title: Lotus japonicus nodules harvested four days after watering withdrawal rep 2 [Lj.nodule.T4.2.S20]

city: Warsaw

first: Weronika

last: Czarnocka

address: Nowoursynowska 166

department: Department of Botany

country: Poland

institute: Warsaw University of Life Sciences

description:
RNA for both plant and bacteria is present
processed data file:
Ljap-RNAseqCounts-withAnn.xlsx
Lj_nodule_T4_2

data_processing:
Preprocessing: Low quality ends and adapter sequences were trimmed off from the Illumina reads with FastX 0.0.13 and Cutadapt 1.7.1 (HannonLab, 2010; Martin, 2011). Subsequently, small reads (length < 35 bp), polyA-reads (more than 90 % of the bases equal A), ambiguous reads (containing N), low-quality reads (more than 50 % of the bases < Q25) and artifact reads (all but three bases in the read equal one base type) were filtered using using FastX 0.0.13 and ShortRead 1.16.3 (Morgan et al, 2009). With Bowtie2 2.2.4 we identified and removed reads that align to phix_illumina (Langmead & Salzberg, 2012).
Mapping: The preprocessed reads of M.truncatula/S.meliloti samples were aligned with Tophat v2.0.13 to a concatenation of reference genomes of Medicago truncatula (MedtrA17-4.0.31 from Ensembl) and Sinorhizobium meliloti (GCA000747295-1.29 from Ensembl) (Trapnell et al, 2009). The preprocessed reads of L.japonicus/M.loti samples were aligned with Tophat v2.0.13 to a concatenation of reference genomes of Lotus japonicus (Lj3.0 from Ensembl) and Mesorhizobium loti (maff303099-1.29 from Ensembl) (Trapnell et al, 2009). Cross-mapping between concatenated plant and bacteria was first evaluated as being much less than 1%. Default Tophat parameter settings were used for mapping, except for ‘min-intron-length=50’, ‘max-intron-length=10,000’, ‘no-coverage-search’ and ‘read-realign-edit-dist=3’. Using Samtools 1.1, reads with a mapping quality smaller than 20 were removed from the alignments (Li et al, 2009). Alignments from different lanes and/or runs were merged per sample.
Genome annotations: For all 4 organisms, we started from the genome annotations as provided by Ensembl Bacteria and Plants. Exon-chains from alternative transcripts were merged with Bedtools v2.17.0 mergeBed (Quinlan et al. 2010) to create unique gene-level coordinates. Information about transcripts was lifted over to the gene-level features. Gene sequences were extracted with Cufflinks v2.2.1 gffread (Trapnell et al. 2010) to compute gene length. For further functional interpretation, the S. meliloti genes were matched with genes from the S. meliloti 1021 strain, M. loti and Agrobacterium tumefaciens. M. loti genes were matched with genes from S. meliloti and Agrobacterium tumefaciens. L. japonicus genes were matched with genes from the Lj2.5 version, M. truncatula and Arabidopsis thaliana TAIR10. M. truncatula genes were matched with genes from L. japonicus and Arabidopsis thaliana TAIR10. All matches were determined at protein level with blastp.
Counting: The number of reads in the alignments that overlap with gene features were counted per sample and per organism with htseq-count 0.6.1p1 (Anders et al, 2014). Following parameters were chosen: -m union --stranded=reverse -a 0 -t exon -i gene id. Further analysis was done for each organism separately. We removed genes for which all samples of the associated organism had less than 1 count-per-million. Raw counts were further corrected between samples using full quantile normalization, as implemented in the EDASeq package from Bioconductor (Risso et al, 2011).
Differential expression analysis: With the EdgeR 3.8.6 package of Bioconductor, a negative binomial generalized linear model (GLM) was fitted against the normalized counts (Robinson et al, 2007). We did not use the normalized counts directly, but worked with offsets. Differential expression was tested for with a GLM likelihood ratio test, also implemented in the EdgeR package. The resulting p-values were corrected for multiple testing with Benjamini-Hochberg to control the false discovery rate (Benjamini  & Hochberg, 1995).
Genome_build: Medicago truncatula: MedtrA17-4.0.31 (from Ensembl). Sinorhizobium meliloti: GCA000747295-1.29 (from Ensembl). Lotus japonicus: Lj3.0 (from Ensembl). Mesorhizobium loti: maff303099-1.29 (from Ensembl).
Supplementary_files_format_and_content: Excel files include FPKM values for each Sample.

organism:
Mesorhizobium loti
Lotus japonicus

source_name: whole root nodules

growth_protocol: Seeds of Lotus japonicus cv. Gifu B-129 and Medicago truncatula cv. Jemalong A17 were treated with 96% sulfuric acid (H2SO4) for 11 min and washed in sterile, de-ionized water for five times. Subsequently, seeds were placed in Petri dishes with 1% water agar and kept in darkness at 4°C for 12 h. After this time the Petri dishes containing L. japonicus seeds were placed up-side-down in a growth chamber (16 h photoperiod, photosynthetic photon flux density (PPFD) of 80–100 µmol m-2s-1 and temperature 25°C) for four days and then inoculated with Mesorhizobium loti strain MAFF303099 culture; whereas Petri dishes with M. truncatula seeds were placed in the same conditions but in normal, down-side-down, position and inoculated with Sinorhizobium meliloti strain Rm1021. Inoculum of both strains was prepared by growing bacteria on Tryptone-Yeast medium (0.5% (w/v) tryptone, 0.3% (w/v) yeast extract, 6 mM CaCl2, pH=6.8) until the value of culture optical density at 600 nm (OD600) was between 0.6 and 0.8. Inoculated seedlings were subsequently placed in pots filled with perlite and watered with inoculum diluted 60-fold. Afterwards, pots were covered with transparent plastic foil for the next 7-10 days to protect seedlings from drying. After inoculation, plants were grown in constant conditions (16 h photoperiod, PPFD of 110–170 µmol m-2s-1 and temperature of 22°C) for 6-8 weeks before harvest and watered three times per week with a carefully measured portion of nitrogen-free Fahraeus medium

extract_protocol:
RNA was obtained from L. japonicus and M. truncatula non-inoculated roots and root nodules either subjected to drought for two (T2) or four (T4) days and control ones (T0). Total RNA extraction was performed using a GeneMATRIX Universal RNA Purification Kit (EURX, Gdańsk, Poland) with the additional step of on-column DNase I digestion.
Per sample, an amount of 1 ug of total RNA was used as input. Using the Illumina TruSeq® Stranded Total RNA Sample Prep Kit (protocol 15031048 version E “October 2013”) rRNA is depleted from the total RNA samples using Ribo-Zero ribosomal RNA reduction chemistry. Illumina Ribo-Zero Plant (seed/root) kit was used for the plant samples, Illumina Ribo-Zero Gram negative bacteria kit was used for the bacterial samples and a mixture of both kits was used for the mixed samples. Subsequently, RNA was purified and fragmented and converted into first strand cDNA in a reverse transcription reaction using random primers. Next, double-stranded cDNA was generated in a second strand cDNA synthesis reaction using DNA Polymerase I and RNAse H. The cDNA fragments were extended with a single ‘A’ base to the 3’ ends of the blunt-ended cDNA fragments after which multiple indexing adapters were ligated introducing different barcodes for each sample. Finally an enrichment PCR was carried out to enrich those DNA fragments that have adapter molecules on both ends and to amplify the amount of DNA in the library. For each run, libraries were equimolar pooled and sequenced in two runs using high 75 cycles NextSeq v2 kits on an Illumina NextSeq 500 instrument.

treatment_protocol: Plants were subjected to drought stress by cessation of watering for 2 and 4 days, whereas control plants were watered normally all the time until tissue harvest. Additional control, constituting plants which were not inoculated with symbiotic bacteria, was grown in the same conditions, but watered with full Fahraeus medium instead of nitrogen-free.

tag: cultivar

value: Gifu B-129

tag: strain

value: root nodule


title: Non-stimulated MPs - 6 days + Gardiquimod 24 h [DC_C-G-2]

status: Public on Feb 26 2019

type: RNA

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

country: Norway

institute: Nofima AS

hyb_protocol: Hybridized according to Agilent Two-Color Microarray-Based Gene Expression Analysis protocol for 4x44k microarrays

scan_protocol: Arrays were scanned with  GenePix 4100A microarray scanner

data_processing: Assessment of spot quality was done with aid of GenePix flags. After filtration of low quality spots, Lowess normalization of log2-expression ratios was performed.

molecule: total RNA

organism: Salmo salar

label_protocol: Amplified and labeled with Low Input Quick Amp Labeling Kit (Agilent).

growth_protocol: Primary salmon mononuclear phagocytes (MPs) isolated from head kidney and cultured in vitro in L-15 medium supplemented with 5% FBS for up to 7 days

extract_protocol: Total RNA was extracted using the RNeasy® Mini Kit (Qiagen)

tag: treatment

value: Gardiquimod 24 h

source_name: control macriphages - 1 day

value: Control


title: Lotus japonicus nodules harvested four days after watering withdrawal rep 1 [Lj.nodule.T4.1.S19]

type: SRA

description:
RNA for both plant and bacteria is present
processed data file:
Ljap-RNAseqCounts-withAnn.xlsx
Lj_nodule_T4_1

library_source: transcriptomic

tag: age

tag: tissue


title: CpG-stimulated MPs - 7 days [DC_CpG-D6-1]

source_name: CpG-stimulated MPs - 7 days

value: CpG 6 days


title: MG_2_5_2_H3K9me3-116174194

city: Athens

first: Mary

last: Goll

state: Select State

address: 120 E. Green Street

department: Genetics

country: USA

institute: University of Georgia

library_source: genomic

data_processing:
Sequenced reads were trimmed using Trimgalore version 4.0 and only reads greater than 20bp were retained. Parameters used trimgalore --length 20 --fastqc --gzip
Reads aligned using BWA version 0.7.15 algorithms algn and samse
Samtools 1.3.1 used to sort and index bam files
IGVtools 2.3.81 to create tdf files viewable in Integrated Genome Viewer. Parameters igvtools count -z 7 -w 100
HOMER version 4.8 create Tag Directories for downstream data analysis
HOMER version 4.8 call peaks using findpeaks style histone size 1000 against input file
HOMER version 4.8 annotatePeaks for metaplot and heatmap generation annotatePeaks parameters -hist 50 -ghist - size 10000
Rstudio for heatmap s
Genome_build: GCF_000002035.6_GRCz10_genomic

molecule: genomic DNA

organism: Danio rerio

source_name: whole embryo

extract_protocol:
Cells lysed using lysis buffer followed by chromatin shearing in Diagenode Bioruptor and histone-DNA complexes were isolated with antibody.
Illumina TruSeq ChIP

tag: hours post fertilization

tag: developmental stage

value: embryo

tag: chip antibody


title: AD_0223

city: Obu

first: Daichi

last: Shigemizu

state: Aichi

address: 7-430 Morioka-cho

country: Japan

institute: National Center for Geriatrics and Gerontology

hyb_protocol: Hybridized for 16 h at 32 ºC with rotary shaker (250 rpm). Hybridization buffer and washing protocol was attached in the 3D-Gene® miRNA oligo chip kit.

scan_protocol: 3D-Gene® Scanner (Toray Industries, Inc.) was used for scanning. Images were quantified using Extraction version 2.0.0.6 (Toray Industries, Inc.)

data_processing: Mean and standard deviation (SD) were calculated using a set of pre-selected negative control signals (background signals) that the top and bottom 5% of which were removed. Signal values greater than mean + 2SD of the background signals were replaced using log2(signal – mean) and labeled effective signals. The remaining signal values were replaced by the minimum of the effective signals – 0.1. Undetected signal values were replaced by the average signal of each miRNA signals. To normalize the signals across different microarrays, a set of pre-selected internal control miRNAs (miR-149-3p, miR-2861 and miR-4463), which had been stably detected in more than 500 serum samples, was used. Each miRNA signal value was standardized with the ratio of the average signal of the three internal control miRNA signals30.

organism: Homo sapiens

source_name: serum

label_protocol: miRNA was labeled using 3D-Gene® miRNA Labeling kit in accordance with the manufacturer's instructions.

extract_protocol: Total RNA was extracted each from 300uL serum samples using 3D-Gene® RNA extraction reagent from liquid sample kit (Toray Industries, Inc.).

tag: diagnosis

value: AD

tag: Sex

value: female


title: MG_4_5_1_H3K9me3-116177188


title: TGCT#5-A5

type: genomic

city: Scottsdale

first: Michael

middle: Thomas

last: Barrett

state: AZ

address: 13400 East Shea Boulevard

department: Molecular Pharmacology and Experimental Therapeutics

institute: Mayo Clinic Arizona

hyb_protocol: Labeled DNA was hybridized without ozone scavenger and chips washed according to manufacture's protocol for 40 hours in a rotating 65°C oven.

