title: Interneurons at P0, biological replicate C

first: Antonio Jesus

last: Hinojosa Garcia

state: London

address: Room 4.4 New Hunt's House, Guy's Campus

department: Centre for Developmenta Neurobiology

institute: King's College London

description: Gene expression data from FACS sorted interneurons from Nkx2-1Cre;RCE:LoxP cortices at P0.

hyb_protocol: Hybridized to Mouse Gene 1.0 ST Array (Affymetrix, 902464) following manufacturer's instructions. Done in “Centro de investigación del cancer” in Salamanca University.

scan_protocol: Washing and scanning were performed using GeneChip System of Affymetrix formed by: GeneChip Hybridization Oven 640, GeneChip Fluidics Station 450 and GeneChip Scanner 7G. Done in “Centro de investigación del cancer” in Salamanca University.

data_processing: Microarray fluorescence intensity data was analysed using the R package BioConductor . Normalization was carried out with the algorithm Robust Multiarray Average (RMA).  (RMA).

source_name: GABAergic interneurons at postnatal day 0, replicate C

label_protocol: Total RNA, 100-300 ng, was amplified using the wild type (WT) Expression Kit (Ambion,4411973), labelled using the GeneChip WT Terminal Labeling Kit (Affymetrix, 900670). Done in “Centro de investigación del cancer” in Salamanca University.

extract_protocol: Total RNA for microarray analysis was extracted and purified using Quiagen Rneasy Micro extraction kit (Quiagen 74004) following manufacturer’s instructions.

treatment_protocol: Mice were anesthetized with sodium pentobarbital and cortices were dissociated in dissociation media removing the meninges and cutting them in small pieces. Next, tissue was digested with papain, mechanically disgregated and run through a FACS sorter (BD FACS aria II, 644832). For detailed experimentas procedures see Catapano et al.J. Neurosci. 2001.

value: cortex

tag: strain

tag: developmental stage

value: Postnatal day 0

tag: neuron subtype

value: Interneurons


title: NCC_R014

status: Public on Jul 31 2018

type: RNA

city: Singapore

first: Vivien

last: Koh

address: 1E Kent Ridge Road

country: Singapore

institute: National University Health System

description: Gene expression data of human gastric tumor

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard Affymetrix scanning protocol

data_processing: Data were processed by the Robust Multi-array Average (RMA) algorithm using Affymetrix Expression Console software.

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: Human stomach

label_protocol: Standard Affymetrix labeling protocol

extract_protocol: Total RNA was isolated using QIAGEN RNeasy Mini Kit following manufacturer's instructions

tag: tissue

value: Gastric tumor


title: Pyramidal cells at P0, biological replicate B

city: London

country: United Kingdom

description: Gene expression data from FACS sorted pyramidal cells from NexCre;RCE:LoxP somatosensory cortices at P0.

label: biotin

organism: Mus musculus

source_name: Pyramidal cells at postnatal day 0, replicate B

value: Pyramidal cells


title: Pyramidal cells at P12, biological replicate A

description: Gene expression data from FACS sorted pyramidal cells from NexCre;RCE:LoxP somatosensory cortices at P12.

source_name: Pyramidal cells at postnatal day 12, replicate A

value: Postnatal day 12


title: Pyramidal cells at P12, biological replicate B

source_name: Pyramidal cells at postnatal day 12, replicate B


title: NCC_R010


title: NCC_R018


title: NCC_R020


title: NCC_R022


title: Interneurons at P10, biological replicate B

description: Gene expression data from FACS sorted interneurons from Nkx2-1Cre;RCE:LoxP cortices at P10.

