC-seq: skewer 0.1.126 is required for trimming raw data. Parameter: -m pe.
ATAC-seq: BWA 0.7.12-r1039 is required for mapping. Parameter: -T 25 -k 18.
ATAC-seq: deepTools3.0.2 is required for sample analysis. Parameter: --corMethod pearson.
ATAC-seq: MACS2 2.1.0 is required for peak calling. Parameter: -q 0.05 --nomode --call-summits --nomodel.
ATAC-seq: homer findMotifsGenome.pl v4.9.1 is required for identifying motif. Parameter: -gc -len 8,10,12,14.
Genome_build: mm10
Supplementary_files_format_and_content: RNA-seq: Gene quantification txt file; ATAC-seq: Signal track bigWig file.

source_name: Lineage–Sca1+cKit+CD34–Flk2– long-term hematopoietic stem cells

extract_protocol:
Lineage–Sca1+cKit+CD34–Flk2– cells were collected and RNA was harvested using RLT reagent. Qiagen RNeasy Mini Kit (Cat#74104) was used for the construction of sequencing libraries. For ATAC-seq samples nuclei were subjected to Tn5 transposase reaction (Illumina Nextera DNA Sample Preparation Kit) following manufacturer’s instructions and DNA was purified using the Agencourt AMPure XP beads (Beckman Coulter).
RNA libraries were prepared for sequencing using standard Illumina protocols. ATAC-seq was performed as originally described in Buenrostro et al. 2013.

treatment_protocol: Long-term hematopoietic stem cells  were isolated from bone marow of WT or Twist1 cKO mice 12 days after irradiation treatment or under steady state

value: irradiation

value: long-term hematopoietic stem cell

value: wild type


title: DM600_6m_rep1_IP

city: La Jolla

first: Gene

last: Yeo

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

data_processing:
Reads were adapter-trimmed using Cutadapt (v1.14) and mapped to human-specific repetitive elements from RepBase (version 18.05) by STAR (v2.4.0i)(Dobin et al., 2013).
Repeat-mapping reads were removed, and remaining reads were mapped to the human genome assembly (hg19) with STAR. PCR duplicate reads were removed using the unique molecular identifier (UMI) sequences in the 5’ adapter and remaining reads retained as ‘usable reads’.
Peaks were called on the usable reads by CLIPper (Lovci et al., 2013) and assigned to gene regions annotated in GENCODE (hg19) with the following descending priority order: CDS, 5’UTR, 3’UTR, proximal intron, and distal intron. Proximal intron regions are defined as extending up to 500 bp from an exon-intron junction. Each peak was normalized to the size-matched input (SMInput) by calculating the fraction of the number of usable reads from immunoprecipitation to that of the usable reads from the SMInput. Peaks were deemed significant at 8-fold enrichment and p-value10-3(Chi-squared test, or Fisher’s exact test if the observed or expected read number in eCLIP or SMInput was below 5).
Assembly: hg19
Supplementary files format and content: bigwig files for input and IP samples as well as beds files for significant eCLIP peaks per experimental group
Library strategy: enhanced CLIP

source_name: DM600 iPSC

growth_protocol: Cortical organoids were maintained in Neurobasal supplemented with 1% B27, 1% GlutaMax, 1% NEAA and 1% Penicillin/Strep and 20 ng/mL FGF2 (Life Technologies)  in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
eCLIP was performed essentially as described in Van Nostrand et al; 2016. Briefly, 20 cortical organoids per group were UV-cross-linked (400 mJ cm-2, 254 nm) and lysed. Lysates were sonicated and treated with RNase I to fragment RNA. Two percent of each lysate sample was stored for preparation of a parallel SMInput library. The remaining lysates were immunoprecipitated using a rabbit anti-CELF2 antibody (MBL XXXX). Bound RNA fragments in the immunoprecipitates were dephosphorylated and 3’-end ligated to an RNA adaptor. Protein-RNA complexes from SMInputs and immunprecipitates were run on an SDS-polyacrylamide gel and transferred to a nitrocellulose membrane. Membrane region comprising of the exact molecular weight of CELF2 (55 kDa) to 75 kDa above were excised, and RNA was released from the complexes with proteinase K.
SMInput samples were dephosphorylated and 3’-end ligated to an RNA adaptor. All RNA samples (immunoprecipitates and SMInputs) were reverse transcribed with AffinityScript (Agilent). cDNAs were 5’-end ligated to a DNA adaptor. cDNA yields were quantified by qPCR, and 100-500 fmal of library was generated with Q5 PCR mix (NEB).

