title: Cell_74

description: Hypothalamic POMC-expressing neuron


title: Cell_79

status: Public on Mar 08 2017

type: SRA

city: Box 289, Addenbrooke’s Hospital

first: Joseph

last: Polex-Wolf

state: Cambridgeshire

address: Wellcome Trust-MRC Institute of Metabolic Science

department: Metabolic Research Laboratories

country: United Kingdom

institute: University of Cambridge

description: Hypothalamic POMC-expressing neuron

library_source: transcriptomic

data_processing:
Basecalls performed using CASAVA 1.7
Reads were aligned to the mouse genome (GRCm38) using Tophat v2.0.11
Counts were determined using Cufflinks v2.2.1
Count normalisation was performed using the edgeR and limma packages in R.
Genome_build: GRCm38
Supplementary_files_format_and_content: Normalized abundance in counts per million (CPM)

molecule: total RNA

organism: Mus musculus

source_name: Hypothalamic neuronal cell

extract_protocol:
GFP-labelled POMC neurons from microdissected Pomc-EGFP murine hypothalami were dissociated into a cell suspension using Papain.  Flurorescence-activating cell sorting (FACS) was then utilised to sort individual GFP-positive neurons into a 96 well plate with lysis buffer and RNase inhibitor.
RNA from the single cell lysate was reverse transcribed and PCR amplified into double stranded cDNA using Clontech SMART-Seq v4 Ultra Low Input RNA Kit.  Amplified cDNA was then used to generate barcoded sequencing libraries using Illumina Nextera XT library preparation kit. The pooled libraries were sequenced on an Illumina HiSeq 4000 instrument at single-end 50bp (SE50).

tag: strain

value: C57/BL6 Tg(Pomc-EGFP)1Low

tag: cell type

value: Pomc-EGFP expressing neuron


title: Cell_92

description: Hypothalamic POMC-expressing neuron


title: Cell_75

description: Hypothalamic POMC-expressing neuron


title: Cell_72

description: Hypothalamic POMC-expressing neuron


title: Cell_73

description: Hypothalamic POMC-expressing neuron


title: Cell_71

description: Hypothalamic POMC-expressing neuron


title: Cell_69

description: Hypothalamic POMC-expressing neuron


title: Cell_70

description: Hypothalamic POMC-expressing neuron


title: Cell_87

description: Hypothalamic POMC-expressing neuron


title: Cell_67

description: Hypothalamic POMC-expressing neuron


title: Cell_83

description: Hypothalamic POMC-expressing neuron


title: GXP GBM6

city: SEONGNAM-SI

first: YOUN JUNG

last: KANG

address: 335 PANGYO-RO

department: MEDICINE

country: South Korea

institute: CHA University

data_processing:
Alignment: TopHat version 2.0.7
Transcriptome Assembly: Cufflinks version 2.0.2
Differential expression: Cuffdiff version 2.0.2
Visualization(heatmap): R version 2.13 (gplots)
Base calls : Casava 1.8.2
Genome_build: Mus Musculus: Mm9
Supplementary_files_format_and_content: Expression file: It is the differential expression for the given two conditions found using Cuffdiff
Supplementary_files_format_and_content: Counts file: This file contains information for the individual counts for the genes for the two conditions
Supplementary_files_format_and_content: FPKM files: This contains the fragments per kilo megabases for different conditions

source_name: brain

extract_protocol:
RNA was harvested using Trizol reagent and extracte using a standard protocol. 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: gliosphere derived from malignant glioma

tag: genotype

tag: passages

value: Passage 1-8


title: Cell_68

description: Hypothalamic POMC-expressing neuron


title: GXP GBM5


title: Cell_65

description: Hypothalamic POMC-expressing neuron


title: Cell_66

description: Hypothalamic POMC-expressing neuron


title: GXP GBM3


title: GXP GBM4


title: Cell_77

description: Hypothalamic POMC-expressing neuron


title: Cell_76

description: Hypothalamic POMC-expressing neuron


title: Cell_112

description: Hypothalamic POMC-expressing neuron


title: GXP GBM2


title: Cell_64

description: Hypothalamic POMC-expressing neuron


title: GXP GBM1


title: GXP neurosphere (NS)

value: postnatal day 1-3 derived neuropheres


title: Cell_63

description: Hypothalamic POMC-expressing neuron


title: Cell_62

description: Hypothalamic POMC-expressing neuron


title: s_L48d_GeneCount

city: Rochester

first: Xuewei

last: Wang

address: 200 1st street

country: USA

institute: Mayo Clinic

data_processing:
Base calling by CASAVA
Alignment by Tophat2 (v2.0.12)
Gene count by featureCounts (v1.4.4)
Normalization by edgeR(v2.6.2)
Genome_build: hg19
Supplementary_files_format_and_content: excel file for gene count

organism: Homo sapiens

source_name: Cellular Dynamics iPSC-derived cardiomyocytes

growth_protocol: manufacturers protocol (Cellular Dynamics)

extract_protocol:
Qiagen RNAeasy minikit
Illumina TruSeq V2

treatment_protocol: 48 hours treatment with trastuzumab (100ug/ml) or lapatinib (2uM)

value: iPSC-derived cardiomyocytes

tag: treatment

value: lapatinib

tag: dose


title: Cell_61

description: Hypothalamic POMC-expressing neuron


title: s_L48c_GeneCount


title: s_L48a_GeneCount


title: Cell_58

description: Hypothalamic POMC-expressing neuron


title: Cell_60

description: Hypothalamic POMC-expressing neuron


title: Cell_59

description: Hypothalamic POMC-expressing neuron


title: s_H48c_GeneCount

value: trastuzumab


title: s_H48d_GeneCount


title: Cell_55

description: Hypothalamic POMC-expressing neuron


title: s_H48b_GeneCount


title: s_H48a_GeneCount


title: Cell_54

description: Hypothalamic POMC-expressing neuron


title: Cell_56

description: Hypothalamic POMC-expressing neuron


title: Cell_52

description: Hypothalamic POMC-expressing neuron


title: Cell_53

description: Hypothalamic POMC-expressing neuron


title: Cell_51

description: Hypothalamic POMC-expressing neuron


title: Cell_50

description: Hypothalamic POMC-expressing neuron


title: Cell_48

description: Hypothalamic POMC-expressing neuron


title: Cell_49

description: Hypothalamic POMC-expressing neuron


title: DNA methylation in NT cells

city: Grand Rapids

first: Yvonne

middle: Nsokika

last: Fondufe-Mittendorf

state: MI

address: 333 Bostwick Ave NE

department: Epigenetics

institute: Van Andel Institute

library_source: genomic

data_processing:
Raw data files had their adapters removed using trim_galore, quality trimming was also done, reads shorter than 20 bp were discarded
Pre-processed fastq files were aligned to human hg19 using bismark
Methylation calling was done on the bamfiles to create browser tracks for CpG, CHG, and CHH sites for each sample, these are in bigbed format
Genome_build: hg19
Supplementary_files_format_and_content: bigbed, browser tracks that contain methylation count and total count of reads per site

molecule: genomic DNA

source_name: Lung Epithelial

growth_protocol: Cell cultures were incubated at 37 degree with humidified air and 5% CO2. Cells were harvested after each treatment. Cells were grown ensuring that 95% of the cells were viable. Harvested cells were centrifuged for five minutes at 200 X g.

extract_protocol: Genomic DNA was extracted using Qiagen Dneasykit according to manusfacturers instructions.

treatment_protocol: Cells were treated with 0.5 uM Sodium Arsenite for 36 days until transformation

value: non-treated lung epithelial cells


title: Cell_46

description: Hypothalamic POMC-expressing neuron


title: DNA methylation in iAsT cells

value: iAs-transformed lung epithelial cells


title: NA12891exosome

city: Stanford

first: Emiy

middle: K

last: Tsang

state: CA

address: 300 Pasteur Dr

department: Pathology

institute: Stanford University

description: small RNA

data_processing:
Sequencing adapters were trimmed with Trimmomatic (v0.27) and were also provided to Novoalign (v3.00.02), which handled incomplete adapter trimming while mapping. The reads were mapped in two steps where they were first mapped to miRBase (release 20) and piRNABank then unmapped reads were aligned to the human reference genome (hg19).
The reads that mapped to the reference genome were assigned to transcripts annotated in Gencode (version 17), miRBase or piRNABank using HTSeq (v0.5.4p3).
The read counts from the first mapping step were added to those generated by HTSeq to get a single read count per transcript.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file including counts for each Sample

source_name: lymphoblastoid cell line exosomes

growth_protocol: CEPH/UTAH family EBV-transformed peripheral blood B lymphoblastoid cell lines (LCLs) (Cat# XC01463) were purchased from Coriell Institute for Medical Research and were grown in RPMI 1640 supplemented with 10% fetal calf serum (Gibco, Life Technologies) and 1x penicillin/streptomycin (Life Technologies) in humidified 5% CO2 to 150 x 106 cells while maintaining a maximum density of 2\times 106 cells/ml.  Fetal calf serum was depleted of bovine exosomes prior to use by overnight centrifugation at 120,000 x g.

extract_protocol:
Small RNA from Trizol-lysed LCLs and exosomes was isolated from 1 µg total RNA using the TruSeq Small RNA Sample Prep Kit (Illumina, San Diego) with minor modifications.
Small RNA libraries were constructed following standard Illumina protocols. PCR-amplified small RNA libraries were gel purified with 3% NuSieve GTG low-melt agarose (Lonza, Rockland) and target bands of 147–157 nt, containing adapter sequence of 125 nt, were excised and column purified (Qiagen, Germantown).

treatment_protocol: Exosomes were isolated by differential centrifugation and filtration through a 200 nm Acrodisc (PAL Corp, Ann Arbor).

value: EBV transformed peripheral blood B lymphocytes

tag: compartment

value: exosome

tag: individual


title: NA12890exosome

description: small RNA


title: Cell_57

description: Hypothalamic POMC-expressing neuron


title: NA12892exosome

description: small RNA


title: Cell_47

description: Hypothalamic POMC-expressing neuron


title: NA12889exosome

description: small RNA


title: NA12888exosome

description: small RNA


title: s_L48b_GeneCount


title: Cell_43

description: Hypothalamic POMC-expressing neuron


title: NA12887exosome

description: small RNA


title: Cell_42

description: Hypothalamic POMC-expressing neuron


title: NA12886exosome

description: small RNA


title: Cell_41

description: Hypothalamic POMC-expressing neuron


title: NA12885exosome

description: small RNA


title: Cell_38

description: Hypothalamic POMC-expressing neuron


title: NA12883exosome

description: small RNA


title: NA12882exosome

description: small RNA


title: Cell_39

description: Hypothalamic POMC-expressing neuron


title: Cell_37

description: Hypothalamic POMC-expressing neuron


title: Cell_45

description: Hypothalamic POMC-expressing neuron


title: Cell_44

description: Hypothalamic POMC-expressing neuron


title: Cell_34

description: Hypothalamic POMC-expressing neuron


title: Cell_35

description: Hypothalamic POMC-expressing neuron


title: Cell_36

description: Hypothalamic POMC-expressing neuron


title: Cell_33

description: Hypothalamic POMC-expressing neuron


title: NA12877exosome

description: small RNA


title: NA12879exosome

description: small RNA


title: Cell_31

description: Hypothalamic POMC-expressing neuron


title: NA12878exosome

description: small RNA


title: NA12881exosome

description: small RNA


title: AD1

city: Anyang

first: Yun

last: Song

state: Henan

address: Huanghe Street No. 83

country: China

institute: Institute of cotton research of CAAS

data_processing:
Illumina Hiseq 4000 platform was used to sequence these libraries, and 100 bp paired-end reads were generated.
TopHat2 was used to map these reads to the G. hirsutum transcripts with the help of genome annotation
The mapped reads were assembled by Cufflinks
Differentially expressed genes (DEGs) were identified using Cuffdiff
Genome_build: http://mascotton.njau.edu.cn/html/Data/Genomefhsequence/2015/04/20/16ab0945-19e9-49f7-a09e-8e956ec866bf.html
Supplementary_files_format_and_content: tsv files include RPKM values for each Sample

organism: Gossypium hirsutum

source_name: AZD treated cotton seedlings

growth_protocol: Cotton seeds were surface-sterilized with 0.1% mercuric chloride for 5 min, rinsed with sterile water. The sterilized seeds were sown in MS medium containing 1% agar for 4 days, and grown in a growth chamber at 25°C under 16 h light/8 h dark condition.

