title: N7-2_Normal-MatureLuminal_10 nM E2_24 hours_13-89MLE2-DC1219_RNA-seq

description: mRNA-seq

value: normal mature luminal cells

value: ER+

tag: her2 status

tag: age

value: 12 nM E2

value: 26 hours


title: SLX-14710.i703_i507

status: Public on May 27 2019

type: SRA

city: Dresden

first: Meritxell

last: Huch

address: Pfotenhauerstrasse 108

country: Germany

institute: Max Planck Institute of Molecular Cell Biology and Genetics

library_source: transcriptomic

data_processing:
Download ERCC sequences from Thermofisher (https://assets.thermofisher.com/TFS-Assets/LSG/manuals/cms_095047.txt) and append them to mouse genome
Create star index using STAR 2.6.0c. Command: `~/bin/STAR --runThreadN 10 --runMode genomeGenerate --genomeDir /ssd/rulands/Genomes/Mouse/GRCm38_ERCC/star_index_overhang49 --genomeFastaFiles /ssd/rulands/Genomes/Mouse/GRCm38_ERCC/GRCm38.p6.all.ERCC.fa --sjdbGTFfile /ssd/rulands/Genomes/Mouse/GRCm38_ERCC/Mus_musculus.GRCm38.93.ERCC.gtf --sjdbOverhang 49`
Perform alignment using STAR 2.6.0c. Command: `~/bin/STAR --runThreadN 10 --genomeDir /ssd/rulands/Genomes/Mouse/GRCm38_ERCC/star_index_overhang49/ --readFilesIn /scratch/rulands/Liver_Embryo_Meri_Huch/fastq --readFilesCommand zcat --outFileNamePrefix /scratch/rulands/Liver_Embryo_Meri_Huch/aligned_reads/ --outSAMtype BAM SortedByCoordinate --sjdbGTFfile /ssd/rulands/Genomes/Mouse/GRCm38_ERCC/Mus_musculus.GRCm38.93.ERCC.gtf`
Generate count matrix using subread 1.6.2. Command: `~/bin/subread-1.6.2-Linux-x86_64/bin/featureCounts -T 10 -t exon -g gene_id -a /ssd/rulands/Genomes/Mouse/GRCm38_ERCC/Mus_musculus.GRCm38.93.ERCC.gtf -Q 30 -o counts.csv *.bam`; sed 1d counts.csv | cut -f1,7- | sed s/Geneid/id/ > counts_final_ercc.txt
Reading count matrix from `counts_final_ercc.txt` and metadata into scanpy 1.3.3 (code will be available on https://github.com/fabianrost84/prior_et_al_2019.git upon publication)
Quality control on cells (code will be available on https://github.com/fabianrost84/prior_et_al_2019.git upon publication)
Normalisation using scran (code will be available on https://github.com/fabianrost84/prior_et_al_2019.git upon publication)
Batch effect correction using mnn_correct (code will be available on https://github.com/fabianrost84/prior_et_al_2019.git upon publication)
Genome_build: Ensemble GRCm38, release 93
Supplementary_files_format_and_content: raw count and normalized counts

molecule: total RNA

organism: Mus musculus

extract_protocol:
E10.5 and E13.5 mouse livers were collected, digested into single cells and sorted by FACS to isolate Lgr5-GFP positive cells or bulk liver cells from each timepoint.
The Illumina Nextera XT DNA preparation kit (FC-131-1096) was used to prepare libraries.

tag: strain background

value: male Lgr5-EGFP-IRES-creERT2 mice maintained on a C57BL/6 background, mated with MF1 female

tag: embryonic day

tag: cell type

value: liver hepatoblast cells

tag: sorting

value: Bulk


title: SLX-14710.i703_i508


title: N7-2_Normal-MatureLuminal_Vehicle_24 hours_13-89MLveh-DC1219_RNA-seq

city: Chicago

first: Hari

last: Singhal

state: IL

address: 929 E 57th St

department: Ben May Department for Cancer Research

country: USA

institute: University of Chicago

description: mRNA-seq

data_processing:
VIPER pipeline at CFCE, DFCI was used to perform RNA-seq analyses. The FASTQ files were filtered and good quality reads were groomed and subsequently aligned to HG19 genome build using STAR.
Relative expression of transcripts were calculated by subjecting STAR output (BAM files) to Cufflinks package.
Cufflinks assemblies obtained from Cufflinks package were merged using cuffmerge. For every model system, cufflink assemblies of each of the treatments were merged with the cufflinks assemblies of the respective vehicle-treated samples.
The output from Cuffmerge along with the corresponding TopHat output (BAM files) were subjected to Cuffdiff to calculate transcript expression.
Genes that were up or down regulated by at least two fold were used for downstream analyses.
Genome_build: HG19
Supplementary_files_format_and_content: Readcount matrix containing expression levels of genes in each of the samples is provided

molecule: polyA RNA

organism: Homo sapiens

source_name: Sorted mature luminal cells

growth_protocol:
Histologically confirmed normal breast samples were obtained from reduction mammoplasty specimens, where family history is generally not known, through the Pathology Departments of the Brigham and Women’s Hospital and Beth Israel Deaconess Medical Center. These breast specimens are in excess of normal diagnostic requirements, hence are normally discarded and are completely de-identified except for patient age. The tissue is collected under the Dana-Farber/Harvard Cancer Center (DF/HCC) institutional review board (IRB)-approved protocol 10-458.
Primary breast tumors were obtained from cancer surgery specimens through the Pathology Department of the Dana-Farber/Harvard Cancer Center. Any leftover remaining tumor tissue following clinical requirements was made available. The tissue is collected under the Dana-Farber/Harvard Cancer Center (DF/HCC) institutional review board (IRB)-approved protocol 10-458. These specimens are de-identified except for patient age, tumor type, grade/stage, and tumor receptor status (ER/PR/HER2).

extract_protocol:
The tissue was collected fresh and sterile from the operating room and transported on ice to the pathologist in the absence of formalin fixative. Following pathological examination, tissue in excess of diagnostic requirements was collected and subsequently de-identified at the tissue bank. The tissue was then transported on ice to the laboratory. Samples that were collected in the evening were stored in media at 4C overnight. The duration from surgery to the commencement of tissue dissociation did not exceed 24 hrs, the majority of the samples were processed on the same day as surgery.
Fragments of normal ER+ breast tissue were of insufficient cell number to utilize FACS after they were dissociated as described above, so epithelial cell enrichment was performed by utilizing magnetic EasySEP EpCAM beads (StemCell Technologies). Once the cells were washed in cold PBS, the appropriate amount of selection media and magnetic particles was added and incubated on ice for 15 minutes. Next, the tube was placed on the magnet at room temperature for five minutes and eluted with chilled media and this process was repeated for a total of four times to enrich for the ER+/EpCAM+ epithelial tumor cells.
Immuno-labelling of normal cells was performed at 4C using PBS as a buffer and wash solution. Incubating the cell pellet with 0.1 mg/ml DNase, 1 mg/ml rat immunoglobulin and a 1/10 dilution of anti-CD16/CD32 receptor antibody for 10 min. was sufficient to block non-specific antibody binding. The cell suspension was then made up to a final concentration of 106 cells /40 l with dilution buffer. For primary human breast tissue, antibodies directed against human lineage markers CD31 (endothelial cells), CD45 (leukocytes) and CD235a (red blood cells) were used to prepare a Lin- cell population, and these PE-linked antibodies were negatively selected against.
Primary antibodies were added at optimized dilutions and incubated for 25 min at 4C. The suspension was then washed, filtered using 40uM tube cap filters (Falcon) and centrifuged. Cells were resuspended in 0.5 g/ml propidium iodide (Sigma) before cell analysis and sorting to allow for only the selection of viable cells. Cell analysis and sorting was performed on either a FACS DIVA or FACS Aria (BD Biosciences) using a sheath pressure of 30 psi and nozzle size of 70 um. Cells were sorted into polystyrene FACS tubes (Westnet #352063) and collected into a mixture of 50% primary MEC media and 50% CDT. Reanalysis of the sorted populations routinely revealed a purity of more than 95%.

treatment_protocol: Freshly sorted cells were resuspended in cell culture media and treated with either vehicle or estradiol for 24 hours. Post treatment, cells were harvaested and RNA was extracted for further downstream analyses. Finer details are provided in the methods section of the paper.

tag: tissue type

tag: er status

tag: pr status

tag: type

tag: grade

tag: drug treatment

value: 11 nM E2

tag: hormone exposure time

value: 25 hours


title: N7-1_Normal-MatureLuminal_10 nM E2_24 hours_13-89ML_E2_RNA-seq

description: mRNA-seq

value: 10 nM E2

value: 24 hours


title: NEG_8

city: Oulu

first: Antti

last: Haapalainen

address: Aapistie 5A

department: CRC

country: Finland

institute: University of Oulu

description: sequencing was done in 1 lane

data_processing:
The base calling was done using bcl2fastq (v. 2.17)
Read alignment was done using star (2.5.2b) to hg38 human genome reference
Genewise read counts were calculated using subread (v1.5.1)
Genome_build: Human GRCh38
Supplementary_files_format_and_content: files are tab delimited text files containing the genewise read counts for each sample

source_name: HTR-8/Svneo cells

growth_protocol: The HTR-8/Svneo cells were cultured in RPMI 1640 medium supplemented with 10 % fetal bovine serum, 100 U/ml penicillin and 100 mg/ml streptomycin

extract_protocol:
RNA was isolated by RNeasy Micro Kit
Library preparation was done according to Illumina TruSeq® Stranded mRNA Sample Preparation Guide (part # 15031047)

treatment_protocol: The transfection with siRNA was done either with 30-40 nM siRNA pair or 30-40 nM siRNA universal negative control and using approximately 70 000 cells and duoble transfection. The first transfection was done in suspension (30 nM siRNA) and the second transfection in adherent cells (40mM).

tag: cell line

value: trophoblast

tag: tissue

value: placenta

tag: treatment

value: siRNA universal negative control


title: T3-rep2_JG3B-2-20151001-IDX7_RNAseq

description: mRNA-seq

source_name: ER+ breast tumor

value: ER+ breast tumor

value: positive

value: negative

value: ductal

value: II


title: NEG_9

description: sequencing was done in 1 lane


title: NEG_7

description: sequencing was done in 1 lane


title: SLX-14710.i704_i502

source_name: E10.5_liver_Lgr5GFP pos

value: Lgr5GFP pos


title: N7-1_Normal-MatureLuminal_Vehicle_24 hours_13-89ML_veh_RNA-seq

description: mRNA-seq

value: normal mature luminal cells

value: ER+

value: Vehicle


title: N6-2_Normal-MatureLuminal_10 nM E2_24 hours_13-79MLE2-DC1219_S7_R1_RNA-seq

description: mRNA-seq


title: SLX-14710.i703_i503

value: male Lgr5-EGFP-IRES-creERT2 mice maintained on a C57BL/6 background, mated with MF1 female

value: liver hepatoblast cells


title: ROBO1_6

description: sequencing was done in 1 lane

value: silenced with siRNA of ROBO1


title: SLX-14710.i703_i502


title: SLX-14710.i703_i506


title: ROBO1_5

description: sequencing was done in 1 lane


title: SLX-14710.i703_i505


title: SLX-14710.i702_i511

value: Bulk


title: E2Ba/F3-gp130 cells stimulated with 100ng/ml Hyper IL-6 (exon-level)

type: RNA

city: Duesseldorf

first: Birgit

last: Knebel

address: Auf'm Hennekamp 65

department: Cinical Biochemistry and Pathobiochemistry

institute: German Diabetes Center

description: RNA expression value derived from Expression Console software; core-exon analysis

hyb_protocol: Amplified cDNA was hybridized on Affymetrix Mouse Gene ST 1.0 arrays (Affymetrix)

scan_protocol: Detection of probe intensities was performed using a GeneChip scanner 3000 7G (GDAS 1.4 package, Affymetrix).

data_processing: The data were analyzed with Affymetrix Expression  Console  using default analysis settings for RNA analyses  for  gene default and exon default .CHP files.

label: biotin

label_protocol: 150 ng total RNAwas amplified using the Ambion WT Expression Kit and the WT Terminal Labeling Kit (Affymetrix, Freiburg, Germany).

growth_protocol: Ba/F3 cell lines were cultured in DMEM with 1% PenStrep and 10%FCS with recombinant Hyper-IL-6 (10 ng/ml cell culture supernatant) in 10 cm cell culture plattes  and were splitted in a ratio from 1:10000 to 1:5

extract_protocol: Total RNA extraction was made with RNeasy mini kit (Qiagen, Hilden, Germany) including DNAse digestion according to the manufacturer's instructions. RNA quality was evaluated using an Agilent 2100 Bioanalyzer and only high quality RNA (RIN > 8) was used for microarray analysis.