value: DM600 iPSC

value: induced pluripotent stem cell

value: Myotonic dystrophy

value: 6 months


title: ATAC-seq_IR_KO

value: Twist1 cKO


title: RNA-seq_IR_WT


title: RNA-seq_H_KO


title: U-IRI D30 #2

description: Single cell RNA

value: 30 days after IRI


title: DM1200_6m_rep2_IP

source_name: Dm1200 iPSC

value: Dm1200 iPSC


title: DM1200_6m_rep2_INPUT


title: RNA-seq_IR_KO


title: DM1200_6m_rep1_IP


title: RNA-seq_H_WT


title: DM600_6m_rep2_INPUT


title: DM600_6m_rep2_IP


title: Control2_6m_rep2_INPUT

source_name: KIN iPSc

value: KIN iPSc

value: WT


title: Control2_6m_rep1_IP


title: Control1_6m_rep2_IP

source_name: CVB24 iPSC

value: CVB24 iPSC


title: CRDU_S2


title: HICA_S2


title: Control1_6m_rep1_INPUT


title: Control1_6m_rep2_INPUT


title: CRDU_S3


title: Control2_6m_rep1_INPUT


title: DM1200_6m_rep1_INPUT


title: Control2_6m_rep2_IP


title: M-HDAC-4.H10

city: Yokohama

first: Andrew

middle: Tae-Jun

last: Kwon

state: Kanagawa

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

department: IMS

institute: RIKEN

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

source_name: MCF7 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.