extract_protocol:
The cotton seedlings were harvested for RNA extraction. RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: 4-d-old cotton seedlings were transferred into MS medium containing DMSO and 5 μΜ AZD for 24 h, respectively.

tag: age

value: 5 days post germination

value: wildtype

tag: tissue

value: seedling


title: AD2


title: AA2

source_name: DMSO treated cotton seedlings


title: NA12880exosome

description: small RNA


title: AD3


title: NA12893cell

description: small RNA

source_name: lymphoblastoid cell line

value: cell


title: AA3


title: AA1


title: Cell_30

description: Hypothalamic POMC-expressing neuron


title: NA12890cell

description: small RNA


title: Cell_29

description: Hypothalamic POMC-expressing neuron


title: NA12892cell

description: small RNA


title: Cell_28

description: Hypothalamic POMC-expressing neuron


title: Cell_40

description: Hypothalamic POMC-expressing neuron


title: NA12884exosome

description: small RNA


title: NA12891cell

description: small RNA


title: Cell_32

description: Hypothalamic POMC-expressing neuron


title: NA12889cell

description: small RNA


title: Cell_27

description: Hypothalamic POMC-expressing neuron


title: Cell_26

description: Hypothalamic POMC-expressing neuron


title: NA12888cell

description: small RNA


title: NA12887cell

description: small RNA


title: NA12885cell

description: small RNA


title: NA12886cell

description: small RNA


title: Cell_23

description: Hypothalamic POMC-expressing neuron


title: Cell_22

description: Hypothalamic POMC-expressing neuron


title: Cell_25

description: Hypothalamic POMC-expressing neuron


title: Cell_24

description: Hypothalamic POMC-expressing neuron


title: NA12884cell

description: small RNA


title: NA12880cell

description: small RNA


title: NA12882cell

description: small RNA


title: NA12881cell

description: small RNA


title: Akt-LEC 2

city: New York

first: Olivier

last: Elemento

state: NY

address: 1305 York Avenue

institute: WEILL MEDICAL COLLEGE OF CORNELL UNIV

data_processing:
Illumina Casava1.8 software used for basecalling.
RNAseq: Sequence reads were aligned to mm9 using TopHat with default parameters
RNAseq: FPKM were obtained using CuffLinks with upper-quartile and GC normalization
Genome_build: mm9
Supplementary_files_format_and_content: RNAseq: tab-delimited FPKM values for each Refseq gene.

molecule: polyA RNA

source_name: mouse lung endothelial cells transduced with a lentivirus encoding a constitutively active myristyolated Akt molecule

extract_protocol:
RNA was harvested using Trizol treatment
Illumina TruSeq PE 51x2 (RNA-seq)

value: Endothelial cells

tag: genotype/variation


title: Cell_19

description: Hypothalamic POMC-expressing neuron

value: C57/BL6 Tg(Pomc-EGFP)1Low


title: Cell_18

description: Hypothalamic POMC-expressing neuron

value: Pomc-EGFP expressing neuron


title: Cell_20

description: Hypothalamic POMC-expressing neuron


title: Cell_17

description: Hypothalamic POMC-expressing neuron


title: NA12883cell

description: small RNA


title: Cell_14

description: Hypothalamic POMC-expressing neuron


title: Cell_15

description: Hypothalamic POMC-expressing neuron


title: Cell_21

description: Hypothalamic POMC-expressing neuron


title: NA12877cell

description: small RNA


title: NA12878cell

description: small RNA


title: Cell_16

description: Hypothalamic POMC-expressing neuron


title: Cell_13

description: Hypothalamic POMC-expressing neuron


title: Cell_12

description: Hypothalamic POMC-expressing neuron


title: Cell_11

description: Hypothalamic POMC-expressing neuron


title: Cell_10

description: Hypothalamic POMC-expressing neuron


title: Cell_8

description: Hypothalamic POMC-expressing neuron


title: Cell_9

description: Hypothalamic POMC-expressing neuron


title: Cell_6

description: Hypothalamic POMC-expressing neuron


title: Cell_3

description: Hypothalamic POMC-expressing neuron


title: Cell_7

description: Hypothalamic POMC-expressing neuron


title: Cell_2

description: Hypothalamic POMC-expressing neuron


title: Cell_1

description: Hypothalamic POMC-expressing neuron


title: terrestrial leaf rep3

city: Seoul

first: Juhyun

last: Kim

state: Seoul

address: Daehak-ro 1, Gwanak-gu

department: School of Biological Science

institute: Seoul National University

data_processing:
Solexa's Sequencing-by-Synthesis utilizes four proprietary nucleotides possessing reversible fluorophore and termination properties.
RNA-seq reads were de novo assembled and mapped using Trinity and TopHat programs and the relative transcript levels were calculated by FPKM using Cufflinks software
Supplementary_files_format_and_content: text files include FPKM values for each Sample

organism: Ranunculus trichophyllus

source_name: shoot

growth_protocol: 22ºC, 60 ± 10% humidity, 16h light/8h dark condition

extract_protocol:
Fresh seedlings without cotyledon and hypocotyl were frozen on liquid nitrogen, and RNA was harvested using RNeasy plant mini kit (Qiagen)
Purified mRNAs were converted to dsDNA with random hexamer. Overhanged dsDNA fragments were trimed and adaptors were ligated to the fragments. PCR-based fragment enrichment were performed to build library templates

treatment_protocol: 1 week seedlings were soaked for preparing aquatic samples

value: leaf + shoot apical meristem

value: 11 days


title: aquatic leaf rep2


title: terrestrial leaf rep2


title: aquatic leaf rep1

value: leaf

value: 14 days


title: terrestrial leaf rep1


title: S. pneumoniae ptvR_deletion (TH5031)

city: Beijing

first: Jing-Ren

last: Zhang

state: Beijing

address: Qinghuayuan Street

department: Center for Infectious Disease Research, School of Medicine

institute: Tsinghua University

description: rpsl1 (StreptomycinR); ∆spd_0096 (markerless_deletion)

data_processing:
Base calliing: Illumina Casava software
Quality control: FastQC v0.11.5
Trimming: Trimmomatic v0.32
S. pneumoniae reads were mapped with Rockhopper 2.0.3
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated internally by Rockhopper version 2.03 after aligning reads.
Genome_build: Streptococcus pneumoniae D39 (accession NC_008533, assembly GCF_000014365.1) was used directly in the analysis
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample.

organism: Streptococcus pneumoniae

source_name: ptvR knockout S. pneumoniae cells

growth_protocol: S. pneumoniae strains wild-type and ptvR deletion mutant were grown in THY medium to mid-log phase (OD620~0.5) in tubes at 37ºC with 5% CO2.

extract_protocol:
Total RNA was extracted with the Trizol reagent (Invitrogen, Beijing, China) based on the supplier’s instructions
The ribosomal RNA was removed from total RNA (~2 µg) with RiboZeroTM Magnetic Kit (EpiCentre, Cleveland, OH). The processed RNA samples were used to prepare double-stranded complementary DNA (cDNA) libraries with the M-MuLV Reverse Transcriptase and NEBNext® mRNA Second Strand Synthesis Module. The cDNA molecules were fragmented by sonication, and further processed for end repair, adaptor attachment, and sequence amplification.

tag: strain background

value: ptvR knockout mutant


title: aquatic leaf rep3


title: S. pneumoniae WT (TH4527)

description: rpsl1 (StreptomycinR)

source_name: wild-type S. pneumoniae cells

value: wild-type ptvR


title: R_s_lag_phase_TEX_pos

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

country: Germany

institute: ZB MED - Information Centre for Life Sciences

data_processing:
FastQ quality trimming using FastX (version 0.0.13)  and a cut-off value of 20
Fastq to fasta conversion using FastX  FastX (version 0.0.13)
Size filtering: discarding reads shorter than 20 nt (READemption version 0.3.5)
Read mapping using segemehl version 0.2.0  (READemption version 0.3.5)
Coverage calculation and normalisation (READemption version 0.3.5)
Genome_build: NC_007488.2, NC_007489.1, NC_007490.2, NC_007493.2, NC_007494.2, NC_009007.1, NC_009008.1
Supplementary_files_format_and_content: wig

organism: Cereibacter sphaeroides 2.4.1

source_name: bacterial cells

growth_protocol: Rhodobacter sphaeroides was grown in low aeration (25-30 µM oxygen)

extract_protocol:
Total RNA was isolated using the hot phenol method followed by two chloroform-isoamyl alcohol treatments and precipitation with sodium acetate and ethanol. RNA was resolved in RNase free water (Roth) and concentrations were determined at a NanoDrop 1000 Spectrophotometer (Peqlab). The sample was treated with DNaseI (Invitrogen) to remove DNA.
The libraries were generated by Vertis Biotechnologie AG (Munich, Germany). The samples were poly(A)-tailed by using poly(A) polymerase. The 5'-PPP were removed using tobacco acid pyrophosphatase (TAP) followed by the ligation of the RNA adapter to the 5'-monophosphate of the RNA. First-strand cDNA synthesis was performed with an oligo(dT)-adapter primer and the M-MLV reverse transcriptase. The resulting cDNA was PCR-amplified to reach a concentration of 20-30 ng/μl using a high fidelity DNA polymerase. The cDNA was purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics) and was analyzed by capillary electrophoresis. The primers used for PCR amplification were designed for TruSeq sequencing according to the instructions of Illumina

tag: phase

value: lag

value: with TEX (terminator exonuclease treatment)


title: R_s_stationary_phase_TEX_neg

value: stationary

value: without TEX (terminator exonuclease treatment)


title: R_s_transitional_phase_TEX_pos

value: transitional


title: R_s_stationary_phase_TEX_pos


title: R_s_exponential_phase_TEX_pos

value: exponential


title: R_s_lag_phase_TEX_neg


title: R_s_exponential_phase_TEX_neg


title: Cell_4

description: Hypothalamic POMC-expressing neuron


title: Cell_5

description: Hypothalamic POMC-expressing neuron


title: RM rep 4

first: Kurt

last: Stueber

address: Carl von Linne-Weg 10

department: Genome Centre

institute: Max Planck Institute for Plant Breeding Research

data_processing: VCF allele frequencies using coverage data, program: GATK.3.1-1, functions: GATK UnifiedGenotype and GATK VariantFiltration

organism: Hordeum vulgare

source_name: apex tissue

growth_protocol: Plants were grown in the greenhouse under long day conditions (16h, 22°C day; 8h, 18°C night)

extract_protocol:
Shoot apical meristem at Waddington stage 5.5 was removed and frozen in liquid nitrogen. RNA was extracted using the Qiagen RNeasy Plant Mini Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: developmental stage

value: Waddington stage 5.5

tag: genetic background

value: Near isogenic lines in Morex

tag: phenotype

value: long awn


title: RM rep 3


title: RM rep 2


title: N. parvum in planta 12 wpi rep1

city: Davis

first: Mélanie

last: Massonnet

state: California

address: 2105 Robert Mondavi Institute-North Building

department: Viticulture and Enology

institute: University of California, Davis

description: Sample name: L-IW_12W_A

data_processing:
Forward reads from the dataset of in vitro culture were trimmed using the FASTX-Toolkit v.0.0.13 (http://hannonlab.cshl.edu/fastx_toolkit/index.html) to 50 bp in order to obtain results comparable to the ones obtained in the in planta experiment.
Quality trimming of raw reads was done with Sickle v.1.210 with a threshold of 20 (Q>20).
Adapter contamination removal was done with Scythe v.0.991
Bowtie2 v.2.2.327 was used to map the processed reads to the denovo assembly with the following options: -q --end-to-end --sensitive --no-unal.
Counts of uniquely mapped reads (mapping quality Q > 30) were extracted from the bowtie2 alignments using the script sam2counts.py v.0.91
Genome_build: de novo assembly. The FASTA file of transcript sequences is available on the series record.
Supplementary_files_format_and_content: Nparvum_invitro_inplanta_counts.txt : tab delimited text file, raw read counts determined by mapping the trimmed sequencing reads

organism:
Vitis vinifera
Neofusicoccum parvum

source_name: Cabernet Sauvignon stem

growth_protocol: A plug (1cm x 1cm) of active growing mycelia was used to inoculate a new Petri dish with media, mycelia was grown at room temperature. Potted V. vinifera plants were inoculated with N. parvum UCD646So mycelia.