treatment_protocol: Ba/F3-gp130 cell lines were washed four times with sterile PBS and incubated in serum-free DMEM for 3 h. Equal numbers of cells (2 x 10^6) were stimulated  for 1h at 37°C with 50µl GFP-PFC emulsion in 1ml serum free DMEM medium (1 h at 37°C). As a positive stimulation control Ba/F3-gp130 cells were incubated for 1h at 37°C with 100ng/ml Hyper IL-6 in serum free medium (Samples E2, E4, E6)

tag: cell line vendor

value: Ba/F3 (DSMZ no.:ACC 300)

tag: transfection

value: untransfected

tag: stimulation

value: 100ng/ml Hyper IL-6


title: SLX-14710.i702_i508

tag: strain background


title: N6-1_Normal-MatureLuminal_Vehicle_24 hours_13-79ML_veh_RNA-seq

description: mRNA-seq

tag: her2 status

tag: age

value: 24 hours


title: ROBO1_4

description: sequencing was done in 1 lane

tag: cell type

value: trophoblast

value: placenta


title: N6-1_Normal-MatureLuminal_10 nM E2_24 hours_13-79ML_E2_RNA-seq

description: mRNA-seq

tag: tissue type

value: 10 nM E2


title: D6Ba/F3-gp130-CIR3 stimulated with GFP-PFC (exon-level)

value: GFP-PFC (50µl/ml)


title: SLX-14710.i702_i507

tag: embryonic day

tag: sorting


title: E6Ba/F3-gp130 cells stimulated with 100ng/ml Hyper IL-6 (exon-level)


title: SLIT2_2

description: sequencing was done in 1 lane

value: silenced with siRNA of SLIT2


title: N6-2_Normal-MatureLuminal_Vehicle_24 hours_13-79MLveh-DC1219_S6_R1_RNA-seq

description: mRNA-seq

tag: er status

tag: pr status

tag: type


title: N5_Normal-MatureLuminal_10 nM E2_24 hours_12-52ML_E2_250ng1_RNA-seq

description: mRNA-seq

tag: grade

tag: drug treatment

tag: hormone exposure time


title: SLX-14710.i702_i506

value: Lgr5GFP pos


title: D2Ba/F3-gp130-CIR3 stimulated with GFP-PFC (exon-level)

tag: cell line


title: D4Ba/F3-gp130-CIR3 stimulated with GFP-PFC (exon-level)

tag: cell line vendor


title: E4Ba/F3-gp130 cells stimulated with 100ng/ml Hyper IL-6 (exon-level)

tag: transfection


title: SLIT2_3

description: sequencing was done in 1 lane

tag: tissue

tag: treatment


title: N5_Normal-MatureLuminal_10 nM E2_24 hours_12-52ML_E2_400ng2_RNA-seq

description: mRNA-seq

value: normal mature luminal cells

tag: her2 status


title: SLIT2_1

description: sequencing was done in 1 lane


title: C2Ba/F3-gp130-CIR2 stimulated with GFP-PFC (exon-level)

tag: stimulation


title: SLX-14710.i702_i503

tag: strain background

tag: cell type


title: N5_Normal-MatureLuminal_Vehicle_24 hours_12-52ML_veh_RNA-seq

description: mRNA-seq

tag: tissue type

value: ER+

tag: age


title: Tabak_onlyPL_group3

city: Zurich

first: Hubert

last: Rehrauer

address: Winterthurerstr. 190

department: FGCZ

country: Switzerland

institute: ETH Zurich / University of Zurich

data_processing:
Reads were aligned with STAR aligner with the options --outFilterType BySJout --outFilterMatchNmin 30 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.05 --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMultimapNmax 50 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --chimScoreMin 15 --chimScoreSeparation 10 --outSAMstrandField intronMotif
Alignments were counted with the featureCounts function
Genome_build: Canis_familiaris/Ensembl/CanFam3.1/Annotation/Version-2015-05-20
Supplementary_files_format_and_content: text files holding match counts per gene

organism: Canis lupus familiaris

extract_protocol:
Following surgery, placentae were separated from uteri, rinsed with phosphate-buffered saline (PBS) and immersed in RNAlater® for 24h at +4°C. After 24h, tissue material was stored at -80°C until RNA isolation. RNA was isolated using Trizol reagent.
Illumina TruSeq RNA Sample Prep Kit v2 was used with 100-1000ng/per sample of total RNA for the construction of sequencing libraries.

tag: animal status

value: clinically healthy, cross-breed

value: 2-8 years

tag: pregancy stage


title: D5Ba/F3-gp130-CIR3 (exon-level)

value: unstimulated


title: C6Ba/F3-gp130-CIR2 stimulated with GFP-PFC (exon-level)


title: SLX-14710.i702_i502

value: male Lgr5-EGFP-IRES-creERT2 mice maintained on a C57BL/6 background, mated with MF1 female

tag: embryonic day

value: liver hepatoblast cells

tag: sorting


title: C5Ba/F3-gp130-CIR2 (exon-level)

value: Ba/F3 (DSMZ no.:ACC 300)


title: C3Ba/F3-gp130-CIR2 (exon-level)


title: D1Ba/F3-gp130-CIR3 (exon-level)


title: D3Ba/F3-gp130-CIR3 (exon-level)


title: SLX-14710.i701_i511

value: Bulk


title: N4_Normal-MatureLuminal_10 nM E2_24 hours_12-38ML_E2_RNA-seq

description: mRNA-seq

tag: er status

tag: pr status

tag: type

tag: grade

tag: drug treatment


title: N4_Normal-MatureLuminal_Vehicle_24 hours_12-38ML_veh_RNA-seq

description: mRNA-seq

value: Vehicle

tag: hormone exposure time


title: C1Ba/F3-gp130-CIR2 (exon-level)

tag: cell line

tag: cell line vendor

tag: transfection


title: SLX-14710.i701_i508

tag: strain background


title: N3_Normal-MatureLuminal_10 nM E2_24 hours_12-36ML_E2_RNA-seq

description: mRNA-seq

tag: her2 status

value: 24 hours


title: Sakine_onlyPL_group3

tag: tissue


title: B6Ba/F3-gp130-CIR1 stimulated with GFP-PFC (exon-level)

tag: cell type

tag: stimulation


title: Sila_onlyPL_group3

tag: animal status

tag: age

tag: pregancy stage


title: C4Ba/F3-gp130-CIR2 stimulated with GFP-PFC (exon-level)


title: Senta_onlyPL_group2

value: prepartum


title: N3_Normal-MatureLuminal_Vehicle_24 hours_12-36ML_veh_RNA-seq

description: mRNA-seq

tag: tissue type

tag: er status


title: B4Ba/F3-gp130-CIR1 stimulated with GFP-PFC (exon-level)


title: SLX-14710.i701_i507

tag: embryonic day

tag: sorting


title: Kimba_onlyPL_group2

value: placenta


title: B5Ba/F3-gp130-CIR1 (exon-level)


title: Amy_onlyPL_group2


title: B3Ba/F3-gp130-CIR1 (exon-level)


title: SLX-14710.i701_i506


title: N2_Normal-MatureLuminal_10 nM E2_24 hours_13-80ML_E2_RNA-seq

description: mRNA-seq

tag: pr status

tag: type

tag: grade

tag: drug treatment

value: 10 nM E2


title: SLX-14710.i701_i505


title: N2_Normal-MatureLuminal_Vehicle_24 hours_13-80ML_veh_RNA-seq

description: mRNA-seq

tag: hormone exposure time


title: N1_Normal-MatureLuminal_10 nM E2_24 hours_13-12ML_E2_RNA-seq

description: mRNA-seq


title: SLX-14710.i701_i503

tag: strain background


title: Gold_onlyPL_group1

value: mid-gestation


title: SLX-14710.i701_i502


title: Kurtulus_onlyPL_group1


title: N1_Normal-MatureLuminal_Vehicle_24 hours_13-12ML_veh_RNA-seq

description: mRNA-seq

tag: her2 status


title: AC2siRNA_1

status: Public on May 26 2019

city: Cambridge

first: Danish

last: Memon

address: Robinson Way

country: United Kingdom

institute: CRUK Cambridge Institute, University of Cambridge

description: strand-specific RNA-seq

data_processing:
Basecalling was performed using Illumina CASAVA version 1.8.2
Paired-end sequencing reads (75 nt) were obtained from all sequencing libraries and aligned to the human reference genome hg19 using the splice-aware alignment software Mapsplice (version v2.7.6) with default parameters, except for options specifying library type (fr-firststrand). Gene annotation was taken from Ensembl release 74.
Gene abundance were obtained by summing up reads that mapped to the the exonic regions using RSubread::featureCounts.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: RPKM values for all samples

source_name: Lung cancer cells

growth_protocol: Non-small-cell lung cancer cell line H460 was purchased from ATCC. The cells were cultured in RPMI-1640 supplemented with 10% fetal bovine serum, passaged every three days, and tested routinely for mycoplasma contamination.

extract_protocol:
Total RNA from three biological replicates of non-target siRNA and AC093323.3 siRNA treated H460 cells were extracted using the RNeasy mini kit (QIAGEN, 74104) and sent for PolyA sequencing.
Indexed PolyA libraries were prepared using 200ng of total RNA and 14 cycles of amplification with the Agilent SureSelect Strand Specific RNA Library Prep Kit for Illumina Sequencing (Agilent, Cat No: G9691A). Libraries were quantified by qPCR using a Kapa Library Quantification Kit for Illumina sequencing platforms (Kapa Biosystems Inc., Cat No: KK4835). Paired-end 75bp sequencing was carried out by clustering 1.9 pM of the pooled libraries on a NextSeq 500 sequencer (Illumina Inc.).

treatment_protocol: For knockdown experiments, 50nM siRNAs were transfected using the Lipofectamine RNAiMAX transfection reagent (ThermoFisher, 13778075) for 48 hours before sample collection. siRNAs were purchased from Dharmacon with ON-TARGETplus modification. siRNA sequences used were as follow: siHKlincR1_1, GCGGAUGACUUCAGCAUUA; siHKlincR1_2, GAAGUAUACUCGUGUGCUU. ON-TARGETplus Non-targeting (NT) siRNA #1 (Dharmacon, D-001810-01-05) was used as a negative control.

tag: cell line

tag: sirna

tag: replicate


title: AC2siRNA_3

description: strand-specific RNA-seq


title: AC2siRNA_2

description: strand-specific RNA-seq


title: A5Ba/F3-gp130 cells (exon-level)

source_name: A5Ba/F3-gp130 cells

tag: cell line vendor

tag: cell type

tag: transfection

value: untransfected

tag: stimulation


title: NTsiRNA_3

description: strand-specific RNA-seq

value: non-target siRNA


title: NTsiRNA_1

description: strand-specific RNA-seq


title: NTsiRNA_2

description: strand-specific RNA-seq


title: B1Ba/F3-gp130-CIR1 (exon-level)


title: HJ293

city: Davis

first: Hong

last: Ji

state: CA

address: County Rd 98 & Hutchison Drive

institute: University of California Davis

description: processed data file: countsTable_Ji_human.txt

data_processing:
All fastq files were adapter trimmed prior to alignment. Files were aligned against Human (GRch37/Ensembl) or Mouse reference genome (GRCm38/mm10). Sequence alignment was performed using Bowtie2 and RSEM.
Post-alignment, raw read counts were extracted and normalized to account for difference in read depth using DESeq.
Following normalization, gene read counts were filtered to remove low read values: maximum Reads Per Kilobase of transcript, per Million mapped reads (RPKM) across all samples must be ≥ 1.
Differentially expressed genes (DEGs) were identified using DESeq, and genes with an FDR adjusted p-value (q-value) < 0.01 and fold of change ≥1.2, were considered significant.
P values were calculated by student t test for each individual gene, and Benjamini and Hochberg correction was applied to generate FDR (q-value).
Genome_build: Mouse GRCm38/mm10, human GRCh37
Supplementary_files_format_and_content: countsTable_Ji_mouse.txt: Tab-delimited text file includes reads for each sample, gene ID, gene name, chr, start, end and strand (+ or -).
Supplementary_files_format_and_content: countsTable_Ji_human.txt: Tab-delimited text file includes reads for each sample, gene ID, gene name, chr, start, end and strand (+ or -).

source_name: bronchial epithelial cells

growth_protocol: Human bronchial epithelial cells were grown to 70-90% confluence in keratinocyte serum free medium supplemented with human recombinant Epidermal Growth Factor and Bovine Pituitary Extract (Life Technologies, Carlsbad, CA). All mice were maintained in a barrier facility and handled under Institutional Animal Care and Use Committee-approved procedures.

extract_protocol:
RNA was purified using the RNeasy Mini Kit (Qiagen, Valencia, CA) according to manufacturer’s instructions.
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Following purification, the mRNA was fragmented and reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA). cDNA libraries were sequenced on an Illumina HiSeq™ 2000 platform.

treatment_protocol: Control plasmid and TET1 CRISPR activation plasmid (Santa Cruz Biotechnology, Dallas, TX) was transfected into HBECs using Lipofectamine® 2000 (Thermo Fisher Scientific, Florence, KY) and Opti-MEM medium according to manufacturer’s protocol. House dust mite (HDM) extract (Dermatophagoides pteronyssinus) was purchased from Greer Laboratories (Lenoir, NC). For an acute model of allergic airway inflammation, on days 0 and 7, mice were sensitized intraperitoneally with 100 μg of HDM (representing 33µg of protein; 11µg of Der p1; 5 EU of endotoxin) in 100 μL of PBS plus alum or an equivalent amount of PBS alone. On days 14, 19 and 21, mice were challenged intratracheally with 100 μg of HDM in 50 μL of PBS or PBS alone. On day 23, lung tissues were harvested for DNA/RNA extraction.