scan_protocol: All microarray slides were scanned using an Agilent 2565C DNA scanner and the images were analyzed with Agilent Feature Extraction version 11.0 using default settings.

data_processing: Data was extracted from the TIFF files using Agilent FE 10.  The aCGH data was assessed with a series of QC metrics then analyzed using an aberration detection algorithm (ADM2)[23]. The latter identifies all aberrant intervals in a given sample with consistently high or low log ratios based on the statistical score derived from the average normalized log ratios of all probes in the genomic interval multiplied by the square root of the number of these probes. This score represents the deviation of the average of the normalized log ratios from its expected value of zero and is proportional to the height h (absolute average log ratio) of the genomic interval, and to the square root of the number of probes in the interval.

source_name: Testicular germ cell cancer

label_protocol: DNAs from FFPE-derived DNA samples were digested for 1 minute with DNAse1. In each case 1 ul of 10x DNase 1 reaction buffer and 2 μl of DNase 1 dilution buffer were added to 7 μl of DNA sample and incubated at room temperature then transferred to 70°C for 30 minutes to deactivate DNase 1. Sample and reference templates were then labeled with Cy-5 dUTP and Cy-3 dUTP respectively using a BioPrime labeling kit (Invitrogen, Carlsbad, CA) according to our published protocols [22]. All labeling reactions were assessed using a Nanodrop assay (Nanodrop, Wilmington, DE) prior to mixing and hybridization to CGH arrays (Agilent Technologies, Santa Clara, CA).

growth_protocol: Formalin fixed paraffin embedded tumor samples were obtained from and reviewed by the Mayo Clinic Department of Anatomic Pathology

extract_protocol: Excess paraffin is removed with a scalpel from individual 40-60um scrolls which are then washed with 1ml Xylene for 5 minutes.  The samples are filtered through a 35um mesh and resuspended in a final concentration of 10ug/ml DAPI prior to flow sorting with an Influx cytometer (Becton-Dickinson, San Jose, CA) with ultraviolet excitation and DAPI emission collected at >450 nm. DNA content and cell cycle were analyzed using the software program MultiCycle (Phoenix Flow Systems, San Diego, CA). DNAs were extracted using Qiagen micro kits (Qiagen Valencia, CA).

tag: origin

value: Transplant

tag: site

value: Primary

tag: histology

value: Seminoma

tag: ploidy

source_name: Reference pooled 46XX

tag: sample type

value: Normal female genome


title: Lotus japonicus nodules harvested two days after watering withdrawal rep 2 [Lj.nodule.T2.2.S16]

description:
RNA for both plant and bacteria is present
processed data file:
Ljap-RNAseqCounts-withAnn.xlsx
Lj_nodule_T2_2


title: Lotus japonicus nodules harvested from well-watered plants rep 2 [Lj.nodule.T0.2.S12]

description:
RNA for both plant and bacteria is present
processed data file:
Ljap-RNAseqCounts-withAnn.xlsx
Lj_nodule_T0_2


title: Lotus japonicus nodules harvested two days after watering withdrawal rep 1 [Lj.nodule.T2.1.S15]

description:
RNA for both plant and bacteria is present
processed data file:
Ljap-RNAseqCounts-withAnn.xlsx
Lj_nodule_T2_1


title: MG_4_5_1_Input-116191097


title: TGCT#4-A3

value: Choriocarcinoma


title: MG_2_5_2_Input-116173213


title: MG_4_5_2_H3K9me3-116179145


title: Lotus japonicus nodules harvested from well-watered plants rep 1 [Lj.nodule.T0.1.S11]

description:
RNA for both plant and bacteria is present
processed data file:
Ljap-RNAseqCounts-withAnn.xlsx
Lj_nodule_T0_1


title: BeWo_Forskolin_treated_Rep_2

city: Karachi

first: Muhammad

middle: Furqan

last: Bari

state: Sindh

address: Suparco Road, Ojha campus

department: Department of Pathology

country: Pakistan

institute: Dow University of Health Sciences

hyb_protocol: Standard methods were used as recommended by the Affymetrix

scan_protocol: GeneChip Scanner 3000 from affymetrix

data_processing: R statistical program and bioconductor packages; Pathway Studio Software (version 10.0; Ariadne Genomics/Elsevier) was used for systems biology analysis; PANTHER software (Protein Analysis Through Evolutionary Relationships; http://www.pantherdb.org/genes/batchIdSearch.jsp) was used to classify genes into distinct categories of molecular functions and biological processes

label: Biotin

growth_protocol: BeWo (CCL-98; ATCC) and JEG-3 (HTB-36, ATCC) cell lines were a gift from Julie Lafond (Université du Québèc À Montréal). BeWo cells were cultured in F-12K medium while JEG-3 cells were cultured in MEM (Sigma Aldrich). Both media contain 10% Fetal Bovine Serum (Gibco, Thermofisher Scientific) and Penicillin/Streptomycin (100 U/ml, Lonza), as well as other supplements as reported by the supplier. Cells were cultured in T75 cm2 flask at 37ºC, 5% CO2 and humidified atmosphere and subcultured using 0.25% trypsin-EDTA.

extract_protocol: BeWo and JEG-3 cells were treated with forskolin to induce fusion and the double positive cells were sorted using Fluorescent Activated Cell sorting (FACS). The sorted cells were used to extract RNA (RNeasy Mini Kit, Qiagen).

treatment_protocol: In some experiments, cells were treated with different amount of forskolin for 48 hours to induce their differentiation.

tag: cell line

value: BeWo


title: Medicago truncatula non-inoculated roots rep 1 [Mt.root.T0.1.S1]

description:
processed data file:
Mtrun-RNAseqCounts-withAnn.xlsx
Mt_root_1

organism: Medicago truncatula

source_name: whole root systems

value: Jemalong A17

value: root


title: Medicago truncatula non-inoculated roots rep 2 [Mt.root.T0.2.S2]

description:
processed data file:
Mtrun-RNAseqCounts-withAnn.xlsx
Mt_root_2


title: Lotus japonicus non-inoculated roots rep 2 [Lj.root.T0.2.S4]

description:
processed data file:
Ljap-RNAseqCounts-withAnn.xlsx
Lj_root_2

organism: Lotus japonicus


title: BeWo_Forskolin_treated_Rep_1

label_protocol: Standard methods were used as recommended by the Affymetrix


title: TGCT#3-A1

value: Recurrant


title: TGCT#2-A7


title: TGCT#3-2


title: MG_4_5_2_Input-116178178


title: BeWo_control_Rep_3


title: Lotus japonicus non-inoculated roots rep 1 [Lj.root.T0.1.S3]

description:
processed data file:
Ljap-RNAseqCounts-withAnn.xlsx
Lj_root_1

value: Gifu B-129


title: Medicago truncatula nodules harvested four days after watering withdrawal rep 2 [Mt.nodule.T4.2.S18]

description:
RNA for both plant and bacteria is present
processed data file:
Mtrun-RNAseqCounts-withAnn.xlsx
Mt_nodule_T4_2

organism:
Sinorhizobium meliloti
Medicago truncatula

value: root nodule


title: SMMC-7721_PTENα/β-KO-gUSP9X_2

city: shanghai

first: ge

last: mengkai

state: State...

address: shanghai

country: China

institute: Shanghai Jiao Tong University School of Medicine (SJTU-SM)

data_processing:
Reads were mapped to Human Genome Assembly GRC38 by STAR v2.5. Gene and isoform expression quantification was called by RSEM v1.2 with default parameters on GENCODE human v28 gene annotation file.
Differential expression analysis was preformed by Bioconductor package edgeR v3.18.1.
Signifciant differentially expressed genes were chosen according to two criteria: 1) significance level FDR < 0.05; 2) expression level average FPKM values bigger than 1 in either treatment or control groups.
Genome_build: hg9
Supplementary_files_format_and_content: text files include FPKM values for each Sample

growth_protocol: cell lines were maintained in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% FBS

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

treatment_protocol: cell lines were infected by lentivirus containing gRNA and CAS9

tag: cell type

value: hepatocellular carcinoma cell line

tag: genotype/variation

value: PTENa/b-KO

tag: usp9x depletion

value: yes


title: SMMC-7721_PTENα/β-KO-gNS_2


title: TGCT#1-A2

value: Metastasis


title: BeWo_control_Rep_2


title: BeWo_Forskolin_treated_Rep_3


title: MG_6_1_H3K9me3-116188129

value: embryo


title: Medicago truncatula nodules harvested four days after watering withdrawal rep 1 [Mt.nodule.T4.1.S17]

description:
RNA for both plant and bacteria is present
processed data file:
Mtrun-RNAseqCounts-withAnn.xlsx
Mt_nodule_T4_1

tag: cultivar

tag: strain


title: MG_6_1_Input-116175183


title: BeWo_control_Rep_1


title: TGCT#2-A8

value: Embryonal


title: SMMC-7721_gNS-gNS_2

value: parental control


title: TGCT#1-A3

value: Transplant


title: MG_6_2_H3K9me3-116183126


title: JEG-3_Forskolin_treated_Rep_3


title: MG_6_2_Input-116184127


title: Medicago truncatula nodules harvested two days after watering withdrawal rep 1 [Mt.nodule.T2.1.S13]

description:
RNA for both plant and bacteria is present
processed data file:
Mtrun-RNAseqCounts-withAnn.xlsx
Mt_nodule_T2_1

tag: age

tag: tissue


title: MG_ScrambleMO_1_H3K9me3-116188134

description: Scramble Morpholino

tag: hours post fertilization

tag: developmental stage


title: Medicago truncatula nodules harvested two days after watering withdrawal rep 2 [Mt.nodule.T2.2.S14]

description:
RNA for both plant and bacteria is present
processed data file:
Mtrun-RNAseqCounts-withAnn.xlsx
Mt_nodule_T2_2


title: SMMC-7721_gNS-gNS_1


title: Medicago truncatula nodules harvested from well-watered plants rep 2 [Mt.nodule.T0.2.S10]

description:
RNA for both plant and bacteria is present
processed data file:
Mtrun-RNAseqCounts-withAnn.xlsx
Mt_nodule_T0_2


title: SMMC-7721_gNS-gUSP9X_2


title: SMMC-7721_gNS-gUSP9X_1


title: MiaPaCa2_gPTENα/β

value: pancreatic cancer cell line


title: TGCT#1-A1

value: Teratoma

value: Normal female genome


title: Control 4 (female)

city: Berlin

first: Markus

last: Schuelke

state: Berlin

address: Augustenburger Platz 1

department: Neuropediatrics

country: Germany

institute: Charite

description:
Control_4
Control_4_HK500HUMjcaRAADRAAPEI-8_1_9_1

data_processing:
Quality check and trimming of adapter sequences were done with FastQC
The alignment to the human reference sequence (hg19) was done with STAR 2.4.0.1
Transcriptiome analysis was performed with the CUFFLINKS 2.2.1 pipeline
Calculation of FPKM values was done with CUFFQUANT
Calculation of differential gene expression CUFFDIFF
Genome_build: GRCh37.p11 (hg19)
Supplementary_files_format_and_content: CUFFLINKS output files

growth_protocol: Culture of fibroblasts in DMEM supplemented with 15% FBS and 1% penicillin/streptomycin at 37°C in 5% carbondioxide until semi-confluency and yielded by trypsinization

extract_protocol:
RNA extracted with the TRIzol protocol
BGISEQ-500 RNA-Seq library (depletion of tRNAs and of rRNAs)

treatment_protocol: no treatment

tag: subject status

value: healthy age-matched control

tag: gender

value: female

value: wildtype

value: skin biopsy from the forearm

value: fibroblasts


title: TGCT#1-5

tag: origin

value: Primary

value: Embryonal, yolk salk tumor, Teratoma (Mixed)


title: MG_ScrambleMO_1_Input-116183127

description: Scramble Morpholino

tag: chip antibody


title: JEG-3_Forskolin_treated_Rep_1


title: JEG-3_Forskolin_treated_Rep_2


title: Control 2 (male)

description:
Control_2
Control_2_HK500HUMxdhRAADRBAPEI-7-8-7_1

source_name: control_male_cultured human fibroblasts

value: male


title: JEG-3_control_Rep_1


title: Control 3 (female)

description:
Control_3
Control_3_HK500HUMjcaRAAERAAPEI-10_1_11_1


title: s2-WDR5_RRC03082

data_processing:
ChIP-seq reads were mapped to the human reference genome (GRCh37) using Bowtie2 version 2.3.4 with parameters very-sensitive-local.
Duplicate reads were removed by picard version 2.18.4.
Peaks were called with the MACS version 2.1.1.20160309. Metaplots and heat maps were generated using deeptools version 3.1.0.
Genome_build: hg9
Supplementary_files_format_and_content: bed file

source_name: hepatocellular

extract_protocol:
Lysates were clarified from sonicated nuclei and isolated with antibody.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: hepatocellular carcinoma cell line