extract_protocol:
Total RNA was extracted using a CTAB based protocol with a chloroform denaturation step. RNA was cleaned with RNeasy kit (Qiagen, US) including the Dnase treatment on column.
Illumina TruSeq RNA Sample Prep Kit v2 protocol

treatment_protocol: Different growth media: Potato Dextrose Agar, minimal media agar with ground dormant canes of Vitis vinifera L. cv. Cabernet Sauvignon and Vitis vinifera L. cv. Merlot. Stems were collected at seven infection time points: 0 hour post-inoculation (hpi), 3 hpi, 24 hpi, 2 weeks post-inoculation (wpi), 6 wpi, 8 wpi, and 12 wpi.

value: N. parvum-infected Cabernet Sauvignon stem

tag: environmental condition

value: in planta

tag: substrate

value: Cabernet Sauvignon clone FPS 19

tag: time point

value: 12 wpi


title: N. parvum in planta 12 wpi rep2

description: Sample name: L-IW_12W_B

tag: strain


title: N. parvum in planta 8 wpi rep2

description: Sample name: L-IW_8W_B

value: 8 wpi


title: R_s_transitional_phase_TEX_neg


title: RD rep 4

value: short awn


title: N. parvum in planta 12 wpi rep3

description: Sample name: L-IW_12W_C


title: N. parvum in planta 8 wpi rep1

description: Sample name: L-IW_8W_A


title: RM rep 1


title: RD rep 2


title: N. parvum in planta 6 wpi rep2

description: Sample name: L-IW_6W_B

value: 6 wpi


title: RD rep 3


title: N. parvum in planta 6 wpi rep1

description: Sample name: L-IW_6W_A


title: RD rep 1


title: N. parvum in planta 24 hpi rep1

description: Sample name: L-IW_24H_A

value: 24 hpi


title: N. parvum in planta 3 hpi rep3

description: Sample name: L-IW_3H_C

value: 3 hpi


title: N. parvum in planta 2 wpi rep2

description: Sample name: L-IW_2W_B

value: 2 wpi


title: N. parvum in planta 2 wpi rep3

description: Sample name: L-IW_2W_C


title: N. parvum in planta 3 hpi rep2

description: Sample name: L-IW_3H_B


title: N. parvum in planta 24 hpi rep3

description: Sample name: L-IW_24H_C


title: N. parvum in planta 8 wpi rep3

description: Sample name: L-IW_8W_C


title: N. parvum in planta 3 hpi rep1

description: Sample name: L-IW_3H_A


title: NA12879cell

description: small RNA

tag: cell type

value: EBV transformed peripheral blood B lymphocytes

value: cell


title: N. parvum in planta 0 hpi rep2

description: Sample name: L-IW_0H_B

value: 0 hpi


title: N. parvum in planta 0 hpi rep3

description: Sample name: L-IW_0H_C


title: N. parvum in planta 0 hpi rep1

description: Sample name: L-IW_0H_A


title: N. parvum in vitro growing in PDA rep2

description: Sample name: NP3

organism: Neofusicoccum parvum

source_name: Mycelia

value: mycelia

value: in vitro

value: PDA

value: 2 cycles


title: brpT_mutant_Rep3

city: Richmond

first: Ping

last: Xu

state: VA

address: 521 North 11th street

department: Philips Institute for Oral Health Research

institute: Virginia Commonwealth Univ. School of Dentistry

description: replicate 3

data_processing:
Standard Illumina pipeline. Real Time Analysis (RTA v. 1.18.66.3) software used for image processing, intesity extraction and basecalling based on intensities. CHASTITY software used for quality filter of basecalling.
Reads obtained from RNA-sequencing were aligned against the Streptococcus sanguinis SK36 genome using Rockhopper v. 2.03
Analyses were run on default parameter settings with verbose output adjusted for reads to the reverse complement in order to obtain expression data of the brpT mutant compared to wild-type SK36. Significance was represented by a q-value ≤ 0.01 adjusted for a false discovery rate of 1%.
Genome_build: Streptococcus sanguinis reference genome SK36
Supplementary_files_format_and_content: tab-delimited text file includes transcription and translation start/stop site, strand direction, gene name and ID, gene product, raw and normalized counts for each replicate, Reads Per Kilobase of exon per Megabase of library size (RPKM), expression, p-value and Rockhopper's adjusted q-value for the mutant expression vs. the wild-type SK36 expression

organism: Streptococcus sanguinis

source_name: brpT deletion mutant

growth_protocol: Cells were incubated at 37°C under anaerobic conditions in brain-heart infusion media and harvested at late-log phase. The brpT mutant was supplemented with kanamycin (500 µg/ml) for selection of the antibiotic resistance cassette.

extract_protocol:
Cells were lysed and RNA was extracted by FastPrep lysing matrix beads. Clean-up and DNase I treatment was conducted by QIAGEN RNeasy mini kit, according to the manufacterer's protocol. Illlumina RiboZero Magnetic Kit for bacteria was used to deplete ribosomal RNA from 2 µg of total RNA.
NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England BioLabs) was used for the RNA-seq library preparation according to the manufacturer’s protocol. Briefly, ribosomal-depleted RNA was fragmented followed by first-strand cDNA synthesis from random primers using ProtoScript II Reverse Transcriptase (New England BioLabs). Second strand cDNA was synthesized and purified. End repair was performed on the double-stranded cDNA and primed with the addition of 5’-phosphorylated dA-tailed ends using T4 DNA polymerase, Klenow DNA polymerase and T4 polynucleotide kinase (New England BioLabs). This was immediately followed by adaptor ligation (New England BioLabs) and purified. Samples were PCR-amplified for 12 cycles with Phusion HiFi polymerase (New England Biolabs) with paired-end primers and a randomly chosen unique barcode (NEB Next Multiplex Oligs for Illumina - Index Primers 2, 11, 12, 13, 15, 16, 18, 20, 21, 22). Agencourt AMPure XP Beads (Beckman Coulter) were used for all purification steps.

value: parent strain:SK36

tag: growth phase

value: late-log


title: brpT_mutant_Rep5

description: replicate 5


title: brpT_mutant_Rep2

description: replicate 2


title: N. parvum in vitro growing in PDA rep1

description: Sample name: NP1


title: N. parvum in planta 6 wpi rep3

description: Sample name: L-IW_6W_C

value: N. parvum-infected Cabernet Sauvignon stem

value: in planta

value: Cabernet Sauvignon clone FPS 19


title: N. parvum in vitro growing in Merlot rep3

description: Sample name: NM8

value: Merlot clone FPS 03


title: N. parvum in vitro growing in Merlot wood rep2

description: Sample name: NM5


title: N. parvum in vitro growing in Merlot wood rep1

description: Sample name: NM2


title: N. parvum in planta 24 hpi rep2

description: Sample name: L-IW_24H_B


title: brpT_mutant_Rep1

description: replicate 1


title: Wild-type_SK36_Rep3

description: replicate 3

source_name: Wild-type SK36


title: Wild-type_SK36_Rep4

description: replicate 4


title: NA12893exosome

description: small RNA

value: exosome


title: N. parvum in vitro growing in Cabernet Sauvignon wood rep2

description: Sample name: NC4

value: Cabernet Sauvignon clone FPS 08


title: Wild-type_SK36_Rep1

description: replicate 1


title: N. parvum in vitro growing in Cabernet Sauvignon wood rep1

description: Sample name: NC1


title: Wild-type_SK36_Rep2

description: replicate 2


title: INPUT_ChIP_DNMT3B_ICF1p2

status: Public on Mar 07 2017

city: Munich

first: Miriam

last: Gagliardi

state: Bayern

address: Kraepelinstrasse 2-10

institute: Max Planck Institute of Psychiatry

description: Input DNA

data_processing:
DNMT3B and H3K36me3 sequence reads were generated by Illumina's HiSeq2000 platform.  H3K27me3 and H3K4me3 reads were sequenced using the SOLiD platform (Applied Biosystem).
Quality of the short reads of 50 bp were analysed and high quality reads were selected. They were aligned to the human reference genome (hg19) by using Bowtie v. 1.1.1. The parameters used for Bowtie were –a, –m3, –-best, and –-strata.
Data were filtered by uniquely aligned reads and a single read for each starting position was considered.
DNMT3B peak calling was performed using MACS v.1.4.2. The sample enrichments were normalized for cell line specific input. MACS parameter settings were: --bw 200, -p 1e-4  and -m 8,30. Moreover, we detected large peaks using EDD (12), setting:  log_ratio_bin_size 2Kb, -g 5 and -n 20000. Confidence intervals were calculated using the normal approximation method for binomial proportions. The SICER v.1.1 (13) peak-finding algorithm was used to identify the H3K4me3-, H3K27me3- and H3K36me3-enriched sites throughout the genome. For all these histone marks we selected peaks with a false discovery rate (FDR) of 1e-5. We used as window size and gap different values accordingly with the profile of analyzed histone marks. In particular, for H3K4me3 we used window size 200 bp and gap size 200 bp, for H3K27me3 500 bp and 1000 bp, while for H3K36me3 800bo and 4000bp respectively.
Genome_build: hg19

growth_protocol: ICF and control B-LCL were coltured in RPMI-1640 (SIGMA) supplemented with 10% fetal bovine serum.

extract_protocol:
Lysates were clarified from sonicated nuclei. Histone-DNA and DNMT3B-DNA complexes were isolated with specific antibodies. Immunoprecipitated complexes were recovered with protein A sepharose (Pharmacia), washed with low and high salt buffers, reverse-crosslinked, and purified.
DNMT3B and H3K36me3 libraries were prepared according to Illumina's instructions accompanying the Nextera DNA Sample Kit. H3K27me3 and H3K4me3 libraries were prepared according to SOLiD protocol (Applied Biosystem).

value: cell line

tag: genotype

tag: chip antibody


title: N. parvum in vitro growing in Cabernet Sauvignon wood rep3

description: Sample name: NC5


title: INPUT_ChIP_DNMT3B_Ctrl2

description: Input DNA


title: INPUT_ChIP_DNMT3B_ICF1p1

description: Input DNA


title: brpT_mutant_Rep4

description: replicate 4


title: N. parvum in vitro growing in PDA  rep3

description: Sample name: NP4


title: INPUT_ChIP_DNMT3B_Ctrl1

description: Input DNA


title: N. parvum in planta 2 wpi rep1

description: Sample name: L-IW_2W_A

value: 2 wpi


title: ChIP_DNMT3B_ICF1p1

description: DNMT3B-interacting DNA

value: DNMT3B, Diagenode


title: ChIP_DNMT3B_ICF1p2

description: DNMT3B-interacting DNA


title: ChIP_DNMT3B_Ctrl2

description: DNMT3B-interacting DNA


title: ChIP_DNMT3B_Ctrl1

description: DNMT3B-interacting DNA


title: Wild-type_SK36_Rep5

description: replicate 5


title: H3K36me3_ICF1p1_ChIPSeq

description: H3K36me3-enriched DNA

value: H3K36me3, Abcam


title: H3K36me3_Ctrl1_ChIPSeq

description: H3K36me3-enriched DNA


title: Input_H3K36me3_ICF1p1_ChIPSeq

description: Input DNA


title: RRBS_ICF1p1

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequence reads were processed by adaptor trimming (Illumina Pipeline Casava), subjected to quality control (FastQC) and low quality reads were discarded (Trim Galore).
High quality reads were aligned to the reference genome using the Bismark aligner and methylation call was performed with methylation extractor script.
Single CpG methylation percentage was calculated on pooled replicates by dividing the number of methylated Cs by the total coverage on that base using the R library package methylKit. Differentially methylated CpGs were obtained comparing CpG methylation level in each ICF1 sample to the mean CpG methylation percentage of control samples.
Differentially methylated regions (DMRs) between samples were defined as sequences with minimum 10 (less than 2Kb apart) common CpGs with concordant methylation difference (≥ |25%|).
Genome_build: hg19

extract_protocol:
DNA extraction was performed using Wizard Genomic DNA (Promega).
RRBS libraries were prepared and sequenced according to Illumina's instructions.