source_name: GABAergic interneurons at postnatal day 10, replicate B

value: Postnatal day 10


title: NCC_R001


title: Interneurons at P10, biological replicate A

source_name: GABAergic interneurons at postnatal day 10, replicate A


title: Pyramidal cells at P0, biological replicate A

source_name: Pyramidal cells at postnatal day 0, replicate A


title: Interneurons at P10,  biological replicate C

source_name: GABAergic interneurons at postnatal day 10, replicate C


title: Pyramidal cells at P12, biological replicate C

source_name: Pyramidal cells at postnatal day 12, replicate C


title: Pyramidal cells at P0, biological replicate C

source_name: Pyramidal cells at postnatal day 0, replicate C


title: NCC_R003


title: NCC_R004


title: Human peripheral blood mononuclear cells (PBMCs) from a health donor were transfected with a control mimics

city: Changsha

first: Jian

last: Ma

state: Hunan

address: 110  Xiangya  Road

department: Cancer  Research Institute

country: China

institute: Central South University

description: Expression data for human peripheral blood mononuclear cells (PBMCs) transfected with control mimics (150 μM) for 36hrs.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45℃ on Affymetrix Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: peripheral blood mononuclear cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 μg total RNA.

growth_protocol: The human PBMCs from a health donor were cultured in both RPMI-1640 medium supplemented with 10% fetal bovine serum. Cultures were incubated at 37°C in a humidified incubator at 5% CO2.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Cells were grown in RPMI-1640 medium (with 2% serum), and were transfected with a negative control microRNA mimics (or EBV Bart6-3p mimics) for 36 hours.

tag: agent

value: control mimics


title: Human peripheral blood mononuclear cells (PBMCs) from a health donor were transfected with a EBV Bart 6-3p mimics

description: Expression data for human peripheral blood mononuclear cells (PBMCs) transfected with EBV Bart 6-3p mimics  (150 μM) for 36 hours.

value: EBV Bart 6-3p mimics


title: Interneurons at P0, biological replicate A

source_name: GABAergic interneurons at postnatal day 0, replicate A


title: Interneurons at P0, biological replicate B

source_name: GABAergic interneurons at postnatal day 0, replicate B


title: BT474_shMEL #2

city: Seoul

first: Hyeong-Seok

last: Joo

address: Wangsimni-ro

department: Institute of Personalized Medicine

country: South Korea

institute: Hanyang University

hyb_protocol: Biotinylated cRNAs were hybridized with standard Illumina hybridization protocol.

scan_protocol: Arrays were scanned on an Illumina BeadArray Reader following the standard Illumina scanning protocol.

data_processing: Standard Illumina GenomeStudio processing of images plus quantile normalization of all samples. Background subtracted.

source_name: Human mammary gland

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep™ RNA amplification kit for Illumina arrays.

growth_protocol: Cells were cultured in RPMI1640 supplemented with 10% FBS

extract_protocol: RNA was extracted with Trizol reagent following the manufacturer's instructions. Quality control was peformed with Agilent Bioanalyzer.

treatment_protocol: BT474 cells were infected with lentiviruses encoding either control or MEL-18 shRNA

tag: disease state

value: ductal carcinoma

tag: cell type

tag: lentivirus

value: shMEL


title: BT474_shMEL #3


title: BT474_shCon #3

value: shCon


title: Single colony of hEKs, biological rep4

city: Lausanne

first: Melissa

last: Maggioni

address: Station 15

department: IBI

country: Switzerland

institute: EPFL

hyb_protocol: cDNAs were hybridized for 17 hr at 45°C on Affymetrix Human Genome U133 Plus 2.0 Array.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G

data_processing: Raw data was extracted from the scanned images and analyzed with the Affymetrix Power Tools software package (Affymetrix). Normalized expression signals were calculated from Affymetrix CEL files using RMA normalization method

source_name: Single colony of hEKs

label_protocol: 5ug of amplified cDNA were labelled with the FL-ovation cDNA BIOTIN MODULE v2

growth_protocol: Single-cell derived colonies of hTECs and single colonies of hEKs were cultivated for 10 days on a feeder layer of lethally irradiated mouse embryonic fibroblasts (3T3-J2)  in medium (cFAD) consisting of a 3:1 mixture of DMEM and Ham's F12 medium supplemented with 10% FBS, 0.4 μg/ml hydrocortisone, 10-6M cholera toxin, 5 μg/ml insulin, 2 x 10-9 M 3,3',5-Triiodo-L-Thyronin (T3)

extract_protocol: Total RNA was extracted using the miRNeasy Mini Kit (QUIAGEN) according to the manufacturer's instructions. First strand cDNAs were  synthetized from 20 ng of each sample RNA and were amplified with the Nugen Ovation Pico WTA System V2, according to the manufacturer's instructions.

