title: 3 Gy [HR5]

status: Public on Oct 15 2020

type: SRA

city: Fontenay-aux-Roses

first: Guillaume

last: Vares

country: France

institute: IRSN

library_source: transcriptomic

data_processing:
Sequencing was performed on a HiSeq 4000 machine (Illumina) to generate 150 nucleotide paired-end reads at a depth of at least 40 million reads.
Reads were mapped to the hg19 reference human genome using tophat2 software (v2.1.1), assembled and quantified using the cufflinks software suite (v2.2.1)
Genome_build: hg19
Supplementary_files_format_and_content: Individual gene counts and differential expression

molecule: total RNA

organism: Homo sapiens

source_name: CH-2879 Chondrosarcoma cells

extract_protocol:
RNA was extracted using Trizol and a column-based PureLink RNA Mini Kit (Invitrogen, Carlsbad, CA, USA).
RNA-sequence libraries were prepared with the TruSeq Stranded mRNA NeoPrep kit (Illumina, San Diego, CA, USA).

tag: cell line

tag: cell type

value: Chondrosarcoma cells

tag: dose

value: 3 Gy


title: 2 Gy [HR4]

value: 2 Gy


title: 0.5 Gy [HR3]


title: 0 Gy [HA1]

value: 0 Gy


title: 0.1 Gy [HR2]


title: 5 Gy [HR6]

value: 5 Gy


title: rad53_DNAPOL2_input

status: Public on Aug 31 2019

city: Taipei

first: Cheng-Fu

last: Kao

address: 128, Academia Rd., Sec. 2, Nankang

department: Institute of Cellular and Organismic Biology

country: Taiwan

institute: Academia Sinica

data_processing:
FASTQ files from biological and technical replicates for each sample were merged. Reads were aligned to the sacCer3 reference genome (release R64-2-1) using Bowtie2 version 2.2.5 in ‘very-sensitive’ mode
Aligned reads were filtered and indexed using SAMtools. Reads were adjusted so that the genome average was set at 1-fold enrichment, then data from immunoprecipitated samples were divided by data from input samples.
Heatmaps were generated using deepTools. Transcription frequency was calculated by a sum of signal in a range TSS to TSS + 200 bp of each yeast gene adapted from the results of NET-seq (Nature 469, 368-373 (2011))

organism: Saccharomyces cerevisiae

source_name: log phase treated with 25mM hydroxyurea

growth_protocol: yeast cell were cultured to exponetial phase

extract_protocol:
The formaldehyde-crosslinked cell pellets were transferred to to a 2-ml flat-bottom screw-cap tube containing 300 μl glass beads, and disrupt the cells in a mini beadbeater for 5 min or until 90% of cells are disrupted. Sonicate samples in a cold Bioruptor sonicator bath at maximum output, cycling 30 sec on, 30 sec off, for a total of 30 min. Centrifuge samples for 30 min at 16,000 × g, 4°C, and transfer the supernatant to a new 1.5-ml siliconized microcentrifuge tube.After sonication, solubilized chromatin will stay in the supernatant.
Libraries were prepared using the Ovation Ultralow v2 kit (NuGEN, catalog #0344).

treatment_protocol: 25mM hydroxyurea

tag: strain bkgd

value: W303a Pol2-3xFLAG

tag: chip antibody

value: none (input)

tag: tissue

value: log phase yeast culture treated with 25mM hydroxyurea


title: H3K4A_DNAPOL2_input


title: rad53_Rpb3_input


title: WT_DNAPOL2_input


title: WT_Rpb3_input


title: SC_Old_8

city: Basel

first: Sophie

last: Brachat

address: Novartis Campus

department: Muskuloskeletal

country: Switzerland

institute: Novartis Institutes For Biomedical Research

data_processing:
read alignment using STAR-2.5.2b; --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000
Star-2.5.2b counting
Genome_build: NCBI GRCm38.p5
Supplementary_files_format_and_content: AAB529_cts.txt raw count: Tab delimited, GeneID||GeneID||GeneSymbol||Length|| samples
Supplementary_files_format_and_content: AAB529_fpkm.txt FPKM: Tab delimited, GeneID||GeneID||GeneSymbol||Length|| samples
Supplementary_files_format_and_content: AAB529_tpm.txt Transcripts per million: Tab delimited, GeneID||GeneID||GeneSymbol||Length|| samples

molecule: polyA RNA

organism: Mus musculus

source_name: Spinal cord

extract_protocol:
Mice were PBS-perfused, whole spinal cords were removed, flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent. Adult Brain Dissociation Kit (Miltenyi Biotec, 130-107-677) and relative protocol on gentleMACS Octo Dissociator with Heaters (Miltenyi Biotec, 130-096-427) were used to generate single cells suspension from brain tissues. Microglia cells were identified as Cd11b+ and Cd45+ by Fluorescence-activated cell sorting (FACS) and RNA isolated with RNeasy Plus Micro Kit (Qiagen, 74034).
TruSeq RNA Library Preparation Kit v2

tag: strain

tag: genotype

value: wild type

tag: age

value: 23 months

value: Whole spinal cord

tag: treatment

value: vehicle


title: SC_Old_7


title: SC_Old Rep_8

value: 5 days Csf1r inhibitor, followed by 7 days recovery


title: SC_Old Rep_7


title: rad53_H3K4A_Rpb3_input


title: SC_Young_8

value: 3 months


title: SC_Old Rep_6


title: SC_Old_6


title: SC_Young_6


title: H3K4A_Rpb3_input


title: rad53_H3K4A_DNAPOL2_input


title: SC_Old Rep_5


title: SC_Old_5


title: SC_Young_5


title: SC_Young_3


title: SC_Old_3


title: SC_Old_4


title: SC_Old Rep_4


title: SC_Old Rep_2


title: SC_Old_2


title: SC_Old_1


title: SC_Young_2


title: SC_Young_4


title: SC_Old Rep_3


title: SC_Young_1


title: SC_Young_7


title: M_Young_8

source_name: Brain

value: FACS-sorted microglia


title: M_Old_8


title: SC_Old Rep_1


title: M_Old_7


title: M_Old Rep_8


title: M_Young_6


title: M_Old Rep_7


title: M_Old_6


title: M_Old Rep_6


title: M_Young_5


title: M_Old Rep_5


title: M_Old_5


title: M_Old_3


title: M_Old Rep_3


title: M_Old_1


title: M_Old_4


title: M_Young_3


title: M_Old Rep_2


title: M_Old Rep_1


title: M_Young_1


title: M_Young_7


title: Ground_R9wt_D1

city: beijing

first: zhao

middle: xue

last: tong

address: chaoyang District

country: China

institute: beijing institute of genomics

data_processing:
Quality control analysis of the FASTQ format sequencing raw data was performed using FastQC software
FASTQ format sequencing reads were mapped to the mm9 reference genome using Tophat version 2.0.9 software with the default parameters
R package edgeR was used to identify differentially expressed genes with a threshold of fold change ≥ 2 and p < 0.05.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample ...

source_name: R9 cells cultured on ground for 1 day

extract_protocol:
Total RNA from each cell sample was extracted by using TRIzol reagent following the manufacturer’s instructions.
Libraries were constructed using Illumina mRNA-Seq library preparation kits. The concentration and size distribution of the libraries were determined by using an ABI 7500 instrument and an Agilent Bioanalyzer DNA 2000 chip (Agilent Technologies, Santa Clara, CA, USA), respectively. Qualified libraries were subjected to sequencing on an Illumina HiSeq 3000 Genome Analyzer platform with 2 ´ 100-bp paired-end reads.

value: mESC

tag: growth

value: cultured on ground for 1 day


title: Space_R9wt_D1

source_name: R9 cells cultured in space for 1 day

value: cultured in space for 1 day


title: Ground _R9wt_D5

source_name: R9 cells cultured on ground for 5 day

value: cultured on ground for 5 days


title: Ground_R9del_D1

source_name: R9 knockout cells cultured on ground for 1 day


title: Space_R9del_D5

source_name: R9 knockout cells cultured in space for 5 day

value: cultured in space for 5 days


title: Space_R9del_D1

source_name: R9 knockout cells cultured in space for 1 day


title: Ground _R9del_D5

source_name: R9 knockout cells cultured on ground for 5 day


title: M_Old_2


title: M_Young_2


title: Lung.MI-2

type: RNA

city: Charlestown

first: Kamila

last: Naxerova

state: MA

address: 149 13th Street

department: Center For Systems Biology

country: USA

institute: Massachusetts General Hospital / Harvard Medical School

hyb_protocol: According to the manufacturer's instructions (Affymetrix)

data_processing: R/Bioconductor, RMA, and removal of all probes that do not belong to the main array content

label: biotin

label_protocol: Ovation Pico WTA System V2 (NuGEN)

extract_protocol: PicoPure RNA extraction kit (Thermofisher Scientific)

tag: disease state

value: myocardial infarction

value: macrophage

value: Lung

tag: time

value: Day 4


title: Lung.Control-3

scan_protocol: According to the manufacturer's instructions (Affymetrix)

value: control


title: Lung.Stroke-3

value: stroke

value: Day 6


title: Lung.Stroke-2


title: Lung.MI-1

value: Day 1


title: Lung.Control-1


title: Lung.Sepsis-3

value: sepsis


title: Lung.Stroke-1


title: Liver.Stroke-1

value: Liver


title: DLD-1-miR-21-1

city: New Taipei City

first: Pei-Ming

last: Yang

address: No. 301, Yuantong Rd., Zhonghe Dist.

department: Graduate Institute of Cancer Biology and Drug Discovery

institute: Taipei Medical University

hyb_protocol: OneArray Plus Hybridization Protocol

scan_protocol: Agilent 0.1 XDR Protocol

data_processing: Scanned images are analyzed by Feature extraction10.5.1.1 software (Agilent Technologies, USA), an image analysis and normalization software is used to quantify signal and background intensity for each feature.

source_name: DLD-1-miR-21, control

label_protocol: Target preparation was performed using an Eberwine-based amplification method with Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion, AM1753) to generate amino-allyl antisense RNA(aa-aRNA). Labeled aRNA coupled with NHS-CyDye was prepared and purified prior to hybridization. Purified coupled aRNA was quantified using NanoDrop ND-1000; pass criteria for CyDye incorporation efficiency at > 15 dye molecular/1000nt.

growth_protocol: DLD-1-miR-Vec and DLD-1-miR-21 cells were cultured in RPMI-1640 medium supplemented with 10% FBS, 1 mM sodium pyruvate, 1% L-glutamine, 1% antibiotic-antimycotic solution, 0.5 mg/mL G418, and incubated at 37°C in a humidified incubator containing 5% CO2.

extract_protocol: RNA was prepared using the GENEzol TriRNA Pure Kit following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer.

treatment_protocol: To establish stable miR-21-overexpressing DLD-1 (DLD-1-miR-21) and corresponding vector-overexpressing (DLD-1-miR-Vec) cell lines, parental DLD-1 cells were transfected with a plasmid encoding human miR-21 or its control vector (pCMV-MIR) using the PolyJet transfection reagent. Stable clones were selected with 1 mg/mL G418 for 2 months. Single clones were selected based on expression of the green fluorescent protein (GFP) reporter and then pooled together for subsequent experiments.

value: human colorectal cells

tag: genotype/variation

value: overexpressing miR-21


title: Lung.Control-4

value: Day 8


title: Lung.Sepsis-2


title: Liver.Sepsis-1


title: Liver.Stroke-3


title: Liver.Stroke-2


title: DLD-1-miR-Vec-1

source_name: DLD-1-miR-Vec, control

value: overexpressing vector


title: Lung.Sepsis-1


title: Lung.Control-2


title: Liver.Sepsis-2


title: DLD-1-miR-Vec-2


title: Lung.MI-3


title: Liver.MI-3


title: DLD-1-miR-21-2


title: Control-PEC biological replicate_2

city: Bhopal

first: Sanjeev

last: Shukla

state: Madhya Prades

address: Bhopal Bypass Road, Bhauri Bhopal 462 066 Madhya Pradesh, INDIA

department: Biological Sciences

country: India

institute: Indian Institute of Science Education and Research Bhopal

description: Global gene expression and splicing analysis in control-PEC treated head and neck cancer cells

hyb_protocol: The standard protocol of 900720- GeneChip® kit was followed for hybridization, wash and staining.

scan_protocol: GeneChip Command Software (AGCC4.3.3) was used for imaging and acquisition.

data_processing: The data was processed with Transcriptome Analysis Console (TAC) version 4.0 and CHP files were generated with sst-rma-combined dadg normalization.

source_name: H157 cells

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix protocol from 100 ng total RNA.

growth_protocol: H157 cells were cultured in ECACC recommended media in a humidified chamber at 37 °C with 5% CO2.

extract_protocol: Total RNA was isolated using trizol as per the manufacturer's instructions.