title: IgG_RIP_ICF1p2

description: Not specific interacting RNA

data_processing:
The sequenced reads were mapped using TopHat2, following the same parameter as above described for RNA-Seq dataset.
Cufflinks settings were the following: max intron length 300000, min isoform fraction 0.1, pre-mRNA fraction 0.15, using effective length correction. For each cell line we considered only genes with input FPKM ≥ 1 and with enrichment values in DNMT3B immunoprecipitated (IP) sample over background (log2(FPKMDNMT3B/FPKMIgG)) ≥ 1.5. The enrichment of exons in DNMT3B immunoprecipitated RNA fraction over background (IgG fraction) was calculated according to the following steps.
Using HTSeq we counted the mapped reads on non-overlapping exon list as described above. Then, we measured the differential exon abundance in DNMT3B and IgG immunoprecipitated transcripts using DESeq2, considering exons with p-value ≤ 0.05 and log2 (DNMT3B/IgG) ≥1.5.
RIP-seq inputs are listed as "RNAseq_experiment2" files.
Genome_build: hg19

extract_protocol:
Native RNA immunoprecipitation experiment was performed using the Magna RIP RNA-Binding Protein Immunoprecipitation Kit (Millipore) according to the manufacturer’s instructions. Anti-DNMT3B from Diagenode was used to performed RIP assay. Immunoprecipitated fractions were cleaned from DNA contamination using TurboDNA-free kit.
Library construction were performed according to Illumina's instructions.

tag: rip antibody

value: Rabbit IgG, Millipore


title: RRBS_Ctrl1


title: RRBS_ICF1p2


title: DNMT3B_RIP_ICF1p1

description: DNMT3B-interacting RNA


title: DNMT3B_RIP_Ctrl2

description: DNMT3B-interacting RNA


title: DNMT3B_RIP_Ctrl1

description: DNMT3B-interacting RNA


title: IgG_RIP_Ctrl1

description: Not specific interacting RNA


title: IgG_RIP_ICF1p1

description: Not specific interacting RNA


title: IgG_RIP_Ctrl2

description: Not specific interacting RNA


title: RNAseq_ICF1p2_experiment2

data_processing:
Reads were mapped to the reference genome using TopHat2 v.2.0.13. In the first step we aligned the reads against the transcriptome. We used the following non-default TopHat2 parameters: -r 250, -m 2, --min-coverage-intron 50, --max-coverage-intron 100000, —mate-std-dev 50, —segment-length 17.
The counts of sequenced reads per annotated gene were derived with the use of htseq-count script distributed with HTSeq. We used the R library package DESeq2 v.1.8.2
The relative isoform abundance estimation was performed using BitSeq
Genome_build: hg19

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Life Technologies) and purified from residual DNA contaminant using the TURBO DNA-freeTM Kit (Ambion, Austin, TX) according to the manufacturer’s instructions. RNA quality was checked on the Agilent 2100 Bioanalyzer and quantity was measured using the Qubit instrument (Life Technologies).
Library construction were performed according to Illumina's instructions.


title: RNAseq_ICF1p1_experiment2


title: RNAseq_ICF1p2_experiment1


title: RNAseq_Ctrl1_experiment2


title: RNAseq_ICF1p1_experiment1


title: RNAseq_Ctrl2_experiment2


title: RNAseq_Ctrl2_experiment1


title: RNAseq_Ctrl1_experiment1


title: Input_H3K36me3_Ctrl1_ChIPSeq

description: Input DNA


title: RRBS_Ctrl3


title: NC Mock

city: Boston

first: Pin-Ji

last: Lei

state: Massachusetts

address: 100 Blossom Street

department: Department of Radiation Oncology

institute: Massachusetts General Hospital

data_processing:
RNASeq raw data quality control by FastQC
RNASeq raw data clean performed by cutadapt
RNASeq data mapping to hg19 reference genome by tophat2 with at most 2 mismatch for each reads. Cufflinks was used for differential expression gene analysis,gene expression value with more than 2 fold change was defined differential expression genes.
Genome_build: hg19
Supplementary_files_format_and_content: txt format file for RNASeq gene expression level in each sample.

source_name: Wildtype, mock infection

extract_protocol:
For RNASeq 10ug total RNA was used, and mRNA purification was performed using oligo-dT magnic beads(NEBNext PolyA mRAN magnetic isolation module # E7490). mRNA was fragmented and reverse transcript into 200-400bp dscDNA for library construction(NEB # E7525 # E6111).
Rubicon ThruPLEX DNA-seq 48D kit was used for RNASeq  library construction. Brifely, about 100ng dscDNA was used as initiation for end repair and prepared for adaptor ligation. After adaptor ligation, PCR amplification with 15 cycles for each library and gel selection was used for library size selection and purification.

tag: cell line

value: wildtype


title: siTTLL12 Mock

source_name: TTLL12 knockdown, mock infection


title: siTTLL12 Sev

source_name: TTLL12 knockdown, Sendai virus infection


title: CD5-high rep3

first: Xiaoyang

last: Jin

state: -- Please, Select --

address: 15 Datun Road, Chaoyang District

institute: Institute of Biophysics, CAS

data_processing:
Sequenced reads were mapped to hg19 whole genome using tophat v2.1.0 with parameters --phred64-quals
The numbers of reads mapped to each gene were calculated using htseq-count (version 0.6.1p1) with parameters --stranded=no. GENCODE release 19 was used as gene annotation source.
Genome_build: hg19
Supplementary_files_format_and_content: text files with raw read counts. The file raw-count.txt contains the raw read counts for all six samples in one file.

source_name: conventional dendritic cells_CD5_high

extract_protocol:
Library was prepared using 200 ng of RNA and the Illumina TruSeq™ RNA Sample Preparation v2 Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: blood

value: blood conventional dendritic cells

tag: surface marker

value: CD5 high expression


title: CD5-high rep2


title: CD5-low rep2

source_name: conventional dendritic cells_CD5_low

value: CD5 low expression


title: NC Sev

source_name: Wildtype, Sendai virus infection


title: CD5-low rep1


title: CD5-low rep3


title: DNMT3B_RIP_ICF1p2

description: DNMT3B-interacting RNA


title: CD5-high rep1


title: S935 - Undifferentiated pleomorphic sarcoma

city: Toulouse

first: Frédéric

last: Chibon

address: 2 avenue Hubert Curien

department: Team 19 - INSERM UMR1037

country: France

institute: Cancer Research Center of Toulouse

description: Unstranded library

data_processing:
Low-quality 5' and 3' ends were trimmed using Sickle (Phred score <20). Overlapping reads were merged using SeqPrep and split in half with a Awk routine. Paired-ends with one read shorter than 30 bp were discarded.
Transcriptomic (coding RefSeq genes from Hg19 UCSC Table Browser fixed on 2014/01) alignments were performed by TopHat2. Once aligned, paired-end reads that mapped at multiple locations on transcriptome, low-quality (score <20) and discordant paired-end reads were discarded using SAMtools. MarkDuplicates removed PCR duplicates.
Htseq-count computed gene expression.
Miscellaneous filters, statistics and plots were performed by R.
Genome_build: Hg19
Supplementary_files_format_and_content: Gene expressions were normalized using DESeq2

source_name: Undifferentiated pleomorphic sarcoma

extract_protocol:
RNA extraction from frozen samples was performed using a standard TRIzol (Life Technologies) / chloroform extraction followed by 100% ethanol precipitation and RNA purification using the RNeasy Mini Kit (Qiagen) with a DNase treatment (RNase-Free DNase Set, Qiagen). RNA were quantified using a Nanodrop 1000 spectrophotometer (Thermo Scientific) and were qualified with the Agilent 2100 Bioanalyzer (Agilent) using the Agilent RNA 6000 Nano Kit (Agilent) according to the manufacturer’s instructions. An ERCC RNA Spike-In Mix (Life technologies) was added to each RNA as recommended by the manufacturer.
The RNA-seq libraries were prepared using a modified TruSeq RNA Sample Prep Kit v2 protocol. Briefly, 0.5 μg of total RNA was used for poly-A based mRNA enrichment selection followed by fragmentation by divalent cations resulting into fragments of 80-250nt, with the major peak at 130nt. Double stranded cDNA was end repaired, 3´adenylated and the 3´-“T” nucleotide of barcoded Illumina adapters was used for the adapter ligation. The ligation product was amplified with 12 cycles of PCR and quality controlled in Agilent DNA 7500 Bioanalyzer assay (Agilent). Each library was sequenced using TruSeq SBS Kit v3-HS, in paired end mode with the read length 2x76bp. We generated minimally 35 million paired end reads passing filter for each frozen tissue RNA-seq library in a fraction of a sequencing lane on HiSeq2000 (Illumina, Inc) following the manufacturer’s protocol. Image analysis, base calling and base quality scoring of the run were processed by integrated primary analysis software - Real Time Analysis (RTA 1.13.48) and followed by generation of FASTQ sequence files by CASAVA (v1.8).