tag: infect

value: lentivirus

value: WDR5 (NOVAS, Cat# NBP1-30063)


title: MG_ScrambleMO_2_H3K9me3-116173211

description: Scramble Morpholino

value: embryo


title: MG_Smarca2MO_1_Input-116189140

description: Smarca2 Morpholino


title: MG_ScrambleMO_2_Input-116179142

description: Scramble Morpholino


title: SMMC-7721_PTENα/β-KO-gNS_1

value: PTENa/b-KO


title: JEG-3_control_Rep_3


title: Medicago truncatula nodules harvested from well-watered plants rep 1 [Mt.nodule.T0.1.S9]

description:
RNA for both plant and bacteria is present
processed data file:
Mtrun-RNAseqCounts-withAnn.xlsx
Mt_nodule_T0_1

value: Jemalong A17

value: root nodule


title: JEG-3_control_Rep_2


title: MG_Smarca2MO_2_H3K9me3-116175180

description: Smarca2 Morpholino


title: Control 1 (male)

description:
Control_1
Control_1_HK500HUMxdhRAACRBAPEI-5-6-5_1


title: s2-PTEN-L_RRC03084

value: PTENα/β (a gift from Professor Yuxin Yin)


title: Patient 2

description:
Patient_2
Patient_2_HK500HUMxdhRAABRBAPEI-3-4-3_1

source_name: patient_cultured human fibroblasts

value: patient with a mutation in the ELOVL1 gene

value: ELOVL1 p.S165F


title: MG_Smarca2MO_2_Input-116183131

description: Smarca2 Morpholino


title: Patient 1

description:
Patient_1
Patient_1_HK500HUMxdhRAAARBAPEI-1-2-1_1


title: s2-input_RRC03080


title: MiaPaCa2_gNS

value: pancreatic cancer cell line

value: parental control


title: TGCT#1-3

value: Transplant

tag: site

tag: histology

value: Seminoma

tag: ploidy

value: Normal female genome


title: SC_GM12878_6UnitDevice5_U4

status: Public on Feb 25 2019

city: Blacksburg

first: Chang

last: Lu

state: VA

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

department: Chemical Engineering

institute: Virginia Tech

description: MID-RNA-Seq data. Name format: Cell Number(single cell SC)_Cell-Line_Device type and number_Unit Number

data_processing:
Raw reads were trimmed with TrimGalore 0.4.1 and Cutadapt 1.12
2 million trimmed reads were sub-sampled and aligned to the genome using Tophat 2.1.1
Aligned reads were analysed with Cufflinks 2.2.1 to obtain FPKM gene counts
Genome_build: hg19, mm9
Supplementary_files_format_and_content: The gene counts are reported in FPKM_tracking files

molecule: polyA RNA

source_name: GM12878 cell line

growth_protocol: GM12878 cells(Coriell) were cultured in RPMI 1640 medium (11875-093, Gibco) plus 15% fetal bovine serum (26140-079, Gibco) and 100 U/ml penicillin-streptomycin (15140-122,Gibco).  MEF cells were obtained from ATCC(SCRC-1040) and cultured in DMEM (ATCC 30-2002) with 15% FBS and 1%PS . Both cell lines were cultured at 37 ℃ in a humidified incubator with 5% CO2. Cells were sub-cultured every 2-3 days to maintain them in exponential growth phase.

extract_protocol:
MEF cells were harvested at 80% confluence. They were detached by incubating with 0.25% trypsin with 0.1% EDTA (Thermo Fisher 25200056) for 1 min. Cells were centrifuged at 120 × g for 5 min. Then the supernatant was discarded and cells were resuspended in PBS and diluted to a concentration of 3.2 × 10^5 cells/ml. GM12878 cells were harvested in their exponential phase, centrifuged under the same set of conditions and resuspended in PBS and diluted to the same concentration.This solution was then promptly used for single cell capture on the MID-RNA-Seq device.
Library preparation was performed using the Nextera XT library preparation kit (Illumina FC-131-1024) using 5 μl of purified RNA following manufacturer's instructions. Bulk RNA-seq samples from a 1000 cells were prepared with Takara Bio SMART-Seq V4 Kit (634894). Libraries were sequenced on Illumina HiSeq 4000/HiSeq X with single-end 50 bp read or paired-end 150 bp reads.

tag: cell line


title: SC_GM12878_6UnitDevice3_U2


title: SC_GM12878_6UnitDevice3_U3


title: SC_GM12878_6UnitDevice5_U5


title: 1000cells_GM12878_1

description: MID-RNA-Seq data. Name format: Cell Number(single cell SC)_Cell-Line_Replicate Number


title: SC_GM12878_6UnitDevice4_U6


title: SC_GM12878_6UnitDevice4_U1


title: SC_GM12878_6UnitDevice4_U4


title: SC_GM12878_6UnitDevice5_U3


title: SC_GM12878_6UnitDevice3_U6


title: SC_GM12878_6UnitDevice5_U1


title: SC_GM12878_6UnitDevice4_U2


title: SC_GM12878_6UnitDevice5_U2


title: SC_GM12878_6UnitDevice3_U5


title: SC_GM12878_6UnitDevice4_U5


title: SC_GM12878_6UnitDevice4_U3


title: SC_GM12878_6UnitDevice3_U4


title: SC_GM12878_6UnitDevice3_U1


title: SC_GM12878_6UnitDevice2_U6


title: SC_GM12878_6UnitDevice2_U4


title: SC_GM12878_6UnitDevice2_U5


title: MG_Smarca2MO_1_H3K9me3-116187136

description: Smarca2 Morpholino


title: SC_GM12878_6UnitDevice1_U6


title: SC_GM12878_6UnitDevice2_U2


title: SC_GM12878_6UnitDevice2_U3


title: SC_GM12878_6UnitDevice2_U1


title: SC_GM12878_6UnitDevice1_U4


title: SC_GM12878_6UnitDevice1_U5


title: Fis3

city: Hangzhou

first: Xiao

middle: Dong

last: Xu

state: Zhejiang province

address: Administrative Building,3 East Qingchun Road, Hangzhou, Zhejiang, China.

institute: Department of General Surgery,Sir Run Run Shaw Hospital,School of Medicine,Zhejiang University

data_processing:
bcl2fastq software were used for basecalling.
In order to guarantee the data quality which was used to analysis, the useful Perl script was used to filter the original data (Raw Data).The steps are: 1) trim Smart-seq2 public primer sequence from the Reads; 2) remove the contaminated reads for adapters; 3) remove the low quality reads; and 4) remove the reads whose N base more than 5% for total bases.
Sequenced reads were mapped to hg38 using Bowtie2 v2.2.3 software.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0. and Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from  Trapnell, C. et al., Nat. Biotechnol, 2010.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: Human pancreatic cancer cell

growth_protocol: Human Panc-1 cells were grown in DMEM medium supplemented with 10% FBS at 37°C in 5% CO2.

extract_protocol:
RNA was harvested using Trizol reagent. NEBNext® UltraTM RNA Library Prep Kit for Illumina  was used with 3 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: Human pancreatic cancer cell


title: NC1


title: Fis1


title: SC_GM12878_6UnitDevice1_U1


title: (R)-Criz + CDDP_2

city: Paris

first: Noémie

last: Robil

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

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

organism: Mus musculus

source_name: Solid tumor

growth_protocol: Subcutaneous MCA205 tumors were established by injecting 500,000 WT MCA205 cells (in 100 µL PBS) into the right flank of WT C57BL/6 mice, until tumors became palpable

extract_protocol:
Tumors were harvested at day 10 after treatments and immediately immersed in the RNAlater RNA Stabilization Reagent (Qiagen, Hilden, Germany) and total RNA was extracted with the RNeasy Plus Mini Kit (Qiagen) following the manufacturers’ instructions.
TruSeq mRNA Stranded Illumina

treatment_protocol: Mice received two times intraperitoneal injections 0.25 mg/ Kg-1 CDDP plus 50 mg/ Kg-1 (R)-crizotinib in 200 µL solvent (10 % Tween-80, 10 % PEG400, 4 % DMSO, 76 % physiological saline; v:v), or 200  µL solvent only as controls, at day 0 and day2.

value: tumor

tag: agent

value: cisplatin plus crizotinib


title: SMMC-7721_PTENα/β-KO-gUSP9X_1

value: hepatocellular carcinoma cell line

tag: genotype/variation

tag: usp9x depletion

value: yes


title: NC2


title: Ctrl_3

tag: strain


title: Fis2


title: Sample_168_MTL: Luminal Treated tdTomato 3

city: Toronto

first: Julie

middle: M

last: Livingstone

state: Ontario

address: 661 University Avenue

country: Canada

institute: Ontario Institute for Cancer Research

data_processing:
Alignment, STAR, v.2.5.2a, default parameters
Generation of gene level abundance estimates, STAR, v.2.5.2a, default parameters
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: .txt, gene abundance estimates

source_name: Mammary gland

extract_protocol:
RNA was isolated using the PicoPure RNA Isolation Kit (Arcturus). RNA concentrations and RNA quality were measured using a bioanalyzer (Agilent) (0.095-193ng/ul; RIN 1-10). cDNA was generated from 2 ng of RNA with the SMARTer stranded total RNA-seq kit – pico input mammalian (Takara). cDNA fragments were indexed and amplified before being cleaned up (Beckman) and depleted of ribosomal RNA (Takara). cDNA libraries were amplified over 15 cycles of PCR. cDNA libraries were sequenced on a NextSeq 500 system (Illumina) in paired-end 75 mode.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: Mammary gland

tag: lineage

value: Luminal

value: tdTomato

tag: treatment

value: E+P


title: NC3


title: SC_GM12878_6UnitDevice1_U3


title: SC_GM12878_6UnitDevice1_U2


title: Ctrl_4


title: Ctrl_1


title: Sample_168_MGL: Luminal Treated eGFP 3

value: eGFP


title: (R)-Criz + CDDP_1


title: Sample_168_MGS: Stromal Treated eGFP 3

value: Stromal


title: Ctrl_2


title: (R)-Criz + CDDP_4


title: Sample_168_MTS: Stromal Treated tdTomato 3


title: Sample_166_MTS: Stromal Treated tdTomato 2


title: (R)-Criz + CDDP_3


title: 1000cells_GM12878_2


title: Sample_149_MGL: Luminal Treated eGFP 1


title: Sample_149_MTS: Stromal Treated tdTomato 1


title: Sample_166_MGS: Stromal Treated eGFP 2


title: Sample_166_MGL: Luminal Treated eGFP 2


title: Sample_138_MTL: Luminal Untreated tdTomato 3

value: Untreated


title: Sample_149_MTL: Luminal Treated tdTomato 1


title: Sample_111_MTL: Luminal Untreated tdTomato 1


title: Sample_124_MGL: Luminal Untreated eGFP 2


title: Sample_150_MTL: Luminal Untreated tdTomato 4


title: Sample_149_MGS: Stromal Treated eGFP 1


title: Sample_166_MTL: Luminal Treated tdTomato 2


title: Sample_150_MTS: Stromal Untreated tdTomato 4


title: Sample_150_MGL: Luminal Untreated eGFP 4


title: Sample_138_MGL: Luminal Untreated eGFP 3


title: Sample_138_MGS: Stromal Untreated eGFP 3


title: Sample_138_MTS: Stromal Untreated tdTomato 3


title: Sample_111_MGS: Stromal Untreated eGFP 1


title: Sample_124_MGS: Stromal Untreated eGFP 2


title: Sample_111_MTS: Stromal Untreated tdTomato 1


title: NR3-E1-cre

city: Cologne

first: Ali

middle: T

last: Abdallah

address: Joseph Stelzmann Str. 26

department: Medical Faculty

institute: University of Cologne

description:
DIFFEXPR_EXPORT319_DATASET396.xlsx
DIFFEXPR_EXPORT328_DATASET402.xlsx

data_processing:
RNA sequencing was performed with a Nextseq 500 sequencer (Illumina, San Diego, CA, USA).
The cDNA libraries were generated using a TruSeq Stranded mRNA Sample Preparation Kit (Illumina).
The RNA-Seq data analysis was performed with an in-house pipeline embedded in the QuickNGS workflow management system.
Generation of the fastq files and adapter removal were completed
using the Illumina demultiplexing and conversion software bcl2fastq [https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html]).
Quality control checks of the RNA-Seq data were done with fastqc available online
(http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Subsequently, the reads were aligned to the mm10 reference genome sequence using  STAR 2.5.2b with default parameters.
In the quantification step, reads were counted with featureCounts from the subread package v1.5.1 available online. (http://subread.sourceforge.net).
The TPM (Transcripts per Million) values were computed using the stringtie package.
Differential expression analysis was then performed by the DESeq2 package.
Genome_build: mm10
Supplementary_files_format_and_content: Excel File for each condition containing TPM values, FoldChanges, Pvalues and Various annotations.