value: VPA


title: M-HDAC-4.H11

description: C1 CAGE

value: TSA


title: M-HDAC-4.H09

description: C1 CAGE


title: M-HDAC-4.H07

description: C1 CAGE

value: Control


title: M-HDAC-4.H12

description: C1 CAGE


title: M-HDAC-4.H03

description: C1 CAGE


title: DM600_6m_rep1_INPUT


title: M-HDAC-4.G12

description: C1 CAGE


title: M-HDAC-4.G08

description: C1 CAGE


title: M-HDAC-4.H02

description: C1 CAGE


title: M-HDAC-4.H06

description: C1 CAGE


title: M-HDAC-4.G07

description: C1 CAGE


title: M-HDAC-4.H04

description: C1 CAGE


title: M-HDAC-4.H05

description: C1 CAGE


title: M-HDAC-4.H01

description: C1 CAGE


title: M-HDAC-4.H08

description: C1 CAGE


title: M-HDAC-4.G09

description: C1 CAGE


title: Control1_6m_rep1_IP


title: M-HDAC-4.G10

description: C1 CAGE


title: M-HDAC-4.G03

description: C1 CAGE


title: M-HDAC-4.G02

description: C1 CAGE


title: M-HDAC-4.G01

description: C1 CAGE


title: M-HDAC-4.F12

description: C1 CAGE


title: M-HDAC-4.F08

description: C1 CAGE


title: M-HDAC-4.G06

description: C1 CAGE


title: M-HDAC-4.F06

description: C1 CAGE


title: M-HDAC-4.F10

description: C1 CAGE


title: M-HDAC-4.G11

description: C1 CAGE


title: M-HDAC-4.F07

description: C1 CAGE


title: M-HDAC-4.F02

description: C1 CAGE


title: M-HDAC-4.F04

description: C1 CAGE


title: M-HDAC-4.E12

description: C1 CAGE


title: M-HDAC-4.F01

description: C1 CAGE


title: M-HDAC-4.G04

description: C1 CAGE


title: M-HDAC-4.E08

description: C1 CAGE


title: M-HDAC-4.E09

description: C1 CAGE


title: M-HDAC-4.F03

description: C1 CAGE


title: M-HDAC-4.E05

description: C1 CAGE


title: M-HDAC-4.E06

description: C1 CAGE


title: M-HDAC-4.E01

description: C1 CAGE


title: M-HDAC-4.E04

description: C1 CAGE


title: M-HDAC-4.D10

description: C1 CAGE


title: M-HDAC-4.E03

description: C1 CAGE


title: M-HDAC-4.G05

description: C1 CAGE


title: M-HDAC-4.F09

description: C1 CAGE


title: M-HDAC-4.F05

description: C1 CAGE


title: M-HDAC-4.D12

description: C1 CAGE


title: M-HDAC-4.D05

description: C1 CAGE


title: M-HDAC-4.D06

description: C1 CAGE


title: M-HDAC-4.D07

description: C1 CAGE


title: M-HDAC-4.E11

description: C1 CAGE


title: M-HDAC-4.E10

description: C1 CAGE


title: M-HDAC-4.D04

description: C1 CAGE


title: M-HDAC-4.D01

description: C1 CAGE


title: M-HDAC-4.C11

description: C1 CAGE


title: M-HDAC-4.C12

description: C1 CAGE


title: M-HDAC-4.D11

description: C1 CAGE


title: M-HDAC-4.C08

description: C1 CAGE


title: M-HDAC-4.D09

description: C1 CAGE


title: M-HDAC-4.F11

description: C1 CAGE


title: M-HDAC-4.C06

description: C1 CAGE


title: M-HDAC-4.C07

description: C1 CAGE


title: M-HDAC-4.B12

description: C1 CAGE


title: M-HDAC-4.E02

description: C1 CAGE


title: M-HDAC-4.B10

description: C1 CAGE


title: M-HDAC-4.B11

description: C1 CAGE


title: M-HDAC-4.D08

description: C1 CAGE


title: M-HDAC-4.C05

description: C1 CAGE


title: M-HDAC-4.B08

description: C1 CAGE


title: M-HDAC-4.B06

description: C1 CAGE


title: M-HDAC-4.B05

description: C1 CAGE


title: M-HDAC-4.E07

description: C1 CAGE


title: M-HDAC-4.B02

description: C1 CAGE


title: M-HDAC-4.D03

description: C1 CAGE


title: M-HDAC-4.C10

description: C1 CAGE


title: M-HDAC-4.B01

description: C1 CAGE


title: M-HDAC-4.D02

description: C1 CAGE


title: M-HDAC-4.C02

description: C1 CAGE


title: M-HDAC-4.A12

description: C1 CAGE


title: M-HDAC-4.A10

description: C1 CAGE


title: M-HDAC-4.C03

description: C1 CAGE


title: M-HDAC-4.A09

description: C1 CAGE


title: M-HDAC-4.C04

description: C1 CAGE


title: M-HDAC-4.B09

description: C1 CAGE


title: M-HDAC-4.C09

description: C1 CAGE


title: M-HDAC-4.C01

description: C1 CAGE


title: M-HDAC-4.A05

description: C1 CAGE


title: M-HDAC-4.B07

description: C1 CAGE


title: M-HDAC-4.A07

description: C1 CAGE


title: M-HDAC-4.A04

description: C1 CAGE


title: M-HDAC-4.A03

description: C1 CAGE


title: M-HDAC-4.B03

description: C1 CAGE


title: M-HDAC-4.A02

description: C1 CAGE


title: M-HDAC-4.B04