tag: tumor type

value: Undifferentiated pleomorphic sarcoma

tag: metastasis

value: Yes

tag: tumor localization

value: Upper limb

tag: trio fusion

value: No


title: S934 - Liposarcoma - dedifferentiated

description: Unstranded library

source_name: Liposarcoma - dedifferentiated

value: Liposarcoma - dedifferentiated

value: Internal trunk


title: S936 - Myxofibrosarcoma

description: Unstranded library

source_name: Myxofibrosarcoma

value: Myxofibrosarcoma

value: Lower limb


title: S937 - Leiomyosarcoma

description: Unstranded library

source_name: Leiomyosarcoma

value: Leiomyosarcoma


title: S928 - Undifferentiated pleomorphic sarcoma

description: Unstranded library


title: S933 - Undifferentiated pleomorphic sarcoma

description: Unstranded library

value: Trunk wall


title: S925 - Liposarcoma - pleomorphic

description: Unstranded library

source_name: Liposarcoma - pleomorphic

value: Liposarcoma - pleomorphic


title: S930 - Undifferentiated pleomorphic sarcoma

description: Unstranded library


title: S927 - Liposarcoma - pleomorphic

description: Unstranded library


title: S929 - Leiomyosarcoma

description: Unstranded library


title: S926 - Undifferentiated pleomorphic sarcoma

description: Unstranded library


title: S932 - Myxofibrosarcoma

description: Unstranded library


title: S931 - Undifferentiated pleomorphic sarcoma

description: Unstranded library


title: S924 - Undifferentiated pleomorphic sarcoma

description: Unstranded library


title: S923 - Leiomyosarcoma

description: Unstranded library


title: S921 - Myxofibrosarcoma

description: Unstranded library


title: S922 - Undifferentiated pleomorphic sarcoma

description: Unstranded library


title: S920 - Liposarcoma - dedifferentiated

description: Unstranded library


title: S917 - Liposarcoma - pleomorphic

description: Unstranded library


title: S915 - Leiomyosarcoma

description: Unstranded library


title: S919 - Leiomyosarcoma

description: Unstranded library


title: S910 - Liposarcoma - dedifferentiated

description: Unstranded library


title: S912 - Leiomyosarcoma

description: Unstranded library


title: S906 - Liposarcoma - dedifferentiated

description: Unstranded library


title: S908 - Liposarcoma - dedifferentiated

description: Unstranded library


title: S907 - Undifferentiated pleomorphic sarcoma

description: Unstranded library


title: S905 - Myxofibrosarcoma

description: Unstranded library


title: S901 - Liposarcoma - dedifferentiated

description: Unstranded library


title: S899 - Undifferentiated pleomorphic sarcoma

description: Unstranded library


title: S903 - Low grade fibromyxoid sarcoma

description: Unstranded library

source_name: Low grade fibromyxoid sarcoma

value: Low grade fibromyxoid sarcoma


title: S904 - Leiomyosarcoma

description: Unstranded library


title: S887 - Undifferentiated pleomorphic sarcoma

description: Unstranded library


title: S882 - Liposarcoma - dedifferentiated

description: Unstranded library


title: S879 - Leiomyosarcoma

description: Unstranded library

value: Gyneacological area


title: S883 - Leiomyosarcoma

description: Unstranded library


title: S877 - Low grade fibromyxoid sarcoma

description: Unstranded library


title: S886 - Liposarcoma - dedifferentiated

description: Unstranded library


title: S881 - Undifferentiated pleomorphic sarcoma

description: Unstranded library


title: S876 - Leiomyosarcoma

description: Unstranded library


title: S911 - Undifferentiated pleomorphic sarcoma

description: Unstranded library


title: S916 - Leiomyosarcoma

description: Unstranded library


title: S918 - Undifferentiated pleomorphic sarcoma

description: Unstranded library


title: S909 - Undifferentiated pleomorphic sarcoma

description: Unstranded library


title: S874 - Liposarcoma - dedifferentiated

description: Unstranded library


title: S864 - Liposarcoma - dedifferentiated

description: Unstranded library


title: S862 - Undifferentiated pleomorphic sarcoma

description: Unstranded library


title: S863 - Undifferentiated pleomorphic sarcoma

description: Unstranded library


title: S861 - Myxofibrosarcoma

description: Unstranded library


title: S871 - Liposarcoma - dedifferentiated

description: Unstranded library


title: S873 - Myxofibrosarcoma

description: Unstranded library


title: S860 - Pleomorphic rhabdomyosarcoma

description: Unstranded library

source_name: Pleomorphic rhabdomyosarcoma

value: Pleomorphic rhabdomyosarcoma


title: S867 - Liposarcoma - dedifferentiated

description: Unstranded library


title: S857 - Leiomyosarcoma

description: Unstranded library


title: S900 - Pleomorphic rhabdomyosarcoma

description: Unstranded library


title: S855 - Undifferentiated pleomorphic sarcoma

description: Unstranded library


title: S856 - Leiomyosarcoma

description: Unstranded library


title: S851 - Undifferentiated pleomorphic sarcoma

description: Unstranded library


title: S844 - Undifferentiated pleomorphic sarcoma

description: Unstranded library


title: S841 - Liposarcoma - dedifferentiated

description: Unstranded library


title: S846 - Leiomyosarcoma

description: Unstranded library


title: S838 - Undifferentiated pleomorphic sarcoma

description: Unstranded library


title: S847 - Leiomyosarcoma

description: Unstranded library


title: S830 - Liposarcoma - dedifferentiated

description: Unstranded library


title: S831 - Undifferentiated pleomorphic sarcoma

description: Unstranded library


title: S843 - Myxofibrosarcoma

description: Unstranded library


title: S828 - Pleomorphic rhabdomyosarcoma

description: Unstranded library


title: S829 - Pleomorphic rhabdomyosarcoma

description: Unstranded library


title: S835 - Leiomyosarcoma

description: Unstranded library


title: S823 - Myxofibrosarcoma

description: Unstranded library


title: S826 - Leiomyosarcoma

description: Unstranded library


title: S822 - Undifferentiated pleomorphic sarcoma

description: Unstranded library


title: S832 - Myxofibrosarcoma

description: Unstranded library


title: S815 - Leiomyosarcoma

description: Unstranded library


title: S821 - Liposarcoma - dedifferentiated

description: Unstranded library


title: S858 - Undifferentiated pleomorphic sarcoma

description: Unstranded library


title: S817 - Leiomyosarcoma

description: Unstranded library


title: S820 - Leiomyosarcoma

description: Unstranded library


title: S824 - Liposarcoma - dedifferentiated

description: Unstranded library


title: S814 - Leiomyosarcoma

description: Unstranded library


title: S813 - Leiomyosarcoma

description: Unstranded library


title: S850 - Myxofibrosarcoma

description: Unstranded library


title: S849 - Undifferentiated pleomorphic sarcoma

description: Unstranded library


title: S848 - Undifferentiated pleomorphic sarcoma

description: Unstranded library


title: N004 - Undifferentiated pleomorphic sarcoma

description: Unstranded library


title: S827 - Myxofibrosarcoma

description: Unstranded library


title: N009 - Liposarcoma - dedifferentiated

description: Unstranded library


title: M978 - Leiomyosarcoma

description: Unstranded library

value: GI tract


title: M980 - Undifferentiated pleomorphic sarcoma

description: Unstranded library


title: M979 - Myxofibrosarcoma

description: Unstranded library


title: M992 - Undifferentiated pleomorphic sarcoma

description: Unstranded library


title: M995 - Myxofibrosarcoma

description: Unstranded library


title: M990 - Leiomyosarcoma

description: Unstranded library


title: M985 - Undifferentiated pleomorphic sarcoma

description: Unstranded library


title: M984 - Leiomyosarcoma

description: Unstranded library


title: M983 - Liposarcoma - pleomorphic

description: Unstranded library


title: M982 - Leiomyosarcoma

description: Unstranded library


title: M989 - Leiomyosarcoma

description: Unstranded library


title: M997 - Leiomyosarcoma

description: Unstranded library


title: M981 - Myxofibrosarcoma

description: Unstranded library


title: M986 - Leiomyosarcoma

description: Unstranded library


title: M993 - Myxofibrosarcoma

description: Unstranded library


title: M988 - Leiomyosarcoma

description: Unstranded library


title: M987 - Leiomyosarcoma

description: Unstranded library


title: M999 - Undifferentiated pleomorphic sarcoma

description: Unstranded library


title: M977 - Leiomyosarcoma

description: Unstranded library

value: Head and neck


title: M976 - Undifferentiated pleomorphic sarcoma

description: Unstranded library


title: M994 - Leiomyosarcoma

description: Unstranded library


title: N002 - Undifferentiated pleomorphic sarcoma

description: Unstranded library


title: M996 - Undifferentiated pleomorphic sarcoma

description: Unstranded library


title: N003 - Liposarcoma - dedifferentiated

description: Unstranded library


title: M969 - Liposarcoma - dedifferentiated

description: Unstranded library


title: M965 - Undifferentiated pleomorphic sarcoma

description: Unstranded library


title: M998 - Undifferentiated pleomorphic sarcoma

description: Unstranded library


title: N001 - Undifferentiated pleomorphic sarcoma

description: Unstranded library


title: M964 - Leiomyosarcoma

description: Unstranded library


title: M961 - Myxofibrosarcoma

description: Unstranded library


title: M963 - Leiomyosarcoma

description: Unstranded library


title: Input_H3K4me3_ICF1p1_ChIPSeq

description: Input DNA

value: cell line


title: H3K27me3_Ctrl1_ChIPSeq

description: H3K27me3-enriched DNA

value: H3K27me3, Abcam


title: Input_H3K4me3_Ctrl1_ChIPSeq

description: Input DNA


title: iPSCp_H3K4me3

first: Tae-Young

last: Roh

state: --- Select One ---

address: 52 Ewhayeodae-gil, Seodaemun-gu

department: Life Sciences

institute: Ewha Womans University

data_processing:
Illumina Casava1.6 software used for basecalling.
Sequenced reads were mapped to mm9 genome using CASAVA 1.6
The following reads were removed for down-stream analysis: multiple match, mismatch >2
Sequencing tags were shifted by +75 bp for positive strand and -75 bp for negative strand. The shifted sequencing tags were counted in non-overlapping 200bp genomic windows.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files with BED graph format

source_name: iPSCp

growth_protocol: mouse ES cells were cultured with Mitomycin C (Sigma-Aldrich, St. Louis, MO)-treated STO feeder cell layer on 0.1% gelatin (Sigma-Aldrich, St. Louis, MO)-coated tissue culture dish. Fibroblast cells were cultured with Dulbecco modified Eagle medium (DMEM) containing 10% fetal bovine serum (FBS) and antibiotics.

extract_protocol:
Cells were resuspended with digestion buffer (50mM Tris-HCL, pH7.6, 1mM CaCl2, 0.2% triton X-100) and 5mM butyrate, 0.5mM PMSF, x proteinase inhibitor. The chromatins were digested with Mnase and enzyme was inactivated by adding the stop buffer (10mM Tris, pH7.6, 5mM EDTA). The chromatin was immunoprecipitated with antibodies specific to the H3K4me3 (ab8580, Abcam, Cambridge, UK), and H3K27me3 (07-449, Millipore, Billerica, MA) in RIPA buffer (10 mM Tris, pH7.4, 1mM EDTA, 0.1% SDS, 0.1% Na-Deoxycholate, and 1% Triton X-100). Bead complex was captured by magnetic stand and washed sequentially twice with RIPA buffer, RIPA + 0.3 M NaCl, and LiCl buffer (0.25 M LiCl, 0.5% NP40, 0.5% Na- Deoxycholate) and once with 1X TE + 0.2% Triton X-100, and 1X TE. Proteinase K digestion and phenol/chloroform extraction was performed to isolate the DNA.
Sequencing libraries were manually generated for high-throughput sequencing. Either end of DNA strands was filled using the Epicentre DNA END-Repair kit (Epicentre Biotechnologies, Madison, WI). Adenine was added at 3’ ends by  Taq DNA polymerase (New England Biolabs, Beverly, MA) under dATP conditions. Illumina’s adaptor oligomers was ligated at both ends using Quick Ligation kit (Qiagen, Germantown, MD). After purified twice, DNA libraries are amplified using Solexa primers (Illumina, San Diego, CA) and Phusion PCR master mix (Thermo Scientific, Hudson, NH).

value: partial induced pluripotent stem cell


title: mESC_H3K27me3

source_name: mESC

value: embryonic stem cell


title: Input_H3K27me3_Ctrl1_ChIPSeq

description: Input DNA


title: sFB-G_H3K4me3

source_name: sFB-G

value: skin fibroblast


title: H3K4me3_Ctrl1_ChIPSeq

description: H3K4me3-enriched DNA

value: H3K4me3, Abcam


title: iPSC1_H3K4me3

value: induced pluripotent stem cell


title: sFB-G_H3K27me3


title: iPSC1_H3K27me3


title: sFB_H3K4me3

source_name: sFB


title: mESC_H3K4me3


title: iPSCp_H3K27me3


title: H3K27me3_ICF1p1_ChIPSeq

description: H3K27me3-enriched DNA


title: cFB_H3K4me3

source_name: cFB

value: cardiac fibroblast


title: iPSC2_H3K4me3


title: iPSC2_H3K27me3


title: Single cell Hi-C cell 5

city: Barcelona

first: Andre

middle: J

last: Faure

address: Dr. Aiguader 88

department: EMBL-CRG Systems Biology Unit

country: Spain

institute: Centre for Genomic Regulation (CRG)