treatment_protocol: The head and neck cancer cells, H157 cells were treated with curcumin-PEC and control-PEC at 0h and 24h. H157 cells were harvested at 48h and proceeded for RNA extraction

value: control PEC


title: Kidney.MI-3

value: Kidney

value: Day 5


title: Control-PEC biological replicate_1


title: Curcumin-PEC biological replicate_2

description: Global gene expression and splicing analysis in curcumin-PEC treated head and neck cancer cells

value: curcumin  PEC


title: Kidney.Control-2

value: macrophage


title: Kidney.Control-1


title: Liver.Control-2


title: Liver.MI-2

value: myocardial infarction


title: Liver.Control-3

value: Day 4


title: Heart.Stroke-3

value: Heart


title: Heart.Stroke-2

value: stroke


title: Kidney.Sepsis-1


title: Kidney.Sepsis-3


title: Kidney.Control-4

value: control


title: Kidney.Stroke-1

value: Day 1


title: Liver.Control-1


title: Kidney.Stroke-2


title: Kidney.MI-1


title: Kidney.MI-2


title: Kidney.Stroke-3


title: Kidney.Sepsis-2

value: sepsis

value: Day 6


title: Kidney.Control-3


title: Heart.Stroke-1

value: Day 2


title: Curcumin-PEC biological replicate_1


title: Space_R9wt_D5

source_name: R9 cells cultured in space for 5 day

value: wild type

value: mESC

value: cultured in space for 5 days


title: Heart.Sepsis-3


title: Heart.Control-3


title: M_Old Rep_4

value: 23 months

value: FACS-sorted microglia

value: 5 days Csf1r inhibitor, followed by 7 days recovery


title: M_Young_4

value: 3 months

value: vehicle


title: Heart.Sepsis-2

value: macrophage

value: Day 5


title: Heart.Sepsis-1

value: Heart


title: Brain.Sepsis-3

value: Brain

value: Day 8


title: Slc17a6-EGFP-Rpl10a-JX883 Input Rep2

city: New York

first: Laura

last: Kus

state: NY

address: 1230 York Avenue # 260

department: Heintz Laboratory

institute: The Rockefeller University

data_processing:
FASTX Toolkit 0.0.13 was used to assess the quality of reads and trim trailing adaptors.
Trimmed reads were aligned to annotated exons using the mm10 genome using STAR v2.0.0e_r291 using default settings.
Raw counts of mapped reads were generated with HTSeq framework v0.6.0 using the htseq-count module with the "union" mode and default settings.
Genome_build: mm10
Supplementary_files_format_and_content: Text files of counts

source_name: Thalamus

extract_protocol:
The thalamus was dissected and homogenized and tagged polysomes were immunopurified with monoclonal anti-EGFP antibodies bound to biotinylated-Protein L (Thermo Fisher) coated streptavidin-conjugated magnetic beads (Life Technologies). Total RNA from IPs was purified with the Agilent Nanoprep kit following manufacturer's protocol.
Ribosomal-bound RNA was extracted and treated as described in PMID 24810037, Heiman M, Kulicke R, Fenster RJ, Greengard P, Heintz N. (2014) Cell type-specific mRNA purification by translating ribosome affinity purification (TRAP). Nat Protoc. 9:1282-1291

treatment_protocol: Control mice only. No treatment

tag: molecule

value: Ribosomal-bound RNA

tag: animal line

value: Slc17a6-TRAP JX883

tag: sample type

value: Input


title: Slc17a6-EGFP-Rpl10a-JX883 Input Rep3


title: Slc17a6-EGFP-Rpl10a-JX883 IP Rep3

value: Immunopurified (IP)


title: Slc17a6-EGFP-Rpl10a-JX883 Input Rep1


title: Slc17a6-EGFP-Rpl10a-JX883 IP Rep2


title: Cbln1-EGFP-Rpl10a-NIDA030 Input Rep1

growth_protocol: Not applicable

value: Cbln1-TRAP NIDA030


title: Cbln1-EGFP-Rpl10a-NIDA030 Input Rep3


title: Cbln1-EGFP-Rpl10a-NIDA030 IP Rep2


title: Cbln1-EGFP-Rpl10a-NIDA030 IP Rep3


title: Cbln1-EGFP-Rpl10a-NIDA030 IP Rep1


title: Cbln1-EGFP-Rpl10a-NIDA030 Input Rep2


title: Brain.Sepsis-2

value: sepsis


title: Heart.Control-1

value: control

value: Day 2


title: Brain.MI-2

value: myocardial infarction


title: Brain.MI-3


title: Heart.Control-2


title: Slc17a6-EGFP-Rpl10a-JX883 IP Rep1


title: Brain.Sepsis-1


title: Brain.Control-2


title: Brain.Control-1


title: Brain.MI-1


title: Brain.Control-3


title: MA9c3

city: Tokyo

first: Yasutaka

last: Hayashi

address: 4-6-1 Shirokanedai, Minato-ku

department: Division of Cellular Therapy, Advanced Clinical Research Center

country: Japan

institute: Institute of Medical Science, The University of Tokyo

data_processing:
RNA libraries were sequenced on the Illumina HiSeq2500 System with 2×100 nucleotide paired-end reads according to the manufacturer’s protocol.
Derived reads were processed using cutadapt(1.8.1) and fastx-toolkit(0.0.13) to remove Illumina adaptor sequence and to trim low-quality bases.
Quality of reads were assessed using FastQC.
Processed reads were aligned to GRCm38 reference transcripts using TopHat(2.1.1)-Cufflinks(2.2.1) pipeline to derive gene FPKM values.
Genome_build: GRCm38
Supplementary_files_format_and_content: text files include FPKM values for each Sample

source_name: Bone marrow cells

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen), and the quality and quantity of RNA were checked using Agilent High Sensitivity RNA Screen Tape and Qubit.
RNA libraries were prepared using 1000 ng total RNA with SureSelect Strand-Specific RNA Preparation Kit (Agilent) according to the manufacturer’s protocol.

treatment_protocol: Vehicle Control or 80mg/kg bw DS-5272 was orally administered to leukemic mice 24 hours before leukemia cell extraction.

tag: transduced gene

value: Vehicle Control


title: MA9DS3


title: MA9DS2


title: MA9c2


title: MA9DS1


title: MA9c1


title: Quad_10.2_Exercise_18m

data_processing:
read alignment using STAR-2.5.2b; --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000
Star-2.5.2b counting
Genome_build: NCBI GRCm38.p5
Supplementary_files_format_and_content: AA293_cts.txt raw count: Tab delimited, GeneID||GeneID||GeneSymbol||Length|| samples
Supplementary_files_format_and_content: AA293_fpkm.txt FPKM: Tab delimited, GeneID||GeneID||GeneSymbol||Length|| samples
Supplementary_files_format_and_content: AA293_tpm.txt Transcripts per milliont: Tab delimited, GeneID||GeneID||GeneSymbol||Length|| samples

source_name: Quadriceps muscle

extract_protocol:
Mice were PBS-perfused, tissues were removed, flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent.
TruSeq RNA Library Preparation Kit v2

value: Quadriceps muscle

value: wild type

value: 18 months

tag: gender

value: male

value: Exercised


title: SC_8.2_Sedentary_18m

value: Spinal cord

value: Sedentary


title: Liver.Sepsis-3

tag: cell type

value: macrophage

value: Liver

value: Day 4


title: SC_10.4_Sedentary_18m


title: SC_4.3_Sedentary_18m


title: Quad_10.4_Sedentary_18m


title: Quad_10.1_Exercise_18m


title: SC_7.4_Sedentary_18m


title: Gas_10.2_Exercise_18m

source_name: Gastrocnemius muscle

value: Gastrocnemius muscle


title: Gas_10.1_Exercise_18m


title: Gas_5.2_Sedentary_18m


title: SC_4.1_Exercise_18m

source_name: Spinal cord


title: SC_3.3_Sedentary_10m

value: 10 months


title: Quad_3.3_Sedentary_10m


title: Quad_9.1_Exercise_18m


title: Gas_4.3_Sedentary_18m


title: Quad_9.3_Sedentary_18m


title: Gas_9.1_Exercise_18m


title: SC_10.3_Exercise_18m


title: Gas_3.3_Sedentary_10m


title: Quad_10.3_Exercise_18m


title: SC_7.3_Exercise_18m


title: SC_7.1_Exercise_18m


title: Quad_9.2_Sedentary_18m


title: Quad_8.4_Exercise_18m


title: Quad_3.2_Sedentary_10m


title: Gas_10.4_Sedentary_18m


title: Gas_8.4_Exercise_18m


title: SC_10.2_Exercise_18m


title: Gas_9.3_Sedentary_18m


title: Gas_3.2_Sedentary_10m


title: SC_6.4_Sedentary_18m


title: SC_3.1_Sedentary_10m


title: Quad_8.3_Exercise_18m


title: Quad_8.2_Sedentary_18m


title: Quad_3.1_Sedentary_10m


title: Gas_9.2_Sedentary_18m


title: Gas_8.3_Exercise_18m


title: Gas_3.1_Sedentary_10m


title: Gas_10.3_Exercise_18m


title: SC_10.1_Exercise_18m


title: SC_6.3_Exercise_18m


title: Quad_2.3_Sedentary_10m


title: SC_2.3_Sedentary_10m


title: Gas_7.3_Exercise_18m


title: Gas_8.2_Sedentary_18m


title: Gas_2.3_Sedentary_10m


title: SC_9.3_Sedentary_18m


title: Quad_2.2_Sedentary_10m


title: SC_2.2_Sedentary_10m


title: Quad_7.1_Exercise_18m


title: SC_6.2_Sedentary_18m


title: Gas_2.2_Sedentary_10m


title: Gas_7.1_Exercise_18m


title: SC_2.1_Sedentary_10m


title: Quad_6.4_Sedentary _18m


title: SC_3.2_Sedentary_10m


title: Quad_6.3_Exercise_18m


title: Quad_2.1_Sedentary_10m


title: SC_6.1_Sedentary_18m


title: Gas_5.4_Exercise_18m


title: SC_5.4_Exercise_18m


title: SC_9.2_Sedentary_18m


title: Gas_2.1_Sedentary_10m


title: SC_1.4_Sedentary_10m


title: Quad_7.4_Sedentary_18m


title: Quad_5.4_Exercise_18m


title: Liver.MI-1

value: Day 1


title: Quad_7.3_Exercise_18m


title: Quad_6.2_Sedentary _18m


title: Gas_7.4_Sedentary _18m


title: Gas_1.4_Sedentary_10m


title: SC_5.3_Exercise_18m


title: Quad_1.3_Sedentary_10m


title: Quad_5.3_Exercise_18m


title: Gas_5.1_Exercise_18m


title: Quad_6.1_Sedentary _18m


title: Gas_1.3_Sedentary_10m


title: Gas_6.4_Sedentary_18m


title: SC_8.4_Exercise_18m


title: SC_5.2_Sedentary_18m


title: Quad_5.1_Exercise_18m


title: SC_1.2_Sedentary_10m


title: Quad_1.2_Sedentary_10m


title: Gas_6.2_Sedentary _18m


title: Gas_4.1_Exercise_18m


title: Quad_5.2_Sedentary _18m


title: SC_1.1_Sedentary_10m


title: Gas_5.3_Exercise_18m


title: SC_9.1_Exercise_18m


title: SC_1.3_Sedentary_10m


title: Gas_6.3_Exercise_18m


title: Gas_1.1_Sedentary_10m


title: Spinal cord_WT

city: Hangzhou

first: Zhong-Min

last: Dai

state: Zhejiang

address: 16 Xuelin Street, Xiasha

institute: Hangzhou Normal University

description:
gene_counts.txt
gene_expression.txt
transcript_counts.txt
transcript_expression.txt

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38.p6 whole genome using bowtie2 v2.3.2.
Transcripts Per Million (TPM) and Fragments Per Kilobase Million (FPKM) were calculated using a protocol from Wagner et al., Theory in Biosciences, 2012 and Trapnell et al., Nature Biotechnology, 2010, respectively.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: .txt files include gene and transcript counts, TPM and FPKM values for each Sample

source_name: Spinal cord_WT

extract_protocol:
Spinal cord were removed, immersed in RNAstore solution (CWBiotech) and stored in -80oC, and RNA was harvested using Trizol reagent (Sangon).
VAHTS™ mRNA-seq V2 Library Prep Kit for Illumina® (Vazyme Biotech) was used with 1 ug of total RNA for the construction of sequencing libraries.