value: human bronchial epithelial cells (HBEC)

tag: treatment

value: control


title: A3Ba/F3-gp130 cells (exon-level)

source_name: A3Ba/F3-gp130 cells


title: HJ292


title: E-EEQ-MBP

city: Frederick

first: Shuo

last: Gu

state: MD

address: 1050 Boyles Str. Building 560 Room 11-6B

institute: National Cancer Institute

description: E.coli and A.a RNase III proteins were incubated each with the dsRNA substrate corresponding to the FF or MBP coding sequence

data_processing:
3ʹ adaptor sequences were removed by customized scripts. Reads without the 3′ adaptor sequences or shorter than 6 nt were discarded
Map to substrate sequence (FF-luc or MBP) by using Bowtie (version 1.1.1) with the command "bowtie -v 0 --best --sam"
The resulting SAM files were converted to BAM files, sorted, indexed by SAMtools, and eventually visualized with IGV.
Length distribution analysis of mapped reads and cleavage sites analysis were carried out subsequently by customized scripts.
The consensuses motif of preferred cleavage sites or mappable reads was identified by Weblogo
Genome_build: N/A
Supplementary_files_format_and_content: Length distribution of all samples

organism: Escherichia coli

source_name: In vitro cleavage products

extract_protocol:
RNAs from the cleavage assay were extracted by using Trizol.
Sequencing libraries were prepared using a protocol similar to what described in Illumina® TruSeq® RNA sample preparation kit with a customized 3' adaptor sequence
3' Adaptor Sequence : CTGTTAACNNNNNNNNNNNNNNNTGGAATTCTC

treatment_protocol: RNase III cleavage reactions were done using 4 mg of purified His-tagged protein and 500 ng of either FF-luc or MBP dsRNA as the substrate in New England Biolabs Buffer 2 (10 mM Tris-HCl (pH 7.9), 10 mM MgCl2, 50 mM NaCl, 1 mM dithiothreitol) and incubated for 30 min at 37°C (EcRNase III) or 30min at 60°C (AaRNase III).

tag: dsrna substrate

value: maltose-binding protein (MBP)


title: HJ295

value: TET1 activation


title: A4Ba/F3-gp130 cells stimulated with GFP-PFC (exon-level)

value: GFP-PFC (50µl/ml)


title: E-E65Q165-MBP


title: E-E38Q165-MBP


title: E-E65-MBP


title: E-E65Q165-FF

value: Firefly (FF)


title: E-EEQ-FF


title: E-Q165-FF


title: Nescafe_onlyPL_group1

tag: animal status

value: clinically healthy, cross-breed

tag: age

value: 2-8 years

tag: pregancy stage

tag: tissue


title: E-Q165-MBP


title: E-E38Q165-FF


title: A2Ba/F3-gp130 cells stimulated with GFP-PFC (exon-level)

value: Ba/F3 (DSMZ no.:ACC 300)


title: GA13V_336

city: Seoul

first: Won-Ji

last: Ryu

address: 262 Seonsanno, Seodaemun-Gu

country: South Korea

institute: Yonsei University

description:
processed data file:
cuffnorm_genes.fpkm_table.txt
Vehicle_PrimaryResistance_DEG_analysis.txt
Vehicle_Responder_DEG_analysis.txt
Vehicle_AcquiredResistance_DEG_analysis.txt

data_processing:
Xenome-0.1.1 software classify Xenograft RNA-seq human (hg19) and mouse (mm9) genome reference.
The paired-end reads were aligned to a human genome reference (UCSC hg19) using TopHat2 version 2.0.12.
The aligned TopHat2 reads were assembled into transcripts using cufflinks package 2.1.0.
cuffnorm was used for gene expression value. (Fragments Per Kilobase of transcript per Million mapped reads).
Genome_build: mm9, hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: gastric cancer PDX tumor_vehicle

growth_protocol: 6-week-old male athymic nude mice (Japan SLC, Inc., Japan) or male NOG mice (NOD/Shi-scid, IL-2 Rγ null; CIEA, JAPAN) were used for each PDX model and were acclimatized for 1 week. The patient tumors were sliced into 3 × 3 × 3-mm3 fragments; then, these fragments were subcutaneously implanted into their flanks. The drug treatment was initiated when the mean tumor volume reached between 100–150 mm3, and the mice were randomly assigned into specific treatment groups.

extract_protocol:
Total RNA was extracted from tumor-rich area using Trizol, according to the manufacturer's instructions.
Library was constructed by SureSelect XT Human All Exon V5 kit according to the manufacture's protocol.

treatment_protocol: The FOLFOX regimen was delivered with the following schedule: leucovorin (5 mg/kg/day) was injected intraperitoneally, followed by 5-FU (15 mg/kg/day) after 20 min once a day. Oxaliplatin (5 mg/kg/day) was injected intraperitoneally once a week.

tag: host mouse strain

value: Nude mouse

value: gastric cancer PDX tumor

value: vehicle


title: E-E38-MBP


title: E-E65-FF


title: HJ294


title: GA13V_331


title: E-WT-MBP-2


title: E-E38-FF


title: A1Ba/F3-gp130 cells (exon-level)

source_name: A1Ba/F3-gp130 cells

value: unstimulated


title: E-WT-MBP-1


title: GA13FOLFOX_340

description:
processed data file:
cuffnorm_genes.fpkm_table.txt
Vehicle_Responder_DEG_analysis.txt

source_name: gastric cancer PDX tumor_FOLFOX

value: FOLFOX

tag: phenotype

value: Responder


title: E-WT-FF-4


title: E-WT-FF-3


title: CNV-Rep1

city: Cincinnati

first: Rebekah

last: Karns

state: OH

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

institute: Cincinnati Children's Hospital Medical Center

description: intestinal epithelial cells harvested from the intestine of C57Bl6J mouse housed in conventional conditions

data_processing:
Sequence reads were aligned to the mm10 genome using the Illumina sequence analysis pipeline.
RPKM were computed from aligned reads and baselined to the median across all samples.
Genome_build: mm10
Supplementary_files_format_and_content: text files with RPKM for each transcript across each sample

source_name: intestine

growth_protocol: Conventionally-housed C57Bl/6J mice were maintained in specific-pathogen free colonies, while germ-free mice were maintained in plastic isolators, fed autoclaved feed and water, and monitored to ensure absence of microbes.

extract_protocol:
Intestinal epithelial cell were harvested from mouse intestine and RNA was isolated using the Rneasy Kit and reverse transcription with Verso reverse transcriptase.
Directional polyA RNAseq according to standard Illumina protocols

tag: background

tag: conditions

value: conventional

tag: cell population

value: intestinal epithelial cells


title: GA13FOLFOX_326

description:
processed data file:
cuffnorm_genes.fpkm_table.txt
Vehicle_AcquiredResistance_DEG_analysis.txt

value: AcquiredResistance


title: GA13FOLFOX_337

description:
processed data file:
cuffnorm_genes.fpkm_table.txt
Vehicle_PrimaryResistance_DEG_analysis.txt

value: PrimaryResistance


title: E-WT-FF-2


title: GF-Rep2

description: intestinal epithelial cells harvested from the intestine of C57Bl6J mouse housed in germ free conditions

value: germ free


title: E-WT-FF-1


title: HJ291

description: processed data file: countsTable_Ji_mouse.txt

source_name: KO lung

tag: genotype/variation

tag: gender

value: Male

value: Lung

value: House dust mite (HDM)


title: GF-Rep1


title: GA13V_334


title: HJ289

value: Saline


title: HJ288

value: Female


title: GA13FOLFOX_323


title: GA13V_322


title: HJ287-2

source_name: WT lung


title: GA13FOLFOX_316


title: CNV-Rep2


title: HJ286


title: A-Q161-MBP

organism: Aquifex aeolicus

value: maltose-binding protein (MBP)


title: HJ285


title: HJ284


title: GA13FOLFOX_324

value: Nude mouse


title: GA13FOLFOX_325

value: gastric cancer PDX tumor


title: Single-cell Hi-C data of zygote 3

city: Wuhan

first: shaoli

last: zhou

state: Hubei

address: shizishan street

department: National Key Laboratory of Crop Genetic Improvement

country: China

institute: Huazhong Agricultural University

library_source: genomic

data_processing:
Library strategy: Single cell Hi-C
The Nuc_processing software was used to take paired sequenced fastq files to create processed single-cell Hi-C contact files (ncc). The Nuc_dymanic software (parameter: -s 8 2 1 0.5 0.2 0.1 0.05 0.02 0.01 0.005) was used to calculated single cell genome structure, the output files (pdb) were for viewing the 3D genome structures in pymol.
Genome_build: RGAP version 7.0
Supplementary_files_format_and_content: For ncc and pdb file were all blank-delimited text files of output of Nuc_processing and Nuc_dynamic softwares, respectively.

molecule: genomic DNA

organism: Oryza sativa Japonica Group

source_name: Unicellular zygote of rice

growth_protocol: Rice seeds were germinated and grown in a greenhouse or in paddy field.

extract_protocol:
After isolation, cells were immediately aspirated with a glass micropipette and blown out to 0.53 M mannitol (pH 5.7, adjusted with 0.1 M MES) containing 2% (v/v) formaldehyde by using a glass micropipette system. After 15 minutes, the cells were aspirated and blown out to fresh 0.53 M mannitol without formaldehyde for washing, Finally, the fixed clean cells were aspirated one by one, and blown into a 200 μl PCR well containing 7.7 μl Dpn II buffer (1X), at 4°C and kept on ice for next steps.
For the precise protocol for library construction, please see the paper of this data linked to. Briefly,7.7 μl 1×Dpn II buffer containing single cell was heated in 62 °C for 7 min to directly lyse cell and to loosen the nuclear membrane.For each well, 0.3 μl (3 U) Dpn II (R0543, NEB) was added after cooling, and incubate at 37 °C for 14 hours.Denature Dpn II at 62 °C for 10 min. Add 2 μl ligation mixture (1 μl 10×T4 ligase buffer, 1 μl (400 U) T4 DNA ligase, M0202, NEB),hold at 16 °C for 4.5 hours, then at room temperature for 30 min.Denature ligase and de-crosslink at 65 °C for 6 hours. DNA amplification was applied with REPLI-g Single Cell Kit (150345, QIAGEN).Shear DNA to 150-500 bp range by sonication.Finally,contruct the library for illumina sequencing by following the classic steps including end repairing, adaptor ligation, and DNA amplification.

value: Unicellular zygote isolated from florets (6-8 hours after pollination)

tag: cultivar

value: Dongjin


title: Single-cell Hi-C data of shoot cell 2

source_name: Single shoot cell of rice

tag: cell type

value: Shoot cell isolated from 12-day-after-germination seedling


title: A-E64-MBP


title: Single-cell Hi-C data of zygote 2


title: A-Q161-FF

value: Firefly (FF)


title: Single-cell Hi-C data of shoot cell 1


title: HJ290


title: A-E64-FF


title: J2.LDM.IP

city: Beijing

first: Bao-Fa

last: Sun

address: Da-Tun Road

institute: Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)

description:
Jinhua pig LDM m6A IP rep2
J-LDM-m6A-peak-rep2.xls

data_processing:
Reads were aligned to the reference genome (Sscrofa10.2/susScr3) using Tophat (v2.0.14)
To call m6A peaks, the longest isoform of each pig gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform, windows with reads counts <1/20 of the top window in both m6A-IP and input sample were excluded. For each gene, threads count in each window was normalized by the median count of all windows of that gene. Fisher’s exact test was used to identify the differential windows between IP and input samples. The window was called as positive if falsediscovery rate (FDR) < 1% and log 2 (Enrichment Score) ≥ 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak (or window): reads count of the IP sample in the current peak/window (a), median reads count of the IP sample in all 100 bp windows on the current mRNA (b), reads count of the input sample in the current peak/window (c), and and median reads count of the input sample in all 100 bp windows on the current mRNA (d). The enrichment score of each window was calculated as (a× d)/(b× c).
Genome_build: susScr3
Supplementary_files_format_and_content: m6A peaks in longissimus dorsi muscles of Landrace and Jinhua pigs.

organism: Sus scrofa

source_name: pig muscle tissue

extract_protocol:
Two males of the Landrace (a Danish pig breed) and two males of the Jinhua (a Chinese pig breed with higher levels of intramuscular fat) at 180-day-old were used in this study. Total RNA was extracted from tissue by TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples, mRNA was sonicated and subjected to IP using m6A antibody (Synaptic Systems, 202003).
Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit (Illumina).

tag: breed

value: Jinhua

value: muscle


title: Single-cell Hi-C data of sperm 4

source_name: Single sperm of rice

value: Sperm isolated from rice stamens


title: A-E37-MBP


title: SPF UVneg-369

city: Graz

first: Karin

last: Wagner

state: Styria

address: Stiftingtalstrasse 24

department: Molecular Biology

country: Austria

institute: Medical University Graz

hyb_protocol: Affymetrix Mouse Gene 2.0 ST Array (Cat No. 902118); Affymetrix GeneChip® HT hybridization, Wash and Stain Kit (Cat No. 900720); Affymetrix Genechip® fluidics station 450: protocol FS450_0002 for Cartridge Arrays

scan_protocol: Affymetrix Scanner: GCS3000; AGCC (Command Console Software AGCC 4.0.0)

data_processing: Affymetrix Genexpression Console (1.3.1) using Affymetrix default analysis settings for generation of CEL-files.

label: Biotin

source_name: dorsal skin, SPF UV-

label_protocol: 500ng for Affymetrix WT PLUS Reagent Kit P/N 703147 Rev5, (Cat No. 902280)

growth_protocol: All the animals were bred and housed in germ-free conditions.