data_processing:
Library strategy: Single cell Hi-C
Basecalls performed using Phred quality score (Q score)
ChIP-seq reads were aligend to the GRCm38/mm10 mouse genome reference using Bowtie 2 v2.1.050 and filtered to retain reads with mapping quality >30.
ChIP-seq peaks were called using MACS2 v2.1.0.2015073157 with a minimum FDR cutoff of 0.01 (-q 0.01), except for broad features (H3K27me3, H3K36me3 and H3K9me3) where a cutoff of 0.05 was used (-q 0.05).
ChIP-seq peaks were filtered to remove those not corresponding to the canonical chromosomes.
RNA-seq reads were aligned to the reference genome GRCm38/mm10, downloaded from the Ensembl database ftp.ensembl.org using Gsnap version gmap-2014-12-17. Only uniquely mapped reads were used for further analysis. Gene counts from SAM files were obtained using htseq-count version 0.6.1 with mode intersection non-empty, -s reverse. The gene annotation was extracted from Ensembl Gene Release 75. Differential gene expression analysis was conducted using Bioconductor R (R-3.1.2) package DESeq2 version 1.6.3. An adjusted p Value threshold of 0.05 was used to determine differential gene expression. Expression values are FPKM (read number normalized across samples by DESeq size factor and across genes by gene length) calculated using custom R-scripts.
Single cell Hi-C reads were initially processed using the NucProcessing software package (available upon request). Processed reads were aligned to the GRCm38/mm10 mouse genome reference using Bowtie 2 and filtered to retain reads that formed a valid Hi-C contact junction between two RE1 resriction sites. Output files were further processed to perform extra, single-cell specific processing and cleanup. These remove any pairs that represent only a single observation of a specific RE1-RE1 ligation junction after PCR amplification, while at least two separate, albeit sometimes identical, molecules must be paired-end sequenced to confirm a ligation junction. Next the sequence pairs were filtered to remove those with promiscuous ends: where the RE1 fragment at either end was involved in more than one ligation event. Finally, the redundancy in amplified RE1-RE1 ligation events was removed to create a single list of paired RE1 fragment ends.
Genome_build: mm10
Supplementary_files_format_and_content: A summary table of results (.txt) from the analysis of the RNA-seq samples includes expression estimates for all genes (Ensembl Gene Release 75; GRCm38/mm10). Expression values are FPKM (read number normalized across samples by DESeq size factor and across genes by gene length) calculated using custom R-scripts.
Supplementary_files_format_and_content: bed files (.bed) are tab-delimited text files containing chromosomal coordinates of all ChIP-seq peaks (chromosome name, start, end).
Supplementary_files_format_and_content: Single cell Hi-C txt file (.txt) is a tab-separated text format containing the Hi-C contacts. After the header line, each individual contact is represented on a line consisting of chromosome_1 seq_pos_1 chromosome_2seq_pos_2
Supplementary_files_format_and_content: Single cell genome structure pdb file (.pdb) is protein data bank format. Atom type N is used to indicate restrained particles. Atom type C is used to represent unrestrained backbone particles. Residue number corresponds to the particle and increases every 100 kb. Chain letter represents the chromosome. The last column represents the particle sequence position.
Supplementary_files_format_and_content: HDF5 file (.hdf5) used to calculate distances between genomic loci and depth in the single cell structures. The hierarchy format is;name :: String -- the name of the NucFrame;bin_size :: Int -- the bin_size of the nuc files;chrms :: ["X", "1", ..] -- all of the chromosomes that are present;bp_pos/chrm :: [Int] -- The start bp index of each particle in each chrm;position/chrm :: [[[Float]]] -- (model, bead_idx, xyz);expr_contacts/chrm/chrm :: [[Int]] -- (bp, bp), raw contact count;dists/chrm/chrm :: [[Float]] -- (bead_idx, bead_idx), distanes between beads;depths/i/alpha :: Float -- alpha value used to calculate depths;depths/i/chrm/ :: [Float] -- (bead_idx, ), depth of point from surface i;alpha_shape/k/simplices :: [[Int]] -- (n_simplicies, k), indices of k simplices;alpha_shape/k/ab :: [(a, b)] -- (n_simplicies, 2), a and b values for k-simplices;surface_dist/alpha_val/tag :: optional tag for this value of alpha;surface_dist/alpha_val/i/surface_size :: size of surface i for alpha

source_name: mESCs

growth_protocol: All mouse embryonic stem cells (mESCs) were cultured on 0.2 % gelatin in 2i media (NDiff B27 base medium, Stem Cell Sciences Ltd, catalogue no: SCS-SF-NB-02, supplemented with 1 uM PD0325901, 3 uM CHIR99021 and 20 ng/ml LIF). Haploid mESCs were sorted every 4 passages to enrich for haploid cells as previously described in Leeb M & Wutz A, Nature, 2011

extract_protocol:
5-10 million Haploid mouse ES cells were fixed for 5 min with 2 % formaldehyde in PBS and then the reaction was quenched for another 5 min in 0.125 M glycine. Nuclei were then extracted by incubating cells on ice for 30 min (inverting every 10 min) in 10 mM Tris pH 8.0, 10 mM NaCl, 0.2 % NP-40 (IGEPAL CA-630) and protease inhibitor cocktail (Roche).
Single cell Hi-C libraries were prepared using Illumina's Nextera XT sample kit with the following modifications. Briefly, biotinylated junctions were captured on streptavidin M-280 dynabeads and digested with AluI enzyme. Then tagmentaion was carried out using 1:10 to 1:100 dilution of Amplicon Tagment Mix. After tagmentation DNA was PCR amplified with Illumina primers for 9 + 15 cycles and library fragments of ~300-700 bp (insert plus adaptor and PCR primer sequences) were isolated using AMPure beads (Beckman). The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the MiSeq following the manufacturer's protocols.

value: haploid mESCs derived from strain 129/Ola


title: cFB_H3K27me3


title: Single cell Hi-C cell 6


title: Single cell Hi-C cell 8

data_processing:
Library strategy: Single cell Hi-C
Basecalls performed using Phred quality score (Q score)
ChIP-seq reads were aligend to the GRCm38/mm10 mouse genome reference using Bowtie 2 v2.1.050 and filtered to retain reads with mapping quality >30.
ChIP-seq peaks were called using MACS2 v2.1.0.2015073157 with a minimum FDR cutoff of 0.01 (-q 0.01), except for broad features (H3K27me3, H3K36me3 and H3K9me3) where a cutoff of 0.05 was used (-q 0.05).
ChIP-seq peaks were filtered to remove those not corresponding to the canonical chromosomes.
RNA-seq reads were aligned to the reference genome GRCm38/mm10, downloaded from the Ensembl database ftp.ensembl.org using Gsnap version gmap-2014-12-17. Only uniquely mapped reads were used for further analysis. Gene counts from SAM files were obtained using htseq-count version 0.6.1 with mode intersection non-empty, -s reverse. The gene annotation was extracted from Ensembl Gene Release 75. Differential gene expression analysis was conducted using Bioconductor R (R-3.1.2) package DESeq2 version 1.6.3. An adjusted p Value threshold of 0.05 was used to determine differential gene expression. Expression values are FPKM (read number normalized across samples by DESeq size factor and across genes by gene length) calculated using custom R-scripts.
Single cell Hi-C reads were initially processed using the NucProcessing software package (available upon request). Processed reads were aligned to the GRCm38/mm10 mouse genome reference using Bowtie 2 and filtered to retain reads that formed a valid Hi-C contact junction between two RE1 resriction sites. Output files were further processed to perform extra, single-cell specific processing and cleanup. These remove any pairs that represent only a single observation of a specific RE1-RE1 ligation junction after PCR amplification, while at least two separate, albeit sometimes identical, molecules must be paired-end sequenced to confirm a ligation junction. Next the sequence pairs were filtered to remove those with promiscuous ends: where the RE1 fragment at either end was involved in more than one ligation event. Finally, the redundancy in amplified RE1-RE1 ligation events was removed to create a single list of paired RE1 fragment ends.
Genome_build: mm10
Supplementary_files_format_and_content: A summary table of results (.txt) from the analysis of the RNA-seq samples includes expression estimates for all genes (Ensembl Gene Release 75; GRCm38/mm10). Expression values are FPKM (read number normalized across samples by DESeq size factor and across genes by gene length) calculated using custom R-scripts.
Supplementary_files_format_and_content: bed files (.bed) are tab-delimited text files containing chromosomal coordinates of all ChIP-seq peaks (chromosome name, start, end).
Supplementary_files_format_and_content: Single cell Hi-C txt file (.txt) is a tab-separated text format containing the Hi-C contacts. After the header line, each individual contact is represented on a line consisting of chromosome_1 seq_pos_1 chromosome_2seq_pos_2
Supplementary_files_format_and_content: Single cell genome structure pdb file (.pdb) is protein data bank format. Atom type N is used to indicate restrained particles. Atom type C is used to represent unrestrained backbone particles. Residue number corresponds to the particle and increases every 100 kb. Chain letter represents the chromosome. The last column represents the particle sequence position.
Supplementary_files_format_and_content: Single cell CENP-A coordinate file (.xyz). CENP-A superposition coordinates are represented in xyz format and may be viewed using molecular graphics software such as PyMol. The xyz format contain centromere positions after fitting to the corresponding genome structure. Atom type O was used to represent centromere positions.
Supplementary_files_format_and_content: HDF5 file (.hdf5) used to calculate distances between genomic loci and depth in the single cell structures. The hierarchy format is;name :: String -- the name of the NucFrame;bin_size :: Int -- the bin_size of the nuc files;chrms :: ["X", "1", ..] -- all of the chromosomes that are present;bp_pos/chrm :: [Int] -- The start bp index of each particle in each chrm;position/chrm :: [[[Float]]] -- (model, bead_idx, xyz);expr_contacts/chrm/chrm :: [[Int]] -- (bp, bp), raw contact count;dists/chrm/chrm :: [[Float]] -- (bead_idx, bead_idx), distanes between beads;depths/i/alpha :: Float -- alpha value used to calculate depths;depths/i/chrm/ :: [Float] -- (bead_idx, ), depth of point from surface i;alpha_shape/k/simplices :: [[Int]] -- (n_simplicies, k), indices of k simplices;alpha_shape/k/ab :: [(a, b)] -- (n_simplicies, 2), a and b values for k-simplices;surface_dist/alpha_val/tag :: optional tag for this value of alpha;surface_dist/alpha_val/i/surface_size :: size of surface i for alpha


title: Single cell Hi-C cell 7


title: Input_H3K27me3_ICF1p1_ChIPSeq

description: Input DNA


title: Single cell Hi-C cell 3


title: Single cell Hi-C cell 4


title: sFB_H3K27me3


title: Single cell Hi-C cell 1


title: Single cell Hi-C cell 2


title: H3K4me3_ICF1p1_ChIPSeq

description: H3K4me3-enriched DNA


title: D2_9mnths_WaterControl_1040

city: Bar Harbor

first: Pete

last: Williams

state: Maine

address: 600 Main Street

institute: The Jackson Laboratory

data_processing:
fastq were alinged to a DBA/2J mm10 genome using Tophat v 2.0.7 and Bowtie 2.0.6
HTSeq was used to quantity gene expression
Genes with read count greater than 5 in atleast 10 samples were retained
Supplementary_files_format_and_content: csv containing library size normanlized counts in CPM

source_name: Retinal ganglion cells

extract_protocol: Prior to cell collection, all surfaces and volumes were cleaned with 70% ethanol and RNaseZap (ThermoFisher Scientific) solution followed by dH20. Mice were euthanized, eyes enucleated and placed immediately into ice-cold HBSS. Retinas were dissected from the eyes (4 or 9 mo of age, no axon degeneration confirmed by PPD staining) in HBSS on ice and placed directly into 100 μl of a custom HBSS (Gibco), dispase (5 U/ml) (Stemcell Technologies), DNase I (2000 U/ml) (Worthington Biochemical) and SUPERase (1 U/μl) (ThermoFisher Scientific) solution. All retinas were from eyes that had no glaucomatous axon degeneration by PPD staining and analysis. Retinas were incubated for 20 mins at 37 °C and shaken at 350 RPM in an Eppendorf Thermomixer R followed by gentle trituration using a 200 μl pipette. Samples were blocked in 2% BSA, SUPERase (1 U/μl) in HBSS, and stained with conjugated antibodies against Cd11b, Cd11c, Cd34, Cd45.2, GFAP, Thy1.2 as well as DAPI. This cocktail allowed other retina cell types to be accurately removed during FACS. FACS was performed on a FACSAria (BD Biosciences). Thy1.2+ (and negative for all other markers) RGCs were sorted into 300μl buffer RLT + 1% β-ME, vortexed and frozen at -80°C until further processing.