treatment_protocol: Single colonies were isolated with cloning ring

tag: gender

value: male

value: Epidermis

value: cultivated Human Epidermal derived Keratinocytes (hEKs)


title: m19-humBBz CD4 CAR T cells, biological rep1 [RNA-seq]

type: SRA

city: Tampa

first: Gongbo

last: Li

state: Florida

address: 3011 W Holly Dr. MRC 2068

country: USA

institute: Moffitt Cancer Center

library_source: transcriptomic

data_processing:
The libraries sequenced on two NextSeq high-output 2x75 paired-end sequencing runs in order to generate approximately 40 million pairs of reads per sample
Sequence reads were aligned to the human reference genome in a splice-aware fashion using Tophat2, allowing for accurate alignments of sequences across introns.
Aligned reads were quantitated at the gene level using HTseq. Normalization, expression modeling, and difference testing were performed using DESeq.
Genome_build: hg19

source_name: m19-humBBz CD4 CAR T cells

growth_protocol: Mouse T cells were isolated from mouse spleens using a negative T cell enrichment kit at day 0. Isolated T cells were activated with anti-mouse dynabeads and 30 IU/ml IL2 for 4 days. At day 1 and day 2 T cells were spin-transduced with retroviral supernatant at 2000×g for 1 hr at 32 °C. Complete medium with fresh IL2 were added at day 3. At day 4 CAR T cells were collected, beads removed, and ready for treatment.

extract_protocol:
After stimulation, live CD4+ CAR T cells were sorted into Trizol. RNA was isolated according to manufacturer’s instructions and evaluated for quality
mRNA enrichment and cDNA library preparation were performed using the Illumina Tru-seq stranded mRNA sample prep kit.  Final RNA-seq libraries were reviewed for size and quality on the Agilent TapeStation, followed by quantitative PCR-based quantitation with the Kapa Library Quantification Kit

treatment_protocol: CAR T cells were incubated with 3T3-mCD19 cells at 10:1 ratio for 48 hr.

tag: car

value: Spleen T cells

tag: t-cell subpopulation


title: m19-humBBz CD4 CAR T cells, biological rep3 [RNA-seq]


title: m19-humBBz CD4 CAR T cells, biological rep2 [RNA-seq]


title: 1_D5

city: Seattle

first: Raghav

last: Chawla

state: WA

address: 3720 15th Ave NE

department: Department of Genome Sciences

institute: University of Washington

description: scRNA-seq of B-cell enriched splenocytes from control mice sacrificed 5 dpi was performed using the 10x Genomics Chromium platform.

data_processing:
Cell Ranger 1.3.0 was used for sample demultiplexing, read alignment, filtering, barcode counting, and UMI counting.
Genome_build: custom_genome.fa
Supplementary_files_format_and_content: Hd5/hf matrix

source_name: Splenocytes enriched for B cells

extract_protocol:
10x Genomics Chromium platform, V1 kit/protocol, per manufacturer's recommendations.
10x Genomics Chromium platform, V1 kit/protocol, per manufacturer's recommendations.

treatment_protocol: 12- to 15-week old mice were immunized i.p. with 200ul of 20% by volume sheep red blood cells diluted in 1x PBS. Mice were sacrificed 5 days post immunization. Red blood cells were lysed using ACK lysing buffer and B cells were enriched using an immunomagnetic negative selection kit.