description: C1 CAGE


title: M-HDAC-4.A08

description: C1 CAGE


title: M-HDAC-3.H09

description: C1 CAGE


title: M-HDAC-4.A06

description: C1 CAGE


title: M-HDAC-3.H11

description: C1 CAGE


title: M-HDAC-4.A11

description: C1 CAGE


title: M-HDAC-4.A01

description: C1 CAGE


title: M-HDAC-3.H05

description: C1 CAGE


title: M-HDAC-3.H10

description: C1 CAGE


title: M-HDAC-3.H04

description: C1 CAGE


title: M-HDAC-3.H12

description: C1 CAGE


title: M-HDAC-3.H08

description: C1 CAGE


title: M-HDAC-3.H03

description: C1 CAGE


title: M-HDAC-3.H07

description: C1 CAGE


title: M-HDAC-3.H06

description: C1 CAGE


title: M-HDAC-3.H02

description: C1 CAGE


title: M-HDAC-3.H01

description: C1 CAGE


title: M-HDAC-3.G10

description: C1 CAGE


title: M-HDAC-3.G11

description: C1 CAGE


title: M-HDAC-3.G09

description: C1 CAGE


title: M-HDAC-3.G02

description: C1 CAGE


title: M-HDAC-3.G12

description: C1 CAGE


title: M-HDAC-3.G04

description: C1 CAGE


title: M-HDAC-3.G01

description: C1 CAGE


title: M-HDAC-3.G05

description: C1 CAGE


title: M-HDAC-3.G07

description: C1 CAGE


title: M-HDAC-3.G08

description: C1 CAGE


title: M-HDAC-3.G06

description: C1 CAGE


title: M-HDAC-3.F10

description: C1 CAGE


title: M-HDAC-3.F04

description: C1 CAGE


title: M-HDAC-3.F12

description: C1 CAGE


title: M-HDAC-3.F08

description: C1 CAGE


title: M-HDAC-3.F07

description: C1 CAGE


title: M-HDAC-3.F05

description: C1 CAGE


title: M-HDAC-3.F01

description: C1 CAGE


title: M-HDAC-3.F03

description: C1 CAGE


title: M-HDAC-3.F02

description: C1 CAGE


title: M-HDAC-3.G03

description: C1 CAGE


title: M-HDAC-3.E10

description: C1 CAGE


title: M-HDAC-3.E09

description: C1 CAGE


title: M-HDAC-3.E11

description: C1 CAGE


title: M-HDAC-3.E08

description: C1 CAGE


title: M-HDAC-3.F06

description: C1 CAGE


title: M-HDAC-3.E01

description: C1 CAGE


title: M-HDAC-3.E05

description: C1 CAGE


title: M-HDAC-3.F09

description: C1 CAGE


title: M-HDAC-3.D12

description: C1 CAGE


title: M-HDAC-3.E12

description: C1 CAGE


title: M-HDAC-3.D11

description: C1 CAGE


title: M-HDAC-3.E07

description: C1 CAGE


title: M-HDAC-3.E06

description: C1 CAGE


title: M-HDAC-3.E02

description: C1 CAGE


title: M-HDAC-3.E04

description: C1 CAGE


title: M-HDAC-3.D06

description: C1 CAGE


title: M-HDAC-3.F11

description: C1 CAGE


title: M-HDAC-3.D08

description: C1 CAGE


title: M-HDAC-3.E03

description: C1 CAGE


title: M-HDAC-3.D05

description: C1 CAGE


title: M-HDAC-3.D03

description: C1 CAGE


title: M-HDAC-3.D10

description: C1 CAGE


title: M-HDAC-3.D09

description: C1 CAGE


title: M-HDAC-3.C11

description: C1 CAGE


title: M-HDAC-3.C07

description: C1 CAGE


title: M-HDAC-3.C10

description: C1 CAGE


title: M-HDAC-3.C09

description: C1 CAGE


title: M-HDAC-3.C08

description: C1 CAGE


title: M-HDAC-3.D07

description: C1 CAGE


title: M-HDAC-3.D04

description: C1 CAGE


title: M-HDAC-3.C03

description: C1 CAGE


title: M-HDAC-3.C02

description: C1 CAGE


title: M-HDAC-3.D02

description: C1 CAGE


title: M-HDAC-3.D01

description: C1 CAGE


title: M-HDAC-3.C04

description: C1 CAGE


title: M-HDAC-3.C12

description: C1 CAGE


title: M-HDAC-3.C06

description: C1 CAGE


title: M-HDAC-3.B12

description: C1 CAGE


title: M-HDAC-3.B10

description: C1 CAGE


title: M-HDAC-3.C05

description: C1 CAGE


title: M-HDAC-3.B04

description: C1 CAGE


title: M-HDAC-3.B03

description: C1 CAGE


title: M-HDAC-3.B11

description: C1 CAGE


title: M-HDAC-3.B08

description: C1 CAGE


title: M-HDAC-3.B01

description: C1 CAGE


title: M-HDAC-3.B09

description: C1 CAGE


title: M-HDAC-3.B07

description: C1 CAGE


title: M-HDAC-3.A07

description: C1 CAGE


title: M-HDAC-3.A10

description: C1 CAGE


title: M-HDAC-3.A08

description: C1 CAGE


title: M-HDAC-2.H12

description: C1 CAGE


title: M-HDAC-3.A06

description: C1 CAGE


title: M-HDAC-3.A01

description: C1 CAGE


title: M-HDAC-3.A12

description: C1 CAGE


title: M-HDAC-3.C01

description: C1 CAGE


title: M-HDAC-3.A04