source_name: CcnE1-/-HCC Clone 3

growth_protocol: All cells were isolated after perfusion of tumorous or control livers. Hepatoma cell lines were cultivated in petri dishes containing DMEM with 20% v/v FBS, 10 mg/ml insulin, 10 mg/ml hydrocortisone hemisuccinate, 0.25 mg/ml amphotericin B, 1 mM phenobarbital and 20 ng/ml Epidermal Growth Factor until cells were passagable.

extract_protocol:
Cells were harvested from plate in Quiazol and stored on liquid nitrogen and -80 °C, RNA was isolated using PureLink RNA Mini Kit (Cat#12183018A, Invitrogen). The construction of sequencing libraries was performed using 800 ng to 1 ug of total RNA.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: For adenoviral infection, hepatoma cells were cultured in standard DMEM medium containing 2% FCS and 5% Penicillin/Streptomycin, 0.2% Gentamycin. After overnight incubation, cells were washed and cultured in standard DMEM containing 10% FCS, 1% Penicillin/Strepromycin, 0.2% Gentamycin until harvest.

value: Liver

value: Adv-Cre/EGFP

tag: genotype

value: CcnE1-KO (CcnE1-/-)

tag: phenotype

value: Non-Responder


title: Sample_124_MTS: Stromal Untreated tdTomato 2


title: Sample_124_MTL: Luminal Untreated tdTomato 2


title: Sample_150_MGS: Stromal Untreated eGFP 4


title: Sample_111_MGL: Luminal Untreated eGFP 1


title: R4-E1C2-GFP

source_name: CcnE1f/fpreCL Clone 4

value: Adv-EGFP

value: WT (CcnE1f/f/ Cdk2f/f)

value: Responder


title: R1-E1-cre

description:
DIFFEXPR_EXPORT316_DATASET394.xlsx
DIFFEXPR_EXPORT328_DATASET402.xlsx

source_name: CcnE1-/-preCL Clone 1


title: R2-E1-cre

source_name: CcnE1-/-preCL Clone 2


title: NR1-E1-GFP

source_name: CcnE1f/fHCC Clone 1

value: WT (CcnE1f/f)


title: R3-E1C2-GFP

source_name: CcnE1f/fpreCL Clone 3


title: NR1-E1-cre

source_name: CcnE1-/-HCC Clone 1


title: R4-E1C2-cre

source_name: CcnE1-/-preCL Clone 4

value: CcnE1/Cdk2-KO (CcnE1-/-/ Cdk2-/-)


title: Ref-Hep1

description:
DIFFEXPR_EXPORT310_DATASET390.xlsx
DIFFEXPR_EXPORT313_DATASET392.xlsx
DIFFEXPR_EXPORT316_DATASET394.xlsx
DIFFEXPR_EXPORT319_DATASET396.xlsx

source_name: Reference hepatocytes Mouse 1

value: untreated


title: Ref-Hep2

source_name: Reference hepatocytes Mouse 2


title: R1-E1-GFP

source_name: CcnE1f/fpreCL Clone 1


title: Ref-Hep3

source_name: Reference hepatocytes Mouse 3


title: NR2-E1-GFP

source_name: CcnE1f/fHCC Clone 2


title: NR2-E1-cre

source_name: CcnE1-/-HCC Clone 2


title: R3-E1C2-cre

source_name: CcnE1-/-preCL Clone 3


title: R2-E1-GFP

source_name: CcnE1f/fpreCL Clone 2


title: NR3-E1-GFP

source_name: CcnE1f/fHCC Clone 3


title: stool_B8_rep0

city: Saint Louis

first: Erica

middle: Kay

last: Barnell

state: MO

address: 4444 Forest Park

department: McDonnell Genome Institute

institute: Washington University School of Medicine

description:
26954
Transcriptome Expression Data

hyb_protocol: Approximately 100ng of DNase-free RNA was amplified with the Ambio WT-pico kit with hybridization to the Affymetrix Human Transcriptome Array 2.0 as per the manufacturer's protocol.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner.

data_processing: The data was normalized using the Single Space Transformation-Robust Multiarray Analysis and analyzed using the Affymetrix Expression Console.

label: biotin

source_name: Stool sample; hyperplastic polyp on colonoscopy

label_protocol: Total mRNA was prepared and labeled according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2017, Thermo Fisher Scientific).

extract_protocol: Total nucleic acid was extracted using the standard protocol on the bead-based Nucli-SENS easyMag.

treatment_protocol: Approximately 20 grams of stool were transferred to a 50mL conical tube with 30mL HBSS, 0.05% Tween-20, and 0.01% RNase inhibitor. Samples were rotated at 4 degrees Celsius for 10 minutes and solution was centrifuged at 500g for 10 minutes. Human cells were resuspended in lysis buffer.

value: Stool

tag: disease status

value: Benign

tag: Sex

value: Male

tag: age (yr)