tag: age (months)

tag: treatment

value: Water Control


title: D2_9mnths_WaterControl_1043


title: D2_9mnths_WaterControl_1002


title: D2_9mnths_WaterControl_1071


title: D2_9mnths_WaterControl_1042


title: D2_9mnths_WaterControl_1003


title: D2_9mnths_WaterControl_360


title: D2_9mnths_WaterControl_1044


title: D2_9mnths_NAM_2004

value: Nicotinamide 500mg/kg/d


title: D2_9mnths_WaterControl_1045


title: D2_9mnths_NAM_2002


title: D2_9mnths_NAM_2006


title: D2_9mnths_WaterControl_2023


title: D2_9mnths_WaterControl_299


title: D2_9mnths_WaterControl_1077


title: D2_9mnths_WaterControl_1004


title: D2_9mnths_WaterControl_306


title: D2_9mnths_NAM_2003


title: D2_9mnths_NAM_2012


title: D2_9mnths_WaterControl_1072


title: D2_9mnths_NAM_2009


title: D2_9mnths_WaterControl_1073


title: Gpnmb_9mnths_WaterControl_1384


title: D2_9mnths_NAM_2001


title: D2_9mnths_WaterControl_1000


title: D2_9mnths_WaterControl_1041


title: D2_9mnths_WaterControl_1076


title: Gpnmb_9mnths_WaterControl_481


title: Gpnmb_9mnths_WaterControl_478


title: Gpnmb_9mnths_WaterControl_1383


title: Gpnmb_9mnths_WaterControl_2055


title: Gpnmb_9mnths_WaterControl_2053


title: Gpnmb_9mnths_WaterControl_469


title: Gpnmb_9mnths_WaterControl_396


title: Gpnmb_9mnths_WaterControl_2045


title: Gpnmb_4mnths_WaterControl_2050


title: Gpnmb_4mnths_WaterControl_2056


title: Gpnmb_4mnths_WaterControl_2057


title: D2_4mnths_WaterControl_2027


title: D2_4mnths_WaterControl_2030


title: Gpnmb_4mnths_WaterControl_2047


title: Gpnmb_4mnths_WaterControl_2041


title: Gpnmb_4mnths_WaterControl_2049


title: D2_9mnths_WaterControl_2036


title: D2_9mnths_WaterControl_246


title: Gpnmb_4mnths_WaterControl_2051


title: Gpnmb_4mnths_WaterControl_2052


title: D2_9mnths_WaterControl_1070


title: Gpnmb_4mnths_WaterControl_2058


title: D2_9mnths_WaterControl_2024


title: D2_4mnths_WaterControl_2034


title: D2_9mnths_WaterControl_262


title: D2_9mnths_WaterControl_250


title: Gpnmb_4mnths_WaterControl_2042


title: D2_4mnths_WaterControl_2021


title: D2_4mnths_WaterControl_2020


title: D2_4mnths_WaterControl_2018


title: D2_4mnths_WaterControl_2019


title: D2_4mnths_WaterControl_2038


title: D2_4mnths_WaterControl_2026


title: KO Adults rep3

city: La Jolla

first: Shujuan

last: Chen

address: 9500 Gilman Drive

department: Pharmacology

institute: University of California, San Diego

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: Excel files include RPKM values for each Sample.

source_name: KO Adults, pulverized small intestine

extract_protocol:
Entire small intestines (SI) were dissected from mice, sectioned, snap frozen in liquid nitrogen, and stored at -80ºC. Frozen tissues were pulverized for further RNA by using Trizol extraction.
The mRNA libraries were prepared by using illuminaTruSeq Stranded mRNA Library Prep Kit (cat: RS-122-2101) for strand-specific sequencing and sequenced using an Illumina HiSeq 2500 by running 36 cycles.

tag: developmental stage

value: adult

tag: age

value: 10 weeks old

tag: genotype/variation

value: NCoR1 intestinal KO

value: small intestine


title: KO Adults rep2

tag: strain


title: WT Adults rep3

source_name: WT Adults, pulverized small intestine

value: wild type


title: KO Adults rep1


title: WT Adults rep1


title: KO neonates rep1

source_name: KO neonates, pulverized small intestine

value: neonate

value: Post natal day 12


title: KO neonates rep2


title: Chd4 ChIP replicate 2

data_processing:
Basecalls performed using Phred quality score (Q score)
ChIP-seq reads were aligend to the GRCm38/mm10 mouse genome reference using Bowtie 2 v2.1.050 and filtered to retain reads with mapping quality >30.
ChIP-seq peaks were called using MACS2 v2.1.0.2015073157 with a minimum FDR cutoff of 0.01 (-q 0.01), except for broad features (H3K27me3, H3K36me3 and H3K9me3) where a cutoff of 0.05 was used (-q 0.05).
ChIP-seq peaks were filtered to remove those not corresponding to the canonical chromosomes.
Genome_build: mm10
Supplementary_files_format_and_content: bed files (.bed) are tab-delimited text files containing chromosomal coordinates of all ChIP-seq peaks (chromosome name, start, end).

extract_protocol:
ChIP-seq samples were prepared as described in Morey et al, 2015. Briefly, 5 million mESCs were removed from the dish using accutase and resuspended in 2i media. mESCs were then fixed in 1 % formaldehyde for 10 min before adding 0.0125 M glycine for 5 min to quench the reaction. Chromatin was then immunoprecipitated with 5 ug of antibody
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: cell type

value: strain 129 mESCs

value: anti-Chd4:Abcam (ab70469)


title: WT neonates rep2

source_name: WT neonates, pulverized small intestine


title: WT neonates rep3


title: Mbd3 ChIP replicate 1

value: anti-FLAG M2:Sigma (F3165)


title: CHD4-WT RNA-seq (72h) replicate 2

data_processing:
Basecalls performed using Phred quality score (Q score)
ChIP-seq reads were aligend to the GRCm38/mm10 mouse genome reference using Bowtie 2 v2.1.050 and filtered to retain reads with mapping quality >30.
ChIP-seq peaks were called using MACS2 v2.1.0.2015073157 with a minimum FDR cutoff of 0.01 (-q 0.01), except for broad features (H3K27me3, H3K36me3 and H3K9me3) where a cutoff of 0.05 was used (-q 0.05).
ChIP-seq peaks were filtered to remove those not corresponding to the canonical chromosomes.
RNA-seq reads were aligned to the reference genome GRCm38/mm10, downloaded from the Ensembl database ftp.ensembl.org using Gsnap version gmap-2014-12-17. Only uniquely mapped reads were used for further analysis. Gene counts from SAM files were obtained using htseq-count version 0.6.1 with mode intersection non-empty, -s reverse. The gene annotation was extracted from Ensembl Gene Release 75. Differential gene expression analysis was conducted using Bioconductor R (R-3.1.2) package DESeq2 version 1.6.3. An adjusted p Value threshold of 0.05 was used to determine differential gene expression. Expression values are FPKM (read number normalized across samples by DESeq size factor and across genes by gene length) calculated using custom R-scripts.
Single cell Hi-C reads were initially processed using the NucProcessing software package (available upon request). Processed reads were aligned to the GRCm38/mm10 mouse genome reference using Bowtie 2 and filtered to retain reads that formed a valid Hi-C contact junction between two RE1 resriction sites. Output files were further processed to perform extra, single-cell specific processing and cleanup. These remove any pairs that represent only a single observation of a specific RE1-RE1 ligation junction after PCR amplification, while at least two separate, albeit sometimes identical, molecules must be paired-end sequenced to confirm a ligation junction. Next the sequence pairs were filtered to remove those with promiscuous ends: where the RE1 fragment at either end was involved in more than one ligation event. Finally, the redundancy in amplified RE1-RE1 ligation events was removed to create a single list of paired RE1 fragment ends.
Genome_build: mm10
Supplementary_files_format_and_content: A summary table of results (.txt) from the analysis of the RNA-seq samples includes expression estimates for all genes (Ensembl Gene Release 75; GRCm38/mm10). Expression values are FPKM (read number normalized across samples by DESeq size factor and across genes by gene length) calculated using custom R-scripts.
Supplementary_files_format_and_content: bed files (.bed) are tab-delimited text files containing chromosomal coordinates of all ChIP-seq peaks (chromosome name, start, end).
Supplementary_files_format_and_content: Single cell Hi-C txt file (.txt) is a tab-separated text format containing the Hi-C contacts. After the header line, each individual contact is represented on a line consisting of chromosome_1 seq_pos_1 chromosome_2seq_pos_2
Supplementary_files_format_and_content: Single cell genome structure pdb file (.pdb) is protein data bank format. Atom type N is used to indicate restrained particles. Atom type C is used to represent unrestrained backbone particles. Residue number corresponds to the particle and increases every 100 kb. Chain letter represents the chromosome. The last column represents the particle sequence position.

extract_protocol:
For RNA-seq samples, 0.5 million cells were pelleted and RNA extracted using the RNA extraction kit (QIAGEN).
Library preparation for sequencing was performed according to standard methods. First RiboZero (depletion of ribosomal RNA), then 60-100ng of depleted RNA was used as the input into the Bioo Scientific NextFlex rapid directional RNA kit (#5138-08).


title: Input for Chd4/Mbd3 ChIP replicate 2


title: Mbd3 ChIP replicate 3


title: CHD4-KO RNA-seq (0h) replicate 3


title: D2_4mnths_WaterControl_2017


title: CHD4-WT RNA-seq (0h) replicate 1


title: WT neonates rep1


title: Mbd3 ChIP replicate 2


title: Input for Chd4/Mbd3 ChIP replicate 1


title: Chd4 ChIP replicate 1


title: CHD4-KO RNA-seq (72h) replicate 3


title: CHD4-WT RNA-seq (0h) replicate 2


title: CHD4-KO RNA-seq (72h) replicate 2


title: CHD4-WT RNA-seq (72h) replicate 1


title: Chd4 ChIP replicate 3


title: CHD4-KO RNA-seq (0h) replicate 2


title: CHD4-KO RNA-seq (72h) replicate 1


title: CHD4-KO RNA-seq (0h) replicate 1


title: KO neonates rep3


title: Limonium bicolor Leaf of the control

city: Jinan

first: Baoshan

last: Wang

state: Shandong

address: No.88 East Wenhua Road, Jinan 250014, Shandong, China

department: College of Life Sciences

institute: Shandong Normal University

description: Sample 1

data_processing:
The raw RNA-Seq reads of all samples were first pulled together for assemblage into contigs.
De novo assembly was conducted using the SOAPdenovo-Trans software, where contigs less than 300 bp were excluded before further analyses.
Then the transcripts were referred to the non-redundant protein database (Nr) of NCBI.
Supplementary_files_format_and_content: Tab-delimited .txt file reports RPKMs.

organism: Limonium bicolor

source_name: Leaf of the control

growth_protocol: Greenhouse cultivation

extract_protocol:
The fourth leaves were collected from the control and NaCl-treated seedlings. Total RNA was extracted using Total Plant RNA Extraction Kit (Karroten, Beijing, China) and purified by the RNAeasy Mini RNA kit’ (Qiagen, Germany) including on-column DNase digestion. The Poly(A) RNA was isolated from purified total RNA (at least 4 μg) using two rounds of purification with oligo d(T) beads (Dynabeads).
First-strand cDNA was generated using random hexamer-primed reverse transcription. After second strand cDNA synthesis and adaptor ligation, cDNA fragments of approximately 200 bp were isolated by gel electrophoresis.

treatment_protocol: The control and 200 mM NaCl treatment

value: seedling

tag: stress

value: Control

value: leaf


title: Population Hi-C (haploid)

data_processing:
Library strategy: Hi-C
Basecalls performed using Phred quality score (Q score)
ChIP-seq reads were aligend to the GRCm38/mm10 mouse genome reference using Bowtie 2 v2.1.050 and filtered to retain reads with mapping quality >30.
ChIP-seq peaks were called using MACS2 v2.1.0.2015073157 with a minimum FDR cutoff of 0.01 (-q 0.01), except for broad features (H3K27me3, H3K36me3 and H3K9me3) where a cutoff of 0.05 was used (-q 0.05).
ChIP-seq peaks were filtered to remove those not corresponding to the canonical chromosomes.
RNA-seq transcript abundance estimates for all annotated mouse transcripts (Ensembl v71, GRCm38/mm10) and ERCC spike-in sequences were obtained using Kallisto v0.42.4 (arXiv:1505.02710).
RNA-seq gene-level abundances were summarized from transcript-level estimates using the tximport R package.
Population Hi-C reads were processed using the HiCUP software package (http://www.bioinformatics.babraham.ac.uk/projects/hicup/overview/). Processed reads were aligned to the GRCm38/mm10 mouse genome reference using Bowtie 2 and filtered to retain reads that formed a valid Hi-C contact junction between two RE1 resriction sites.
Single cell Hi-C reads were initially processed using the NucProcessing software package (available upon request). Processed reads were aligned to the GRCm38/mm10 mouse genome reference using Bowtie 2 and filtered to retain reads that formed a valid Hi-C contact junction between two RE1 resriction sites. Output files were further processed to perform extra, single-cell specific processing and cleanup. These remove any pairs that represent only a single observation of a specific RE1-RE1 ligation junction after PCR amplification, while at least two separate, albeit sometimes identical, molecules must be paired-end sequenced to confirm a ligation junction. Next the sequence pairs were filtered to remove those with promiscuous ends: where the RE1 fragment at either end was involved in more than one ligation event. Finally, the redundancy in amplified RE1-RE1 ligation events was removed to create a single list of paired RE1 fragment ends.
Genome_build: mm10
Supplementary_files_format_and_content: bed files (.bed) are tab-delimited text files containing chromosomal coordinates of all ChIP-seq peaks (chromosome name, start, end).
Supplementary_files_format_and_content: tsv files (.tsv) contain gene-level abundance estimates for all genes.
Supplementary_files_format_and_content: Single cell Hi-C txt file (.txt) is a tab-separated text format containing the Hi-C contacts. After the header line, each individual contact is represented on a line consisting of chromosome_1 seq_pos_1 chromosome_2seq_pos_2
Supplementary_files_format_and_content: Population Hi-C txt file (.txt) is a tab-separated text format containing all the chromosomal coordinates for Hi-C contacts and the number observed (chromosome_A start position_A end position_A chromosome_B start position_B end position_B number observed)
Supplementary_files_format_and_content: Single cell genome structure pdb file (.pdb) is protein data bank format. Atom type N is used to indicate restrained particles. Atom type C is used to represent unrestrained backbone particles. Residue number corresponds to the particle and increases every 100 kb. Chain letter represents the chromosome. The last column represents the particle sequence position.