description: C1 CAGE


title: M-HDAC-3.A09

description: C1 CAGE


title: M-HDAC-3.B05

description: C1 CAGE


title: M-HDAC-2.H09

description: C1 CAGE


title: M-HDAC-3.B06

description: C1 CAGE


title: M-HDAC-2.H10

description: C1 CAGE


title: M-HDAC-3.B02

description: C1 CAGE


title: M-HDAC-3.A02

description: C1 CAGE


title: M-HDAC-2.H06

description: C1 CAGE


title: M-HDAC-2.H11

description: C1 CAGE


title: M-HDAC-3.A03

description: C1 CAGE


title: M-HDAC-3.A05

description: C1 CAGE


title: M-HDAC-2.H03

description: C1 CAGE


title: M-HDAC-3.A11

description: C1 CAGE


title: M-HDAC-2.H04

description: C1 CAGE


title: M-HDAC-2.H02

description: C1 CAGE


title: M-HDAC-2.H08

description: C1 CAGE


title: M-HDAC-2.H01

description: C1 CAGE


title: M-HDAC-2.G12

description: C1 CAGE


title: M-HDAC-2.H07

description: C1 CAGE


title: M-HDAC-2.G10

description: C1 CAGE


title: M-HDAC-2.G11

description: C1 CAGE


title: M-HDAC-2.H05

description: C1 CAGE


title: M-HDAC-2.G07

description: C1 CAGE


title: M-HDAC-2.G06

description: C1 CAGE


title: M-HDAC-2.G08

description: C1 CAGE


title: M-HDAC-2.G03

description: C1 CAGE


title: M-HDAC-2.G04

description: C1 CAGE


title: M-HDAC-2.F10

description: C1 CAGE


title: M-HDAC-2.G05

description: C1 CAGE


title: M-HDAC-2.F09

description: C1 CAGE


title: M-HDAC-2.F03

description: C1 CAGE


title: M-HDAC-2.E10

description: C1 CAGE


title: M-HDAC-2.G01

description: C1 CAGE


title: M-HDAC-2.F08

description: C1 CAGE


title: M-HDAC-2.F07

description: C1 CAGE


title: M-HDAC-2.E11

description: C1 CAGE


title: M-HDAC-2.F04

description: C1 CAGE


title: M-HDAC-2.E07

description: C1 CAGE


title: M-HDAC-2.F11

description: C1 CAGE


title: M-HDAC-2.E06

description: C1 CAGE


title: M-HDAC-2.F12

description: C1 CAGE


title: M-HDAC-2.G02

description: C1 CAGE


title: M-HDAC-2.F01

description: C1 CAGE


title: M-HDAC-2.F05

description: C1 CAGE


title: M-HDAC-2.E03

description: C1 CAGE


title: M-HDAC-2.F06

description: C1 CAGE


title: M-HDAC-2.F02

description: C1 CAGE


title: M-HDAC-2.E02

description: C1 CAGE


title: M-HDAC-2.G09

description: C1 CAGE


title: M-HDAC-2.E12

description: C1 CAGE


title: M-HDAC-2.E01

description: C1 CAGE


title: M-HDAC-2.E09

description: C1 CAGE


title: M-HDAC-2.E08

description: C1 CAGE


title: M-HDAC-2.D05

description: C1 CAGE


title: M-HDAC-2.E05

description: C1 CAGE


title: M-HDAC-2.D08

description: C1 CAGE


title: M-HDAC-2.D03

description: C1 CAGE


title: M-HDAC-2.D06

description: C1 CAGE


title: M-HDAC-2.D07

description: C1 CAGE


title: M-HDAC-2.C09

description: C1 CAGE


title: M-HDAC-2.C06

description: C1 CAGE


title: M-HDAC-2.C10

description: C1 CAGE


title: M-HDAC-2.C08

description: C1 CAGE


title: M-HDAC-2.E04

description: C1 CAGE


title: M-HDAC-2.C05

description: C1 CAGE


title: M-HDAC-2.D12

description: C1 CAGE


title: M-HDAC-2.B11

description: C1 CAGE


title: M-HDAC-2.D01

description: C1 CAGE


title: M-HDAC-2.B12

description: C1 CAGE


title: M-HDAC-2.C01

description: C1 CAGE


title: M-HDAC-2.D11

description: C1 CAGE


title: M-HDAC-2.D04

description: C1 CAGE


title: M-HDAC-2.C12

description: C1 CAGE


title: M-HDAC-2.D02

description: C1 CAGE


title: M-HDAC-2.C11

description: C1 CAGE


title: M-HDAC-2.D09

description: C1 CAGE


title: M-HDAC-2.B08

description: C1 CAGE


title: M-HDAC-2.C02

description: C1 CAGE


title: M-HDAC-2.D10

description: C1 CAGE


title: M-HDAC-2.C07

description: C1 CAGE


title: M-HDAC-2.B01

description: C1 CAGE


title: M-HDAC-2.A12

description: C1 CAGE


title: M-HDAC-2.A10

description: C1 CAGE


title: M-HDAC-2.A08

description: C1 CAGE


title: M-HDAC-2.B09

description: C1 CAGE


title: M-HDAC-2.A05

description: C1 CAGE


title: M-HDAC-2.A04

description: C1 CAGE


title: M-HDAC-2.C04

description: C1 CAGE


title: M-HDAC-2.B07

description: C1 CAGE


title: M-HDAC-2.B06

description: C1 CAGE


title: M-HDAC-2.A07

description: C1 CAGE


title: M-HDAC-2.B04

description: C1 CAGE


title: M-HDAC-2.B10