value: postnatal day 7


title: Quad_4.1_Exercise_18m


title: SC_5.1_Exercise_18m


title: SC_8.3_Exercise_18m


title: Quad_1.4_Sedentary_10m


title: Gas_1.2_Sedentary_10m


title: Blimp1-Treg (CD4+CD25+Thy1.1-Blimp1+) B1

city: Beijing

first: Xundong

last: Wei

address: 1st West Beichen, Chaoyang

department: CAS Key Laboratory of Pathogenic Microbiology and Immunology

institute: Institute of Microbiology, Chinese Academy of Sciences (CAS)

data_processing:
Illumina Casava1.8 software used for basecalling.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads Vontaining ploy-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index of  the reference genome was built using Bowtie v2.2.3 and paired-end clean reads were  aligned to the reference genome using TopHat  v2.0.12.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene, considering the effect of sequencing depth and gene length for the reads count at the same time.(Trapnell, Cole, et al., Nat. Biotechnol 2010)
Genome_build: mm9
Supplementary_files_format_and_content: excel files include FPKM values for each sample

source_name: lymph node

extract_protocol:
Lymphocytes were isolated from the LN of 35EbiT-Blimp1-GFP mice and enriched for CD4+ T cells using magnetic beads. Then, CD25+CD62LlowThy1.1+Blimp1- and CD25+CD62LlowThy1.1-Blimp1+ Tregs were sorted to a typical purity of >90% using Thy1.1, CD25, CD62L and CD4 Abs.  SMART-SeqTM v4 UltraTM Low Input RNA Kit for Illumina was used with 10 pg-10 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: lymph node

value: 6 to 8 weeks

tag: mice

value: 35EbiT × Blimp1-GFP KI

tag: cell type/genotype

value: Blimp1-Treg (CD4+CD25+Thy1.1-Blimp1+)


title: Blimp1-Treg (CD4+CD25+Thy1.1-Blimp1+) B4

tag: tissue


title: Quad_1.1_Sedentary_10m

value: Quadriceps muscle

tag: strain

value: wild type


title: Ebi3-Treg (CD4+CD25+Thy1.1+Blimp1-) E3

value: Thy1.1+Blimp1- (Ebi3-Tregs)


title: Blimp1-Treg (CD4+CD25+Thy1.1-Blimp1+) B2


title: Ebi3-Treg (CD4+CD25+Thy1.1+Blimp1-) E4


title: Ebi3-Treg (CD4+CD25+Thy1.1+Blimp1-) E2


title: Ebi3-Treg (CD4+CD25+Thy1.1+Blimp1-) E1


title: P12_mVc_60

city: Delhi

first: Debarka

last: Sengupta

state: Delhi

address: IIIT Delhi, Okhla Phase 3

department: Computational Biology and Computer Science

institute: Indraprastha Institute of Information Technology

data_processing:
BAM files produced using  STAR aligner  with mm10 as  the reference genome.
Raw counts obtained using HTSeq  version 0.6.0.
The refseq genes are tracked for analysis.
Genome_build: mm10
Supplementary_files_format_and_content: The .csv file contains the count table for all individual cells

source_name: p12  Visual cortex

extract_protocol:
Single cells enriched by FACS were captured by C1 Single-cell Auto Prep System(Fluidigm).  polyA RNA from each single cell was reverse transcribed and cDNA amplified using SMARTer kit (SMARTer Ultra Low RNA Kit for the Fluidigm C1 System,Clontech#634936)
1ng of amplified cDNA was used as input to prepare sequencing libraries with the NexteraXT DNA Kit (Illumina #fc-131-1096) and with dual indices (PN FC-131-1002; Illumina)

value: p12  Visual cortex

value: Endothelial

tag: genotype

value: wildtype


title: P12_mVc_58

value: Astrocyte


title: P12_mVc_59


title: P12_mVc_56

value: Newly formed Oligodendrocyte


title: P12_mVc_57

value: OPC


title: P12_mVc_55

value: Microglia


title: Quad_4.3_Sedentary _18m

tag: age

value: 18 months

value: male

value: Sedentary


title: Gas_6.1_Sedentary _18m

value: Gastrocnemius muscle

tag: treatment


title: P12_mVc_53


title: P12_mVc_52


title: P12_mVc_50

value: unannotated


title: P12_mVc_51


title: Spinal cord_cKO

source_name: Spinal cord_cKO

value: Spinal cord

value: postnatal day 7


title: P12_mVc_46


title: P12_mVc_44


title: P12_mVc_43


title: Blimp1-Treg (CD4+CD25+Thy1.1-Blimp1+) B3

value: lymph node

value: 6 to 8 weeks

value: 35EbiT × Blimp1-GFP KI

value: Blimp1-Treg (CD4+CD25+Thy1.1-Blimp1+)


title: P12_mVc_47

value: p12  Visual cortex


title: P12_mVc_41

value: wildtype


title: P12_mVc_42

value: Astrocyte


title: P12_mVc_40

value: Newly formed Oligodendrocyte


title: P12_mVc_39

value: Endothelial


title: P12_mVc_38


title: P12_mVc_37


title: P12_mVc_33


title: P12_mVc_36


title: P12_mVc_34

value: Microglia


title: P12_mVc_54


title: P12_mVc_31


title: P12_mVc_49


title: P12_mVc_27


title: P12_mVc_26


title: P12_mVc_25


title: P12_mVc_48

value: OPC


title: P12_mVc_28


title: P12_mVc_23


title: P12_mVc_24


title: P12_mVc_45


title: P12_mVc_22


title: P12_mVc_20


title: P12_mVc_18


title: P12_mVc_15


title: P12_mVc_19


title: P12_mVc_17


title: P12_mVc_16


title: P12_mVc_14


title: P12_mVc_35


title: P12_mVc_9


title: P12_mVc_29


title: P12_mVc_8


title: P12_mVc_30


title: P12_mVc_7


title: P12_mVc_10


title: P12_mVc_32


title: P12_mVc_11


title: P12_mVc_13

value: purple


title: P12_mVc_6


title: P12_mVc_5


title: P12_mVc_2


title: P12_mThal_21

source_name: p12  Thalamus

value: p12  Thalamus


title: P12_mVc_3


title: P12_mVc_21


title: P12_mVc_1


title: P12_mThal_19


title: P12_mThal_18


title: P12_mThal_17


title: P12_mThal_20


title: P12_mVc_12


title: P12_mThal_15


title: P12_mThal_16


title: P12_mThal_13


title: P12_mThal_10


title: P12_mThal_12


title: P12_mThal_8


title: P12_mThal_9


title: P12_mThal_7


title: P12_mThal_5


title: P12_mH_67

source_name: p12  Hippocampus

value: p12  Hippocampus


title: P12_mThal_6


title: P12_mH_66


title: P12_mThal_4


title: P12_mThal_2


title: P12_mThal_3


title: P12_mH_65

value: unannotated


title: P12_mH_64


title: P12_mH_60


title: P12_mH_57


title: P12_mH_63


title: P12_mH_59


title: P12_mH_56


title: P12_mH_58


title: P12_mH_62


title: P12_mH_61


title: P12_mH_55


title: P12_mThal_14


title: P12_mH_52


title: P12_mH_54


title: P12_mH_51


title: P12_mVc_4


title: P12_mThal_11


title: P12_mThal_1


title: P12_mH_68


title: P12_mH_49


title: P12_mH_47


title: P12_mH_50


title: P12_mH_44


title: P12_mH_45


title: P12_mH_42


title: P12_mH_43


title: P12_mH_48


title: P12_mH_40


title: P12_mH_38


title: P12_mH_36


title: P12_mH_53


title: P12_mH_34


title: P12_mH_41


title: P12_mH_32


title: P12_mH_30


title: P12_mH_35


title: P12_mH_31


title: P12_mH_39


title: P12_mH_29


title: P12_mH_33


title: P12_mH_26


title: P12_mH_25


title: P12_mH_24


title: P12_mH_27


title: P12_mH_23


title: P12_mH_22


title: P12_mH_46


title: P12_mH_21


title: P12_mH_20


title: P12_mH_16

value: Myelinating Oligodendrocyte


title: P12_mH_17


title: P12_mH_18


title: P12_mH_13


title: P12_mH_15


title: P12_mH_28


title: P12_mH_10


title: P12_mH_12


title: P12_mH_9


title: P12_mH_3


title: P12_mH_11


title: P12_mH_5


title: P12_mH_7


title: mAdultVc_62

source_name: adult brain Visual cortex

value: adult brain Visual cortex


title: P12_mH_37


title: P12_mH_1


title: P12_mH_2


title: P12_mH_4


title: P12_mH_14


title: mAdultVc_59


title: mAdultVc_60


title: mAdultVc_61


title: mAdultVc_58


title: P12_mH_6


title: mAdultVc_57


title: P12_mH_19


title: mAdultVc_56


title: mAdultVc_55


title: mAdultVc_54


title: mAdultVc_51


title: mAdultVc_53


title: mAdultVc_49


title: mAdultVc_50


title: P12_mH_8


title: mAdultVc_46


title: mAdultVc_47


title: mAdultVc_45


title: mAdultVc_42


title: mAdultVc_43


title: mAdultVc_48


title: mAdultVc_41


title: mAdultVc_40


title: mAdultVc_39


title: mAdultVc_37


title: mAdultVc_44


title: mAdultVc_33


title: mAdultVc_32


title: mAdultVc_38


title: mAdultVc_30


title: mAdultVc_31


title: mAdultVc_34


title: mAdultVc_36


title: mAdultVc_27


title: mAdultVc_52


title: mAdultVc_26


title: mAdultVc_25


title: mAdultVc_35


title: mAdultVc_20


title: mAdultVc_21


title: mAdultVc_17


title: mAdultVc_29


title: mAdultVc_15


title: mAdultVc_28


title: mAdultVc_13


title: mAdultVc_10


title: mAdultVc_11


title: mAdultVc_24


title: mAdultVc_6


title: mAdultVc_5


title: mAdultVc_4


title: mAdultVc_23


title: mAdultVc_22


title: mAdultVc_1


title: E18.5mThal_50

source_name: e18.5  brain Visual cortex

value: e18.5  brain Visual cortex


title: mAdultVc_18


title: mAdultVc_19


title: mAdultVc_16


title: E18.5mThal_48


title: mAdultVc_14


title: mAdultVc_12


title: mAdultVc_2


title: E18.5mThal_44


title: mAdultVc_8


title: E18.5mThal_43

value: Neurons


title: E18.5mThal_42


title: mAdultVc_7


title: E18.5mThal_39


title: mAdultVc_3


title: mAdultVc_9


title: E18.5mThal_51


title: E18.5mThal_35


title: E18.5mThal_34


title: E18.5mThal_33


title: E18.5mThal_46


title: E18.5mThal_47


title: E18.5mThal_49


title: E18.5mThal_45


title: E18.5mThal_29


title: E18.5mThal_41


title: E18.5mThal_27


title: E18.5mThal_40


title: E18.5mThal_38


title: E18.5mThal_24


title: E18.5mThal_36


title: E18.5mThal_37


title: E18.5mThal_23


title: E18.5mThal_22


title: E18.5mThal_21


title: E18.5mThal_32


title: E18.5mThal_17


title: E18.5mThal_31


title: E18.5mThal_16


title: E18.5mThal_15


title: E18.5mThal_30


title: E18.5mThal_13


title: E18.5mThal_10


title: E18.5mThal_12


title: E18.5mThal_28


title: E18.5mThal_14


title: E18.5mThal_20


title: E18.5mThal_25


title: E18.5mThal_26


title: E18.5mThal_19


title: E18.5mThal_6


title: E18.5mThal_18


title: E18.5mThal_2


title: E18.5mThal_1


title: E18.5_mVc_71


title: E18.5mThal_3


title: E18.5_mVc_70


title: E18.5mThal_11


title: E18.5mThal_9


title: E18.5_mVc_63


title: E18.5mThal_8


title: E18.5mThal_4


title: E18.5mThal_5


title: E18.5_mVc_61


title: E18.5_mVc_69


title: E18.5_mVc_57


title: E18.5_mVc_67


title: E18.5_mVc_59


title: E18.5mThal_7


title: E18.5_mVc_56


title: E18.5_mVc_54


title: E18.5_mVc_53


title: E18.5_mVc_65


title: E18.5_mVc_49


title: E18.5_mVc_62


title: E18.5_mVc_66


title: E18.5_mVc_64


title: E18.5_mVc_60


title: E18.5_mVc_46


title: E18.5_mVc_58


title: E18.5_mVc_48


title: E18.5_mVc_68


title: E18.5_mVc_52


title: E18.5_mVc_43


title: E18.5_mVc_51


title: E18.5_mVc_47


title: E18.5_mVc_40


title: E18.5_mVc_50


title: E18.5_mVc_55


title: E18.5_mVc_42


title: E18.5_mVc_44


title: E18.5_mVc_39


title: E18.5_mVc_41


title: E18.5_mVc_32


title: E18.5_mVc_38


title: E18.5_mVc_33


title: E18.5_mVc_31


title: E18.5_mVc_35


title: E18.5_mVc_34


title: E18.5_mVc_30


title: MB135_p2_siXY_2

city: Seattle

first: Stephen

last: Tapscott

state: WASHINGTON

address: 1100 Fairview N. Ave

department: Human Biology

institute: Fred Hutch Cancer Research Center

description: pulse 2 H3.X/Y knockdown

data_processing:
Filtered un-qualified reads indicated by the filter flag within the sequency identifier.
Aligned raw reads to genome build hg38 using Taphat-2.1.0.
Profiled gene expression using features collected from Ensembl v88 and hit-counting function summarizedOverlaps() from BioConductor's GenomicAlignments pacakge.
Identified robust DUX4 targets genes by using DESeq2 comparing pulse 1 siContrl samples to negative controls. The alternative hypothesis was set to |log fold change| > 4 and adjusted p-value threshold to 0.05.
Genome_build: hg38
Supplementary_files_format_and_content: se_pulse_EnsV88.rda contains a BioConductor's SummarizedExperiment instance storing gene feature ranges (Ensembl V88), phenotype data and counts/RPKM. And se_pulse_EnsV88.CSV is the gene count.
Supplementary_files_format_and_content: GSE72379_se_H3XY.rda is a SummarizedExperiment instance containing H3.X/Y family features, phenoty data and counts/RPKM for H3.X/Y family genes. GSE72379_se_H3XY.csv contains H3.X/Y family gene counts.
Supplementary_files_format_and_content: GSE85461_MB135_se_EnsV88.rda stores a SummarizedExperiment instance containing gene feaures, counts/RPKM for GSE85461 MB135 samples.
Supplementary_files_format_and_content: pulse1_continues_lfc.csv contains log fold change of pulse 1 sample (pulse 1 siContrl vs neg_controls) and continues sampls (DUX+ vs DUX-) from GSE85461 MB135 samples.