tag: ethnicity

value: Caucasian/white

tag: smoking status

value: No

tag: family history

tag: set

value: Not Used


title: stool_B6_rep0

description:
26953
Transcriptome Expression Data

value: Yes


title: stool_B1_rep0

description:
26901
Transcriptome Expression Data

value: Female


title: stool_B7_rep0

description:
27218
Transcriptome Expression Data


title: stool_B4_rep0

description:
26926
Transcriptome Expression Data


title: stool_B3_rep0

description:
26904
Transcriptome Expression Data


title: stool_C116_rep0

description:
27800 C
Transcriptome Expression Data

source_name: Stool sample; cancer on colonoscopy

value: Stage IV

value: Training


title: stool_B5_rep0

description:
26927
Transcriptome Expression Data


title: stool_B2_rep0

description:
26925
Transcriptome Expression Data


title: stool_C117_rep0

description:
27801 C
Transcriptome Expression Data

value: Stage I


title: stool_C114_rep0

description:
27798 C
Transcriptome Expression Data

value: Stage II


title: stool_N110_rep0

description:
27796 N
Transcriptome Expression Data

source_name: Stool sample; no findings on colonoscopy

value: Normal


title: stool_N108_rep0

description:
27794 N
Transcriptome Expression Data


title: stool_N111_rep0

description:
27797 N
Transcriptome Expression Data

value: Testing


title: stool_C113_rep0

description:
27785 C
Transcriptome Expression Data


title: stool_N109_rep0

description:
27795 N
Transcriptome Expression Data


title: stool_P98_rep0

description:
27787 P
Transcriptome Expression Data

source_name: Stool sample; precancerous adenoma on colonoscopy

value: Adenoma


title: stool_P99_rep0

description:
27788 P
Transcriptome Expression Data


title: stool_P101_rep0

description:
27790 P
Transcriptome Expression Data


title: stool_C115_rep0

description:
27799 C
Transcriptome Expression Data


title: stool_C112_rep0

description:
27802 C
Transcriptome Expression Data

value: Stage III


title: stool_N107_rep0

description:
27793 N
Transcriptome Expression Data


title: stool_P102_rep0

description:
27791 P
Transcriptome Expression Data


title: stool_P100_rep0

description:
27789 P
Transcriptome Expression Data


title: stool_C110_rep0

description:
27783 C
Transcriptome Expression Data


title: stool_C108_rep0

description:
27781 C
Transcriptome Expression Data


title: stool_C111_rep0

description:
27784 C
Transcriptome Expression Data


title: stool_N106_rep0

description:
27792 N
Transcriptome Expression Data


title: stool_C109_rep0

description:
27782 C
Transcriptome Expression Data


title: stool_P97_rep0

description:
27786 P
Transcriptome Expression Data


title: stool_P96_rep0

description:
27738 P
Transcriptome Expression Data


title: stool_C106_rep0

description:
27779 C
Transcriptome Expression Data


title: stool_P95_rep0

description:
27737 P
Transcriptome Expression Data


title: stool_C105_rep0

description:
27739 C
Transcriptome Expression Data


title: stool_P94_rep0

description:
27736 P
Transcriptome Expression Data


title: stool_C107_rep0

description:
27780 C
Transcriptome Expression Data


title: stool_P89_rep0

description:
27723 P
Transcriptome Expression Data


title: stool_P88_rep0

description:
27722 P
Transcriptome Expression Data


title: stool_N104_rep0

description:
27733 N
Transcriptome Expression Data


title: stool_P93_rep0

description:
27735 P
Transcriptome Expression Data


title: stool_N103_rep0

description:
27732 N
Transcriptome Expression Data


title: stool_P90_rep0

description:
27724 P
Transcriptome Expression Data


title: stool_P87_rep0

description:
27721 P
Transcriptome Expression Data


title: stool_P85_rep0

description:
27719 P
Transcriptome Expression Data


title: stool_C101_rep0

description:
27726 C
Transcriptome Expression Data


title: stool_C104_rep0

description:
27729 C
Transcriptome Expression Data


title: stool_P91_rep0

description:
27725 P
Transcriptome Expression Data


title: stool_P84_rep0

description:
27718 P
Transcriptome Expression Data


title: stool_P86_rep0

description:
27720 P
Transcriptome Expression Data


title: stool_C102_rep0

description:
27727 C
Transcriptome Expression Data


title: stool_P82_rep0

description:
27716 P
Transcriptome Expression Data


title: stool_P92_rep0

description:
27730 P
Transcriptome Expression Data


title: stool_N105_rep0

description:
27734 N
Transcriptome Expression Data


title: stool_C100_rep0

description:
27714 C
Transcriptome Expression Data


title: stool_N102_rep0

description:
27731 N
Transcriptome Expression Data


title: stool_N101_rep0

description:
27715 N
Transcriptome Expression Data


title: stool_C103_rep0

description:
27728 C
Transcriptome Expression Data


title: stool_P83_rep0

description:
27717 P
Transcriptome Expression Data


title: stool_P81_rep0

description:
27713 P
Transcriptome Expression Data


title: stool_P77_rep0

description:
27709 P
Transcriptome Expression Data


title: stool_C99_rep0

description:
27700 C
Transcriptome Expression Data


title: stool_P78_rep0

description:
27710 P
Transcriptome Expression Data


title: stool_N94_rep0

description:
27702 N
Transcriptome Expression Data


title: stool_P79_rep0

description:
27711 P
Transcriptome Expression Data


title: stool_N100_rep0

description:
27708 N
Transcriptome Expression Data


title: stool_P80_rep0

description:
27712 P
Transcriptome Expression Data


title: stool_N96_rep0

description:
27704 N
Transcriptome Expression Data


title: stool_N92_rep0

description:
27607 N
Transcriptome Expression Data


title: stool_N90_rep0

description:
27605 N
Transcriptome Expression Data


title: stool_N93_rep0

description:
27701 N
Transcriptome Expression Data


title: stool_C97_rep0

description:
27698 C
Transcriptome Expression Data


title: stool_N85_rep0

description:
27600 N
Transcriptome Expression Data


title: stool_N95_rep0

description:
27703 N
Transcriptome Expression Data


title: stool_N87_rep0

description:
27602 N
Transcriptome Expression Data


title: stool_C98_rep0

description:
27699 C
Transcriptome Expression Data


title: stool_C96_rep0

description:
27599 C
Transcriptome Expression Data


title: stool_C93_rep0

description:
27596 C
Transcriptome Expression Data


title: stool_N89_rep0

description:
27604 N
Transcriptome Expression Data


title: stool_N88_rep0

description:
27603 N
Transcriptome Expression Data


title: stool_N98_rep0

description:
27706 N
Transcriptome Expression Data


title: stool_N99_rep0

description:
27707 N
Transcriptome Expression Data


title: stool_N97_rep0

description:
27705 N
Transcriptome Expression Data


title: stool_N91_rep0

description:
27606 N
Transcriptome Expression Data


title: stool_N86_rep0

description:
27601 N
Transcriptome Expression Data


title: stool_C94_rep0

description:
27597 C
Transcriptome Expression Data


title: stool_C90_rep0

description:
27593 C
Transcriptome Expression Data


title: stool_C92_rep0

description:
27595 C
Transcriptome Expression Data


title: stool_C95_rep0

description:
27598 C
Transcriptome Expression Data


title: stool_C91_rep0

description:
27594 C
Transcriptome Expression Data


title: stool_C89_rep0

description:
27592 C
Transcriptome Expression Data


title: stool_C88_rep0

description:
27591 C
Transcriptome Expression Data


title: stool_C85_rep0

description:
27588 C
Transcriptome Expression Data


title: stool_C87_rep0

description:
27590 C
Transcriptome Expression Data


title: stool_C82_rep0

description:
27564 C
Transcriptome Expression Data


title: stool_C86_rep0

description:
27589 C
Transcriptome Expression Data


title: stool_P75_rep0

description:
27586 P
Transcriptome Expression Data


title: stool_P70_rep0

description:
27560 P
Transcriptome Expression Data


title: stool_C84_rep0

description:
27566 C
Transcriptome Expression Data


title: stool_P73_rep0

description:
27584 P
Transcriptome Expression Data


title: stool_N81_rep0

description:
27555 N
Transcriptome Expression Data


title: stool_P76_rep0

description:
27587 P
Transcriptome Expression Data


title: stool_N84_rep0

description:
27558 N
Transcriptome Expression Data


title: stool_N83_rep0

description:
27557 N
Transcriptome Expression Data


title: stool_C79_rep0

description:
27553 C
Transcriptome Expression Data


title: stool_P69_rep0

description:
27559 P
Transcriptome Expression Data


title: stool_P72_rep0

description:
27562 P
Transcriptome Expression Data


title: stool_C80_rep0

description:
27554 C
Transcriptome Expression Data


title: stool_N82_rep0

description:
27556 N
Transcriptome Expression Data


title: stool_N80_rep0

description:
27548 N
Transcriptome Expression Data


title: stool_N79_rep0

description:
27547 N
Transcriptome Expression Data


title: stool_P71_rep0

description:
27561 P
Transcriptome Expression Data


title: stool_C83_rep0

description:
27565 C
Transcriptome Expression Data


title: stool_P67_rep0

description:
27551 P
Transcriptome Expression Data


title: stool_P65_rep0

description:
27549 P
Transcriptome Expression Data


title: stool_P68_rep0

description:
27552 P
Transcriptome Expression Data


title: stool_P74_rep0

description:
27585 P
Transcriptome Expression Data


title: stool_C81_rep0

description:
27563 C
Transcriptome Expression Data


title: stool_P66_rep0

description:
27550 P
Transcriptome Expression Data


title: stool_P64_rep0

description:
27544 P
Transcriptome Expression Data


title: stool_N78_rep0

description:
27546 N
Transcriptome Expression Data


title: stool_N77_rep0

description:
27545 N
Transcriptome Expression Data


title: stool_N74_rep0

description:
27440 N
Transcriptome Expression Data


title: stool_N76_rep0

description:
27442 N
Transcriptome Expression Data


title: stool_N69_rep0

description:
27435 N
Transcriptome Expression Data


title: stool_N70_rep0

description:
27436 N
Transcriptome Expression Data


title: stool_C77_rep0

description:
27431 C
Transcriptome Expression Data


title: stool_N72_rep0

description:
27438 N
Transcriptome Expression Data


title: stool_N71_rep0

description:
27437 N
Transcriptome Expression Data


title: stool_N75_rep0

description:
27441 N
Transcriptome Expression Data


title: stool_P63_rep0

description:
27543 P
Transcriptome Expression Data


title: stool_C72_rep0

description:
27426 C
Transcriptome Expression Data


title: stool_C75_rep0

description:
27429 C
Transcriptome Expression Data


title: stool_N73_rep0

description:
27439 N
Transcriptome Expression Data


title: stool_P58_rep0

description:
27420 P
Transcriptome Expression Data


title: stool_C71_rep0

description:
27425 C
Transcriptome Expression Data


title: stool_N67_rep0

description:
27392 N
Transcriptome Expression Data


title: stool_C76_rep0

description:
27430 C
Transcriptome Expression Data


title: stool_P62_rep0

description:
27424 P
Transcriptome Expression Data


title: stool_C74_rep0

description:
27428 C
Transcriptome Expression Data


title: stool_C78_rep0

description:
27432 C
Transcriptome Expression Data


title: stool_N62_rep0

description:
27387 N
Transcriptome Expression Data


title: stool_C70_rep0

description:
27434 C
Transcriptome Expression Data


title: stool_P60_rep0

description:
27422 P
Transcriptome Expression Data


title: stool_N61_rep0

description:
27386 N
Transcriptome Expression Data


title: stool_P61_rep0

description:
27423 P
Transcriptome Expression Data


title: stool_N64_rep0

description:
27389 N
Transcriptome Expression Data


title: stool_N65_rep0

description:
27390 N
Transcriptome Expression Data


title: stool_C73_rep0

description:
27427 C
Transcriptome Expression Data


title: stool_N66_rep0

description:
27391 N
Transcriptome Expression Data


title: stool_P57_rep0

description:
27433 P
Transcriptome Expression Data


title: stool_P59_rep0

description:
27421 P
Transcriptome Expression Data


title: stool_N63_rep0

description:
27388 N
Transcriptome Expression Data


title: stool_N68_rep0

description:
27393 N
Transcriptome Expression Data


title: stool_C67_rep0

description:
27383 C
Transcriptome Expression Data


title: stool_C68_rep0

description:
27384 C
Transcriptome Expression Data


title: stool_C69_rep0

description:
27385 C
Transcriptome Expression Data


title: stool_P54_rep0

description:
27380 P
Transcriptome Expression Data


title: stool_P55_rep0

description:
27381 P
Transcriptome Expression Data


title: stool_P56_rep0

description:
27382 P
Transcriptome Expression Data


title: stool_P52_rep0

description:
27378 P
Transcriptome Expression Data


title: stool_P51_rep0

description:
27377 P
Transcriptome Expression Data


title: stool_C62_rep0

description:
27365 C
Transcriptome Expression Data


title: stool_N59_rep0

description:
27373 N
Transcriptome Expression Data


title: stool_C66_rep0

description:
27369 C
Transcriptome Expression Data


title: stool_P50_rep0

description:
27376 P
Transcriptome Expression Data


title: stool_C60_rep0

description:
27363 C
Transcriptome Expression Data


title: stool_N60_rep0

description:
27374 N
Transcriptome Expression Data


title: stool_C64_rep0

description:
27367 C
Transcriptome Expression Data


title: stool_C65_rep0

description:
27368 C
Transcriptome Expression Data


title: stool_P53_rep0

description:
27379 P
Transcriptome Expression Data


title: stool_P49_rep0

description:
27375 P
Transcriptome Expression Data


title: stool_C59_rep0

description:
27362 C
Transcriptome Expression Data


title: stool_C63_rep0

description:
27366 C
Transcriptome Expression Data


title: stool_N56_rep0

description:
27370 N
Transcriptome Expression Data


title: stool_P45_rep0

description:
27356 P
Transcriptome Expression Data


title: stool_P47_rep0

description:
27358 P
Transcriptome Expression Data


title: stool_N58_rep0

description:
27372 N
Transcriptome Expression Data


title: stool_P48_rep0

description:
27359 P
Transcriptome Expression Data


title: stool_C61_rep0

description:
27364 C
Transcriptome Expression Data


title: stool_P44_rep0

description:
27355 P
Transcriptome Expression Data


title: stool_C58_rep0

description:
27361 C
Transcriptome Expression Data


title: stool_N57_rep0

description:
27371 N
Transcriptome Expression Data


title: stool_P46_rep0

description:
27357 P
Transcriptome Expression Data


title: stool_C57_rep0

description:
27360 C
Transcriptome Expression Data


title: stool_P42_rep0

description:
27353 P
Transcriptome Expression Data


title: stool_P43_rep0

description:
27354 P
Transcriptome Expression Data


title: stool_N53_rep0

description:
27348 N
Transcriptome Expression Data


title: stool_C47_rep0

description:
27335 C
Transcriptome Expression Data


title: stool_C56_rep0

description:
27344 C
Transcriptome Expression Data


title: stool_C51_rep0

description:
27339 C
Transcriptome Expression Data


title: stool_C48_rep0

description:
27336 C
Transcriptome Expression Data


title: stool_P34_rep0

description:
27329 P
Transcriptome Expression Data


title: stool_N52_rep0

description:
27347 N
Transcriptome Expression Data


title: stool_P39_rep0

description:
27346 P
Transcriptome Expression Data


title: stool_C46_rep0

description:
27334 C
Transcriptome Expression Data


title: stool_P40_rep0

description:
27351 P
Transcriptome Expression Data


title: stool_C52_rep0

description:
27340 C
Transcriptome Expression Data


title: stool_C45_rep0

description:
27333 C
Transcriptome Expression Data


title: stool_C55_rep0

description:
27343 C
Transcriptome Expression Data


title: stool_C54_rep0

description:
27342 C
Transcriptome Expression Data


title: stool_P35_rep0

description:
27330 P
Transcriptome Expression Data


title: stool_N54_rep0

description:
27349 N
Transcriptome Expression Data


title: stool_P33_rep0

description:
27328 P
Transcriptome Expression Data


title: stool_C50_rep0

description:
27338 C
Transcriptome Expression Data


title: stool_P36_rep0

description:
27331 P
Transcriptome Expression Data


title: stool_N51_rep0

description:
27326 N
Transcriptome Expression Data


title: stool_N50_rep0

description:
27323 N
Transcriptome Expression Data


title: stool_P38_rep0

description:
27345 P
Transcriptome Expression Data


title: stool_P32_rep0

description:
27327 P
Transcriptome Expression Data


title: stool_N55_rep0

description:
27350 N
Transcriptome Expression Data


title: stool_P41_rep0

description:
27352 P
Transcriptome Expression Data


title: stool_C53_rep0

description:
27341 C
Transcriptome Expression Data


title: stool_P37_rep0

description:
27332 P
Transcriptome Expression Data


title: stool_N49_rep0

description:
27324 N
Transcriptome Expression Data


title: stool_C49_rep0

description:
27337 C
Transcriptome Expression Data


title: stool_P30_rep0

description:
27315 P
Transcriptome Expression Data


title: stool_C34_rep0

description:
27301 C
Transcriptome Expression Data


title: stool_P31_rep0