description: C1 CAGE


title: M-HDAC-1.H12

description: C1 CAGE


title: M-HDAC-1.H11

description: C1 CAGE


title: M-HDAC-1.H08

description: C1 CAGE


title: M-HDAC-2.B03

description: C1 CAGE


title: M-HDAC-2.B02

description: C1 CAGE


title: M-HDAC-2.B05

description: C1 CAGE


title: M-HDAC-2.A11

description: C1 CAGE


title: M-HDAC-2.C03

description: C1 CAGE


title: M-HDAC-2.A01

description: C1 CAGE


title: M-HDAC-1.H10

description: C1 CAGE


title: M-HDAC-1.H02

description: C1 CAGE


title: M-HDAC-1.H09

description: C1 CAGE


title: M-HDAC-1.G05

description: C1 CAGE


title: M-HDAC-1.G11

description: C1 CAGE


title: M-HDAC-1.H05

description: C1 CAGE


title: M-HDAC-2.A06

description: C1 CAGE


title: M-HDAC-1.H04

description: C1 CAGE


title: M-HDAC-1.F11

description: C1 CAGE


title: M-HDAC-1.G01

description: C1 CAGE


title: M-HDAC-2.A09

description: C1 CAGE


title: M-HDAC-1.H06

description: C1 CAGE


title: M-HDAC-1.F09

description: C1 CAGE


title: M-HDAC-1.H07

description: C1 CAGE


title: M-HDAC-1.F08

description: C1 CAGE


title: M-HDAC-2.A02

description: C1 CAGE


title: M-HDAC-1.G04

description: C1 CAGE


title: M-HDAC-2.A03

description: C1 CAGE


title: M-HDAC-1.H01

description: C1 CAGE


title: M-HDAC-1.G08

description: C1 CAGE


title: M-HDAC-1.F06

description: C1 CAGE


title: M-HDAC-1.F03

description: C1 CAGE


title: M-HDAC-1.F04

description: C1 CAGE


title: M-HDAC-1.G02

description: C1 CAGE


title: M-HDAC-1.G09

description: C1 CAGE


title: M-HDAC-1.G12

description: C1 CAGE


title: M-HDAC-1.G10

description: C1 CAGE


title: M-HDAC-1.E12

description: C1 CAGE


title: M-HDAC-1.G07

description: C1 CAGE


title: M-HDAC-1.E11

description: C1 CAGE


title: M-HDAC-1.E09

description: C1 CAGE


title: M-HDAC-1.G03

description: C1 CAGE


title: M-HDAC-1.E10

description: C1 CAGE


title: M-HDAC-1.F05

description: C1 CAGE


title: M-HDAC-1.H03

description: C1 CAGE


title: M-HDAC-1.E08

description: C1 CAGE


title: M-HDAC-1.F12

description: C1 CAGE


title: M-HDAC-1.G06

description: C1 CAGE


title: M-HDAC-1.F10

description: C1 CAGE


title: M-HDAC-1.F07

description: C1 CAGE


title: M-HDAC-1.F02

description: C1 CAGE


title: M-HDAC-1.D12

description: C1 CAGE


title: M-HDAC-1.D09

description: C1 CAGE


title: M-HDAC-1.E01

description: C1 CAGE


title: M-HDAC-1.D10

description: C1 CAGE


title: M-HDAC-1.F01

description: C1 CAGE


title: M-HDAC-1.E03

description: C1 CAGE


title: M-HDAC-1.E06

description: C1 CAGE


title: M-HDAC-1.E05

description: C1 CAGE


title: M-HDAC-1.E07

description: C1 CAGE


title: M-HDAC-1.E02

description: C1 CAGE


title: M-HDAC-1.D11

description: C1 CAGE


title: M-HDAC-1.D08

description: C1 CAGE


title: M-HDAC-1.D07

description: C1 CAGE


title: M-HDAC-1.E04

description: C1 CAGE


title: M-HDAC-1.D04

description: C1 CAGE


title: M-HDAC-1.D03

description: C1 CAGE


title: M-HDAC-1.D02

description: C1 CAGE


title: M-HDAC-1.D01

description: C1 CAGE


title: M-HDAC-1.C12

description: C1 CAGE


title: M-HDAC-1.C10

description: C1 CAGE


title: M-HDAC-1.C11

description: C1 CAGE


title: M-HDAC-1.C06

description: C1 CAGE


title: M-HDAC-1.C07

description: C1 CAGE


title: M-HDAC-1.C08

description: C1 CAGE


title: M-HDAC-1.C09

description: C1 CAGE


title: M-HDAC-1.C04

description: C1 CAGE


title: M-HDAC-1.D06

description: C1 CAGE


title: M-HDAC-1.C03

description: C1 CAGE


title: M-HDAC-1.B11

description: C1 CAGE


title: M-HDAC-1.C02

description: C1 CAGE


title: M-HDAC-1.B10

description: C1 CAGE


title: M-HDAC-1.B04

description: C1 CAGE


title: M-HDAC-1.B08

description: C1 CAGE


title: M-HDAC-1.B09

description: C1 CAGE


title: M-HDAC-1.B12

description: C1 CAGE


title: M-HDAC-1.C01

description: C1 CAGE


title: M-HDAC-1.B02

description: C1 CAGE


title: M-HDAC-1.D05

description: C1 CAGE


title: M-HDAC-1.B06

description: C1 CAGE


title: M-HDAC-1.B03

description: C1 CAGE


title: M-HDAC-1.B05

description: C1 CAGE


title: M-HDAC-1.B07

description: C1 CAGE


title: M-HDAC-1.A11