source_name: MB135iDUX4 myoblast

growth_protocol: MB135iDUX4 cells were grown in F10 medium supplemented with 10% FBS, 1% pen/strep, 10pg/mL fgf, 1uM dexamethasone, and 10ug/mL blasticidin

extract_protocol:
Total RNA was extracted from whole cells using NucleoSpin RNA kit (Macherey-Nagel) following the manufacturer's instructions.
RNA-seq libraries were prepared from total RNA using the TruSeq RNA Sample Prep v2 Kit (Illumina, Inc., San Diego, CA, USA) and a Sciclone  NGSx Workstation (PerkinElmer, Waltham, MA, USA).
RNA-seq libraries were pooled (15-plex) and clustered onto two flow cell lanes.

treatment_protocol: cells were plated 200,000 cells/well in a 6-well dish. Prior to each pulse cells were treated with siRNA overnight, then pulsed with doxycycline for 6 hours and harvested 18 hours later

value: MB135iDUX4 myoblast

value: pulse 2 siXY KD

tag: genome


title: MM1S_shEV_rep3

city: Durham

first: Greg

last: Wang

state: NC

address: 3 Genome Court

department: Duke Department of Pharmacology and Cancer Biology  and Duke Cancer Institute

institute: Duke University School of Medicine, and Department of Biochemistry and Biophysics, UNC at Chapel Hill (adjunct)

data_processing:
Basecalls by Casava
Alignment by MapSplice2
Genome to transcriptome coordiantes by UBU (https://github.com/mozack/ubu/wiki)
Gene expression estimates by RSEM using Sept 2011 UCSC knownGene transcript definitions
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited matrix of gene level count estimates

source_name: MM1S cells

growth_protocol: MM1S cells were grown in RPMI1640 plus 10% FBS and 1% antibiotics.

extract_protocol:
RNA was extracted by using Qiagen RNeasy Mini Kit. Illumina Truseq sample prep kit v2 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: For knocking down PHF19 experiment, MM1S cells were infected with lentivirus encoding empty vectro (shEV controls) or sh-PHF19. For RNA-seq experiments, cells were grown in regular medium and collected.

tag: cell line

tag: shRNA

value: empty vector


title: MM1S_shEV_rep2


title: MM1S_shEV_rep1


title: MM1S_PHF19-KD_rep1


title: MM1S_KD_Rescued_rep2

value: shRNA-resistant PHF19


title: MM1S_KD_Rescued_rep1


title: MM1S_PHF19-KD_rep4


title: MM1S_PHF19-KD_rep2


title: MM1S_PHF19-KD_rep3


title: E18.5_mVc_45

value: wildtype


title: E18.5_mVc_29


title: E18.5_mVc_28


title: E18.5_mVc_27


title: E18.5_mVc_37


title: E18.5_mVc_36


title: MB135_p2_siCntrl_1

description: pulse 2 control knockdown

value: pulse 2 control KD


title: E18.5_mVc_26


title: MB135_p2_siCntrl_2

description: pulse 2 control knockdown


title: MB135_p1_siXY_3

description: pulse 1 H3.X/Y knockdown

value: pulse 1 siXY KD


title: E18.5_mVc_25


title: MB135_p2_siXY_3

description: pulse 2 H3.X/Y knockdown


title: MB135_p1_siXY_2

description: pulse 1 H3.X/Y knockdown


title: E18.5_mVc_24


title: MB135_p1_siXY_1

description: pulse 1 H3.X/Y knockdown


title: MB135_p1_siCntrl_3

description: pulse 1 control knockdown

value: pulse 1 control KD


title: MB135_p2_siXY_1

description: pulse 2 H3.X/Y knockdown


title: MB135_p1_siCntrl_2

description: pulse 1 control knockdown


title: E18.5_mVc_22


title: MB135_neg_control_3

description: negative control without DUX4 induction

value: negative control


title: E18.5_mVc_19


title: E18.5_mVc_17


title: MB135_neg_control_1

description: negative control without DUX4 induction


title: E18.5_mVc_21


title: E18.5_mVc_16


title: E18.5_mVc_18


title: MB135_p2_siCntrl_3

description: pulse 2 control knockdown


title: MB135_p1_siCntrl_1

description: pulse 1 control knockdown


title: E18.5_mVc_20


title: MB135_neg_control_2

description: negative control without DUX4 induction


title: E18.5_mVc_9


title: E18.5_mVc_11


title: E18.5_mVc_10


title: E18.5_mVc_12


title: E18.5_mVc_7


title: E18.5_mVc_23


title: E18.5_mVc_5


title: E18.5_mVc_8


title: E18.5_mVc_3


title: E18.5_mVc_2


title: E18.5_mVc_1


title: H3: tSKPs-FBs

city: Chengdu

first: Ru

state: Sichuan

address: No.37 Guo Xue Xiang

department: Dermatology

institute: West China hospital

data_processing:
IlluminaHiSeqTM 2000 software used for base calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the human genome using Tophat v2.0.12
The gene expression level was presented by using RPKM method, which was calculated based on the length of the gene and sequencing discrepancies.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene.
RPKM values could be used for comparing the difference of gene expression in two conditions.
Genome_build: human genome
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: tSKPs-FBs

extract_protocol:
trizol
RNA libraries were prepared for sequencing using standard illumina protocols

tag: location

value: dermis

tag: passage

value: Human foreskin


title: E18.5_mVc_15


title: E18.5_mVc_14


title: E18.5_mVc_13


title: 6419c5-EPHA2-KO1-B

first: Jinyang

last: Li

state: New York

address: 1230 York Ave

data_processing:
Alignment-independent quantification using Salmon
Genome_build: mm10
Supplementary_files_format_and_content: TPM values of for all samples

source_name: 6419c5 pancreatic tumor cell clone

growth_protocol: pancreatic tumor cells were subcutaneously implanted into C57BL/6 mice. Sorted tumor cell samples were prepared from tumors 3 weeks following implantation.

extract_protocol:
RNA was extracted using Qiagen Rneasy Micro Kit.
500 ng of total RNA was used for the preparation of sequencing libraries using NEB RNA-seq library preparation kit with standard protocol. RNA-seq libraries were sequenced on an Illumina Nextseq 550 high-throughput sequencer.

treatment_protocol: no treatment administrated

tag: condition

value: in vivo sorted tumor cells

value: mouse pancreatic tumor cells


title: D0-165

city: Nanjing

first: Wang

last: Hongsheng

state: Jiangsu

address: 12 Jiangwangmiao Street, Xuanwu District

institute: Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College

description:
Sample 37
Venous blood
Langhans giant cells
processed data file: RawCounts.xlsx
processed data file: NormalizedCounts.xlsx

data_processing:
Technique replicates were pooled together then mapped to hg19 with tophat2 using parameters --bowtie1 --no-coverage-search --library-type fr-unstranded -G --transcriptome-index
Reads per gene were calculated with htseq-count with ensembl 75 gene annotation.
Reads counts were normalized by DESeq2 and then performed gene differential expression analysis with DESeq2.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: RawCounts.xlsx: Table for raw counts in Excel file.
Supplementary_files_format_and_content: NormalizedCounts.xlsx: Table for normalized counts in Excel file.

source_name: PBMC

extract_protocol:
RNA extracted by Qiagen RNeasy Micro Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Adherent monocytes

tag: time point

value: Day 0

tag: donor


title: D0-301

description:
Sample 39
Venous blood
Langhans giant cells
processed data file: RawCounts.xlsx
processed data file: NormalizedCounts.xlsx


title: 6419c5-EPHA2-KO2-A


title: 6419c5-EPHA2-KO1-C


title: D10-301-4

description:
Sample 36
Venous blood
Langhans giant cells
processed data file: RawCounts.xlsx
processed data file: NormalizedCounts.xlsx

value: Day 10


title: 6419c5-EPHA2-KO2-B


title: D10-301-15

description:
Sample 34
Venous blood
Langhans giant cells
processed data file: RawCounts.xlsx
processed data file: NormalizedCounts.xlsx


title: E18.5_mVc_6

value: e18.5  brain Visual cortex

value: Neurons


title: 6419c5-B


title: 6419c5-C


title: E18.5_mVc_4


title: H2: FBs

source_name: FBs


title: 6419c5-A


title: D10-58-M

description:
Sample 32
Venous blood
Langhans giant cells
processed data file: RawCounts.xlsx
processed data file: NormalizedCounts.xlsx

value: Media


title: 6694c2-EPHA2-KO2-B

source_name: 6694c2 pancreatic tumor cell clone


title: 6694c2-EPHA2-KO2-D


title: H1: tSKPs

source_name: tSKPs


title: 6419c5-EPHA2-KO2-C


title: 6694c2-EPHA2-KO2-C


title: D10-165-4

description:
Sample 30
Venous blood
Langhans giant cells
processed data file: RawCounts.xlsx
processed data file: NormalizedCounts.xlsx


title: 6694c2-EPHA2-KO2-A


title: 6694c2-EPHA2-KO1-D


title: D10-165-M

description:
Sample 29
Venous blood
Langhans giant cells
processed data file: RawCounts.xlsx
processed data file: NormalizedCounts.xlsx


title: D10-165-15

description:
Sample 28
Venous blood
Langhans giant cells
processed data file: RawCounts.xlsx
processed data file: NormalizedCounts.xlsx


title: 6419c5-EPHA2-KO1-A


title: D6-301-4

description:
Sample 27
Venous blood
Langhans giant cells
processed data file: RawCounts.xlsx
processed data file: NormalizedCounts.xlsx

value: Day 6


title: D6-301-M

description:
Sample 26
Venous blood
Langhans giant cells
processed data file: RawCounts.xlsx
processed data file: NormalizedCounts.xlsx


title: D6-301-15

description:
Sample 25
Venous blood
Langhans giant cells
processed data file: RawCounts.xlsx
processed data file: NormalizedCounts.xlsx


title: 6694c2-EPHA2-KO1-A


title: 6694c2-D


title: D10-58-4

description:
Sample 33
Venous blood
Langhans giant cells
processed data file: RawCounts.xlsx
processed data file: NormalizedCounts.xlsx


title: D6-58-4

description:
Sample 24
Venous blood
Langhans giant cells
processed data file: RawCounts.xlsx
processed data file: NormalizedCounts.xlsx


title: 6694c2-EPHA2-KO1-B


title: 6694c2-C


title: D10-58-15

description:
Sample 31
Venous blood
Langhans giant cells
processed data file: RawCounts.xlsx
processed data file: NormalizedCounts.xlsx


title: D6-58-15

description:
Sample 22
Venous blood
Langhans giant cells
processed data file: RawCounts.xlsx
processed data file: NormalizedCounts.xlsx


title: D6-58-M

description:
Sample 23
Venous blood
Langhans giant cells
processed data file: RawCounts.xlsx
processed data file: NormalizedCounts.xlsx


title: D6-165-4

description:
Sample 21
Venous blood
Langhans giant cells
processed data file: RawCounts.xlsx
processed data file: NormalizedCounts.xlsx


title: D6-165-M

description:
Sample 20
Venous blood
Langhans giant cells
processed data file: RawCounts.xlsx
processed data file: NormalizedCounts.xlsx


title: D3-301-4

description:
Sample 18
Venous blood
Langhans giant cells
processed data file: RawCounts.xlsx
processed data file: NormalizedCounts.xlsx

value: Day 3


title: D3-301-M

description:
Sample 17
Venous blood
Langhans giant cells
processed data file: RawCounts.xlsx
processed data file: NormalizedCounts.xlsx


title: D3-301-15

description:
Sample 16
Venous blood
Langhans giant cells
processed data file: RawCounts.xlsx
processed data file: NormalizedCounts.xlsx


title: 6694c2-EPHA2-KO1-C


title: D3-58-4

description:
Sample 15
Venous blood
Langhans giant cells
processed data file: RawCounts.xlsx
processed data file: NormalizedCounts.xlsx