extract_protocol: miRNeasy Mini Kit inclusive DNase digest (Qiagen; Hilden, Germany; Cat No. 217004)

treatment_protocol: UVB exposure was performed in a sterile environment.

value: dorsal skin


title: SPF UVneg-370


title: SPF UVneg-368


title: A-E37-FF


title: Single-cell Hi-C data of sperm 3


title: SPF UVpos-366

source_name: dorsal skin, SPF UV+


title: SPF UVpos-367


title: J1.LDM.IP

description:
Jinhua pig LDM m6A IP rep1
J-LDM-m6A-peak-rep1.xls


title: Single-cell Hi-C data of sperm 2


title: A-WT-MBP-2


title: J1.LDM.input

description:
Jinhua pig LDM m6A input rep1
J-LDM-m6A-peak-rep1.xls


title: Single-cell Hi-C data of zygote 1


title: L2.LDM.IP

description:
Landrace pig LDM m6A IP rep2
L-LDM-m6A-peak-rep2.xls

value: Landrace


title: GF UVneg-364

source_name: dorsal skin, GF UV-


title: Single-cell Hi-C data of sperm 1


title: Single-cell Hi-C data of egg 4

source_name: Single egg of rice

value: Egg isolated from rice non-pollinated florets


title: A-WT-MBP-1


title: A-WT-FF-3


title: L2.LDM.input

description:
Landrace pig LDM m6A input rep2
L-LDM-m6A-peak-rep2.xls


title: Single-cell Hi-C data of egg 3


title: J2.LDM.input

description:
Jinhua pig LDM m6A input rep2
J-LDM-m6A-peak-rep2.xls


title: GF UVneg-363


title: A-WT-FF-2


title: GF UVneg-362


title: SPF UVpos-365


title: GF UVpos-360

source_name: dorsal skin, GF UV+


title: GF UVpos-361


title: Single-cell Hi-C data of egg 2


title: A-WT-FF-1


title: L1.LDM.input

description:
Landrace pig LDM m6A input rep1
L-LDM-m6A-peak-rep1.xls


title: GF-H3K9Ac-Rep1

data_processing:
Raw reads were mapped to the mm10 genome usign Bowtie and peaks were identified with MACS.
Data were visualized and analyzed using BioWardrobe.
Genome_build: mm10
Supplementary_files_format_and_content: peak files

extract_protocol:
Intestinal epithelial cellswere harvested from mouse intestine and chromatin was immunoprecipitated with rabbit anti-H3K9Ac
Sequencing was performed using the Illumina HiSeq2500 according to standard protocols.

value: germ free

tag: antibody

value: intestinal epithelial cells


title: CNV-H3K9Ac-Rep1

value: conventional


title: Single-cell Hi-C data of egg 1


title: L1.LDM.IP

description:
Landrace pig LDM m6A IP rep1
L-LDM-m6A-peak-rep1.xls


title: lib16878

status: Public on May 25 2019

city: Seattle

first: Daniel

middle: J

last: Campbell

state: Washington

address: 1201 Ninth Avenue

institute: Benaroya Research Institute

description:
raw_counts.txt
norm_counts.txt

data_processing:
Base-calling and demultiplexing were performed automatically on BaseSpace (Illumina) to generate FASTQ files.
The FASTQ files were processed in order to remove reads of zero length (fastq_trimmer v.1.0.0), remove adapter sequences (fastqmcf tool v.1.1.2) and perform quality trimming from both ends until a minimum base quality ≥ 30 (FASTQ quality trimmer tool v.1.0.0).
Reads were aligned to the human reference genome (build hg38) with TopHat (v.1.4.0) and read counts per Ensembl gene ID were quantified with htseq-count (v.0.4.1).
Quality metrics for the FASTQ and BAM/SAM files were generated with FastQC (v.0.11.3) and Picard (v.1.128).
Processing of FASTQ and BAM/SAM files was executed on the Galaxy workflow platform of Globus genomics.
Samples with a total number of fastq reads below 10^6, mapped reads below 70% or median CV coverage > 1 were excluded from further analysis.
Genome_build: hg38
Supplementary_files_format_and_content: raw_counts: Gene counts as determined by htseq-count. Ensembl Gene IDs were mapped to HGNC gene symbols using biomaRt (GRCh38.p10). Genes were filtered for protein coding genes and those with an expression of CPM > 2 in at least 10% of the libraries.
Supplementary_files_format_and_content: norm_counts: Gene filtering performed as for the raw_counts. Gene expression levels represent counts per million using normalized library sizes (Robinson & Oshlack, 2010).

source_name: blood

extract_protocol:
500 cells per population were sorted into lysis buffer using a BD FACSARIA III or FACSFUSION instruments (BD Biosciences), and cDNA was prepared using the SMARTSeq v4 Ultra Low Input RNA Kit for Sequencing (Takara).
Library construction was performed using the NexteraXT DNA sample preparation kit (Illumina) using half the recommended volumes and reagents.
sequencing run: Dual-index, single-read sequencing of pooled libraries was run on a HiSeq2500 sequencer (Illumina) with 58-base reads and a target depth of 5 million reads per sample.

treatment_protocol: For blood samples, human PBMCs were isolated using Ficoll-Hypaque (GE-Healthcare; GE17-1440-02) gradient separation. For RNAseq CD4+ T cells were enriched using CD4 microbeads (Miltenyi; 130-045-101) and 4x106 cells/ml were resuspended in RPMIc with 50 U/ml IL-2 (Immunotools; 11340023) in a 24-well and stimulated for 20h with 25µl/ml ImmunoCult CD3/CD28 T cell activator (Stemcell; 10971) prior to staining and cell sorting.  For isolation of skin T cells, subcutaneous fat was removed before skin was minced with dissection scissors and surgical scalpel. Approximately 1cm^2 of skin was digested overnight in 5%CO2 at 37°C with 3ml of digestion mix containing 0.8mg/ml Collagenase Type 4 (Worthington; #LS004186) and 0.02mg/ml DNase (Sigma-Aldrich; DN25) in RPMIc. Samples were filtered, washed with RPMI and PBS and stained for flow cytometry/cell sorting.

value: blood

tag: donor id

value: E

tag: collection site

value: Salzburg


title: lib16840

description:
raw_counts.txt
norm_counts.txt

source_name: skin

value: skin

value: B

value: Seattle


title: lib16852

description:
raw_counts.txt
norm_counts.txt

value: C


title: lib16837

description:
raw_counts.txt
norm_counts.txt


title: lib16831

description:
raw_counts.txt
norm_counts.txt

value: A


title: lib16853

description:
raw_counts.txt
norm_counts.txt


title: lib16877

description:
raw_counts.txt
norm_counts.txt


title: lib16829

description:
raw_counts.txt
norm_counts.txt


title: lib16854

description:
raw_counts.txt
norm_counts.txt


title: lib16839

description:
raw_counts.txt
norm_counts.txt


title: lib16843

description:
raw_counts.txt
norm_counts.txt


title: lib16836

description:
raw_counts.txt
norm_counts.txt


title: lib16838

description:
raw_counts.txt
norm_counts.txt


title: lib16856

description:
raw_counts.txt
norm_counts.txt

value: D


title: lib16855

description:
raw_counts.txt
norm_counts.txt


title: lib16828

description:
raw_counts.txt
norm_counts.txt


title: lib16827

description:
raw_counts.txt
norm_counts.txt


title: lib16830

description:
raw_counts.txt
norm_counts.txt


title: GF UVpos-359


title: lib16844

description:
raw_counts.txt
norm_counts.txt


title: JEG3 sample B

city: CINCINNATI

first: Xuzhe

last: Zhang

state: Ohio

address: 3333 Burnet Avenue

department: Human Genetics

data_processing:
Reads were aligned with TopHat 2.1.1 to the human GRCh37 Ensembl cDNA build.
Reads were counted and normalized using Cufflinks 2.2.1.
Genome_build: GRCh37
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample.

source_name: JEG3 cell line

growth_protocol: JEG3 choriocarcinoma cell line was obtained from ATCC (ATCC® HTB-36™) and cultured in DMEM medium supplemented with 10% FBS, glutaMAX (2 mM), penicillin (100 U/ml), and streptomycin (100 μg/ml). BeWo choriocarcinoma cell line was obtained from ATCC (ATCC® CCL-98™) and cultured in DMEM/F12 medium supplemented with 10% FBS, glutaMAX (2 mM), penicillin (100 U/ml), and streptomycin (100 μg/ml). All cell lines were cultured at 37°C and 5% CO2.

extract_protocol:
Total RNA was extracted from cells using the RNeasy Mini kit (Qiagen) followed by on-column DNase I treatment.
RNA-seq libraries were prepared using the SureSelect Strand-Specific RNA Library Prep for Illumina Multiplexed Sequencing kit (Agilent).

value: Choriocarcinoma

tag: cell line


title: BeWo sample B

source_name: BeWo cell line

value: BeWo


title: JEG3 sample A


title: Day 6 (T6)

city: Fuzhou

first: Yue

last: Zhicao

state: Fujian

address: Institute of Life Sciences, Fuzhou University

department: Institute of Life Sciences

institute: Fuzhou University

description: Rat footpad skin was irradiated at Day 4 and extracted at Day 6

data_processing:
Image analysis and basecalling was performed using the Illumina Pipeline v1.5+. Raw sequences are transformed into Clean Tags after following steps of data-processing using customized workflow developed by Shenzhen Huada Gene Sci-Tech Company.
1. 3' adaptor sequence removal: since Tags are only 21nt long while the sequencing reads are 35nt long, raw sequences are with 3' adaptor sequences
2. Empty reads removal (reads with only 3' adaptor sequences but no tags)
3. Low quality tags removal (Tags with unknown sequences 'N')
4. Removal of tags which are too long or too short, leaving Tags of 21nt long
5. Removal of Tags with a copy number of 1 (probably be sequencing error)
6. Generate Clean Tags
A virtual libraries is build to contain all the possible CATG+17 bases length sequences of the reference gene sequences (Rattus norvegicus genome assemblies: Rattus norvegicus Rnor_6.0).
All clean tags were mapped to the reference sequences and only 1bp mismatch is considered. Clean tags mapped to reference sequences from multiple genes were filtered.
Remainder clean tags were designed as unambiguous clean tags. The number of unambiguous clean tags for each gene was calculated and then normalized to TPM (number of transcripts per million clean tags).
(Morrissy, A. S., R. D. Morin, et al . 2009. "Next-generation tag sequencing for cancer gene expression profiling." Genome Res.)
Genome_build: NCBI Rattus norvegicus Rnor_6.0
Supplementary_files_format_and_content: txt file with gene expression level

organism: Rattus norvegicus

source_name: footpad skin

growth_protocol: Rats were housed under normal diurnal condition with free access to food and water.

extract_protocol:
Rat footpad skin was irradiated at Day 1, Day 2, Day 4, Day 5 at 10Gy X 4 to mimic the fractioned delivery scheme used in clinic. The irradiation was performed using a Varian Clinac 23ex linear accelerator. Nine MeV electron beam was delivered at a dose rate of 500 cGy/min. Footpad skin from the hindlimb was collected at Day 0, Day 3, Day 6, Day 9, and total RNAs were extracted. After quality check, RNAs were processed for NGS in BGI, Shengzhen, China. The sequencing results were annotated according to a NCBI database.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain

value: Sprague Dawley

value: footpad skin


title: Day 3 (T3)

description: Rat footpad skin was irradiated at Day 2 and extracted at Day 3


title: BeWo sample A


title: Day 9 (T9)

description: Rat footpad skin was irradiated at Day 5 and extracted at Day 9


title: Day 0 (T0)

description: Rat footpad skin extracted at day 1 and extracted at Day 1


title: rna_seq_s4XCol-rep1_RRAS07929-V

city: Shanghai

first: Hui

address: Rd, Fenglin

institute: SIPPE

data_processing:
RNA-seq data were used with DEGseq2, Statistical analysis was performed using R(version 3.4.1)
Genome_build: tair10
Supplementary_files_format_and_content: txt

organism: Arabidopsis thaliana

source_name: Arabidopsis seedling

growth_protocol: All seeds were germinated in MS-medium (1% sucrose and 0.8% agar), after vernalizing at 4°C for 3d.  Plants were grown in a greenhouse under a 16h light/8h dark photoperiod for 10 days.

extract_protocol:
total RNA was used for sequencing with standard Illumina protocols
Sequencing libraries were constructed according to a standard protocol (Illumina).

tag: ecotype

value: columbia

value: seedling

tag: age

value: 10 days after vernalization

tag: genomic type


title: chip_seq_4XCol_Input.rep2

data_processing:
Hi-C data were analyzed with HiC-Pro and Jucier software
ChIP-seq data were analyzed with BWA and Mac2 software
RNA-seq data were used with DEGseq, Statistical analysis was performed using R(version 3.4.1)
Genome_build: tair10
Supplementary_files_format_and_content: matrix files for Hi-C, peak files for chip-seq and txt file for rna-seq

extract_protocol:
Hi-C experiments were performed essentially as Grob,Mol Cell,2014 described;the extracted genomic DNA was used for chip-seq with antibody H3K4me3, H3K27me3 and H3; total RNA was used for sequencing with standard Illumina protocols
Sequencing libraries were constructed according to a standard protocol (Illumina).