description:
27316 P
Transcriptome Expression Data


title: stool_C41_rep0

description:
27308 C
Transcriptome Expression Data


title: stool_P29_rep0

description:
27314 P
Transcriptome Expression Data


title: stool_C42_rep0

description:
27309 C
Transcriptome Expression Data


title: stool_C44_rep0

description:
27311 C
Transcriptome Expression Data


title: stool_C40_rep0

description:
27307 C
Transcriptome Expression Data


title: stool_N47_rep0

description:
27296 N
Transcriptome Expression Data


title: stool_C43_rep0

description:
27310 C
Transcriptome Expression Data


title: stool_C37_rep0

description:
27304 C
Transcriptome Expression Data


title: stool_C31_rep0

description:
27298 C
Transcriptome Expression Data


title: stool_C28_rep0

description:
27239 C
Transcriptome Expression Data


title: stool_P28_rep0

description:
27313 P
Transcriptome Expression Data


title: stool_C32_rep0

description:
27299 C
Transcriptome Expression Data


title: stool_C25_rep0

description:
27236 C
Transcriptome Expression Data


title: stool_C38_rep0

description:
27305 C
Transcriptome Expression Data


title: stool_C33_rep0

description:
27300 C
Transcriptome Expression Data


title: stool_C39_rep0

description:
27306 C
Transcriptome Expression Data


title: stool_C29_rep0

description:
27240 C
Transcriptome Expression Data


title: stool_N45_rep0

description:
27294 N
Transcriptome Expression Data


title: stool_N46_rep0

description:
27295 N
Transcriptome Expression Data


title: stool_C35_rep0

description:
27302 C
Transcriptome Expression Data


title: stool_C36_rep0

description:
27303 C
Transcriptome Expression Data


title: stool_C27_rep0

description:
27238 C
Transcriptome Expression Data


title: stool_C30_rep0

description:
27297 C
Transcriptome Expression Data


title: stool_C24_rep0

description:
27235 C
Transcriptome Expression Data


title: stool_C26_rep0

description:
27237 C
Transcriptome Expression Data


title: stool_C23_rep0

description:
27234 C
Transcriptome Expression Data


title: stool_N41_rep0

description:
27225 N
Transcriptome Expression Data


title: stool_N48_rep0

description:
27325 N
Transcriptome Expression Data


title: stool_C21_rep0

description:
27232 C
Transcriptome Expression Data


title: stool_C20_rep0

description:
27231 C
Transcriptome Expression Data


title: stool_N38_rep0

description:
27222 N
Transcriptome Expression Data


title: stool_C19_rep0

description:
27230 C
Transcriptome Expression Data


title: stool_P25_rep0

description:
27219 P
Transcriptome Expression Data


title: stool_N36_rep0

description:
26972 N
Transcriptome Expression Data


title: stool_N37_rep0

description:
27221 N
Transcriptome Expression Data


title: stool_C18_rep0

description:
27229 C
Transcriptome Expression Data


title: stool_N43_rep0

description:
27227 N
Transcriptome Expression Data


title: stool_N44_rep0

description:
27228 N
Transcriptome Expression Data


title: stool_P24_rep0

description:
26971 P
Transcriptome Expression Data


title: stool_N40_rep0

description:
27224 N
Transcriptome Expression Data


title: stool_N32_rep0

description:
26963 N
Transcriptome Expression Data


title: stool_P26_rep0

description:
27220 P
Transcriptome Expression Data


title: stool_N35_rep0

description:
26966 N
Transcriptome Expression Data


title: stool_C22_rep0

description:
27233 C
Transcriptome Expression Data


title: stool_N33_rep0

description:
26964 N
Transcriptome Expression Data


title: stool_N34_rep0

description:
26965 N
Transcriptome Expression Data


title: stool_N30_rep0

description:
26961 N
Transcriptome Expression Data


title: stool_N42_rep0

description:
27226 N
Transcriptome Expression Data


title: stool_P20_rep0

description:
26967 P
Transcriptome Expression Data


title: stool_N31_rep0

description:
26962 N
Transcriptome Expression Data


title: stool_P23_rep0

description:
26970 P
Transcriptome Expression Data


title: stool_P22_rep0

description:
26969 P
Transcriptome Expression Data


title: stool_P21_rep0

description:
26968 P
Transcriptome Expression Data


title: stool_N39_rep0

description:
27223 N
Transcriptome Expression Data


title: stool_C17_rep0

description:
26959 C
Transcriptome Expression Data


title: stool_N28_rep0

description:
26958 N
Transcriptome Expression Data


title: stool_P18_rep0

description:
26950 P
Transcriptome Expression Data


title: stool_N29_rep0

description:
26960 N
Transcriptome Expression Data


title: stool_C12_rep0

description:
26949 C
Transcriptome Expression Data


title: stool_C14_rep0

description:
26952 C
Transcriptome Expression Data


title: stool_N20_rep0

description:
26941 N
Transcriptome Expression Data


title: stool_C16_rep0

description:
26957 C
Transcriptome Expression Data


title: stool_C15_rep0

description:
26956 C
Transcriptome Expression Data


title: stool_P19_rep0

description:
26955 P
Transcriptome Expression Data


title: stool_N21_rep0

description:
26942 N
Transcriptome Expression Data


title: stool_N19_rep0

description:
26940 N
Transcriptome Expression Data


title: stool_N18_rep0

description:
26939 N
Transcriptome Expression Data


title: stool_P17_rep0

description:
26938 P
Transcriptome Expression Data


title: stool_C13_rep0

description:
26951 C
Transcriptome Expression Data


title: stool_N27_rep0

description:
26948 N
Transcriptome Expression Data


title: stool_P16_rep0

description:
26937 P
Transcriptome Expression Data


title: stool_P27_rep0

description:
27312 P
Transcriptome Expression Data


title: stool_N23_rep0

description:
26944 N
Transcriptome Expression Data


title: stool_N16_rep0

description:
26930 N
Transcriptome Expression Data


title: stool_N26_rep0

description:
26947 N
Transcriptome Expression Data


title: stool_P14_rep0

description:
26935 P
Transcriptome Expression Data


title: stool_P15_rep0

description:
26936 P
Transcriptome Expression Data


title: stool_P12_rep0

description:
26933 P
Transcriptome Expression Data


title: stool_N17_rep0

description:
26931 N
Transcriptome Expression Data


title: stool_N24_rep0

description:
26945 N
Transcriptome Expression Data


title: stool_P11_rep0

description:
26932 P
Transcriptome Expression Data


title: stool_N25_rep0

description:
26946 N
Transcriptome Expression Data


title: stool_P13_rep0

description:
26934 P
Transcriptome Expression Data


title: stool_N14_rep0

description:
26928 N
Transcriptome Expression Data


title: stool_P10_rep0

description:
26923 P
Transcriptome Expression Data


title: stool_P6_rep0

description:
26912 P
Transcriptome Expression Data


title: stool_N7_rep0

description:
26908 N
Transcriptome Expression Data


title: stool_N11_rep0

description:
26917 N
Transcriptome Expression Data


title: stool_C8_rep0

description:
26913 C
Transcriptome Expression Data


title: stool_C10_rep0

description:
26915 C
Transcriptome Expression Data


title: stool_P9_rep0

description:
26922 P
Transcriptome Expression Data


title: stool_N6_rep0

description:
26900 N
Transcriptome Expression Data


title: stool_C11_rep0

description:
26916 C
Transcriptome Expression Data


title: stool_N8_rep0

description:
26909 N
Transcriptome Expression Data


title: stool_P7_rep0

description:
26924 P
Transcriptome Expression Data


title: stool_P4_rep0

description:
26902 P
Transcriptome Expression Data


title: stool_C9_rep0

description:
26914 C
Transcriptome Expression Data


title: stool_P5_rep0

description:
26903 P
Transcriptome Expression Data


title: stool_N10_rep0

description:
26911 N
Transcriptome Expression Data


title: stool_N9_rep0

description:
26910 N
Transcriptome Expression Data


title: stool_P2_rep0

description:
26844 P
Transcriptome Expression Data


title: stool_C2_rep0

description:
26841 C
Transcriptome Expression Data


title: stool_C6_rep0

description:
26906 C
Transcriptome Expression Data


title: stool_C1_rep0

description:
26840 C
Transcriptome Expression Data


title: stool_N22_rep0

description:
26943 N
Transcriptome Expression Data


title: stool_C5_rep0

description:
26905 C
Transcriptome Expression Data


title: stool_N13_rep0

description:
26919 N
Transcriptome Expression Data


title: stool_C7_rep0

description:
26907 C
Transcriptome Expression Data


title: stool_P3_rep0

description:
26845 P
Transcriptome Expression Data


title: stool_N12_rep0

description:
26918 N
Transcriptome Expression Data


title: stool_C4_rep0

description:
26843 C
Transcriptome Expression Data


title: stool_P8_rep0

description:
26921 P
Transcriptome Expression Data


title: stool_P1_rep0

description:
26839 P
Transcriptome Expression Data


title: T4ph_mNETseq_muB_rep1

city: Oxford

first: Kinga

last: Kamieniarz-Gdula

address: South Parks Road

department: Sir William Dunn School of Pathology

country: United Kingdom

institute: University of Oxford

data_processing:
library strategy: Mammalian Native elongating transcript sequencing (mNET-seq)
reads in FASTQ files were trimmed with cutadapt using following settings: -a TGGAATTCTCGG -A GATCGTCGGACT -e 0.05 -m 10 --times 1
trimmed reads were mapped with STAR 2.5b to hg19
last transcribed nucleotides positions from each read were retrieved using in house developed script based on R Bioconductor libraries similarily to (Nojima et al., 2016)
Those positions were further used to calculate genome-wide, sequencing depth normalized coverage utilized for downstream analysis and visualization
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files: genome-coverage files for all samples

growth_protocol: HeLa cells were maintained in DMEM with 10% fetal bovine serum.

extract_protocol:
Nascent RNAs were purified from Pol II IP products of solubilized chromatin (Nojima et al., Nature Protocols, 2016, PMID: 2684442).
Libraries were prepared according to the protocols of TruSeq Small RNA Library Preparation kit (RS-200-0012, Illumina).

treatment_protocol: siRNAs from Dharmacon were transfected for 48 hrs according to RNAiMAX reagent protocol at the concentrations indicated.

tag: cell line

value: HeLa TREX Flip-In

tag: genotype/treatment

value: PCF11 PAS1 deletion clone muB

tag: antibody

value: Pol II T4ph (active motif, 61361, clone 6D7)

tag: molecule subtype

value: Pol II bound RNA


title: T4ph_mNETseq_wild-type_rep2

value: wild-type control for PCF11 PAS1 deletion


title: stool_N15_rep0

description:
26929 N
Transcriptome Expression Data

value: Stool

value: Caucasian/white

value: No


title: T4ph_mNETseq_muB_rep2


title: T4ph_mNETseq_siPCF11_rep3

value: HeLa cells

value: PCF11 knock-down (5 nM)


title: T4ph_mNETseq_siPCF11_rep1


title: T4ph_mNETseq_siLUC_rep3

value: siLUC control for PCF11 kd (5 nM)


title: stool_N5_rep0

description:
26838 N
Transcriptome Expression Data

value: Male

value: Training


title: chrRNA-seq_muB_rep4

data_processing:
Reads were mapped with STAR 2.5b aligner with index generated from hg19 genome.
For visualisation genome-wide coverage were calculated and normalised for sequencing depth (rpm). BigWig files were generated to visualize the data in the UCSC browser.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files: genome-coverage files for all samples

source_name: HeLa TREX Flip-In

extract_protocol:
Chromatin-bound semi-nascent RNAs were purified as described (Nojima et al., Cell, 2015, PMID: 25910207).
Chromatin RNA-Seq libraries were prepared with NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7760, NEB) according to manufacturer's instructions.

value: chromatin-bound RNA


title: stool_C3_rep0

description:
26842 C
Transcriptome Expression Data


title: T4ph_mNETseq_siLUC_rep1

value: siLUC control for PCF11 knock-down (5 nM)


title: chrRNA-seq_muB_rep3


title: T4ph_mNETseq_wild-type_rep1


title: stool_N1_rep0

description:
26834 N
Transcriptome Expression Data

value: Normal

value: Female

value: Yes

value: Testing


title: stool_N4_rep0

description:
26837 N
Transcriptome Expression Data


title: chrRNA-seq_muB_rep2

value: HeLa TREX Flip-In

value: PCF11 PAS1 deletion clone muB


title: chrRNA-seq_muB_rep1


title: stool_N3_rep0

description:
26836 N
Transcriptome Expression Data


title: chrRNA-seq_siPCF11_rep2

source_name: HeLa cells


title: chrRNA-seq_siLUC_rep2


title: chrRNA-seq_wild-type_rep3

value: wild-type control for PCF11 PAS1 deletion


title: T4ph_mNETseq_siPCF11_rep2

value: PCF11 knock-down (50 nM)

value: Pol II T4ph (active motif, 61361, clone 6D7)

value: Pol II bound RNA


title: T4ph_mNETseq_siLUC_rep2

value: HeLa cells

value: siLUC control for PCF11 kd (50 nM)


title: DoubleKD2_insulin

city: Boston

first: Alfred

last: Ramirez

state: MA

address: One Joslin Place

institute: Joslin Diabetes Center

description:
TRA00073569
PolyA RNA

data_processing:
Illumina Casava 1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence mapped to GRCm38.p4 whole genome using STAR 2.4.2a with relevant parameters --outFilterIntronMotifs RemoveNoncanonicalUnannotated --twopassMode Basic
Count matrices were generated using the R package featureCounts with parameters useMetaFeatures = TRUE, allowMultiOverlap = FALSE, isPairedEnd = TRUE, countMultiMappingReads = FALSE
Genome_build: GRCm38.p4
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include raw counts for each sample.

extract_protocol:
RNA was isolated via a Qiagen RNeasy mini Kit.
RNA libraries were prepared using NEBNext Sample Prep Master Mix kit.

treatment_protocol: Cells were serum starved overnight with DMEM + 0.1% BSA, then mock treated or treated with insulin (100 nM) for 6 h.

tag: cell type

value: Hepatocyte

tag: genotype/variation

value: Double FoxK1/2 KD

value: Insulin

tag: treatment time


title: chrRNA-seq_siPCF11_rep1

tag: tissue

value: chromatin-bound RNA


title: Foxk2KD4_insulin

description:
TRA00073567
PolyA RNA

value: Foxk2 KD

tag: treatment


title: Foxk2KD3_insulin

description:
TRA00073566
PolyA RNA


title: chrRNA-seq_wild-type_rep4


title: chrRNA-seq_wild-type_rep2


title: stool_N2_rep0

description:
26835 N
Transcriptome Expression Data

value: Stool

value: Normal

value: Male

value: Caucasian/white

value: No

value: Training


title: DoubleKD1_insulin

description:
TRA00073568
PolyA RNA


title: Foxk2KD2_insulin

description:
TRA00073565
PolyA RNA


title: Foxk1KD4_insulin

description:
TRA00073563
PolyA RNA

value: Foxk1 KD


title: Foxk2KD1_insulin

description:
TRA00073564
PolyA RNA


title: DoubleKD3_insulin

description:
TRA00073570
PolyA RNA


title: Foxk1KD3_insulin

description:
TRA00073562
PolyA RNA


title: Foxk1KD2_insulin

description:
TRA00073561
PolyA RNA


title: Control3_insulin

description:
TRA00073559
PolyA RNA

value: Control


title: Foxk1KD1_insulin

description:
TRA00073560
PolyA RNA


title: DoubleKD3

description:
TRA00073554
PolyA RNA


title: DoubleKD4

description:
TRA00073555
PolyA RNA


title: Control2_insulin

description:
TRA00073558
PolyA RNA


title: Foxk2KD4

description:
TRA00073551
PolyA RNA


title: DoubleKD1

description:
TRA00073552
PolyA RNA


title: DoubleKD2

description:
TRA00073553
PolyA RNA


title: Foxk2KD2

description:
TRA00073549
PolyA RNA


title: Foxk2KD1

description:
TRA00073548
PolyA RNA


title: Foxk2KD3

description:
TRA00073550
PolyA RNA


title: chrRNA-seq_siLUC_rep1

value: siLUC control for PCF11 knock-down (50 nM)


title: Foxk1KD3

description:
TRA00073546
PolyA RNA


title: Foxk1KD1

description:
TRA00073544
PolyA RNA


title: Control3

description:
TRA00073542
PolyA RNA


title: Foxk1KD4

description:
TRA00073547
PolyA RNA


title: Control2

description:
TRA00073541
PolyA RNA


title: Control4

description:
TRA00073543
PolyA RNA


title: Control1_insulin

description:
TRA00073557
PolyA RNA


title: Control1

description:
TRA00073540
PolyA RNA


title: B17_S13

city: Birmingham

first: Jeremy

middle: Jason

last: Day

state: AL

address: 1825 University Blvd

department: Neurobiology

institute: UAB

data_processing:
Pre-trimming QC with FastQC (version build within trim-galore=0.4.5)
Trimming of low quality bases (Phred score <20) and Illumina adapter with trim-galore=0.4.5
Post-trimming QC with FastQC
Splice-aware alignment with star=2.6.0c. The genome utilized was: /data/project/daylab/Genome-Reference/Genomes/rn6-Ensembl/Rattus_norvegicus.Rnor_6.0.dna.toplevel.fa
Merging of BAM files and index generation with samtools=1.6
Count generation with bioconductor-rsubread=1.26.1 (R version: r-base=3.4.1). The GTF file utilized was: /data/project/daylab/Genome-Reference/Genomes/rn6-Ensembl/rn6-GTF/Rattus_norvegicus.Rnor_6.0.90.gtf
Genome_build: rn6
Supplementary_files_format_and_content: Matrix with differentially expressed genes in Lacz vs Bdnf-I and Lacz vs Bdnf-IV sgRNA comparisons (in separate spreadsheets). Genes are in rows, and columns contain the Ensembl ID, basemean, log2foldchange value, and other gene information (chromosome, location, etc).