title: PFC_mix_H3K79me2_1k_R2

city: Blacksburg

first: Chang

last: Lu

state: VA

address: 235 Goodwin Hall, 635 Prices Fork Road, Virginia Tech

department: Chemical Engineering

institute: Virginia Tech

library_source: genomic

data_processing:
Raw reads were trimmed with TrimGalore 0.4.1 with default setting
Trimmed reads were aligned using bowtie 1.1.2
Reads were extended to 250bp and normalized based on the sequencing depth
Sample was normalized and input subtracted
Sample was converted to BigWig format
Genome_build: mm10
Supplementary_files_format_and_content: Normalized ChIP-seq signal in BigWig format

molecule: genomic DNA

source_name: Prefrontal cortex

extract_protocol:
50 mg of the frozen mouse prefrontal cortex tissue was placed in a glass dounce tissue grinder, add 5 ml of nuclei extraction buffer (0.32 M sucrose, 5 mM CaCl2, 3 mM Mg(Ac)2, 0.1 mM EDTA, 10 mM Tris-HCl and 0.1% Triton X-100), 50 µl of PIC, 5 µl of 100mM PMSF and 5 µl of 1M DTT, and place the grinder on ice. Once the tissue thaws, dounce the tissue with pestle A (D9063, Sigma-Aldrich) for 15 times, followed by douncing with pestle B (D9063, Sigma-Aldrich) for 25 times. Filter the homogenate through a 40-µm cell strainer into a new 15 ml centrifuge tube. Centrifuge the tube at 1000 g for 10 min at 4 °C. Discard the supernatant and gently resuspend the crude nuclei pellet in 500 µl nuclei extraction buffer. Add 5 µl of PIC, 0.5 µl of 100 mM PMSF, and 0.5 µl of 1 M DTT to the nuclei suspension. Transfer the nuclei suspension into a 1.5 mL Eppendorf microcentrifuge tube. Place the tube on ice. Add 750 µl of 50% iodixanol solution, 7.5 µl of PIC, 0.75 µl of 100 mM PMSF and 0.75 µl of 1 M DTT to the tube. Mix the solution well. Centrifuge at 10,000 g for 20 min at 4 °C. Carefully remove all the supernatant. Add 50 µl of PBS, 0.5 µl of PIC, 0.5 µl of 100 mM PMSF to the tube. Incubate on ice for 10 min. Resuspend the nuclei pellet by pipetting up and down gently. Check nuclei concentration with a hemocytometer to get 1000 nuclei per assay. Usually we can get ~150K nuclei after this   protocol.
Library preparation was conduct using the Swift Bio S2 library preparation kit (Swift Biosciences) using ChIP DNA from 1000 nuclei (we can get ~150 pg DNA per assay). Use 2.5 μl of 20x EvaGreen  and 7.5 μl of the low EDTA TE buffer in the 50 μl amplification cycle reaction mix, instead of 10 μl of low EDTA TE buffer and amplification was stopped after samples saw an >3000 RFU increase (BioRad CFX Connect). Amplified DNA was then eluted into 10 μl low EDTA TE buffer where 1 μl could be used for qPCR analysis for preliminary quality control analysis, Kappa DNA quantification, and Tapestation fragment size analysis and the other 5 μl for library pooling. Libraries were pooled at 10 nM for sequencing by Illumina HiSeq 4000 with single-end 50 nt read.

value: 10 weeks

tag: chip antibody


title: PFC_mix_H3K79me2_1k_R1


title: 6694c2-B

tag: cell type


title: PFC_mix_H3K36me3_1k_R2


title: PFC_mix_H3K9me3_1k_R1


title: D3-165-15

description:
Sample 10
Venous blood
Langhans giant cells
processed data file: RawCounts.xlsx
processed data file: NormalizedCounts.xlsx


title: 6694c2-A


title: D3-165-4

description:
Sample 12
Venous blood
Langhans giant cells
processed data file: RawCounts.xlsx
processed data file: NormalizedCounts.xlsx


title: PFC_mix_H3K27me3_1k_R4

data_processing:
library strategy: microfluidic oscillatory washing-based chromatin immunoprecipitation followed by sequencing (MOWChIP-seq)
Raw reads were trimmed with TrimGalore 0.4.1 with default setting
Trimmed reads were aligned using bowtie 1.1.2
Reads were extended to 250bp and normalized based on the sequencing depth
Sample was normalized and input subtracted
Sample was converted to BigWig format
Genome_build: mm9
Supplementary_files_format_and_content: Normalized ChIP-seq signal in BigWig format

extract_protocol:
50 mg of the frozen mouse prefrontal cortex tissue was placed in a glass dounce tissue grinder, add 5 ml of nuclei extraction buffer (0.32 M sucrose, 5 mM CaCl2, 3 mM Mg(Ac)2, 0.1 mM EDTA, 10 mM Tris-HCl and 0.1% Triton X-100), 50 µl of PIC, 5 µl of 100mM PMSF and 5 µl of 1M DTT, and place the grinder on ice. Once the tissue thaws, dounce the tissue with pestle A (D9063, Sigma-Aldrich) for 15 times, followed by douncing with pestle B (D9063, Sigma-Aldrich) for 25 times. Filter the homogenate through a 40-µm cell strainer into a new 15 ml centrifuge tube. Centrifuge the tube at 1000 g for 10 min at 4 °C. Discard the supernatant and gently resuspend the crude nuclei pellet in 500 µl nuclei extraction buffer. Add 5 µl of PIC, 0.5 µl of 100 mM PMSF, and 0.5 µl of 1 M DTT to the nuclei suspension. Transfer the nuclei suspension into a 1.5 mL Eppendorf microcentrifuge tube. Place the tube on ice. Add 750 µl of 50% iodixanol solution, 7.5 µl of PIC, 0.75 µl of 100 mM PMSF and 0.75 µl of 1 M DTT to the tube. Mix the solution well. Centrifuge at 10,000 g for 20 min at 4 °C. Carefully remove all the supernatant. Add 50 µl of PBS, 0.5 µl of PIC, 0.5 µl of 100 mM PMSF to the tube. Incubate on ice for 10 min. Resuspend the nuclei pellet by pipetting up and down gently. Check nuclei concentration with a hemocytometer to get 1000 nuclei per assay. Typically we get a total of ~150K nuclei after this procedure.
Library preparation was conducted using Accel-NGS® 2S Plus DNA Library Kit (Swift Biosciences) with ChIP DNA from 1000 nuclei (~150 pg). Use 2.5 μl of 20x EvaGreen  and 7.5 μl of the low EDTA TE buffer in the 50 μl amplification cycle reaction mix, instead of 10 μl of low EDTA TE buffer and amplification was stopped after samples saw an >3000 RFU increase (BioRad CFX Connect). Amplified DNA was then eluted into 10 μl low EDTA TE buffer where 1 μl could be used for qPCR analysis for preliminary quality control analysis, Kappa DNA quantification, and Tapestation fragment size analysis and the other 5 μl for library pooling. Libraries were pooled at 10 nM for sequencing by Illumina HiSeq 4000 with single-end 50 nt read.

value: Prefrontal cortex


title: D6-165-15

description:
Sample 19
Venous blood
Langhans giant cells
processed data file: RawCounts.xlsx
processed data file: NormalizedCounts.xlsx


title: PFC_mix_H3K9me3_1k_R2


title: D3-58-15

description:
Sample 13
Venous blood
Langhans giant cells
processed data file: RawCounts.xlsx
processed data file: NormalizedCounts.xlsx


title: D3-165-M

description:
Sample 11
Venous blood
Langhans giant cells
processed data file: RawCounts.xlsx
processed data file: NormalizedCounts.xlsx


title: D1-301-4

description:
Sample 9
Venous blood
Langhans giant cells
processed data file: RawCounts.xlsx
processed data file: NormalizedCounts.xlsx

value: Day 1


title: PFC_mix_input


title: PFC_mix_H3K27me3_1k_R3


title: cell_Vector_48h_rep1

first: Chen

last: Chuwen

address: No.22, Zhongguancun South Avenue

institute: Peking university

description: Gene expression after 48hr in Vector plasmid transfected SACC-83 cells

hyb_protocol: Each slide was hybridized with 600ngCy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit. Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, limma packages in R.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.11 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genedpring 13.0 (Agilent. Probes that at least 1 out of 2 samples flagged as Detected were maintained.

source_name: cell, 48hr, Vector, replicate 1

label_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity>10.0 pmol Cy3/μg cRNA) was fragmented at 60℃ for 30 minutes in a reaction volume of 22.5μl containing 1xAgilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Human Gene Expression (8*60K) for 17 hours at 65℃ in a rotating Adilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Was Buffer 1 (Agilent) and 1 minute with 37℃ GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

growth_protocol: Cells were maintained in RPMI 1640 medium (Gibco) supplemented with 10% fetal bovine serum (FBS) (Gibco) and incubated at 37ºC in a humidified 5% CO2 incubator.

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: SACC-83 cells were transiently transfected with vector plasmid or plasmid withMRPL23-AS1. The cells were grown in six-well plates to 30-50% confluence and transfected using riboFECTTM CP (RiboBio) according to the manufacturer’s instructions. The cells were harvested after a forty-eight-hour transfection.

value: control


title: cell_si-control_48h_rep1

description: Gene expression after 48hr in si-control transfected SACC-LM cells

treatment_protocol: SACC-LM cells were transiently transfected with siRNA (si) or scrambled siRNA negative control (si-control). The cells were grown in six-well plates to 30-50% confluence and transfected using riboFECTTM CP (RiboBio) according to the manufacturer’s instructions. The cells were harvested after a forty-eight-hour transfection.

value: SACC-LM

value: si-control


title: cell_MRPL23-AS1_48h_rep1

description: Gene expression after 48hr in MRPL23-AS1 plasmid transfected SACC-83 cells

source_name: cell, 48hr, plasmid, replicate 1

value: overexpressing MRPL23-AS1


title: D1-301-M

description:
Sample 8
Venous blood
Langhans giant cells
processed data file: RawCounts.xlsx
processed data file: NormalizedCounts.xlsx


title: D1-58-4

description:
Sample 6
Venous blood
Langhans giant cells
processed data file: RawCounts.xlsx
processed data file: NormalizedCounts.xlsx


title: cell_siRNA_48h_rep1

description: Gene expression after 48hr in siRNA transfected SACC-LM cells


title: D1-301-15

description:
Sample 7
Venous blood
Langhans giant cells
processed data file: RawCounts.xlsx
processed data file: NormalizedCounts.xlsx


title: PFC_mix_H3K27me3_1k_R2


title: D1-165-M

description:
Sample 2
Venous blood
Langhans giant cells
processed data file: RawCounts.xlsx
processed data file: NormalizedCounts.xlsx


title: col-0 +HrcC 3rd rep

city: Thuwal

first: Prof. Heribert

last: HIRT

address: 4700 KAUST

country: Saudi Arabia

institute: KAUST

data_processing:
Reads were quality checked using FASTQC.
Sequenced reads were passed through trimmomatic0.36 to remove adapter contents and low quality sequences.
Trimmed sequences were checked for quality again using FASTQC.
Trimmed sequences were aligned to Arabidopsis thaliana genome using Tophat V2.1.1
FPKM values for each sample and differential expression between samples were calculated using Cufflinks V2.2.1
Genome_build: TAIR10
Supplementary_files_format_and_content: Excel; FPKM values

organism: Arabidopsis thaliana

growth_protocol: 14 days-old seedlings were grown under long-day conditions on sugar-free MS (Murashige and Skoog) plates at 23oC

extract_protocol:
The whole 14 days-old seedlings were used for total RNA extraction.
mRNA library generation followed by paired end sequencing (Hiseq4000)

treatment_protocol: Spray inoculated treatment with Pst hrcC bacterial suspension at an OD600=0.002 for 24 hours

tag: sample type

value: Pst hrcC treated wild type

value: wild type


title: PFC_mix_H3K27me3_1k_R1


title: col-0 ctrl 3rd rep


title: linc1-1 HrcC 3rd rep

value: Pst hrcC treated linc1-1


title: D1-58-M

description:
Sample 5
Venous blood
Langhans giant cells
processed data file: RawCounts.xlsx
processed data file: NormalizedCounts.xlsx

value: Adherent monocytes


title: D3-58-M

description:
Sample 14
Venous blood
Langhans giant cells
processed data file: RawCounts.xlsx
processed data file: NormalizedCounts.xlsx


title: col-0 +HrcC  2nd rep


title: D1-58-15

description:
Sample 4
Venous blood
Langhans giant cells
processed data file: RawCounts.xlsx
processed data file: NormalizedCounts.xlsx


title: linc1-1 ctrl 3rd rep


title: D1-165-4

description:
Sample 3
Venous blood
Langhans giant cells
processed data file: RawCounts.xlsx
processed data file: NormalizedCounts.xlsx


title: linc1-1 HrcC 1st rep


title: linc1-1 HrcC  2nd rep


title: linc1-1 ctrl 1st rep


title: linc1-1 ctrl  2nd rep


title: D1-165-15

description:
Sample 1
Venous blood
Langhans giant cells
processed data file: RawCounts.xlsx
processed data file: NormalizedCounts.xlsx


title: T47D_RES_CL2.6

city: Houston

first: Khandan

last: Keyomarsi

address: 6565 MD Anderson Blvd

institute: UT MD Anderson Cancer Center

description:
biological replicate 2
T47D_RES_CL2-6_GTCCGC

data_processing:
fastqc files were generated using Illumina’s HiSeq Control Analysis Software and Sequencing analysis viewer software according to Illumina’s protocols (CASAVA).
To map the reads of all samples to the human genome (hg19) we used the RNA-STAR* software [Bioinformatics. 2013;29:15–21] using the default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: RNA-seq data tags mapped to hg19 and genes are annotated

source_name: T47D_clone_palbociclib resistant

growth_protocol: T47D cells were maintained in minimum essential medium Eagle alpha modification (alpha MEM) supplemented with 10% FBS, 10mM HEPES, nonessential amino acids, sodium pyruvate, 2mM L-glutamine, insulin, EGF, and hydrocortisone

extract_protocol:
Total RNA was isolated from cell lysates using the Qiagen RNeasy mini Kit with DNase according to manufacturer's protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol:
Palbociclib-resistant cell lines were generated by culturing cells in media supplemented with palbociclib at increasing concentrations for 6 months starting at 1uM and reaching a final dose of 5uM.
Resistant cells were maintained in alpha MEM supplemented with 5mM palbociclib but all experiments were conducted in the absence of palbociclib-supplemented media unless otherwise noted.