tag: genotype

value: WT

tag: days post immunization

value: 5 dpi


title: 1_aCARD11

description: scRNA-seq of B-cell enriched splenocytes from aCARD11 mice sacrificed 5 dpi was performed using the 10x Genomics Chromium platform.

value: Mb1-Cre X aCARD11


title: hTECs clone with refringent colony morphology, biological rep4

source_name: Single-cell derived colony of hTECs with refringent morphology

value: female

value: Thymus

value: cultivated Human Thymic Epithelial Cells (hTECs)


title: Single colony of hEKs, biological rep1

description: YF29 ColA


title: Single colony of hEKs, biological rep2


title: BT474_shMEL #1


title: BT474_shCon #1


title: Single colony of hEKs, biological rep3

description: YF29 ColC


title: hTECs clone with stratified colony morphology, biological rep4

source_name: Single-cell derived colony of hTECs with stratified morphology


title: Rap2.9 con3

city: Erlangen

first: Haina

last: Zhang

state: Bayern

address: Staudtstrasse 5

department: Division of biochemistry

country: Germany

description:
SAMPLE 8
252116913727_4
Gene expression in Rap2.9 overexpressing Arabidopsis leaves under control condition

hyb_protocol: Following fragmentation, 1.65 µg of Cy3-labeled cRNA were hybridisied for 17h at 65°C on 4x44K Agilent Arabidopsis_v4 arrays. Arrays were washed according to the protocol (One-Color Microarray-based gene expression analysis v5.7).

scan_protocol: Microarrays were scanned using Agilent G2565BA Microarray Scanner. Data were extracted using Feature Extraction Version: FE Version 11.0 (Agilent Technologies Germany). Data extraction using protocol GE1_1105_Oct12.

data_processing: txt. Files derived from feature extraction were imported into Genespring GX 12.5 (Silicon Genetics). Data were log2 transformed followed by normalization to the 75th percentile and adjusted to the median of all samples. Subsequently entities present in all replicates in at least one conditions were selected by filtering and subjected to an One-Way-ANOVA test (p-value </= 0.05) corrected by Bejamini-Hochberg-FDR. Entities differentially expressed mean an at least 2-fold change in expression level in all transgenic lines compared to wild-type Col-0 plants were further analysed.

organism: Arabidopsis thaliana

source_name: 35S::Rap2.9-GFP, Arabidopsis leaf, replicate 3

label_protocol: 200ng total RNA was used for preparing Cy3-labeled cRNA as described in the Agilent low input one color microarray-based gene expression analysis protocol.

growth_protocol: Stratification was performed for 3 days at 7 °C in the dark before transfer to a light room with 8 h light per day and constant temperature at 22°C for 20 days. Then, plants were grown in the maize chamber Percivals with 12h supplemental light (60µmol quanta ,m-2 s-1), 12h darkness; temperature 22°C/ 18°C (day/nigth) for 34 days. Relative humidty was adjusted to 60%.

extract_protocol: Total RNA was isolated as described by Logemann et al. (1987), purified using Rneasy Kit (Qiagen).

treatment_protocol: No treatment. All plants were grown in control condition.

tag: ecotype background

value: 35S::Rap2.9-GFP transgenic line

value: leaf


title: hTECs clone with refringent colony morphology, biological rep1

description: Thy14 IV Cl16


title: m1928z CD4 CAR T cells, biological rep3 [RNA-seq]

source_name: m1928z CD4 CAR T cells


title: m1928z CD4 CAR T cells, biological rep2 [RNA-seq]


title: Rap2.9 con1

description:
SAMPLE 7
252116913727_3
Gene expression in Rap2.9 overexpressing Arabidopsis leaves under control condition