tag: tissue


title: rna_seq_s4XCol-rep3_RRAS07931-V


title: chip_seq_Col_H3K4me3.rep2


title: chip_seq_Col_H3K4me3.rep1


title: rna_seq_col-rep3_RRAS07928-V


title: chip_seq_Col_H3K4me3_Input.rep2


title: rna_seq_s4XCol-rep2_RRAS07930-V


title: chip_seq_4XCol_H3K4me3_Input.rep2


title: chip_seq_4XCol_H3K4me3.rep2


title: chip_seq_Col_H3K4me3_Input.rep1


title: chip_seq_4XCol_Input.rep1


title: chip_seq_4XCol_H3K4me3.rep1


title: chip_seq_Col_H3


title: chip_seq_4XCol_H3K27me3.rep1


title: rna_seq_col-rep1_RRAS07926-V


title: chip_seq_4XCol_H3


title: chip_seq_Col_H3K27me3.rep2


title: chip_seq_4XCol_H3K27me3.rep2


title: chip_seq_Col_Input.rep1


title: hic_4XCol.rep1


title: chip_seq_Col_Input.rep2


title: chip_seq_Col_H3K27me3.rep1


title: hic_Col.rep2


title: hic_4XCol.rep2


title: hic_Col.rep1


title: chip_seq_4XCol_H3K4me3_Input.rep1


title: rna_seq_col-rep2_RRAS07927-V


title: D14-400965

first: Peter

middle: W

last: Reddien

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

description:
muscle cell by qPCR collagen expression
140929Red_D14-400965
processed data file; raw read counts:
ReadcountMaster_uniquegenes2_forGEO_onlySinglecells.txt
processed data file; differential expression analysis:
ppolecandidates_singlecell_PvsNP_modelbygroup_forGEO.txt

data_processing:
Basecalls performed using CASAVA version 1.7.0.
Reads were trimmed using Trimmomatic-0.32 to remove Nextera transposon sequences and low quality 3′ base pairs.
Reads were mapped to dd_Smed_v4 planarian transcriptome assembly using bowtie 1 with --best to generate raw read counts file.
Only cells with a total read count of >10,000 from all genes were included in subsequent analysis. Read counts were normalized to cpm.
Cells with collagen (dd_Smed_v4_702_0_1) cpm <40, troponin (dd_Smed_V4_323_0_2) cpm <80, and with tropomyosin (dd_Smed_v4_436_0_1) cpm of 0 were excluded from analysis
Cells with high AGAT expression were excluded from analysis
Reads for isotigs of contigs (all contig ids that vary only by the final number) were summed.
Reads for mitochondrial and ribosomal RNA (dd_Smed_v4_7_0, and dd_Smed_v4_4_1, mtRNA, rRNA_5s) were discarded.
Differential gene expression analysis was performed between posterior pole cells (11 total) and non-posterior-pole muscle cells (90 total) using SCDE analysis.
Genome_build: dd_Smed_v4
Supplementary_files_format_and_content: Raw read counts: Tab-delineated text file includes unnormalized read counts of contigs for all 152 cells. SCDE analyses: tab-delineated text file generated per Kharchenko et al, 2014 for differential gene expression between posterior pole cells (11 total) and non-posterior-pole muscle cells (90 total) that passing quality filters (per data processing steps delineated above). Fold change is indicated as the maximum likelihood estimate (mle) with a lower (lb) and upper bound (ub) and a conservative estimate (ce, equal to lb (positive), ub (negative) or 0 (lb and ub have different signs)) and statistical significance as signed Z-score (Z) and conservative Z-score (cZ, Z score corrected for multiple hypothesis using Holm procedure).

organism: Schmidtea mediterranea

growth_protocol: Asexual Schmidtea mediterranea strain (CIW4) animals starved 7-14 days before surgical resection of midline tail tip regions, or before transverse tail amputation, then resection of midline posterior blastema regions after 72 hours of regeneration.

extract_protocol:
Cells were lysed in total cell lysis buffer supplemented with 1% β-mercaptoethanol
cDNA and sequencing libraries were constructed using SmartSeq2.

treatment_protocol: Single cell suspensions for each region were stained with Hoechst, and non-dividing single cells were sorted by flow cytometry into 96 well plates

value: asexual CIW4

tag: ploidy

value: 2N (non-dividing)

tag: uninjured or regenerating animal

value: uninjured

value: non-pole muscle cell


title: D14-400954

description:
muscle cell by qPCR collagen expression
140929Red_D14-400954
processed data file; raw read counts:
ReadcountMaster_uniquegenes2_forGEO_onlySinglecells.txt
processed data file; differential expression analysis:
ppolecandidates_singlecell_PvsNP_modelbygroup_forGEO.txt


title: D14-400952

description:
muscle cell by qPCR collagen expression
140929Red_D14-400952
processed data file; raw read counts:
ReadcountMaster_uniquegenes2_forGEO_onlySinglecells.txt
processed data file; differential expression analysis:
ppolecandidates_singlecell_PvsNP_modelbygroup_forGEO.txt


title: D14-400957

description:
muscle cell by qPCR collagen expression
140929Red_D14-400957
processed data file; raw read counts:
ReadcountMaster_uniquegenes2_forGEO_onlySinglecells.txt
processed data file; differential expression analysis:
ppolecandidates_singlecell_PvsNP_modelbygroup_forGEO.txt


title: D14-400958

description:
muscle cell by qPCR collagen expression
140929Red_D14-400958
processed data file; raw read counts:
ReadcountMaster_uniquegenes2_forGEO_onlySinglecells.txt
processed data file; differential expression analysis:
ppolecandidates_singlecell_PvsNP_modelbygroup_forGEO.txt

source_name: uninjured_pole_Isolated planarian cell

value: pole muscle cell


title: D14-400959

description:
muscle cell by qPCR collagen expression
140929Red_D14-400959
processed data file; raw read counts:
ReadcountMaster_uniquegenes2_forGEO_onlySinglecells.txt
processed data file; differential expression analysis:
ppolecandidates_singlecell_PvsNP_modelbygroup_forGEO.txt


title: D14-400956

description:
muscle cell by qPCR collagen expression
140929Red_D14-400956
processed data file; raw read counts:
ReadcountMaster_uniquegenes2_forGEO_onlySinglecells.txt
processed data file; differential expression analysis:
ppolecandidates_singlecell_PvsNP_modelbygroup_forGEO.txt


title: D14-400960

description:
muscle cell by qPCR collagen expression
140929Red_D14-400960
processed data file; raw read counts:
ReadcountMaster_uniquegenes2_forGEO_onlySinglecells.txt
processed data file; differential expression analysis:
ppolecandidates_singlecell_PvsNP_modelbygroup_forGEO.txt


title: D14-400953

description:
muscle cell by qPCR collagen expression
140929Red_D14-400953
processed data file; raw read counts:
ReadcountMaster_uniquegenes2_forGEO_onlySinglecells.txt
processed data file; differential expression analysis:
ppolecandidates_singlecell_PvsNP_modelbygroup_forGEO.txt


title: D14-400961

description:
muscle cell by qPCR collagen expression
140929Red_D14-400961
processed data file; raw read counts:
ReadcountMaster_uniquegenes2_forGEO_onlySinglecells.txt
processed data file; differential expression analysis:
ppolecandidates_singlecell_PvsNP_modelbygroup_forGEO.txt


title: D14-400963

description:
muscle cell by qPCR collagen expression
140929Red_D14-400963
processed data file; raw read counts:
ReadcountMaster_uniquegenes2_forGEO_onlySinglecells.txt
processed data file; differential expression analysis:
ppolecandidates_singlecell_PvsNP_modelbygroup_forGEO.txt


title: D14-400962

description:
muscle cell by qPCR collagen expression
140929Red_D14-400962
processed data file; raw read counts:
ReadcountMaster_uniquegenes2_forGEO_onlySinglecells.txt
processed data file; differential expression analysis:
ppolecandidates_singlecell_PvsNP_modelbygroup_forGEO.txt


title: D14-400955

description:
muscle cell by qPCR collagen expression
140929Red_D14-400955
processed data file; raw read counts:
ReadcountMaster_uniquegenes2_forGEO_onlySinglecells.txt
processed data file; differential expression analysis:
ppolecandidates_singlecell_PvsNP_modelbygroup_forGEO.txt


title: D14-400951

description:
muscle cell by qPCR collagen expression
140929Red_D14-400951
processed data file; raw read counts:
ReadcountMaster_uniquegenes2_forGEO_onlySinglecells.txt
processed data file; differential expression analysis:
ppolecandidates_singlecell_PvsNP_modelbygroup_forGEO.txt


title: D16-4594 [nr4A1_4w2]

description:
160517Red_D16-4594
processed data file; raw read counts:
Readcountmaster_tail_mRNAonly_forGEO.txt
processed data file; differential expression analysis:
nr4Avsunc22_RNAi_tail_collapsedisoforms_baseMeanAavg_lessthan100deleted_forGEO.txt

data_processing:
Basecalls performed using CASAVA version 1.7.0.
Reads were trimmed using Trimmomatic-0.32 to remove SmartSeq2 adaptor sequences and low quality 3′ base pairs, and only transcripts with 30bp or more were used for subsequent analysis.
Reads were mapped to dd_Smed_v4 planarian transcriptome assembly using bowtie 1 with --best to generate rawreadcounts file.
Reads for isotigs of contigs (all contig ids that vary only by the final number) were summed.
Reads for mitochondrial and ribosomal RNA (dd_Smed_v4_7_0, and dd_Smed_v4_4_1, mtRNA, rRNA_5s) were discarded.
Differential gene expression analysis was performed between nr4A RNAi and control RNAi heads and tails within each time point (2, 3, 4, and 5 weeks of RNAi) using DESeq.
Transcripts with base meanA average <100 were excluded from analysis
Genome_build: dd_Smed_v4
Supplementary_files_format_and_content: Rawreadcounts: Tab-delineated text file includes unnormalized read counts of contigs. DESeq analyses: tab-delineated text file generated using DESeq differential gene analysis program comparing raw read counts of each transcript in nr4A RNAi vs. control RNAi heads and tails in each of the RNAi time points.

source_name: nr4A_4_Planarian tail

growth_protocol: Asexual Schmidtea mediterranea strain (CIW4) animals starved 7 days before transection of heads and tails for RNA sequencing

extract_protocol:
Resected tissues were homogenized using Qiagen TissueLyser III, and RNA was extracted using TRIzol
cDNA and sequencing libraries were constructed using TruSeq RNA Library Prep Kit V2.

treatment_protocol: Heads were amputated just posterior to the eyes; transverse tail amputation lines were 1/4 of the distance between the tail tip and the posterior aspect of pharynx.

tag: control or nr4a rnai

tag: weeks of control or nr4a rnai

value: Planarian tail


title: D16-4592 [unc22_4w3]

description:
160517Red_D16-4592
processed data file; raw read counts:
Readcountmaster_tail_mRNAonly_forGEO.txt
processed data file; differential expression analysis:
nr4Avsunc22_RNAi_tail_collapsedisoforms_baseMeanAavg_lessthan100deleted_forGEO.txt

source_name: control_4_Planarian tail

value: control


title: D14-400950

description:
muscle cell by qPCR collagen expression
140929Red_D14-400950
processed data file; raw read counts:
ReadcountMaster_uniquegenes2_forGEO_onlySinglecells.txt
processed data file; differential expression analysis:
ppolecandidates_singlecell_PvsNP_modelbygroup_forGEO.txt


title: D16-4597 [nr4A1_5w3]

description:
160517Red_D16-4597
processed data file; raw read counts:
Readcountmaster_tail_mRNAonly_forGEO.txt
processed data file; differential expression analysis:
nr4Avsunc22_RNAi_tail_collapsedisoforms_baseMeanAavg_lessthan100deleted_forGEO.txt

source_name: nr4A_5_Planarian tail


title: D14-400949

description:
muscle cell by qPCR collagen expression
140929Red_D14-400949
processed data file; raw read counts:
ReadcountMaster_uniquegenes2_forGEO_onlySinglecells.txt
processed data file; differential expression analysis:
ppolecandidates_singlecell_PvsNP_modelbygroup_forGEO.txt


title: D16-4593 [nr4A1_4w1]

description:
160517Red_D16-4593
processed data file; raw read counts:
Readcountmaster_tail_mRNAonly_forGEO.txt
processed data file; differential expression analysis:
nr4Avsunc22_RNAi_tail_collapsedisoforms_baseMeanAavg_lessthan100deleted_forGEO.txt


title: D16-4596 [unc22_5w3]

description:
160517Red_D16-4596
processed data file; raw read counts:
Readcountmaster_tail_mRNAonly_forGEO.txt
processed data file; differential expression analysis:
nr4Avsunc22_RNAi_tail_collapsedisoforms_baseMeanAavg_lessthan100deleted_forGEO.txt

source_name: control_5_Planarian tail


title: D16-4591 [unc22_4w2]

description:
160517Red_D16-4591
processed data file; raw read counts:
Readcountmaster_tail_mRNAonly_forGEO.txt
processed data file; differential expression analysis:
nr4Avsunc22_RNAi_tail_collapsedisoforms_baseMeanAavg_lessthan100deleted_forGEO.txt


title: D16-4590 [unc22_4w1]

description:
160517Red_D16-4590
processed data file; raw read counts:
Readcountmaster_tail_mRNAonly_forGEO.txt
processed data file; differential expression analysis:
nr4Avsunc22_RNAi_tail_collapsedisoforms_baseMeanAavg_lessthan100deleted_forGEO.txt


title: A6Ba/F3-gp130 cells stimulated with GFP-PFC (exon-level)

description: RNA expression value derived from Expression Console software; core-exon analysis

data_processing: The data were analyzed with Affymetrix Expression  Console  using default analysis settings for RNA analyses  for  gene default and exon default .CHP files.