description: C1 CAGE


title: M-HDAC-1.A12

description: C1 CAGE


title: M-HDAC-1.B01

description: C1 CAGE


title: M-HDAC-1.A09

description: C1 CAGE


title: M-HDAC-1.A08

description: C1 CAGE


title: M-HDAC-1.A06

description: C1 CAGE


title: M-HDAC-1.A07

description: C1 CAGE


title: M-HDAC-1.A05

description: C1 CAGE


title: M-HDAC-1.A04

description: C1 CAGE


title: M-HDAC-1.A02

description: C1 CAGE


title: M-HDAC-1.A03

description: C1 CAGE


title: H-HDAC-4.H11

description: C1 CAGE

source_name: HepG2 cell line


title: H-HDAC-4.H12

description: C1 CAGE


title: M-HDAC-1.A01

description: C1 CAGE


title: M-HDAC-1.C05

description: C1 CAGE


title: H-HDAC-4.H02

description: C1 CAGE


title: H-HDAC-4.H05

description: C1 CAGE


title: H-HDAC-4.H06

description: C1 CAGE


title: H-HDAC-4.H09

description: C1 CAGE


title: H-HDAC-4.H08

description: C1 CAGE


title: H-HDAC-4.H03

description: C1 CAGE


title: H-HDAC-4.H04

description: C1 CAGE


title: H-HDAC-4.G07

description: C1 CAGE


title: H-HDAC-4.G10

description: C1 CAGE


title: M-HDAC-1.A10

description: C1 CAGE


title: H-HDAC-4.H10

description: C1 CAGE


title: H-HDAC-4.G12

description: C1 CAGE


title: H-HDAC-4.G08

description: C1 CAGE


title: H-HDAC-4.G11

description: C1 CAGE


title: H-HDAC-4.G06

description: C1 CAGE


title: H-HDAC-4.H01

description: C1 CAGE


title: H-HDAC-4.H07

description: C1 CAGE


title: H-HDAC-4.G05

description: C1 CAGE


title: H-HDAC-4.G04

description: C1 CAGE


title: H-HDAC-4.G09

description: C1 CAGE


title: H-HDAC-4.F10

description: C1 CAGE


title: H-HDAC-4.F12

description: C1 CAGE


title: H-HDAC-4.F11

description: C1 CAGE


title: H-HDAC-4.G03

description: C1 CAGE


title: H-HDAC-4.G02

description: C1 CAGE


title: H-HDAC-4.F05

description: C1 CAGE


title: H-HDAC-4.G01

description: C1 CAGE


title: H-HDAC-4.F04

description: C1 CAGE


title: H-HDAC-4.F06

description: C1 CAGE


title: H-HDAC-4.F03

description: C1 CAGE


title: H-HDAC-4.F07

description: C1 CAGE


title: H-HDAC-4.F09

description: C1 CAGE


title: H-HDAC-4.F08

description: C1 CAGE


title: H-HDAC-4.F02

description: C1 CAGE


title: H-HDAC-4.E07

description: C1 CAGE


title: H-HDAC-4.E11

description: C1 CAGE


title: H-HDAC-4.E09

description: C1 CAGE


title: H-HDAC-4.F01

description: C1 CAGE


title: H-HDAC-4.E12

description: C1 CAGE


title: H-HDAC-4.E02

description: C1 CAGE


title: H-HDAC-4.E04

description: C1 CAGE


title: H-HDAC-4.E06

description: C1 CAGE


title: H-HDAC-4.E03

description: C1 CAGE


title: H-HDAC-4.D12

description: C1 CAGE


title: H-HDAC-4.D10

description: C1 CAGE


title: H-HDAC-4.E08

description: C1 CAGE


title: H-HDAC-4.D11

description: C1 CAGE


title: H-HDAC-4.D08

description: C1 CAGE


title: H-HDAC-4.D07

description: C1 CAGE


title: H-HDAC-4.E05

description: C1 CAGE


title: H-HDAC-4.E10

description: C1 CAGE


title: H-HDAC-4.E01

description: C1 CAGE


title: H-HDAC-4.D04

description: C1 CAGE


title: H-HDAC-4.D06

description: C1 CAGE


title: H-HDAC-4.C11

description: C1 CAGE


title: H-HDAC-4.C12

description: C1 CAGE


title: H-HDAC-4.C10

description: C1 CAGE


title: H-HDAC-4.C09

description: C1 CAGE


title: H-HDAC-4.D05

description: C1 CAGE


title: H-HDAC-4.C06

description: C1 CAGE


title: H-HDAC-4.D03

description: C1 CAGE


title: H-HDAC-4.C08

description: C1 CAGE


title: H-HDAC-4.C01

description: C1 CAGE


title: H-HDAC-4.C05

description: C1 CAGE


title: H-HDAC-4.D02

description: C1 CAGE


title: H-HDAC-4.C04

description: C1 CAGE


title: H-HDAC-4.D09

description: C1 CAGE


title: H-HDAC-4.B07

description: C1 CAGE


title: H-HDAC-4.B08

description: C1 CAGE


title: H-HDAC-4.C02

description: C1 CAGE


title: H-HDAC-4.D01

description: C1 CAGE


title: H-HDAC-4.B12

description: C1 CAGE


title: H-HDAC-4.B06

description: C1 CAGE


title: H-HDAC-4.B05

description: C1 CAGE


title: H-HDAC-4.B10

description: C1 CAGE


title: H-HDAC-4.C03

description: C1 CAGE


title: H-HDAC-4.C07

description: C1 CAGE


title: H-HDAC-4.B11

description: C1 CAGE