value: Breast cancer cells

tag: drug sensitivty

value: palbociclib resistant

tag: cell subtype

value: resistant (RES) clone 2


title: col-0 ctrl 2nd rep


title: T47D_CL4.2

description:
biological replicate 2
T47D_CL4-2_ACTTGA

value: resistant clone 4


title: T47D_PAR.2

description:
biological replicate 2
T47D_PAR-2_CAGATC

source_name: T47D_parental_palbociclib sensitive

value: palbociclib sensitive

value: parental (PAR)


title: T47D_CL4.1

description:
biological replicate 1
T47D_CL4-1_TTAGGC


title: col-0 ctrl 1st rep


title: T47D_PAR.3

description:
biological replicate 3
T47D_PAR-3_CTTGTA


title: T47D_PAR.1

description:
biological replicate 1
T47D_PAR-1_CGATGT


title: col-0 +HrcC 1st rep


title: PP_InVivo_5

city: Utrecht

first: Maria

middle: Belen

last: Rabaglino

address: Yalelaan 7

department: Population Health Science

country: Netherlands

institute: Utrecht University

data_processing:
Sequence reads for each sample were mapped to the annotated bovine reference genome (UMD3.1.70) using CLC genomics workbench 12.0 (www.qiagenbioinformatics.com)
Gene expression levels were assessed by counting the number of mapped reads for each Ensembl ID.
Raw counts were processed with the edgeR package for the R software.
Genes with low expression counts (less than 1 count per million) were filtered out before normalization.
The between-samples normalization method applied was TMM (weighted trimmed mean of M-values).
Genome_build: bosTau8
Supplementary_files_format_and_content: tab delimited text file containing raw read counts for each sample.

organism: Bos taurus

source_name: Pregnant at 30 and 60 days of gestation_demi-blastocyst

extract_protocol:
Total RNA from each sample was isolated using the RNeasy Micro Kit (Qiagen, Germantown, MD, USA) according to the manufacture’s cell protocol with the following adjustments for samples maintained in RNAlater; 250 µl of 100% ethanol was used instead of the recommended 350 µL of 70% (v/v) ethanol and isolated RNA was eluted in 12 µl RNase-free water instead of the recommended 22 µl RNase-free water.
Barcoded fragment libraries were constructed using the Bovine Custom Any Deplete Ovation SoLo RNA-Seq System from NuGEN (San Carlos, CA, USA) following the manufacturer’s protocol. DNA integrity of the libraries was assessed using the High Sensitivity D1000 ScreenTape on the Agilent 4200 TapeStation (Santa Clara, CA, USA) and DNA concentration was measured using the KAPA qPCR kit (Boston, MA, USA) following the manufacturer’s protocol. Samples were then multiplexed and sequenced with 1×75bp single-end reads on an Illumina NEXT-seq (Illumina, Inc.San Diego, CA, USA) at the Stanford Functional Genomics Facility (Stanford, CA, USA) according to the manufacturer’s protocol.

treatment_protocol: Blastocysts collected on day 7 of culture were transferred individually into 50 µl drops of embryo biopsy medium (BO-biopsy, IVF Bioscience) placed on the surface of an epoxy-printed well slide to which scratches were made manually in the glass with an 18 gauge needle. Scratches were made to assist in stabilization of the embryo during the biopsy procedure. While visualizing the embryo using an inverted microscope with 20X magnification (Nikon,Diaphot, Tokyo, Japan), a micro-blade fixed to a micromanipulator was gently pressed against the middle of the embryo so that trophectoderm and inner cell mass cells were evenly distributed on both sides. The micro-blade was slowly moved forward and backward until the embryo was completely bisected and the zona pellucida was removed.   One portion of the bisected blastocyst (the smaller or less intact portion if bisection was not uniform) was directly placed into a 0.2 ml tube containing 50 µl of RNAlater (Invitrogen, Carlsbad, CA, USA) and stored at -80°C until RNA-seq analysis.  The other demi-embryo was placed into a 25 µl drop of SOF-BE2 covered in mineral oil and maintained inside an incubator at 38.5o C in a humidified atmosphere of 5% O2, 5% CO2 and 90% N2) for 30 min for re-establishment of the blastocoele after bisection. The demi-embryo was then placed into a plate containing embryo transfer medium (BO-Transfer, IVF Bioscience), loaded into a 0.25 ml embryo transfer straw, and transported to the farm in a portable incubator at 38.5°C (Micro Q Technologies).  The embryo was the transferred into a heifer recipient.

tag: breed

value: Holstein heifers

tag: pregnancy status

value: Pregnant at 30 and 60 days of gestation

value: Demi-blastocyst containing trophectoderm and inner cell mass cells


title: PP_InVivo_2


title: PP_InVivo_3


title: T47D_RES_CL2.4

description:
biological replicate 1
T47D_RES_CL2-4_CCGTCC


title: PP_InVivo_1


title: GH_P_241_14_CAGATC_L005

city: Beltsville

first: Arvind

middle: A

last: Bhagwat

state: MD

address: 10300 Baltimore Avenue

department: ARS, NEA, BARC, EMFSL

institute: United States Department of Agriculture

data_processing:
Illumina RealTime Analysis Software, version 2 was used for basecalling.
Raw data were inspected with the quality control tool, FastQC [http://www.bioinformatics.babraham.ac.uk/projects/fastqc/].
The reads were aligned to the reference  using BWA 0.6.2 aln [Bioinformatics, 25, 1754-1760, (2009)] with a parameter for read trimming of 30 and default parameters otherwise.
Gene expression was caculated using the Partek Genomics Suite 6.6 RNA-Seq Workflow (Partek Inc., St. Louis, MO, USA; http://www.partek.com) and normalized using reads per kilobase of exon model per million mapped reads, RPKM.
Genes with RPKM values less than 5.0 across all samples were filtered, and then the RPKM values were then log base 2 transformed.
Genome_build: NC_016810, S. enterica subsp. enterica serovar Typhimurium SL1344 complete genome; NC_017718, plasmid pCol1B9_SL1344 complete sequence; NC_017719, plasmid pRSF1010_SL1344 complete sequence; and NC_017720, plasmid pSLT_S1344 complete sequence
Supplementary_files_format_and_content: The file aabhagwatprocessed.txt has the format tab-delimited text and contains the filtered and transformed data for the samples in columns and genes in rows.

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: Salmonella enterica serovar strain SG111 with plasmid pBK16

growth_protocol: Salmonella enterica serovar strain SL1344, its opgGH mutant and plasmid borne (opgGH) complemented strains (pBK16) [Microbiology 155, 229-237 (2009); Arch Microbiol. 192, 167-174 (2010)] were streaked on LB agar plates from freezer stocks, and a single colony was inoculated in LB broth and grown at 37 oC in a shaker incubator for 18-20 h. The medium was supplemented as needed with antibiotics at the following concentrations: ampicillin (100 µg ml-1), kanamycin (50 µg ml-1), nalidixic acid (10 µg ml-1).  Osmolarity of growth media was measured with Wescor vapor pressure osmometer (model 5500, Wescor, Inc., Logan UT).

extract_protocol:
RNA was isolated from  Salmonella cells from swarm edges, 7 h from the time cells were spotted on swarm agar plates. Cells were suspended in RNA stabilization reagent [J. Microbiol. Methods 55, 399-409 (2003)] and stored at -70 0 C till proceeding for RNA isolation.  Cells were suspended in hot TRIzol RNA isolation reagent (LifeTechnologies, Carlsbad, CA) and processed for RNA isolation as described [Microbiol Discov. 2013; 1:10. http://dx.doi.org/10.7243/2052-6180-1-10]. RNA was treated with DNase three times (twice on column and once in solution) and DNA contamination was checked by PCR using primers against rpoD and 16S RNA genes.
The messenger RNA population from all RNA samples was enriched by depleting rRNA sequences and strand-specific libraries were constructed as described earlier [Adv Microbiol 4, 25-32 (2014); Arch Microbiol 198, 353-362 (2016)].  Briefly, starting with 8 - 50 ng rRNA-depleted RNA, random-primed cDNA synthesis was done using ScriptSeq v2 RNA-Seq library preparation kit (Epicenter, WI).  cDNA was purified using Agencourt AMPure XP system (BeckmanCoulter, NJ). Libraries were amplified using FailSafe PCR enzyme kit (Epicenter, WI). Typically 12 (50-100 ng starting RNA) or 15 (8 ng starting RNA) PCR cycles were used and reverse primer from the kit was replaced with one of the ScriptSeq Index primers.  After PCR amplification, libraries were purified and size selected (~280 bp) using the Agencourt AMPure XP system (BeckmanCoulter, NJ). Profiles of library insert sizes were verified on the Experion microfluidic platform using 1K DNA chip (Bio-Rad Laboratories, CA).

tag: strain

value: opgGH mutant with pBK16 plasmid


title: GH_P_241_15_GATCAG_L005


title: NP_InVivo_16

source_name: Not pregnant at 30 days of gestation_demi-blastocyst

value: Not pregnant at 30 days of gestation


title: GH_P_241_13_CGATGT_L005


title: GH_243_6_CTTGTA_L005

source_name: Salmonella enterica serovar strain SG111

value: opgGH mutant


title: PFC_mix_H3K36me3_1k_R1

tag: age

value: 10 weeks


title: NP_InVivo_14


title: NP_InVivo_13


title: GH_243_4_TAGCTT_L005


title: NP_InVivo_11


title: NP_InVivo_9


title: NP_InVivo_10


title: NP_InVivo_4


title: NP_InVivo_5


title: NP_InVivo_6


title: NP_InVivo_1


title: NP_InVivo_3


title: NP_InVivo_8


title: PP_8

source_name: Demi-blastocyst containing trophectoderm and inner cell mass cells

extract_protocol:
Total RNA from each sample was isolated using the RNeasy Micro Kit (Qiagen, Germantown, MD, USA) according to the manufacture’s cell protocol with the following adjustments for samples maintained in RNAlater; 250 µl of 100% ethanol was used instead of the recommended 350 µL of 70% (v/v) ethanol and isolated RNA was eluted in 12 µl RNase-free water instead of the recommended 22 µl RNase-free water.
Barcoded fragment libraries were constructed using the Bovine Custom Any Deplete Ovation SoLo RNA-Seq System from NuGEN (San Carlos, CA, USA) following the manufacturer’s protocol.

treatment_protocol: Blastocysts collected on day 7 of culture were transferred individually into 50 µl drops of embryo biopsy medium (BO-biopsy, IVF Bioscience) placed on the surface of an epoxy-printed well slide to which scratches were made manually in the glass with an 18 gauge needle. Scratches were made to assist in stabilization of the embryo during the biopsy procedure. While visualizing the embryo using an inverted microscope with 20X magnification (Nikon,Diaphot, Tokyo, Japan), a micro-blade fixed to a micromanipulator was gently pressed against the middle of the embryo so that trophectoderm (TE) and inner cell mass (ICM) cells were evenly distributed on both sides (Figure 4A and B). The micro-blade was slowly moved forward and backward until the embryo was completely bisected and the zona pellucida was removed. One portion of the bisected blastocyst (the smaller or less intact portion if bisection was not uniform) was directly placed into a 0.2 ml tube containing 50 µl of RNAlater (Invitrogen, Carlsbad, CA, USA) and stored at -80°C until RNA-seq analysis.  The other demi-embryo was placed into a 25 µl drop of SOF-BE2 covered in mineral oil and maintained inside an incubator at 38.5o C in a humidified atmosphere of 5% O2, 5% CO2 and 90% N2) for 30 min for re-establishment of the blastocoele after bisection. The demi-embryo was then placed into a plate containing embryo transfer medium (BO-Transfer, IVF Bioscience), loaded into a 0.25 ml embryo transfer straw, and transported to the farm in a portable incubator at 38.5°C (Micro Q Technologies).