extract_protocol: Total RNA extraction was made with RNeasy mini kit (Qiagen, Hilden, Germany) including DNAse digestion according to the manufacturer's instructions. RNA quality was evaluated using an Agilent 2100 Bioanalyzer and only high quality RNA (RIN > 8) was used for microarray analysis.

tag: cell line vendor

value: Ba/F3 (DSMZ no.:ACC 300)

tag: transfection

value: untransfected

tag: stimulation

value: GFP-PFC (50µl/ml)


title: D16-4595 [nr4A1_4w3]

description:
160517Red_D16-4595
processed data file; raw read counts:
Readcountmaster_tail_mRNAonly_forGEO.txt
processed data file; differential expression analysis:
nr4Avsunc22_RNAi_tail_collapsedisoforms_baseMeanAavg_lessthan100deleted_forGEO.txt


title: D16-4589 [nr4A1_5w2]

description:
160517Red_D16-4589
processed data file; raw read counts:
Readcountmaster_tail_mRNAonly_forGEO.txt
processed data file; differential expression analysis:
nr4Avsunc22_RNAi_tail_collapsedisoforms_baseMeanAavg_lessthan100deleted_forGEO.txt


title: D14-400966

description:
muscle cell by qPCR collagen expression
140929Red_D14-400966
processed data file; raw read counts:
ReadcountMaster_uniquegenes2_forGEO_onlySinglecells.txt
processed data file; differential expression analysis:
ppolecandidates_singlecell_PvsNP_modelbygroup_forGEO.txt

value: regenerating animal 72 hours post transverse amputation

tag: cell type


title: D16-4588 [unc22_5w2]

description:
160517Red_D16-4588
processed data file; raw read counts:
Readcountmaster_tail_mRNAonly_forGEO.txt
processed data file; differential expression analysis:
nr4Avsunc22_RNAi_tail_collapsedisoforms_baseMeanAavg_lessthan100deleted_forGEO.txt


title: D14-400964

description:
muscle cell by qPCR collagen expression
140929Red_D14-400964
processed data file; raw read counts:
ReadcountMaster_uniquegenes2_forGEO_onlySinglecells.txt
processed data file; differential expression analysis:
ppolecandidates_singlecell_PvsNP_modelbygroup_forGEO.txt


title: B2Ba/F3-gp130-CIR1 stimulated with GFP-PFC (exon-level)


title: D16-4582 [unc22_3w1]

description:
160517Red_D16-4582
processed data file; raw read counts:
Readcountmaster_tail_mRNAonly_forGEO.txt
processed data file; differential expression analysis:
nr4Avsunc22_RNAi_tail_collapsedisoforms_baseMeanAavg_lessthan100deleted_forGEO.txt

source_name: control_3_Planarian tail


title: D16-4581 [nr4A1_5w1]

description:
160517Red_D16-4581
processed data file; raw read counts:
Readcountmaster_tail_mRNAonly_forGEO.txt
processed data file; differential expression analysis:
nr4Avsunc22_RNAi_tail_collapsedisoforms_baseMeanAavg_lessthan100deleted_forGEO.txt


title: D16-4583 [unc22_3w2]

description:
160517Red_D16-4583
processed data file; raw read counts:
Readcountmaster_tail_mRNAonly_forGEO.txt
processed data file; differential expression analysis:
nr4Avsunc22_RNAi_tail_collapsedisoforms_baseMeanAavg_lessthan100deleted_forGEO.txt


title: D16-4585 [nr4A1_3w1]

description:
160517Red_D16-4585
processed data file; raw read counts:
Readcountmaster_tail_mRNAonly_forGEO.txt
processed data file; differential expression analysis:
nr4Avsunc22_RNAi_tail_collapsedisoforms_baseMeanAavg_lessthan100deleted_forGEO.txt

source_name: nr4A_3_Planarian tail


title: D16-4579 [nr4A1_2w3]

description:
160517Red_D16-4579
processed data file; raw read counts:
Readcountmaster_tail_mRNAonly_forGEO.txt
processed data file; differential expression analysis:
nr4Avsunc22_RNAi_tail_collapsedisoforms_baseMeanAavg_lessthan100deleted_forGEO.txt

source_name: nr4A_2_Planarian tail


title: D16-4587 [nr4A1_3w3]

description:
160517Red_D16-4587
processed data file; raw read counts:
Readcountmaster_tail_mRNAonly_forGEO.txt
processed data file; differential expression analysis:
nr4Avsunc22_RNAi_tail_collapsedisoforms_baseMeanAavg_lessthan100deleted_forGEO.txt


title: D16-3180 [nr4A_4w2]

description:
160406RedB_D16-3180
processed data file; raw read counts:
Rawreadsmaster_mergedisoforms_head_forGEO.txt
processed data file; differential expression analysis:
nr4Avsunc22_RNAi_head_collapsedisoforms_baseMeanAavg_lessthan100deleted_forGEO.txt

source_name: nr4A_4_Planarian head

value: Planarian head


title: D16-3174 [unc22_5w2]

description:
160406RedB_D16-3174
processed data file; raw read counts:
Rawreadsmaster_mergedisoforms_head_forGEO.txt
processed data file; differential expression analysis:
nr4Avsunc22_RNAi_head_collapsedisoforms_baseMeanAavg_lessthan100deleted_forGEO.txt

source_name: control_5_Planarian head


title: D16-3175 [nr4A_5w2]

description:
160406RedB_D16-3175
processed data file; raw read counts:
Rawreadsmaster_mergedisoforms_head_forGEO.txt
processed data file; differential expression analysis:
nr4Avsunc22_RNAi_head_collapsedisoforms_baseMeanAavg_lessthan100deleted_forGEO.txt

source_name: nr4A_5_Planarian head


title: D16-3173 [nr4A_3w3]

description:
160406RedB_D16-3173
processed data file; raw read counts:
Rawreadsmaster_mergedisoforms_head_forGEO.txt
processed data file; differential expression analysis:
nr4Avsunc22_RNAi_head_collapsedisoforms_baseMeanAavg_lessthan100deleted_forGEO.txt

source_name: nr4A_3_Planarian head


title: D16-3182 [unc22_5w3]

description:
160406RedB_D16-3182
processed data file; raw read counts:
Rawreadsmaster_mergedisoforms_head_forGEO.txt
processed data file; differential expression analysis:
nr4Avsunc22_RNAi_head_collapsedisoforms_baseMeanAavg_lessthan100deleted_forGEO.txt


title: D16-3169 [unc22_3w2]

description:
160406RedB_D16-3169
processed data file; raw read counts:
Rawreadsmaster_mergedisoforms_head_forGEO.txt
processed data file; differential expression analysis:
nr4Avsunc22_RNAi_head_collapsedisoforms_baseMeanAavg_lessthan100deleted_forGEO.txt

source_name: control_3_Planarian head


title: D16-3172 [nr4A_3w2]

description:
160406RedB_D16-3172
processed data file; raw read counts:
Rawreadsmaster_mergedisoforms_head_forGEO.txt
processed data file; differential expression analysis:
nr4Avsunc22_RNAi_head_collapsedisoforms_baseMeanAavg_lessthan100deleted_forGEO.txt


title: D16-3183 [nr4A_5w3]

description:
160406RedB_D16-3183
processed data file; raw read counts:
Rawreadsmaster_mergedisoforms_head_forGEO.txt
processed data file; differential expression analysis:
nr4Avsunc22_RNAi_head_collapsedisoforms_baseMeanAavg_lessthan100deleted_forGEO.txt


title: D16-3170 [unc22_3w3]

description:
160406RedB_D16-3170
processed data file; raw read counts:
Rawreadsmaster_mergedisoforms_head_forGEO.txt
processed data file; differential expression analysis:
nr4Avsunc22_RNAi_head_collapsedisoforms_baseMeanAavg_lessthan100deleted_forGEO.txt


title: D16-4578 [nr4A1_2w2]

description:
160517Red_D16-4578
processed data file; raw read counts:
Readcountmaster_tail_mRNAonly_forGEO.txt
processed data file; differential expression analysis:
nr4Avsunc22_RNAi_tail_collapsedisoforms_baseMeanAavg_lessthan100deleted_forGEO.txt


title: D16-4575 [unc22_2w2]

description:
160517Red_D16-4575
processed data file; raw read counts:
Readcountmaster_tail_mRNAonly_forGEO.txt
processed data file; differential expression analysis:
nr4Avsunc22_RNAi_tail_collapsedisoforms_baseMeanAavg_lessthan100deleted_forGEO.txt

source_name: control_2_Planarian tail


title: D16-3176 [unc22_4w1]

description:
160406RedB_D16-3176
processed data file; raw read counts:
Rawreadsmaster_mergedisoforms_head_forGEO.txt
processed data file; differential expression analysis:
nr4Avsunc22_RNAi_head_collapsedisoforms_baseMeanAavg_lessthan100deleted_forGEO.txt

source_name: control_4_Planarian head


title: D16-4576 [unc22_2w3]

description:
160517Red_D16-4576
processed data file; raw read counts:
Readcountmaster_tail_mRNAonly_forGEO.txt
processed data file; differential expression analysis:
nr4Avsunc22_RNAi_tail_collapsedisoforms_baseMeanAavg_lessthan100deleted_forGEO.txt


title: D16-3179 [nr4A_4w1]

description:
160406RedB_D16-3179
processed data file; raw read counts:
Rawreadsmaster_mergedisoforms_head_forGEO.txt
processed data file; differential expression analysis:
nr4Avsunc22_RNAi_head_collapsedisoforms_baseMeanAavg_lessthan100deleted_forGEO.txt


title: D16-4580 [unc22_5w1]

description:
160517Red_D16-4580
processed data file; raw read counts:
Readcountmaster_tail_mRNAonly_forGEO.txt
processed data file; differential expression analysis:
nr4Avsunc22_RNAi_tail_collapsedisoforms_baseMeanAavg_lessthan100deleted_forGEO.txt


title: D16-3171 [nr4A_3w1]

description:
160406RedB_D16-3171
processed data file; raw read counts:
Rawreadsmaster_mergedisoforms_head_forGEO.txt
processed data file; differential expression analysis:
nr4Avsunc22_RNAi_head_collapsedisoforms_baseMeanAavg_lessthan100deleted_forGEO.txt


title: D16-4586 [nr4A1_3w2]

description:
160517Red_D16-4586
processed data file; raw read counts:
Readcountmaster_tail_mRNAonly_forGEO.txt
processed data file; differential expression analysis:
nr4Avsunc22_RNAi_tail_collapsedisoforms_baseMeanAavg_lessthan100deleted_forGEO.txt


title: D16-4577 [nr4A1_2w1]

description:
160517Red_D16-4577
processed data file; raw read counts:
Readcountmaster_tail_mRNAonly_forGEO.txt
processed data file; differential expression analysis:
nr4Avsunc22_RNAi_tail_collapsedisoforms_baseMeanAavg_lessthan100deleted_forGEO.txt


title: D16-4584 [unc22_3w3]

description:
160517Red_D16-4584
processed data file; raw read counts:
Readcountmaster_tail_mRNAonly_forGEO.txt
processed data file; differential expression analysis:
nr4Avsunc22_RNAi_tail_collapsedisoforms_baseMeanAavg_lessthan100deleted_forGEO.txt


title: D16-3178 [unc22_4w3]

description:
160406RedB_D16-3178
processed data file; raw read counts:
Rawreadsmaster_mergedisoforms_head_forGEO.txt
processed data file; differential expression analysis:
nr4Avsunc22_RNAi_head_collapsedisoforms_baseMeanAavg_lessthan100deleted_forGEO.txt


title: D16-3181 [nr4A_4w3]

description:
160406RedB_D16-3181
processed data file; raw read counts:
Rawreadsmaster_mergedisoforms_head_forGEO.txt
processed data file; differential expression analysis:
nr4Avsunc22_RNAi_head_collapsedisoforms_baseMeanAavg_lessthan100deleted_forGEO.txt


title: D16-4574 [unc22_2w1]

description:
160517Red_D16-4574
processed data file; raw read counts:
Readcountmaster_tail_mRNAonly_forGEO.txt
processed data file; differential expression analysis:
nr4Avsunc22_RNAi_tail_collapsedisoforms_baseMeanAavg_lessthan100deleted_forGEO.txt


title: D16-3177 [unc22_4w2]

description:
160406RedB_D16-3177
processed data file; raw read counts:
Rawreadsmaster_mergedisoforms_head_forGEO.txt
processed data file; differential expression analysis:
nr4Avsunc22_RNAi_head_collapsedisoforms_baseMeanAavg_lessthan100deleted_forGEO.txt


title: D16-3168 [unc22_3w1]

description:
160406RedB_D16-3168
processed data file; raw read counts:
Rawreadsmaster_mergedisoforms_head_forGEO.txt
processed data file; differential expression analysis:
nr4Avsunc22_RNAi_head_collapsedisoforms_baseMeanAavg_lessthan100deleted_forGEO.txt


title: D16-3164 [nr4A_2w2]