organism: Rattus norvegicus

source_name: Hippocampal neuron culture

growth_protocol: Neurons were removed from hippocampal tissue at embryonic day 18, and maintained in vitro for 11 days prior to collection of RNA. Each culture well contained ~250,000 cells.

extract_protocol:
Total RNA from was extracted, DNase-treated, and purified (RNeasy, Qiagen). 1µg of total RNA underwent quality control (Bioanalyzer; all RIN values > 7.0) and library construction for polyA+ RNA sequencing.
Directional polyA+ RNA llibraries were constructed at the UAB Helfin Genomics Core. RNA libraries were quantified and underwent sequencing (~25M total 75bp paired-end reads) on an Illumina sequencing platform (NextSeq 500).

treatment_protocol: Neurons were treated as described with CRISPR sgRNAs and dCas9-VPR fusion lentiviruses on DIV 4. Media was removed and RNA was extracted on DIV 11.

tag: strain

value: Sprague-Dawley

value: Hippocampal neuron culture

tag: age

value: Embryonic day 18, 11 DIV

value: Bdnf-I sgRNA


title: BIV14_S2

value: Bdnf-IV sgRNA


title: BIV15_S3


title: B16_S12


title: B18_S14


title: LZ5_S11

value: Lacz sgRNA


title: LZ4_S10


title: NFIA-SCAstro-1

city: New York

first: Lorenz

last: Studer

state: NY

department: Developmental Biology

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Basecalls performed using CASAVA version 1.4
RNASeq - FASTQ files were aligned using the STAR aligner to hg38.  BAM files were then processed into a counts table using HTSeq and imported into DESeq2 for further analysis
Genome_build: hg38
Supplementary_files_format_and_content: tab delimited files.  RNA seq - fold change compared to rosette cells

source_name: hPSC-derived spinal cord astrocytes

growth_protocol: NSCs maintained in 10ng/ml of EGF, 10ng/ml of FGF; Astrocytes maintained in 10ng/ml LIF and 10ng/ml HB-EGF

extract_protocol:
RNA was isolated from cell pellets resuspended in TRIzol and purified using the RNEasy spin column
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: growth condition

value: N2 media containing LIF/HB-EGF

tag: psc line


title: NFIA-SCAstro-2


title: NFIA-SC-Astro-3


title: LZ2_S9


title: NFIA-Astro-10

source_name: hPSC-derived astrocytes


title: NFIA-Astro-9

tag: prefix


title: NFIA-Astro-8


title: Foxk1KD2

description:
TRA00073545
PolyA RNA

value: Hepatocyte


title: DF_PGE-2_treated

first: Ben

middle: S.

last: Wittner

address: 149 13th Street

department: Center for Cancer Research

institute: Massachusetts General Hospital

data_processing:
Trimmomatic was used to crop reads to length 50 and to remove the TruSeq3-PE-2 Illumina adapters
The reads were then aligned using tophat2 and bowtie1 with the no-novel-juncs argument set with human genome version hg19 and transcriptome defined by the hg19 genes.gtf table from http://genome.ucsc.edu
Reads that did not align or aligned to multiple locations were discarded.
Read counts were determined using htseq-count.
Genome_build: hg19
Supplementary_files_format_and_content: Rows correspond to the gene given in the first column. Columns correspond to specimens.

source_name: human dermal fibroblast cell line DF

extract_protocol:
Total RNA was isolated from the cell lines using RNeasy Mini Kit (Qiagen)
TruSeq Stranded Total RNA Library Prep Kit (Illumina) following low sample protocol

value: DF

value: human dermal fibroblast

value: PGE-2 six hours


title: DF_untreated

value: untreated


title: NFIA-Astro-7


title: BIV11_S1


title: NFIA-Astro-6


title: NFIA-Astro-5


title: NFIA-Astro-4


title: primary Astro-2

source_name: Primary astrocytes (commercial)

value: fetal


title: primary Astro-1


title: Tfh_CFSEneg TSLpoolTfh_CfN

city: Cleveland

first: Peter

middle: A

last: Wilkinson

state: Ohio

address: 2103 Cornell Road

department: Pathology / Systems Biology & Bioinformatics

institute: Case Western Reserve University

description: SampleID: S21

hyb_protocol: Microarray analysis was conducted using 750ng of biotinylated cRNA hybridized to Human RefSeq-12 V4 BeadChips (Illumina) at 58°C for 20 hours, according to Illumina's direct hybridization protocol by the Genomics core at Collaborative Genomics Center (CGC).

scan_protocol: The arrays were scanned using an Illumina iScan scanner and quantified using GenomeStudio software (Illumina).

data_processing: Analysis of the quantified output data was conducted using the limma version 3.22.4 from the R statistical language and other software packages from Bioconductor version 3.0.  Missing values were imputed using the KNN algorithm from the impute R package. Quantile normalization was applied, followed by a log2 transformation.

source_name: tonsils

label_protocol: The hybridized BeadChips were washed, blocked, stained and scanned according to the Illumina's direct hybridization protocol.

growth_protocol: PBMC from healthy donors were sorted for Tfh and non-Tfh cells and then put in culture for 5 days with memory B cells. Cells were sorted and analysed by gene array. Tonsils from healthy donors were sorted for Tfh and non-Tfh cells and then put in culture for 5 days with Germinal centers B cells. Cells were sorted and analysed by gene array.

extract_protocol: Cells were washed twice with cold PBS and lysed with 100 µl of cold RLT buffer (QIAGEN, Germany) supplemented with 1% beta-mercaptoethanol (BM) (Sigma, St. Louis, MO USA), and transferred to 1.7 ml tubes with 250 µl of cold RLT/BM buffer and quickly stored at -80oC. The samples underwent nucleic acid isolation in a designated Pre-PCR room using Qiagen’s RNeasy Micro Kit and underwent DNase I treatment.  Total RNA concentrations were quantified using a NanoDrop 2000c spectrophotometer and quality was assessed using BioRad’s Experion automated electrophoresis system.  With each batch of samples a 500 ng HeLa RNA control and two water non-template negative controls were included.

treatment_protocol: Cells were treated with SEB.

tag: donor

tag: cellsource

value: Tfh


title: Tfh_CFSEpos D2

description: SampleID: S4


title: NFIA-Astro-3


title: NFIA-Astro-2


title: Tfh_CFSEneg D3

description: SampleID: S15


title: Tfh_CFSEneg D2

description: SampleID: S3


title: NFIA-Astro-1


title: Tfh_CFSEneg D1

description: SampleID: S1


title: CRC organoid3-derived, UC pellet

city: Budapest

first: Zoltan

last: Wiener

address: Ulloi ut 26

country: Hungary

institute: Semmelweis University

description: Medium from 3D culture of CRC organoids3 was ultracentrifuged and fibroblasts were treated with the pellet containing Evs

hyb_protocol: 1650 ng of Cy3-labelled cRNA (specific activity >8.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutesfollowing the manufacturers instructions. On completion of the fragmentation reaction, 55ul 2x Gex HiRPM hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome 4 x44K Microarrays (G2519F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent), 1 minute with 37 °C GE Wash buffer 2 (Agilent) and then in Agilent Drying Solution.

scan_protocol: Slides were scanned immediately after washing on Agilent B Scanner, Extended Dynamic Range (100% and 10% laser intensity, 5 micron resolution)

data_processing: Feature Extraction Software 12.0.3.1., default one-color high density protocol (GE1_1200_Jun14). Data were imported into Chipster (https://chipster.csc.fi/) and normalized with the default Agilent 1-color protocol in Chipster (background treatment: normexp, background offset 50, normalize chips: quantile, remove control probes: yes)

source_name: fibroblasts, 18h, UC pellet 3

label_protocol: 200 ng total RNA was reverse transcribed and processed according to Low Input QuickAmp version 6.5. cRNA was purified on Qiagen RNEasy columns.

growth_protocol: Fibroblasts were grown in DMEM 4500 g/l glucose, Pen/Strept, glutamine and 5% EV-free FBS

extract_protocol: RNEasy micro Kit (Qiagen), according to the manufacturer's protocol with on-column Dnase digestion.

treatment_protocol: Medium from organoid cultures containing 7x105 cells or from empty Matrigel droplets were centrifuged at 300 g for 5 min and 2,000 g for 15 min to remove cells and cell debris, respectively. The supernatnant was then ultracentrifuged at 4C, 100,000 g for 70 min. The EV-enriched pellet was re-suspended in the supernatant and fibroblasts were treated with the EV-containing pellet or EV-free supernatant.

value: fibroblasts

tag: cell source


title: Tfh_CFSEneg D5

description: SampleID: S7


title: nonTfh_CFSEpos TSLpoolNonTfh_CfP

description: SampleID: S20

source_name: PBMC

value: nonTfh


title: CRC organoid2-derived, UC pellet

description: Medium from 3D culture of CRC organoids2 was ultracentrifuged and fibroblasts were treated with the pellet containing Evs

source_name: fibroblasts, 18h, UC pellet 2


title: CRC organoid3-derived, UC supnat

description: Medium from 3D culture of CRC organoids3 was ultracentrifuged and fibroblasts were treated with the supernatant without Evs

source_name: fibroblasts, 18h, UC supnat3


title: CRC organoid2-derived, UC supnat

description: Medium from 3D culture of CRC organoids2 was ultracentrifuged and fibroblasts were treated with the supernatant without Evs

source_name: fibroblasts, 18h, UC supnat2


title: nonTfh_CFSEpos D4

description: SampleID: S12


title: Tfh_CFSEpos D5

description: SampleID: S8


title: Tfh_CFSEpos D4

description: SampleID: S6


title: nonTfh_CFSEneg TSLpoolNonTfh_CfN

description: SampleID: S19


title: Tfh_CFSEpos D1

description: SampleID: S2


title: nonTfh_CFSEpos D3

description: SampleID: S18


title: CRC organoid1-derived, UC pellet

description: Medium from 3D culture of CRC organoids1 was ultracentrifuged and fibroblasts were treated with the pellet containing Evs

source_name: fibroblasts, 18h, UC pellet 1


title: Tfh_CFSEpos TSLpoolTfh_CfP

description: SampleID: S22


title: Tfh_CFSEneg D4

description: SampleID: S5


title: nonTfh_CFSEpos D1

description: SampleID: S10


title: nonTfh_CFSEpos D5

description: SampleID: S14


title: nonTfh_CFSEneg D5

description: SampleID: S13


title: CRC organoid1-derived, UC supnat

description: Medium from 3D culture of CRC organoids1 was ultracentrifuged and fibroblasts were treated with the supernatant without Evs