tag: treatment during culture

value: Vehicle


title: PP_9

value: CSF2 (10ng/ml)


title: PP_10


title: GH_243_5_GGCTAC_L005


title: PP_4


title: PP_1


title: PP_7


title: WT_3_ACAGTG_L005

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

source_name: Salmonella enterica serovar strain SL1344

value: wild type


title: PP_3


title: PP_2


title: WT_1_ATCACG_L005


title: WT_2_TGACCA_L005


title: NP_InVivo_12


title: NP_InVivo_15


title: PNP_5

value: Pregnancy lost between 30 and 60 days of gestation


title: PP_5


title: Cbln2-EGFP-Rpl10a-NIDA172 IP Rep4

data_processing:
FASTX Toolkit 0.0.13 was used to assess the quality of reads and trim trailing adaptors.
Trimmed reads were aligned to annotated exons using the mm10 genome using STAR v2.0.0e_r291 using default settings.
Raw counts of mapped reads were generated with HTSeq framework v0.6.0 using the htseq-count module with the "union" mode and default settings.
Genome_build: mm10
Supplementary_files_format_and_content: Text files of counts

source_name: Rostral pons

extract_protocol:
The rostral pons was dissected and homogenized and tagged polysomes were immunopurified with monoclonal anti-EGFP antibodies bound to biotinylated-Protein L (Thermo Fisher) coated streptavidin-conjugated magnetic beads (Life Technologies). Total RNA from IPs was purified with the Agilent Nanoprep kit following manufacturer's protocol.
Ribosomal-bound RNA was extracted and treated as described in PMID 24810037, Heiman M, Kulicke R, Fenster RJ, Greengard P, Heintz N. (2014) Cell type-specific mRNA purification by translating ribosome affinity purification (TRAP). Nat Protoc. 9:1282-1291

tag: molecule

value: Ribosomal-bound RNA

tag: animal line

value: Cbln2-TRAP NIDA172

value: Immunopurified (IP)


title: PNP_3


title: PP_6


title: PNP_2


title: Cbln2-EGFP-Rpl10a-NIDA172 IP Rep3


title: PNP_4


title: Cbln2-EGFP-Rpl10a-NIDA172 IP Rep1


title: TG 5

city: Paris

first: Noémie

last: Robil

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

institute: GenoSplice technology

description:
Right eye
Processed data file: Deseq2_normalized_gene_expression_with_annotations.txt

data_processing:
Sequencing, data quality, reads repartition (e.g., for potential ribosomal contamination), and insert size estimation were performed using FastQC, Picard-Tools, Samtools and rseqc.
Reads were mapped using STAR_2.4.0.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Deseq2_normalized_gene_expression_with_annotations.txt: Tab-delimited text file includes deseq2 normalized expression values for each gene and for each sample. Annotations from Human FAST DB v2016_1 were also provided.

source_name: Retina, human transferrin

extract_protocol:
Retinas (n=4 per group) were frozen immediately after isolation. Total RNA was extracted using Precellys Homogenizer (Ozyme, Bertin) and RNeasy Mini Kit (Qiagen).
TruSeq mRNA stranded (llumina).
PolyA selected, RT, EndRepair, A tailing, Adapter ligation (Illumina).

treatment_protocol: Induction of retinal detachment by subretinal injection of sodium hyaluronate (10µl).

tag: strain/background

tag: genotype/variation

value: expressing human transferrin

tag: gender

value: Male

tag: tissue

value: Retina

tag: treatment

value: Retinal detachment

tag: time

value: 4 days after retinal detachment


title: Cbln2-EGFP-Rpl10a-NIDA172 IP Rep2

first: Laura

address: 1230 York Avenue # 260


title: NP_29


title: PNP_1


title: TG 2

description:
Left eye
Processed data file: Deseq2_normalized_gene_expression_with_annotations.txt


title: NP_27


title: NP_26


title: PNP_6


title: WT 7

source_name: Retina, WT

value: WT

value: Female


title: WT 4


title: NP_28

value: Not pregnant at 30 days of gestation


title: TG 6


title: TG 8


title: WT 3


title: NP_23


title: NP_24


title: NP_25


title: NP_22


title: NP_21


title: D0-58

description:
Sample 38
Venous blood
Langhans giant cells
processed data file: RawCounts.xlsx
processed data file: NormalizedCounts.xlsx

source_name: PBMC

tag: cell type

value: Adherent monocytes

tag: time point

value: Day 0

tag: donor


title: D10-301-M

description:
Sample 35
Venous blood
Langhans giant cells
processed data file: RawCounts.xlsx
processed data file: NormalizedCounts.xlsx

value: Media

value: Day 10


title: WT 5


title: NP_20

value: Vehicle


title: NP_19


title: NP_18


title: piPSC.C2: Epi-piPSC-FL6i_2

city: Columbia

first: Toshihiko

last: Ezashi

state: MO

address: 240a CS Bond Life Sciences Center

department: Animal Sciences

institute: University of Missouri-Columbia

data_processing:
50 bp long, paired end sequencing reads were trimmed for bases with base quality score less than 20.
Trimmed high quality sequencing reads were aligned to the Sus scrofa assembly of the pig genome using TopHat2 (v2.1.0).
Transcript abundances were estimated and differentially expressed transcripts were detected by DESeq2.
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: tab-delimited text file including a normalized count matrix for all samples

organism: Sus scrofa

source_name: piPSC generated with episomal plasmids in the FL6i supplemented medium_2 [iPSC11p11]

growth_protocol: The pESCLC-primary from porcine blastocysts were maintained F condition (pESCLC-F) and some of the pESCLC-F cells were transferred to the FL6i culture condition (pESCLC-FL6i) at culture day 8. Later at culture day 18, some of the pESCLC-FL6i cells were transferred to the FLB2i culture condition (pESCLC-FLB2i).

extract_protocol:
RNAs were extracted with STAT60 (Tel-Test) and 1-bromo-3-chloro-propane (Sigma).
Libraries were constructed following the manufacturer’s protocol with reagents supplied in Illumina’s TruSeq mRNA stranded sample preparation kit.

treatment_protocol: Porcine fetal fibroblasts were reprogrammed with nonintegrating episomal vectors (Addgene #27077, 27078 and 27079). A following day, the transfected cells were placed into three 10 cm dishes previously plated with irradiated mouse embryonic fibroblasts. Next day the culture medium was switched to NHSM basal medium with FGF2 and LIF (FL condition in the 1st dish), FLB2i medium in the 2nd dish and FL6i medium in the 3rd dish. 17-day post transfection, emerged independent colonies were mechanically isolated from the dishes and expanded. A total of two iPSC lines in FL, four lines in FLB2i and eight lines in FL6i conditions were established, respectively. After day 40, all of colonies in FL condition were gradually differentiated in the extended cultivation, Epi-piPSC in FL condition has not been included inthe study.

value: piPSC


title: piPSC.C1: Epi-piPSC-FL6i_1

source_name: piPSC generated with episomal plasmids in the FL6i supplemented medium_1 [iPSC10p12]


title: piPSC.B2: Epi-piPSC-FLB2i_2

source_name: piPSC generated with episomal plasmids in the FLB2i supplemented medium_2 [iPSB5p12]


title: ID6_FGF2.A3: Lv-piPSC-F_2

source_name: lentiviral reprogrammed piPSC grown in F supplemented medium_2 [M1690-A-3-p46]

value: lentiviral reprogrammed piPSC


title: C. elegans_indole 1.0 mM

city: Gyeongsan-Si

first: Jintae

last: Lee

state: Gyeongsangbuk-Do

address: 214-1 Daedong

department: Chemical engineering

country: South Korea

institute: Yeungnam University

hyb_protocol: The fragmented cRNA was resuspended with 2X hybridization buffer and directly pipetted onto assembled Agilent C. elegans (V2) Gene Expression 4X 44K Microarray. The arrays hybridized at 65 oC for 17 h using Agilent Hybridization oven (Agilent Technologies). The hybridized microarrays were washed as the manufacturer’s washing protocol (Agilent Technologies).

scan_protocol: The hybridization images were analyzed by Agilent DNA microarray Scanner (Agilent Technologies, USA).

data_processing: The data quantification was performed using Agilent Feature Extraction software 10.7 (Agilent Technologies, USA). The average fluorescence intensity for each spot was calculated and local background was subtracted.

organism: Caenorhabditis elegans

source_name: worms

label_protocol: For each RNA, the synthesis of target cRNA probes and hybridization were performed using Agilent’s LowInput QuickAmp Labeling Kit (Agilent Technologies) according to the manufacturer’s instructions. Briefly, each 25 ng total RNA and T7 promoter primer mix were incubated at 65 oC for 10 min. cDNA master mix (5X First strand buffer, 0.1M DTT, 10 mM dNTP mix, RNase-Out, and MMLV-RT) was prepared and added to the reaction mixture. The samples were incubated at 40 oC for 2 hours and then the RT and dsDNA synthesis was terminated by incubating at 70 oC for 10 min. The transcription master mix was prepared as the manufacturer’s protocol (4X Transcription buffer, 0.1M DTT, NTP mix, 50% PEG, RNase-Out, Inorganic pyrophosphatase, T7-RNA polymerase, and Cyanine 3-CTP). Transcription of dsDNA was performed by adding the transcription master mix to the dsDNA reaction samples and incubating at 40 oC for 2 hours. Amplified and labeled cRNA was purified on RNase mini column (Qiagen) according to the manufacturer’s protocol. Labeled cRNA target was quantified using ND-1000 spectrophotometer (NanoDrop Technologies, USA). After checking labeling efficiency, each 1650 ng of cyanine 3-labeled cRNA target was carried out the fragmentation of cRNA was performed by adding 10X blocking agent and 25X fragmentation buffer and incubating at 60 oC for 30 min.

growth_protocol: For transcriptional analysis, C. elegans worms (fer-15;fem-1) were scraped from 8 petri dishes  (90 mm plate) and synchronized. Synchronized eggs were incubated for 24 hrs with rotation at 6 rpm at 25oC in M9 buffer. Hatched worms were cultivated in 30 mL of S basal medium in shaking flasks for 24 hrs at 20oC with E. coli OP50 cells which were grown in LB for 24 hrs at 37oC with 180 rpm shaking as food.

extract_protocol:
Worms were separated from E. coli OP50 roughly by standing 15-20 min at room-temperature and worms were harvested by centrifugation at 16,600 g for 10 min. Collected worms were immediately mixed with 1 mL of TRI reagent (Sigma, T9424)
Snap-frozen until RNA was isolated using  a Qiagen RNeasy mini Kit (Valencia, CA, USA).

treatment_protocol: Worms were washed with 30 mL of S basal medium and worms were counted by microscope. About 50,000 worms in 10 mL were exposed to indole (0, 0.1, 0.5, or 1.0 mM) at 20oC for 12 hrs with 180 rpm shaking and, 25 ml overnight cultured E. coli BW25113 tnaA mutant cells were spun and added in the incubation mixture as food.

value: indole 1.0 mM


title: piPSC.B1: Epi-piPSC-FLB2i_1

source_name: piPSC generated with episomal plasmids in the FLB2i supplemented medium_1 [iPSB5p9]


title: NP_16


title: pESC.C2: pESCLC-FL6i_2

source_name: pESCLC grown in the FL6i supplemented medium_2 [PESC2p9]

value: pESCLC


title: ID6_FGF2: Lv-piPSC-F_1

source_name: lentiviral reprogrammed piPSC grown in F supplemented medium_1 [ID6_FGF2]


title: C. elegans_indole 0.5 mM

value: indole 0.5 mM


title: NP_17


title: NP_15


title: pESC.B2: pESCLC-FLB2i_2

source_name: pESCLC grown in the FLB2i supplemented medium_2 [PESB1p6]


title: pESC.B1: pESCLC-FLB2i_1

source_name: pESCLC grown in the FLB2i supplemented medium_1 [PESB1p3]


title: NP_14


title: pESC.C1: pESCLC-FL6i_1

source_name: pESCLC grown in the FL6i supplemented medium_1 [PESC2p3]


title: NP_13

source_name: Demi-blastocyst containing trophectoderm and inner cell mass cells


title: pESC.A2: pESCLC-F_2

description: pESCLC grown in F supplemented medium

source_name: porcine embryonic stem cell (pESC) like cells (pESCLC) grown in FGF2 (F) supplemented medium_2 [PESA2p2]


title: NP_11


title: NP_12

value: CSF2 (10ng/ml)


title: pESC.A1: pESCLC-F_1

description: pESCLC grown in F supplemented medium

source_name: porcine embryonic stem cell (pESC) like cells (pESCLC) grown in FGF2 (F) supplemented medium_1 [PESA1p2]


title: C. elegans_indole 0.1 mM

value: indole 0.1 mM


title: NP_10


title: pESC.P2: pESCLC-primary_2

description: inner cell mass outgrowths from porcine blastocyst

source_name: porcine embryonic primary cells_2 [PES_primary_2]

value: porcine embryonic primary cells


title: pESC.P1: pESCLC-primary_1

source_name: porcine embryonic primary cells_1 [PES_primary_1]


title: NP_8


title: NP_9


title: NP_7


title: s60B-6h-1

city: Chengde

first: Guangcheng

last: Xie

state: Hebei Province

address: Anyuan Road, Shuangqiao District

institute: Chengde Medical University

data_processing:
Basecalls performed using  Solexa pipeline v1.8
The trimmed reads (trimmed 5’,3’-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 (2.0.5)software
The transcript abundances for each sample was estimated with StringTie（1.3.1c）
the FPKM value for gene and transcript level were calculated with R package Ballgown (v2.6.0)
The mRNA reads were aligned to reference genome using STAR(2.5.2b)detecting backesplicec junction reads with CIRCexplore2 (2.2.6)
Genome_build: hg19

source_name: human tonsillar epithelial cells

extract_protocol:
RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis
Total RNA of each sample was used to prepare the RNA sequencing library 1)RNA fragment；2)Random primed first strand cDNA synthesis；3)dUTP based second strand cDNA synthesis;4)Adaptor ligation and PCR amplification.

value: Tonsillar epithelium-drived tonsillar epithelial cell lines

tag: passages

value: human tonsillar


title: s60B-6h-3


title: NP_5


title: NP_6


title: NP_4


title: s60B-mock-3


title: s60B-6h-2


title: human lymphocyte- after activate-2

city: Fukuoka

first: Akiko

last: Fujimura

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

department: Department of Cancer Therapy and Research

institute: Graduate School of Medical Sciences Kyushu University

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Human Gene Expression Microarray 8x60K v2; Agilent Technologies) according to the manufacturer's instructions.