title: H-HDAC-4.B04

description: C1 CAGE


title: H-HDAC-4.B09

description: C1 CAGE


title: H-HDAC-4.B02

description: C1 CAGE


title: H-HDAC-4.B03

description: C1 CAGE


title: H-HDAC-4.A11

description: C1 CAGE


title: H-HDAC-4.A10

description: C1 CAGE


title: H-HDAC-4.B01

description: C1 CAGE


title: H-HDAC-4.A12

description: C1 CAGE


title: H-HDAC-4.A09

description: C1 CAGE


title: H-HDAC-4.A07

description: C1 CAGE


title: H-HDAC-4.A05

description: C1 CAGE


title: H-HDAC-4.A08

description: C1 CAGE


title: H-HDAC-3.H06

description: C1 CAGE


title: H-HDAC-4.A06

description: C1 CAGE


title: H-HDAC-4.A02

description: C1 CAGE


title: H-HDAC-3.H12

description: C1 CAGE


title: H-HDAC-3.H10

description: C1 CAGE


title: H-HDAC-3.H07

description: C1 CAGE


title: H-HDAC-3.H11

description: C1 CAGE


title: H-HDAC-3.H09

description: C1 CAGE


title: H-HDAC-3.H01

description: C1 CAGE


title: H-HDAC-3.H04

description: C1 CAGE


title: H-HDAC-3.H08

description: C1 CAGE


title: H-HDAC-4.A01

description: C1 CAGE


title: H-HDAC-3.H02

description: C1 CAGE


title: H-HDAC-3.G11

description: C1 CAGE


title: H-HDAC-4.A04

description: C1 CAGE


title: H-HDAC-3.G08

description: C1 CAGE


title: H-HDAC-3.H03

description: C1 CAGE


title: H-HDAC-3.G12

description: C1 CAGE


title: H-HDAC-3.G10

description: C1 CAGE


title: H-HDAC-3.G06

description: C1 CAGE


title: H-HDAC-4.A03

description: C1 CAGE


title: H-HDAC-3.G03

description: C1 CAGE


title: H-HDAC-3.G07

description: C1 CAGE


title: H-HDAC-3.G04

description: C1 CAGE


title: H-HDAC-3.H05

description: C1 CAGE


title: H-HDAC-3.F12

description: C1 CAGE


title: H-HDAC-3.G09

description: C1 CAGE


title: H-HDAC-3.F10

description: C1 CAGE


title: H-HDAC-3.G02

description: C1 CAGE


title: H-HDAC-3.G01

description: C1 CAGE


title: H-HDAC-3.F11

description: C1 CAGE


title: H-HDAC-3.F09

description: C1 CAGE


title: H-HDAC-3.F05

description: C1 CAGE


title: H-HDAC-3.F07

description: C1 CAGE


title: H-HDAC-3.E08

description: C1 CAGE


title: H-HDAC-3.E05

description: C1 CAGE


title: H-HDAC-3.E12

description: C1 CAGE


title: H-HDAC-3.E10

description: C1 CAGE


title: H-HDAC-3.F04

description: C1 CAGE


title: H-HDAC-3.E06

description: C1 CAGE


title: H-HDAC-3.F02

description: C1 CAGE


title: H-HDAC-3.E07

description: C1 CAGE


title: H-HDAC-3.F06

description: C1 CAGE


title: H-HDAC-3.E04

description: C1 CAGE


title: H-HDAC-3.F08

description: C1 CAGE


title: H-HDAC-3.E03

description: C1 CAGE


title: H-HDAC-3.G05

description: C1 CAGE


title: H-HDAC-3.E09

description: C1 CAGE


title: H-HDAC-3.E11

description: C1 CAGE


title: H-HDAC-3.F01

description: C1 CAGE


title: H-HDAC-3.D11

description: C1 CAGE


title: H-HDAC-3.E01

description: C1 CAGE


title: H-HDAC-3.F03

description: C1 CAGE


title: H-HDAC-3.D09

description: C1 CAGE


title: H-HDAC-3.D05

description: C1 CAGE


title: H-HDAC-3.E02

description: C1 CAGE


title: H-HDAC-3.D02

description: C1 CAGE


title: H-HDAC-3.D10

description: C1 CAGE


title: H-HDAC-3.D07

description: C1 CAGE


title: H-HDAC-3.C07

description: C1 CAGE


title: H-HDAC-3.C08

description: C1 CAGE


title: H-HDAC-3.C10

description: C1 CAGE


title: H-HDAC-3.D06

description: C1 CAGE


title: H-HDAC-3.C04

description: C1 CAGE


title: H-HDAC-3.D08

description: C1 CAGE


title: H-HDAC-3.C05

description: C1 CAGE


title: H-HDAC-3.C03

description: C1 CAGE


title: H-HDAC-3.D03

description: C1 CAGE


title: H-HDAC-3.C12

description: C1 CAGE


title: H-HDAC-3.D04

description: C1 CAGE


title: H-HDAC-3.C02

description: C1 CAGE


title: H-HDAC-3.C11

description: C1 CAGE


title: H-HDAC-3.C06

description: C1 CAGE


title: H-HDAC-3.D12

description: C1 CAGE


title: H-HDAC-3.C01

description: C1 CAGE


title: H-HDAC-3.B07

description: C1 CAGE


title: H-HDAC-3.B02

description: C1 CAGE


title: H-HDAC-3.C09

description: C1 CAGE


title: H-HDAC-3.B12

description: C1 CAGE


title: H-HDAC-3.D01

description: C1 CAGE


title: H-HDAC-3.A09

description: C1 CAGE