source_name: fibroblasts, 18h, UC supnat1


title: Tfh_CFSEpos D3

description: SampleID: S16


title: 3'mRNAseq_muD

description: nuclear RNA

data_processing:
3’ mRNA-seq data were mapped according to the guidelines of QuantSeq library kit manufacturer (Lexogen). Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx (TopHat 2 component (Kim et al., 2013)). After overview with FastQC reads were trimmed with BBtools (sourceforge.net/projects/bbmap/) script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 .
After trimming control with FastQC curated reads were mapped with STAR2.5b (Dobin et al., 2013) aligner. STAR index was  generated with the GRCh37.p13 assembly and gencode.v19.annotation.gtf annotation file).
Aligned 3’ mRNA-seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome-encoded poly(A) stretches. To do this, first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand, an analogous T-rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T-rich regions by strand-specifically unmasking 20 nucleotide intervals centred at GENCODE 3’ gene ends as well as previously experimentally validated PAS sites detected in all human data sets from (Derti et al., 2012). 3’ mRNA-seq reads falling into those refined strand-specific masks were then removed, and the filtered reads reduced to the most distal nucleotide (3’ end nucleotide).
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files: genome-coverage files, mean from replicates

extract_protocol:
Nuclei were prepared by incubation of cells 5 mins on ice in HLB (10 mM Tris pH 7.5, 10 mM NaCl, 2.5 mM MgCl2, 0.5% NP40), underlayering with HLB+NS buffer (10 mM Tris pH 7.5, 10 mM NaCl, 2.5 mM MgCl2, 0.5% NP40, 10% sucrose) and centrifugation 420 g for 5 min at 4oC. RNA was purified from the nuclei using TRI reagent (Sigma) according to manufacturer’s instructions. Residual DNA was digested using 4U Turbo DNase (Life Tech) for 10 min at 37oC followed by proteinase K digestion for 10 min at 37oC. TRI reagent purification and DNase digestion were repeated. RNA was further acid phenol/chloroform and chloroform extracted, followed by ethanol precipitation. The purified RNA was then resuspended in ultrapure water.
Libraries were prepared according to the protocols of QuantSeq 3’mRNA-Seq library prep kit REV for Illumina (LEXOGEN Cat# SKU 016.24)

value: 3' end of mRNA

value: PCF11 PAS1 deletion clone muD


title: nonTfh_CFSEneg D4

description: SampleID: S11


title: 3'mRNAseq_wt_rep4

description: nuclear RNA

value: wild-type control for PCF11 PAS1 deletion


title: 3'mRNAseq_muB_rep3

description: nuclear RNA

value: PCF11 PAS1 deletion clone muB


title: 3'mRNAseq_muB_rep1

description: nuclear RNA


title: 3'mRNAseq_muA_rep3

description: nuclear RNA

value: PCF11 PAS1 deletion clone muA


title: 3'mRNAseq_muB_rep2

description: nuclear RNA


title: 3'mRNAseq_muA_rep2

description: nuclear RNA


title: nonTfh_CFSEneg D3

description: SampleID: S17


title: nonTfh_CFSEneg D1

description: SampleID: S9


title: 3'mRNAseq_muC

description: nuclear RNA

value: PCF11 PAS1 deletion clone muC


title: pTfh_CFSEneg D4

description:
SampleID: E9
9377361024_C

value: pTfh


title: Matrigel, UC pellet

description: Medium from 3D culture only with Matrigel was ultracentrifuged and fibroblasts were treated with the pellet containing Evs

source_name: fibroblasts, 18h, UC pellet control


title: Matrigel, UC supnat

description: Medium from 3D culture only with Matrigel was ultracentrifuged and fibroblasts were treated with the supernatant without Evs

source_name: fibroblasts, 18h, UC supnat control


title: 3'mRNAseq_muA_rep1

description: nuclear RNA

source_name: HeLa TREX Flip-In


title: CXCR3pos_CFSEpos D6

description:
SampleID: E38
9377361024_B


title: CXCR5neg_CFSEneg D5

description:
SampleID: E49
9377361024_D


title: CXCR5neg_CFSEpos D4

description:
SampleID: E46
9377361013_G


title: CXCR3pos_CFSEneg D2

description:
SampleID: E21
9377361024_A


title: CXCR3pos_CFSEpos D4

description:
SampleID: E30
9377361013_J


title: pTfh_CFSEneg D5

description:
SampleID: E13
9377361013_L


title: pTfh_CFSEneg D1

description:
SampleID: E17
9377358057_G


title: 3'mRNAseq_wt_rep3

description: nuclear RNA


title: pTfh_CFSEpos D2

description:
SampleID: E2
9377361013_E


title: CXCR3pos_CFSEneg D4

description:
SampleID: E29
9377361013_F


title: pTfh_CFSEneg D2

description:
SampleID: E1
9377358057_B


title: pTfh_CFSEpos D3

description:
SampleID: E6
9377358057_F


title: CXCR5neg_CFSEpos D6

description:
SampleID: E54
9377358057_I


title: CXCR3pos_CFSEpos D3

description:
SampleID: E26
9377358057_E


title: pTfh_CFSEpos D5

description:
SampleID: E14
9377358057_C


title: 3'mRNAseq_wt_rep2

description: nuclear RNA


title: CXCR5neg_CFSEpos D3

description:
SampleID: E42
9377358057_D


title: CXCR3pos_CFSEneg D5

description:
SampleID: E33
9377361013_H


title: chrRNA-seq_wild-type_rep1

value: HeLa TREX Flip-In

value: chromatin-bound RNA


title: CXCR5neg_CFSEneg D4

description:
SampleID: E45
9377358055_L


title: 3'mRNAseq_wt_rep1

description: nuclear RNA


title: CXCR3pos_CFSEneg D3

description:
SampleID: E25
9377358055_J


title: CXCR5neg_CFSEpos D5

description:
SampleID: E50
9377358057_A


title: CXCR3pos_CFSEpos D2

description:
SampleID: E22
9377358055_H


title: CXCR3pos_CFSEneg D6

description:
SampleID: E37
9377358055_I


title: 3'mRNAseq_siPCF11_rep3

description: nuclear RNA

source_name: HeLa cells

value: PCF11 knock-down (5 nM)


title: 3'mRNAseq_siPCF11_rep4

description: nuclear RNA

value: PCF11 knock-down (50 nM)


title: 3'mRNAseq_siPCF11_rep2

description: nuclear RNA


title: MYb65_ad7_rep4

city: Kiel

first: Hinrich

last: Schulenburg

address: Am Botanischen Garten 1-9

department: Evolutionary Ecology and Genetics, Zoological Institute

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-quality sequence, then mapped to WS235 whole genome using STAR-2.5.3a
Read counts per gene is extracted via STAR-2.5.3a
Genome_build: WS235
Supplementary_files_format_and_content: tab-delimited text files include Raw reads counts for each Sample ...

organism: Caenorhabditis elegans

source_name: whole body

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

treatment_protocol: Worms were fed to OP50 and Ochrobactrum at the different stage (from L2 to adults)

value: N2/Wide type

tag: time point

value: adults (7 days)

tag: medium

value: mNGM

tag: temperature


title: MYb65_ad1_rep4

value: adults (72h)


title: MYb65_ad3_rep4

value: adults (3 days)


title: 3'mRNAseq_siPCF11_rep1

description: nuclear RNA

tag: molecule subtype

tag: genotype/treatment


title: CXCR5neg_CFSEneg D6

description:
SampleID: E53
9377358055_F


title: MYb65_L3_rep3


title: CXCR3pos_CFSEpos D5

description:
SampleID: E34
9377358055_G


title: MYb71_ad3_rep4


title: MYb65_L2_rep3


title: pTfh_CFSEpos D4

description:
SampleID: E10
9377358055_D


title: pTfh_CFSEpos D1

description:
SampleID: E18
9377358055_C


title: MYb71_ad7_rep4


title: 3'mRNAseq_siLUC_rep4

description: nuclear RNA

value: siLUC control for PCF11 kd (50 nM)


title: pTfh_CFSEneg D3

description:
SampleID: E5
9377358055_B


title: 3'mRNAseq_siLUC_rep3

description: nuclear RNA

value: 3' end of mRNA

value: siLUC control for PCF11 kd (5 nM)


title: MYb71_ad1_rep4


title: MYb71_L4_rep4


title: CXCR5neg_CFSEneg D3

description:
SampleID: E41
9377358055_E


title: 3'mRNAseq_siLUC_rep2

description: nuclear RNA


title: MYb71_L2_rep4


title: Mix_ad3_rep3

value: Mix


title: Mix_ad7_rep3


title: WL31

city: Hershey

first: Wei

last: Li

state: PA

address: 500 University Drive, PO Box 850, MC H085

institute: Penn State Hershey College of Medicine

description:
stable cell line
ln229-RY from GVRY

data_processing:
Sequencing data were analyzed using Strand NGS. Briefly, reads were aligned to reference human genome and annotation file (GRCh38, build 38, RefSeq genes and transcripts, 2017_01_13). After filtering the reads by minimal 10 in at least one sample, Audic Claverie Test was performed when comparing each pair of samples. During the analysis, Benjamini Hochberg FDR correction was used for multiple testing corrections and the p-value cut-off was set as 0.05. After this processing, fold change was calculated and the threshold was set as ≥2 folds. For Hierarchical clustering analysis, genes showing changes above 2 folds were used. For ingenuity pathway analysis, 2-fold was used as the cut-off. Direct relationships were chosen.
Genome_build: GRCh38, build 38, RefSeq genes and transcripts, 2017_01_13
Supplementary_files_format_and_content: TXT file

source_name: LN229 GBM cell line

growth_protocol: LN229 cells were seeded in neural sphere medium in 96-well Ultra Low Cluster Plates.  After 24-48 hours, medium was replaced with regular DMEM culture medium containing 10% FBS. The spheroids were incubated at 37°C with 5% CO2 for 2-3 weeks.

extract_protocol:
Total RNA was extracted using Trizol (Thermo Fisher Scientific) by following the manufacture’s manual instruction.
The cDNA libraries were prepared using the NEXTflex™ Illumina Rapid Directional RNA-Seq Library Prep Kit (BioO Scientific) as per the manufacturer’s instructions. Briefly, polyA RNA was purified from 100 ng of total RNA using oligo (dT) beads. The extracted mRNA fraction was subjected to fragmentation, reverse transcription, end repair, 3’– end adenylation, and adaptor ligation, followed by PCR amplification and SPRI bead purification (Beckman Coulter). The unique barcode sequences were incorporated in the adaptors for multiplexed high-throughput sequencing. The final product was assessed for its size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit (Agilent Technologies). Pooled libraries were diluted to 2 nM in EB buffer (Qiagen) and then denatured using the Illumina protocol. The denatured libraries were diluted to 10 pM by pre-chilled hybridization buffer and loaded onto a TruSeq Rapid flow cell on an Illumina HiSeq 2500 and run for 50 cycles using a single-read recipe according to the manufacturer's instructions.

treatment_protocol: 96 tumor spheroids were collected and dissociated with Accutase. Cells were sorted based on ZsGreen and mCherry signals by FACS.

tag: cell type

value: glioblastoma

tag: cell line


title: Mix_L4_rep3


title: Mix_ad1_rep3


title: WL30

description:
stable cell line
ln229-GV from GVRY


title: Mix_L2_rep3


title: OP_ad7_rep3


title: MYb71_L3_rep4


title: OP_ad3_rep3


title: OP_L4_rep3


title: OP_ad1_rep3


title: WL28

description:
stable cell line
ln229-GY from GYRV


title: WL27

description:
stable cell line
ln229-RY from GYRY


title: WL29

description:
stable cell line
ln229-RV from GYRV


title: OP_L2_rep4


title: WL26

description:
stable cell line
ln229-GY from GYRY


title: MYb65_ad3_rep3


title: 3'mRNAseq_siLUC_rep1

description: nuclear RNA

value: siLUC control for PCF11 knock-down (5 nM)


title: MYb65_ad7_rep3


title: MYb65_ad1_rep3


title: OP_L3_rep4


title: Mix_L3_rep3


title: WL25

description:
stable cell line
ln229-RV from GVRV


title: MYb71_ad3_rep3


title: MYb71_ad1_rep3


title: WT_PFC_biological rep 06

city: Toyoake

first: Hideo

last: Hagihara

address: 1-98 Dengakugakubo, Kutsukake-cho

department: Institute for Comprehensive Medical Science

institute: Fujita Health University

description: Gene expression data from the PFC of wild-type mouse

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner 3000 (GCS3000)

data_processing: The data were analyzed with Affymetrix Expression Cosole (version 1.1). The normalization used in RMA is quantile normalization.

source_name: PFC of wild-type mouse

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

extract_protocol: Trizol extraction of total RNA and cleanup byRNeasy Micro kit (QIAGEN) was performed according to the manufacturer's instructions.

tag: tissue

value: Medial prefrontal cortex

tag: genotype

value: wildtype


title: WT_PFC_biological rep 05


title: WL24

description:
stable cell line
ln229-GV from GVRV


title: WT_PFC_biological rep 03


title: MYb71_L4_rep3

tag: strain

tag: treatment


title: WT_PFC_biological rep 04


title: WT_PFC_biological rep 02


title: MYb71_L3_rep3


title: WT_PFC_biological rep 01


title: MYb71_L2_rep3


title: Mix_L4_rep2


title: MYb71_ad7_rep3