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

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

source_name: human lymphocyte after activate, healthy volunteer #2

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

extract_protocol: Total RNA was isolated from tissues using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega)

tag: cell

value: lymphocytes


title: s60B-mock-2


title: human lymphocyte- after activate-1

source_name: human lymphocyte after activate, healthy volunteer #1


title: human lymphocyte- before activate-1

source_name: human lymphocyte before activate, healthy volunteer #1


title: NP_2

tag: pregnancy status

value: Not pregnant at 30 days of gestation


title: NP_1


title: s60B-mock-1


title: NP_3


title: m6A-seq replicate1

city: Ithaca

first: Ji

last: Wan

address: 303 Biotech 526 Campus Road

institute: Cornell University

data_processing:
Sequencing reads were mapped to genome and ENsembl genes by STAR
P-site of ribosome protected fragment (RPF) (13th nt) was extracted
Genome_build: GRCH38
Supplementary_files_format_and_content: ribosome occupancy file of Ensembl mRNAs (according to psite of RPF)

extract_protocol:
Rnase I Digestion, RNA dephosphorylation, Size Selection
Poly-A Tailing, cDNA synthesis, Size selection, circularization, DNA precipitation, Linearization, PCR amplification

treatment_protocol: cycloheximide for 3 mins (100 ug/ml)

tag: cell line

value: control


title: RIP-seq with YTHDF1 antibody

description:
S19D0349_S6_L003
processed data file: RIP_profile.txt

source_name: RIP-seq with YTHDF1 antibody

tag: rip antibody

value: YTHDF1 antibody (Proteintech, 17479-1-AP, 00074471)


title: mRNA-seq from whole cell lysate

description:
S19D0348_S5_L003
input

source_name: mRNA-seq from whole cell lysate


title: mRNA-seq after YTHDF1 knockdown with shY1-2

description:
S18H0271.R1.fq.gz
processed data file: indiviual_ribosome_rna_profile.txt

value: YTHDF1 knockdown with shY1


title: mRNA-seq fom control cells

description:
S18H0269.R1.fq.gz
processed data file: indiviual_ribosome_rna_profile.txt

source_name: mRNA-seq fom control cells


title: mRNA-seq after YTHDF1 knockdown with shY1-1

description:
S18H0270.R1.fq.gz
processed data file: indiviual_ribosome_rna_profile.txt


title: Ribo-seq fom control cells

description:
C_S20_L005
processed data file: indiviual_ribosome_rna_profile.txt

source_name: Ribo-seq fom control cells


title: Ribo-seq after YTHDF1 knockdown with shY1-2

description:
Y-4_S19_L005
processed data file: indiviual_ribosome_rna_profile.txt


title: C. elegans_indole control

source_name: worms

value: indole control


title: Ribo-seq after YTHDF1 knockdown with shY1-1


title: m6A-seq replicate2


title: hSVP Exosomes-Donor 7

city: Philadelphia

first: Sezin

last: Aday

state: Pennsylvania

address: 210 South 33rd Street, Skirkanich Hall

institute: University of Pennsylvania

description: Exosomes isolated from hSVP

data_processing:
Immediately after a run,threshoulds were determined and data was analyzed using the QuantStudio™ 6 Flex Software. Spike-in control values were checked to determine the accuracy of RNA isolation and cDNA reaction. If a miRNA is expressed (i.e. Ct<40) in all donors of a group, it was considered as a valid miRNA for the comparison.
Different hSVP exosomes were compared to check whether they express a certain miRNA or not. If a miRNA had Ct value <40, it was considered as an epresseed miRNA in the hSVP exosomes..

label: SYBR Green

source_name: Human saphenous vein pericytes

label_protocol: A synthetic analog of the non-human Caenorhabditis elegans microRNA-39 (cel-miR-39; Qiagen, Hilden, Germany) was spiked in (10 μl of a 5 fmol/μl stock) to normalize RNA extraction efficiency. cDNA synthesis and real-time qPCR was performed using the miRCURY LNA™ Universal RT microRNA PCR system (Exiqon, Denmark). The cDNA products were transferred to the microRNA PCR Human Panels (I + II; version 3) and run using QuantStudio 6 Flex Real-Time PCR System (Applied Biosystems, Foster City, CA, USA).

growth_protocol: Human saphenous vein pericytes (hSVPs) were cultured on 0.5% gelatin+20 µg/mL fibronectin coated plates in EGM-2 (Lonza). After the attachment of the cells, the medium was replaced by EGM-2 (without SingleQuot FBS; Lonza, Basel, Switzerland) containing 2% exosome-depleted FBS from Gibco (Waltham, MA, USA) and cells were put into hypoxia incubator (2% O2). The conditioned media were collected from the confluent pericyte cultures every 3 days and centrifuged at 300 × g for 10 minutes to remove cells. Then, supernatant was transferred into a new centrifuge tube and spun at 16,000 × g for 30 minutes to remove any remaining cell debris. The supernatant was transferred into a new falcon and kept at -80 °C until use. On the day of the isolation, supernatants were thawed on ice and then, exosome isolation was performed using Exo-SpinTM columns from Cell Guidance Systems (Cambridge, UK) according to the manufacturer’s instructions.

extract_protocol: Total RNA was extracted from isolated exosomes using the miRNeasy Mini Kit (Qiagen, Hilden, Germany), according to the manufacturer’s instructions.

treatment_protocol: Human saphenous vein pericytes were cultured under hypoxia (2% O2) and the exosomes were isolated from cell media using Exo-SpinTM columns from Cell Guidance Systems (Cambridge, UK).

tag: passage number


title: hSVP Exosomes-Donor 8

description: Exosomes isolated from hSVP


title: VSV-IP

status: Public on Aug 30 2019

city: Guangzhou

first: Xin

last: Jia

state: Guangdong

address: 135 XinGangXi Road

department: College of Life Sciences

institute: Sun Yat-sen University

description: co-immunoprecipitated RNAs

data_processing:
Illumina Bcl2FastQ  software used for basecalling.
Adaptor and low-quality bases were trimmed with Trimmomatictools(version:0.36), and the clean reads undergone rRNA deleting through RNAcentral to get effective reads.Genomic alignment (hg19 from UCSC genome browser) was using Tophat(version:2.0.13)to get uniquely mapping reads.
RIPseekre(version 1.18.0) was employed to perform peak calling.Then using Hommer(version:4.8) to annotate  the Peaks.The nucleotides in Peaks region were used for detection of the consensus motif by DREME (version:  4.11.1) and MEME(version:4.11.1). Motif central enrichment was performed by CentriMo (version:4.11.1).  Differential peak enrichment was determined by Pyicoenrich(version:2.0.7).
Genome_build: hg19
Supplementary_files_format_and_content: files include RPKM values for each Sample

source_name: A549 Cells with VSV infection

growth_protocol: The A549 cells were purchased from ATCC and  cultured in endotoxin-free DMEM (GIBCO), supplemented with 10% FBS (GIBCO) and 1% penicillin-streptomycin (GIBCO).

extract_protocol:
A549 cells were infected for 8 hrs and the total RNAs of input and co-immunoprecipitated RNAs of ZNFX1 were extracted by Trizol.
cDNA libraries were prepared using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina (ENB, USA). Libraries were sequenced on the Hiseq X Ten following the manufacturer's protocols.

value: A549 epithelial cells

tag: agent

value: vesicular stomatitis virus (VSV)


title: WGBS_SKN_3

city: Santiago de Compostela

first: Carmen

last: Rivas

address: Avda Barcelona

department: CIMUS

country: Spain

institute: Universidad de Santiago de Compostela

data_processing:
Raw ChIP sequencing reads were aligned using BWA version 0.7.17 with default parameters. After alignment, we sorted the bam files using samtools, then igvtools was used to generate wig files (igvtools count -w 25 -e 200). Finally, bigWig files were obtained using wigToBigWig.
Raw RNA sequencing reads were aligned using STAR version 2.5.3a with default parameters. The bigWig files were generated similarly as ChIP-seq.
Raw reads from whole-genome bisulfite sequencing were aligned using BWA (version 0.6.1). Low-quality sequence at the 3′ ends were trimmed. After alignment, we filtered duplicated or poorly mapping reads (>2% mismatches or aberrant insert size). Samtools (version 0.1.18) in mpileup mode was applied to call CpG methylation. We used igvtools to generate the tdf files.
Genome_build: hg19, mm10 and dm6 for human, mouse and drosophila data, respectively
Supplementary_files_format_and_content: bigWig, tdf

source_name: SKN-3 cells

growth_protocol: SKN-3 cells were cultured in Dulbecco's modified Eagles' medium (DMEM, Invitrogen) with 10% fetal bovine serum (FBS, Sigma).

extract_protocol:
DNA was extracted from flash frozen cell pelets of about 5 million cells using DNeasy Blood & Tissue Kit from QIAGEN Cat. #69509
NxSeq AmpFREE Low DNA Library Kit (Lucigen). Samples were then bisulfite converted using the EZ-DNA Methylation Gold Kit (Zymo Research). DNA was amplified by 9 cycles of PCR using the Kapa Hifi Uracil + DNA polymerase (KAPA Biosystems).

value: Patient-derived head and neck squamous cell carcinoma cell line

tag: genotype

value: NSD1 mutant


title: VSV-input

description: total RNA


title: WGBS_Fadu

source_name: Fadu cells

growth_protocol: Fadu cells were cultured in Dulbecco's modified Eagles' medium (DMEM, Invitrogen) with 10% fetal bovine serum (FBS, Sigma).

extract_protocol:
DNA was extracted from flash frozen cell pelets of about 5 million cells using DNeasy Blood & Tissue Kit from QIAGEN Cat. #69507
NxSeq AmpFREE Low DNA Library Kit (Lucigen). Samples were then bisulfite converted using the EZ-DNA Methylation Gold Kit (Zymo Research). DNA was amplified by 9 cycles of PCR using the Kapa Hifi Uracil + DNA polymerase (KAPA Biosystems).

value: Fadu

value: NSD1 wild-type


title: WGBS_Cal27

source_name: Cal 27 cells

growth_protocol: Cal27 cells were cultured in Dulbecco's modified Eagles' medium (DMEM, Invitrogen) with 10% fetal bovine serum (FBS, Sigma).

extract_protocol:
DNA was extracted from flash frozen cell pelets of about 5 million cells using DNeasy Blood & Tissue Kit from QIAGEN Cat. #69506
NxSeq AmpFREE Low DNA Library Kit (Lucigen). Samples were then bisulfite converted using the EZ-DNA Methylation Gold Kit (Zymo Research). DNA was amplified by 9 cycles of PCR using the Kapa Hifi Uracil + DNA polymerase (KAPA Biosystems).


title: WGBS_SCC_4

source_name: SCC-4 cells

growth_protocol: SCC-4 cells were cultured in DMEM:F12 medium (Invitrogen) with 10% fetal bovine serum (Sigma) and 400 ng/ml hydrocortisone (Sigma).

extract_protocol:
DNA was extracted from flash frozen cell pelets of about 5 million cells using DNeasy Blood & Tissue Kit from QIAGEN Cat. #69508
NxSeq AmpFREE Low DNA Library Kit (Lucigen). Samples were then bisulfite converted using the EZ-DNA Methylation Gold Kit (Zymo Research). DNA was amplified by 9 cycles of PCR using the Kapa Hifi Uracil + DNA polymerase (KAPA Biosystems).