description:
160406RedB_D16-3164
processed data file; raw read counts:
Rawreadsmaster_mergedisoforms_head_forGEO.txt
processed data file; differential expression analysis:
nr4Avsunc22_RNAi_head_collapsedisoforms_baseMeanAavg_lessthan100deleted_forGEO.txt

source_name: nr4A_2_Planarian head


title: D16-3166 [unc22_5w1]

description:
160406RedB_D16-3166
processed data file; raw read counts:
Rawreadsmaster_mergedisoforms_head_forGEO.txt
processed data file; differential expression analysis:
nr4Avsunc22_RNAi_head_collapsedisoforms_baseMeanAavg_lessthan100deleted_forGEO.txt


title: D16-3165 [nr4A_2w3]

description:
160406RedB_D16-3165
processed data file; raw read counts:
Rawreadsmaster_mergedisoforms_head_forGEO.txt
processed data file; differential expression analysis:
nr4Avsunc22_RNAi_head_collapsedisoforms_baseMeanAavg_lessthan100deleted_forGEO.txt


title: D16-3163 [nr4A_2w1]

description:
160406RedB_D16-3163
processed data file; raw read counts:
Rawreadsmaster_mergedisoforms_head_forGEO.txt
processed data file; differential expression analysis:
nr4Avsunc22_RNAi_head_collapsedisoforms_baseMeanAavg_lessthan100deleted_forGEO.txt


title: D14-1369 [Ar2]

description:
140228Red_D14-1369
processed data file; raw read counts:
rPole_rawreadcounts_complete_Ar_NAr_forGEO.txt
processed data file; differential expression analysis:
ArvsNAr_complete.txt

data_processing:
Basecalls performed using CASAVA version 1.7.0.
Reads were trimmed using Trimmomatic-0.32 to remove SmartSeq2 adaptor sequences and low quality 3′ base pairs, and only transcripts with 30bp or more were used for subsequent analysis.
Reads were mapped to dd_Smed_v4 planarian transcriptome assembly using bowtie 1 with --best to generate rawreadcounts file.
Differential gene expression analysis was performed between pole-containing and non-pole-containing samples using DESeq
Genome_build: dd_Smed_v4
Supplementary_files_format_and_content: Rawreadcounts: Tab-delineated text file includes unnormalized read counts of contigs. DESeq analyses: tab-delineated text file generated using DESeq differential gene analysis program comparing raw read counts of each transcript in pole-containing vs. non-pole containing pieces

source_name: regenerating_Pole-containing anterior blastema region

growth_protocol: Asexual Schmidtea mediterranea strain (CIW4) animals starved 7-14 days before surgical resections.

treatment_protocol: Head tip regions from uinjured animals were resected after starvation period, as above. Animals were transversely amputated (just posterior to the eyes), and allowed to regenerate for 72 hours before surgical resection of anterior blastema regions to obtain tissue from 72-hour regenerating animals.

value: regenerating animal 72-hours-post transverse amputation


title: D14-1371 [NAr1]

description:
140228Red_D14-1371
processed data file; raw read counts:
rPole_rawreadcounts_complete_Ar_NAr_forGEO.txt
processed data file; differential expression analysis:
ArvsNAr_complete.txt

source_name: regenerating_Non-pole-containing anterior blastema flanking region


title: D14-784 [Ai2]

description:
140206RedB_D14-784
processed data file; raw read counts:
iPole_rawreadcounts_DresdenMap_iA_iNA_forGEO.txt
processed data file; differential expression analysis:
AivsNAi_DresdenMap.txt

source_name: uninjured_Pole-containing head tip region

value: Pole-containing head tip region


title: D14-786 [NAi1]

description:
140206RedB_D14-786
processed data file; raw read counts:
iPole_rawreadcounts_DresdenMap_iA_iNA_forGEO.txt
processed data file; differential expression analysis:
AivsNAi_DresdenMap.txt

source_name: uninjured_Non-pole-containing head tip flanking region


title: D14-788 [NAi3]

description:
140206RedB_D14-788
processed data file; raw read counts:
iPole_rawreadcounts_DresdenMap_iA_iNA_forGEO.txt
processed data file; differential expression analysis:
AivsNAi_DresdenMap.txt

value: Non-pole-containing head tip flanking region


title: D14-783 [Ai1]

description:
140206RedB_D14-783
processed data file; raw read counts:
iPole_rawreadcounts_DresdenMap_iA_iNA_forGEO.txt
processed data file; differential expression analysis:
AivsNAi_DresdenMap.txt


title: D14-401100

description:
muscle cell by qPCR collagen expression
140929Red_D14-401100
processed data file; raw read counts:
ReadcountMaster_uniquegenes2_forGEO_onlySinglecells.txt
processed data file; differential expression analysis:
ppolecandidates_singlecell_PvsNP_modelbygroup_forGEO.txt


title: D14-401097

description:
muscle cell by qPCR collagen expression
140929Red_D14-401097
processed data file; raw read counts:
ReadcountMaster_uniquegenes2_forGEO_onlySinglecells.txt
processed data file; differential expression analysis:
ppolecandidates_singlecell_PvsNP_modelbygroup_forGEO.txt


title: D14-401094

description:
muscle cell by qPCR collagen expression
140929Red_D14-401094
processed data file; raw read counts:
ReadcountMaster_uniquegenes2_forGEO_onlySinglecells.txt
processed data file; differential expression analysis:
ppolecandidates_singlecell_PvsNP_modelbygroup_forGEO.txt


title: D14-1373 [NAr3]

description:
140228Red_D14-1373
processed data file; raw read counts:
rPole_rawreadcounts_complete_Ar_NAr_forGEO.txt
processed data file; differential expression analysis:
ArvsNAr_complete.txt

value: Non-pole-containing anterior blastema flanking region


title: D14-401098

description:
muscle cell by qPCR collagen expression
140929Red_D14-401098
processed data file; raw read counts:
ReadcountMaster_uniquegenes2_forGEO_onlySinglecells.txt
processed data file; differential expression analysis:
ppolecandidates_singlecell_PvsNP_modelbygroup_forGEO.txt


title: D16-3161 [unc22_2w2]

description:
160406RedB_D16-3161
processed data file; raw read counts:
Rawreadsmaster_mergedisoforms_head_forGEO.txt
processed data file; differential expression analysis:
nr4Avsunc22_RNAi_head_collapsedisoforms_baseMeanAavg_lessthan100deleted_forGEO.txt

source_name: control_2_Planarian head


title: D14-1370 [Ar3]

description:
140228Red_D14-1370
processed data file; raw read counts:
rPole_rawreadcounts_complete_Ar_NAr_forGEO.txt
processed data file; differential expression analysis:
ArvsNAr_complete.txt

value: Pole-containing anterior blastema region


title: D14-401093

description:
muscle cell by qPCR collagen expression
140929Red_D14-401093
processed data file; raw read counts:
ReadcountMaster_uniquegenes2_forGEO_onlySinglecells.txt
processed data file; differential expression analysis:
ppolecandidates_singlecell_PvsNP_modelbygroup_forGEO.txt

value: asexual CIW4


title: D16-3167 [nr4A_5w1]

description:
160406RedB_D16-3167
processed data file; raw read counts:
Rawreadsmaster_mergedisoforms_head_forGEO.txt
processed data file; differential expression analysis:
nr4Avsunc22_RNAi_head_collapsedisoforms_baseMeanAavg_lessthan100deleted_forGEO.txt

value: 2N (non-dividing)


title: D14-401095

description:
muscle cell by qPCR collagen expression
140929Red_D14-401095
processed data file; raw read counts:
ReadcountMaster_uniquegenes2_forGEO_onlySinglecells.txt
processed data file; differential expression analysis:
ppolecandidates_singlecell_PvsNP_modelbygroup_forGEO.txt


title: D14-401092

description:
muscle cell by qPCR collagen expression
140929Red_D14-401092
processed data file; raw read counts:
ReadcountMaster_uniquegenes2_forGEO_onlySinglecells.txt
processed data file; differential expression analysis:
ppolecandidates_singlecell_PvsNP_modelbygroup_forGEO.txt


title: D14-401091

description:
muscle cell by qPCR collagen expression
140929Red_D14-401091
processed data file; raw read counts:
ReadcountMaster_uniquegenes2_forGEO_onlySinglecells.txt
processed data file; differential expression analysis:
ppolecandidates_singlecell_PvsNP_modelbygroup_forGEO.txt


title: D16-3162 [unc22_2w3]

description:
160406RedB_D16-3162
processed data file; raw read counts:
Rawreadsmaster_mergedisoforms_head_forGEO.txt
processed data file; differential expression analysis:
nr4Avsunc22_RNAi_head_collapsedisoforms_baseMeanAavg_lessthan100deleted_forGEO.txt


title: D14-1372 [NAr2]

description:
140228Red_D14-1372
processed data file; raw read counts:
rPole_rawreadcounts_complete_Ar_NAr_forGEO.txt
processed data file; differential expression analysis:
ArvsNAr_complete.txt


title: D14-401089

description:
muscle cell by qPCR collagen expression
140929Red_D14-401089
processed data file; raw read counts:
ReadcountMaster_uniquegenes2_forGEO_onlySinglecells.txt
processed data file; differential expression analysis:
ppolecandidates_singlecell_PvsNP_modelbygroup_forGEO.txt


title: D14-785 [Ai3]

description:
140206RedB_D14-785
processed data file; raw read counts:
iPole_rawreadcounts_DresdenMap_iA_iNA_forGEO.txt
processed data file; differential expression analysis:
AivsNAi_DresdenMap.txt

value: uninjured


title: D14-787 [NAi2]

description:
140206RedB_D14-787
processed data file; raw read counts:
iPole_rawreadcounts_DresdenMap_iA_iNA_forGEO.txt
processed data file; differential expression analysis:
AivsNAi_DresdenMap.txt


title: D14-401090

description:
muscle cell by qPCR collagen expression
140929Red_D14-401090
processed data file; raw read counts:
ReadcountMaster_uniquegenes2_forGEO_onlySinglecells.txt
processed data file; differential expression analysis:
ppolecandidates_singlecell_PvsNP_modelbygroup_forGEO.txt

value: non-pole muscle cell


title: D16-3160 [unc22_2w1]

description:
160406RedB_D16-3160
processed data file; raw read counts:
Rawreadsmaster_mergedisoforms_head_forGEO.txt
processed data file; differential expression analysis:
nr4Avsunc22_RNAi_head_collapsedisoforms_baseMeanAavg_lessthan100deleted_forGEO.txt


title: D14-1368 [Ar1]

description:
140228Red_D14-1368
processed data file; raw read counts:
rPole_rawreadcounts_complete_Ar_NAr_forGEO.txt
processed data file; differential expression analysis:
ArvsNAr_complete.txt


title: D14-401088

description:
muscle cell by qPCR collagen expression
140929Red_D14-401088
processed data file; raw read counts:
ReadcountMaster_uniquegenes2_forGEO_onlySinglecells.txt
processed data file; differential expression analysis:
ppolecandidates_singlecell_PvsNP_modelbygroup_forGEO.txt


title: D14-401096

description:
muscle cell by qPCR collagen expression
140929Red_D14-401096
processed data file; raw read counts:
ReadcountMaster_uniquegenes2_forGEO_onlySinglecells.txt
processed data file; differential expression analysis:
ppolecandidates_singlecell_PvsNP_modelbygroup_forGEO.txt


title: D14-401087

description:
muscle cell by qPCR collagen expression
140929Red_D14-401087
processed data file; raw read counts:
ReadcountMaster_uniquegenes2_forGEO_onlySinglecells.txt
processed data file; differential expression analysis:
ppolecandidates_singlecell_PvsNP_modelbygroup_forGEO.txt


title: D14-401084

description:
muscle cell by qPCR collagen expression
140929Red_D14-401084
processed data file; raw read counts:
ReadcountMaster_uniquegenes2_forGEO_onlySinglecells.txt
processed data file; differential expression analysis:
ppolecandidates_singlecell_PvsNP_modelbygroup_forGEO.txt


title: D14-401086

description:
muscle cell by qPCR collagen expression
140929Red_D14-401086
processed data file; raw read counts:
ReadcountMaster_uniquegenes2_forGEO_onlySinglecells.txt
processed data file; differential expression analysis:
ppolecandidates_singlecell_PvsNP_modelbygroup_forGEO.txt


title: D14-401081

description:
muscle cell by qPCR collagen expression
140929Red_D14-401081
processed data file; raw read counts:
ReadcountMaster_uniquegenes2_forGEO_onlySinglecells.txt
processed data file; differential expression analysis:
ppolecandidates_singlecell_PvsNP_modelbygroup_forGEO.txt


title: D14-401080

description:
muscle cell by qPCR collagen expression
140929Red_D14-401080
processed data file; raw read counts:
ReadcountMaster_uniquegenes2_forGEO_onlySinglecells.txt
processed data file; differential expression analysis:
ppolecandidates_singlecell_PvsNP_modelbygroup_forGEO.txt


title: D14-401079

description:
muscle cell by qPCR collagen expression
140929Red_D14-401079
processed data file; raw read counts:
ReadcountMaster_uniquegenes2_forGEO_onlySinglecells.txt
processed data file; differential expression analysis:
ppolecandidates_singlecell_PvsNP_modelbygroup_forGEO.txt