extract_protocol:
5-10 million Haploid mouse ES cells were fixed for 5 min with 2 % formaldehyde in PBS and then the reaction was quenched for another 5 min in 0.125 M glycine. Nuclei were then extracted by incubating cells on ice for 30 min (inverting every 10 min) in 10 mM Tris pH 8.0, 10 mM NaCl, 0.2 % NP-40 (IGEPAL CA-630) and protease inhibitor cocktail (Roche).
Population Hi-C libraries were prepared as follows. Briefly, sonicated DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. Biotinylated junctions were captured on streptavidin M-280 dynabeads and the blunt, phosphorylated ends were treated with Klenow fragment  exo minus) and dATP to yield a protruding 3- 'A' base for ligation of custom adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 10 cycles and library fragments of ~300-700 bp (insert plus adaptor and PCR primer sequences) were isolated using AMPure beads (Beckman). The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the HiSeq2500 following the manufacturer's protocols.

tag: chip antibody


title: Limonium bicolor Leaf of NaCl treatment

description: Sample 2

source_name: Leaf of NaCl treatment

value: 200 mM NaCl


title: WT Adults rep2


title: nuclear RNA (diploid)

data_processing:
Basecalls performed using Phred quality score (Q score)
ChIP-seq reads were aligend to the GRCm38/mm10 mouse genome reference using Bowtie 2 v2.1.050 and filtered to retain reads with mapping quality >30.
ChIP-seq peaks were called using MACS2 v2.1.0.2015073157 with a minimum FDR cutoff of 0.01 (-q 0.01), except for broad features (H3K27me3, H3K36me3 and H3K9me3) where a cutoff of 0.05 was used (-q 0.05).
ChIP-seq peaks were filtered to remove those not corresponding to the canonical chromosomes.
RNA-seq transcript abundance estimates for all annotated mouse transcripts (Ensembl v71, GRCm38/mm10) and ERCC spike-in sequences were obtained using Kallisto v0.42.4 (arXiv:1505.02710).
RNA-seq gene-level abundances were summarized from transcript-level estimates using the tximport R package.
Population Hi-C reads were processed using the HiCUP software package (http://www.bioinformatics.babraham.ac.uk/projects/hicup/overview/). Processed reads were aligned to the GRCm38/mm10 mouse genome reference using Bowtie 2 and filtered to retain reads that formed a valid Hi-C contact junction between two RE1 resriction sites.
Single cell Hi-C reads were initially processed using the NucProcessing software package (available upon request). Processed reads were aligned to the GRCm38/mm10 mouse genome reference using Bowtie 2 and filtered to retain reads that formed a valid Hi-C contact junction between two RE1 resriction sites. Output files were further processed to perform extra, single-cell specific processing and cleanup. These remove any pairs that represent only a single observation of a specific RE1-RE1 ligation junction after PCR amplification, while at least two separate, albeit sometimes identical, molecules must be paired-end sequenced to confirm a ligation junction. Next the sequence pairs were filtered to remove those with promiscuous ends: where the RE1 fragment at either end was involved in more than one ligation event. Finally, the redundancy in amplified RE1-RE1 ligation events was removed to create a single list of paired RE1 fragment ends.
Genome_build: mm10
Supplementary_files_format_and_content: bed files (.bed) are tab-delimited text files containing chromosomal coordinates of all ChIP-seq peaks (chromosome name, start, end).
Supplementary_files_format_and_content: tsv files (.tsv) contain gene-level abundance estimates for all genes.
Supplementary_files_format_and_content: Single cell Hi-C txt file (.txt) is a tab-separated text format containing the Hi-C contacts. After the header line, each individual contact is represented on a line consisting of chromosome_1 seq_pos_1 chromosome_2seq_pos_2
Supplementary_files_format_and_content: Population Hi-C txt file (.txt) is a tab-separated text format containing all the chromosomal coordinates for Hi-C contacts and the number observed (chromosome_A start position_A end position_A chromosome_B start position_B end position_B number observed)
Supplementary_files_format_and_content: Single cell genome structure pdb file (.pdb) is protein data bank format. Atom type N is used to indicate restrained particles. Atom type C is used to represent unrestrained backbone particles. Residue number corresponds to the particle and increases every 100 kb. Chain letter represents the chromosome. The last column represents the particle sequence position.

molecule: nuclear RNA

extract_protocol:
For RNA-seq samples, 0.5 million cells were pelleted and RNA extracted using the RNA extraction kit (QIAGEN).
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.


title: nuclear RNA (haploid)

value: haploid mESCs derived from strain 129/Ola


title: Input (diploid)


title: Holstein_19_HC

city: Kongens Lyngby

first: Haja

middle: N

last: Kadarmideen

address: Richard Petersens Plads, Building 324

department: Department of Applied Mathematics and Computer Science

country: Denmark

institute: Technical University of Denmark

data_processing:
Reads were aligned to the genome assembly Bos taurus UMD3.1 using STAR: ultrafast universal RNA-Seq aligner STAR_2.3.0
Gene expression counts were computed using HTSeq-count
Genome_build: Bos taurus UMD3.1
Supplementary_files_format_and_content: Text files (.txt) containing the Ensembl gene IDs and raw counts (Note: last five rows are general statistics). One file for each sample (38 samples)

organism: Bos taurus

source_name: Liver tissue

extract_protocol:
liver biopsies were collected ,preserved in RNA later,and stored at -80 degree Celcius. mRNA was extracted from the liver tissue samples using the Qiazol, RNeasy® Mini Kit and MaXtract High Density for further RNA-Sequencing.
Illumina TruSeq Stranded mRNA Kit was used with 0.4 ug of total RNA for the construction of sequencing libraries.

tag: breed

value: Holstein

value: High

tag: diet

value: liver


title: H3K4me3 ChIP (diploid)

value: antibody:diagenode (pAb003-050)


title: Nanog ChIP (diploid)

value: antibody:calbiochem (SC1000)


title: Input (haploid)


title: H3K4me3 ChIP (haploid)


title: Holstein_19_C

value: Control (Low Concentrate)

tag: tissue


title: H3K36me3 ChIP (diploid)

value: antibody:abcam (ab9050-100)


title: Jersey_17_HC

value: Jersey


title: Jersey_17_C


title: CTCF ChIP (haploid)

value: antibody:millipore (07-729)


title: H3K36me3 ChIP (haploid)


title: Nanog ChIP (haploid)

value: antidoby:calbiochem (SC1000)


title: Holstein_15_HC

value: Low


title: Holstein_16_HC


title: Jersey_18_HC


title: Holstein_16_C


title: SMC3 ChIP (haploid)

value: antibody:abcam (ab9263)


title: Jersey_18_C


title: H3K9me3 ChIP (haploid)

value: antibody:active motif (39161)


title: H3K27me3 ChIP (haploid)

value: antibody:millipore (07-449)


title: Jersey_14_HC


title: Ezh2 Mutant H3k27me3 sample2

city: Chapel Hill

first: Joshua

last: Starmer

state: NORTH CAROLINA

address: 120 Mason Farm Road

department: Genetics

institute: University of North Carolina at Chapel Hill

data_processing:
Initial processing and basecalling were done using the Illumina Pipeline (v.1.8.2).
Alignment to the mm9 genome was performed using Bowtie.
BAM files were created from bowtiefiles using samtools.
Enriched domains were called using hiddenDomains and MACSv2 using the input and each replicate for control and mutant using default parameters.
bigWig files were created using samtools to count the number of reads (for normalization), bedtools to make bedGraph files and bedGraphToBigWig to convert the bedGraph to bigWig.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: bed files are tab-delimited text files.
Supplementary_files_format_and_content: bigWig files are a binary file format.

source_name: spermatogenic cells, Ezh2 mutant, H3k27me3 ChIP

extract_protocol:
Testes were collected from 6-week-old mice and digested with collagenase, trypsin, and DNaseI. Percoll solution and cell strainers were applied to separate somatic cells from spermatogenic cells. The isolated cells were examined under differential interference contrast optics and 90% of them were spermatogenic cells.
ChIP-seq libraries were prepared according to Illumina instructions and sequenced on Illumina's HiSeq2000 instrument.

tag: strain/background

value: mixed background

value: 6 weeks

value: spermatogenic cells

value: H3K27me3 (ab6002; Abcam)


title: H3K27me3 ChIP (diploid)

value: strain 129 mESCs


title: Jersey_13_HC

value: liver


title: Ezh2 Mutant H3k27me3 sample1


title: Control Input

source_name: spermatogenic cells, control, input


title: Ezh2 Mutant Input

source_name: spermatogenic cells, Ezh2 mutant, input


title: Jersey_13_C


title: Jersey_12_C


title: Jersey_12_HC


title: Control H3k27me3 sample1

source_name: spermatogenic cells, control, H3k27me3 ChIP


title: Holstein_11_C

value: Holstein

value: High


title: Holstein_11_HC


title: TSWT

city: Memphis

first: Amy

last: Abell

state: TN

address: 3774 Walker Ave

department: Biological Sciences

institute: The University of Memphis

description: alligned using mm9 reference genome

data_processing:
Reads were aligned to the murine mm9 reference genome using MapSplice v2.1.4.
Picard Tools v1.88 was used to determine the alignment profile.
SAMtools v1.2 was used to sort and index aligned reads, which were then translated to transcriptome coordinates and filtered for indels, large inserts, and zero mapping quality using UNC Bioinformatics utilities (UBU, https://github.co/mozack/ubu) v1.2.
Transcript abundance for each sample was estimated using RSEM expectation-maximization algorithm
Genome_build: mouse mm9
Supplementary_files_format_and_content: CSV format containing:
Supplementary_files_format_and_content: gene_id, transcript_id(s), length, effective_length, expected_count, TPM, FPKM, and Normalized reads

source_name: Trophoblast Stem Cells

growth_protocol: Cells were cultured in the absence of feeders in 30% TS media (RPMI 1640, 20% fetal bovine serum, 1% penicillin and streptomycin, 1% L-glutamine, 1% sodium pyruvate, and 100 µM β-mercaptoethanol) and 70% MEF-conditioned TS cell media. For maintenance of the stem cell state, TS medium was supplemented with FGF4 (37.5 ng/ml) and Heparin (1 mg/ml).

extract_protocol:
Total RNA was extracted from TS cells using the RNeasy minikit (Qiagen).
Libraries were constructed from 4 µg RNA using KAPA stranded mRNAseq kits and Illumina TruSeq indexed adapters following the manufacturer’s protocol, except half the recommended template DNA was added to the 10 cycle PCR reaction. RNA seq Libraries were prepped by 1 x 75 bp Illumina NextSeq500, 12-plex, single-indexed sequencing.

tag: knock-in

tag: shRNA

value: pLKO vector


title: TSKI4 HDAC6 sh2

description: alligned using mm9 reference genome

value: MAP3K4 K1361R

value: HDAC6 shRNA


title: TSKI4

description: alligned using mm9 reference genome


title: Holstein_9_HC