title: D14-401082

description:
muscle cell by qPCR collagen expression
140929Red_D14-401082
processed data file; raw read counts:
ReadcountMaster_uniquegenes2_forGEO_onlySinglecells.txt
processed data file; differential expression analysis:
ppolecandidates_singlecell_PvsNP_modelbygroup_forGEO.txt


title: D14-401083

description:
muscle cell by qPCR collagen expression
140929Red_D14-401083
processed data file; raw read counts:
ReadcountMaster_uniquegenes2_forGEO_onlySinglecells.txt
processed data file; differential expression analysis:
ppolecandidates_singlecell_PvsNP_modelbygroup_forGEO.txt


title: D14-401076

description:
muscle cell by qPCR collagen expression
140929Red_D14-401076
processed data file; raw read counts:
ReadcountMaster_uniquegenes2_forGEO_onlySinglecells.txt
processed data file; differential expression analysis:
ppolecandidates_singlecell_PvsNP_modelbygroup_forGEO.txt


title: D14-401078

description:
muscle cell by qPCR collagen expression
140929Red_D14-401078
processed data file; raw read counts:
ReadcountMaster_uniquegenes2_forGEO_onlySinglecells.txt
processed data file; differential expression analysis:
ppolecandidates_singlecell_PvsNP_modelbygroup_forGEO.txt


title: D14-401075

description:
muscle cell by qPCR collagen expression
140929Red_D14-401075
processed data file; raw read counts:
ReadcountMaster_uniquegenes2_forGEO_onlySinglecells.txt
processed data file; differential expression analysis:
ppolecandidates_singlecell_PvsNP_modelbygroup_forGEO.txt


title: D14-401073

description:
muscle cell by qPCR collagen expression
140929Red_D14-401073
processed data file; raw read counts:
ReadcountMaster_uniquegenes2_forGEO_onlySinglecells.txt
processed data file; differential expression analysis:
ppolecandidates_singlecell_PvsNP_modelbygroup_forGEO.txt


title: D14-401074

description:
muscle cell by qPCR collagen expression
140929Red_D14-401074
processed data file; raw read counts:
ReadcountMaster_uniquegenes2_forGEO_onlySinglecells.txt
processed data file; differential expression analysis:
ppolecandidates_singlecell_PvsNP_modelbygroup_forGEO.txt


title: D14-401077

description:
muscle cell by qPCR collagen expression
140929Red_D14-401077
processed data file; raw read counts:
ReadcountMaster_uniquegenes2_forGEO_onlySinglecells.txt
processed data file; differential expression analysis:
ppolecandidates_singlecell_PvsNP_modelbygroup_forGEO.txt


title: D14-401072

description:
muscle cell by qPCR collagen expression
140929Red_D14-401072
processed data file; raw read counts:
ReadcountMaster_uniquegenes2_forGEO_onlySinglecells.txt
processed data file; differential expression analysis:
ppolecandidates_singlecell_PvsNP_modelbygroup_forGEO.txt


title: D14-401071

description:
muscle cell by qPCR collagen expression
140929Red_D14-401071
processed data file; raw read counts:
ReadcountMaster_uniquegenes2_forGEO_onlySinglecells.txt
processed data file; differential expression analysis:
ppolecandidates_singlecell_PvsNP_modelbygroup_forGEO.txt


title: D14-401070

description:
muscle cell by qPCR collagen expression
140929Red_D14-401070
processed data file; raw read counts:
ReadcountMaster_uniquegenes2_forGEO_onlySinglecells.txt
processed data file; differential expression analysis:
ppolecandidates_singlecell_PvsNP_modelbygroup_forGEO.txt


title: D14-401068

description:
muscle cell by qPCR collagen expression
140929Red_D14-401068
processed data file; raw read counts:
ReadcountMaster_uniquegenes2_forGEO_onlySinglecells.txt
processed data file; differential expression analysis:
ppolecandidates_singlecell_PvsNP_modelbygroup_forGEO.txt


title: D14-401066

description:
muscle cell by qPCR collagen expression
140929Red_D14-401066
processed data file; raw read counts:
ReadcountMaster_uniquegenes2_forGEO_onlySinglecells.txt
processed data file; differential expression analysis:
ppolecandidates_singlecell_PvsNP_modelbygroup_forGEO.txt


title: D14-401064

description:
muscle cell by qPCR collagen expression
140929Red_D14-401064
processed data file; raw read counts:
ReadcountMaster_uniquegenes2_forGEO_onlySinglecells.txt
processed data file; differential expression analysis:
ppolecandidates_singlecell_PvsNP_modelbygroup_forGEO.txt


title: D14-401065

description:
muscle cell by qPCR collagen expression
140929Red_D14-401065
processed data file; raw read counts:
ReadcountMaster_uniquegenes2_forGEO_onlySinglecells.txt
processed data file; differential expression analysis:
ppolecandidates_singlecell_PvsNP_modelbygroup_forGEO.txt


title: D14-401063

description:
muscle cell by qPCR collagen expression
140929Red_D14-401063
processed data file; raw read counts:
ReadcountMaster_uniquegenes2_forGEO_onlySinglecells.txt
processed data file; differential expression analysis:
ppolecandidates_singlecell_PvsNP_modelbygroup_forGEO.txt


title: D14-401067

description:
muscle cell by qPCR collagen expression
140929Red_D14-401067
processed data file; raw read counts:
ReadcountMaster_uniquegenes2_forGEO_onlySinglecells.txt
processed data file; differential expression analysis:
ppolecandidates_singlecell_PvsNP_modelbygroup_forGEO.txt


title: D14-401062

description:
muscle cell by qPCR collagen expression
140929Red_D14-401062
processed data file; raw read counts:
ReadcountMaster_uniquegenes2_forGEO_onlySinglecells.txt
processed data file; differential expression analysis:
ppolecandidates_singlecell_PvsNP_modelbygroup_forGEO.txt


title: D14-401061

description:
muscle cell by qPCR collagen expression
140929Red_D14-401061
processed data file; raw read counts:
ReadcountMaster_uniquegenes2_forGEO_onlySinglecells.txt
processed data file; differential expression analysis:
ppolecandidates_singlecell_PvsNP_modelbygroup_forGEO.txt


title: D14-401058

description:
muscle cell by qPCR collagen expression
140929Red_D14-401058
processed data file; raw read counts:
ReadcountMaster_uniquegenes2_forGEO_onlySinglecells.txt
processed data file; differential expression analysis:
ppolecandidates_singlecell_PvsNP_modelbygroup_forGEO.txt


title: D14-401059

description:
muscle cell by qPCR collagen expression
140929Red_D14-401059
processed data file; raw read counts:
ReadcountMaster_uniquegenes2_forGEO_onlySinglecells.txt
processed data file; differential expression analysis:
ppolecandidates_singlecell_PvsNP_modelbygroup_forGEO.txt


title: D14-401060

description:
muscle cell by qPCR collagen expression
140929Red_D14-401060
processed data file; raw read counts:
ReadcountMaster_uniquegenes2_forGEO_onlySinglecells.txt
processed data file; differential expression analysis:
ppolecandidates_singlecell_PvsNP_modelbygroup_forGEO.txt


title: D14-401057

description:
muscle cell by qPCR collagen expression
140929Red_D14-401057
processed data file; raw read counts:
ReadcountMaster_uniquegenes2_forGEO_onlySinglecells.txt
processed data file; differential expression analysis:
ppolecandidates_singlecell_PvsNP_modelbygroup_forGEO.txt


title: D14-401085

description:
muscle cell by qPCR collagen expression
140929Red_D14-401085
processed data file; raw read counts:
ReadcountMaster_uniquegenes2_forGEO_onlySinglecells.txt
processed data file; differential expression analysis:
ppolecandidates_singlecell_PvsNP_modelbygroup_forGEO.txt


title: D14-401056

description:
muscle cell by qPCR collagen expression
140929Red_D14-401056
processed data file; raw read counts:
ReadcountMaster_uniquegenes2_forGEO_onlySinglecells.txt
processed data file; differential expression analysis:
ppolecandidates_singlecell_PvsNP_modelbygroup_forGEO.txt


title: D14-401055

description:
muscle cell by qPCR collagen expression
140929Red_D14-401055
processed data file; raw read counts:
ReadcountMaster_uniquegenes2_forGEO_onlySinglecells.txt
processed data file; differential expression analysis:
ppolecandidates_singlecell_PvsNP_modelbygroup_forGEO.txt


title: D14-401053

description:
muscle cell by qPCR collagen expression
140929Red_D14-401053
processed data file; raw read counts:
ReadcountMaster_uniquegenes2_forGEO_onlySinglecells.txt
processed data file; differential expression analysis:
ppolecandidates_singlecell_PvsNP_modelbygroup_forGEO.txt


title: D14-401054

description:
muscle cell by qPCR collagen expression
140929Red_D14-401054
processed data file; raw read counts:
ReadcountMaster_uniquegenes2_forGEO_onlySinglecells.txt
processed data file; differential expression analysis:
ppolecandidates_singlecell_PvsNP_modelbygroup_forGEO.txt


title: D14-401051

description:
muscle cell by qPCR collagen expression
140929Red_D14-401051
processed data file; raw read counts:
ReadcountMaster_uniquegenes2_forGEO_onlySinglecells.txt
processed data file; differential expression analysis:
ppolecandidates_singlecell_PvsNP_modelbygroup_forGEO.txt


title: D14-401050

description:
muscle cell by qPCR collagen expression
140929Red_D14-401050
processed data file; raw read counts:
ReadcountMaster_uniquegenes2_forGEO_onlySinglecells.txt
processed data file; differential expression analysis:
ppolecandidates_singlecell_PvsNP_modelbygroup_forGEO.txt


title: D14-401052

description:
muscle cell by qPCR collagen expression
140929Red_D14-401052
processed data file; raw read counts:
ReadcountMaster_uniquegenes2_forGEO_onlySinglecells.txt
processed data file; differential expression analysis:
ppolecandidates_singlecell_PvsNP_modelbygroup_forGEO.txt


title: D14-401047

description:
muscle cell by qPCR collagen expression
140929Red_D14-401047
processed data file; raw read counts:
ReadcountMaster_uniquegenes2_forGEO_onlySinglecells.txt
processed data file; differential expression analysis:
ppolecandidates_singlecell_PvsNP_modelbygroup_forGEO.txt


title: D14-401046

description:
muscle cell by qPCR collagen expression
140929Red_D14-401046
processed data file; raw read counts:
ReadcountMaster_uniquegenes2_forGEO_onlySinglecells.txt
processed data file; differential expression analysis:
ppolecandidates_singlecell_PvsNP_modelbygroup_forGEO.txt


title: D14-401045

description:
muscle cell by qPCR collagen expression
140929Red_D14-401045
processed data file; raw read counts:
ReadcountMaster_uniquegenes2_forGEO_onlySinglecells.txt
processed data file; differential expression analysis:
ppolecandidates_singlecell_PvsNP_modelbygroup_forGEO.txt


title: D14-401044

description:
muscle cell by qPCR collagen expression
140929Red_D14-401044
processed data file; raw read counts:
ReadcountMaster_uniquegenes2_forGEO_onlySinglecells.txt
processed data file; differential expression analysis:
ppolecandidates_singlecell_PvsNP_modelbygroup_forGEO.txt


title: D14-401048

description:
muscle cell by qPCR collagen expression
140929Red_D14-401048
processed data file; raw read counts:
ReadcountMaster_uniquegenes2_forGEO_onlySinglecells.txt
processed data file; differential expression analysis:
ppolecandidates_singlecell_PvsNP_modelbygroup_forGEO.txt


title: D14-401043

description:
muscle cell by qPCR collagen expression
140929Red_D14-401043
processed data file; raw read counts:
ReadcountMaster_uniquegenes2_forGEO_onlySinglecells.txt
processed data file; differential expression analysis:
ppolecandidates_singlecell_PvsNP_modelbygroup_forGEO.txt


title: D14-401069

description:
muscle cell by qPCR collagen expression
140929Red_D14-401069
processed data file; raw read counts:
ReadcountMaster_uniquegenes2_forGEO_onlySinglecells.txt
processed data file; differential expression analysis:
ppolecandidates_singlecell_PvsNP_modelbygroup_forGEO.txt


title: D14-401042

description:
muscle cell by qPCR collagen expression
140929Red_D14-401042
processed data file; raw read counts:
ReadcountMaster_uniquegenes2_forGEO_onlySinglecells.txt
processed data file; differential expression analysis:
ppolecandidates_singlecell_PvsNP_modelbygroup_forGEO.txt


title: D14-401041

description:
muscle cell by qPCR collagen expression
140929Red_D14-401041
processed data file; raw read counts:
ReadcountMaster_uniquegenes2_forGEO_onlySinglecells.txt
processed data file; differential expression analysis:
ppolecandidates_singlecell_PvsNP_modelbygroup_forGEO.txt


title: D14-401038

description:
muscle cell by qPCR collagen expression
140929Red_D14-401038
processed data file; raw read counts:
ReadcountMaster_uniquegenes2_forGEO_onlySinglecells.txt
processed data file; differential expression analysis:
ppolecandidates_singlecell_PvsNP_modelbygroup_forGEO.txt


title: D14-401039

description:
muscle cell by qPCR collagen expression
140929Red_D14-401039
processed data file; raw read counts:
ReadcountMaster_uniquegenes2_forGEO_onlySinglecells.txt
processed data file; differential expression analysis:
ppolecandidates_singlecell_PvsNP_modelbygroup_forGEO.txt