source_name: 35S::Rap2.9-GFP, Arabidopsis leaf, replicate 1


title: hTECs clone with refringent colony morphology, biological rep3

description: Thy14 IV Cl55


title: WT_LPS_8h_RNAseq_rep2

first: Gopuraja

last: Dharmalingam

address: Faculty of Medicine, Imperial College, Hammersmith Hospital Campus

department: Epigenetics section

institute: MRC London Institute of Medical Sciences

description:
WT8_2
RNA-seq of 8h LPS-stimulated macrophages

data_processing:
The reads were aligned to mouse genome mm9 using Tophat2 with arguments  “--library-type fr-firststrand --b2-very-sensitive --b2-L 25” with gene annotation from Ensembl version 67
Number of reads counts on exons were summarised using Rsubread
Genome_build: mm9
Supplementary_files_format_and_content: reads counts on genes

source_name: Bone marrow-derived macrophages

growth_protocol: Bone marrow cells were isolated from WT or Rad21-/- mice and plated in 10 cm dishes containing 10 ml medium (DMEM containing 10% FCS, 20% L929-conditioned media, 0.05 mM β-mercaptoethanol, PenStrep 1% and Sodium Pyruvate 1mM). 96 hours later media was replaced by fresh media containing 200nM 4-hydroxy-tamoxifen to induce nuclear translocation of ERt2-Cre. Experiments were done at day 7.

extract_protocol:
RNA was extracted from 2 millon cells per condition with RNeasy minikit and using Qiashredder disruption following the manufacturer's instructions (Qiagen). Quality of RNA was assessed using a Bioanalyzer instrument (Agilent) and quantified with Qubit (Invitrogen). ERCC RNA Spike-Ins (Ambion) were added to each purified RNA solution.
750ng of total RNA were used to prepare libraries using the TruSeq stranded total RNA Kit for Illumina following the manufacturer's recommendations. Library quality and quantity were assessed on a Bionalyser and Qubit respectively.

treatment_protocol: Macrophages were subjected to LPS treatment (10ng/ml) and Interferon-gamma treatment (10ng/ml) at the indicated time points (see individual samples).

value: Bone marrow-derived macrophages

tag: stimulation

value: 8 hours of LPS stimulation

value: wild-type


title: WT_LPS_8h_RNAseq_rep3

description:
WT8_3
RNA-seq of 8h LPS-stimulated macrophages


title: Huh7_UV_48h_b_52

city: New York

first: Angela

last: Rasmussen

state: NY

department: Center for Infection and Immunity

institute: Columbia University

hyb_protocol: Individual cRNA samples were hybridized to Agilent human whole-genome oligonucleotide 4X44K microarrays according to the manufacturer's instructions.

scan_protocol: Slides were scanned with an Agilent DNA microarray scanner, and the resulting images were analyzed using Agilent Feature Extractor version 8.1.1.1. This software was used to perform image analysis, including significance of signal and spatial detrending and to apply a universal error model. For these hybridizations, the most conservative error model was applied.

data_processing:
Raw data from Agilent Feature Extractor was normalized using the Quantile Normalization method in GeneData Analyst.  The GeneData Analyst-generated normalized signals are not available.
Matrix shows log2 ratio data (relative to mock-infected values) for DENV-infected and UV DENV-treated Huh7 cells. Probe list was selected after applying a cutoff of p<0.05 in GeneData Analyst.  The Matrix of log2 ratios forms the basis of conclusions in the manuscript and is linked as supplementary file on Series record.

source_name: Huh7_UV_48h, human hepatoma continuous cell line

label_protocol: cRNA probes were generated from each sample by the use of an Agilent one-color LowInput Quick Amp labeling kit (Agilent Technologies, Santa Clara, CA).

growth_protocol: Cells were propagated in complete Dulbecco's minimal essential medium with 10% fetal bovine serum, 100 IU/mL penicillin, and 2.5 ug/mL Plasmocin

extract_protocol: Cells were washed and lysed using TRIzol reagent and total RNA was extracted according the manufacturer's instructions

treatment_protocol: Cells were infected with DENV2/NGC at MOI=10, treated with UV-irradiated DENV2, or mock-infected

tag: cell line

value: hepatoma

tag: treatment

value: treated with UV-irradiated DENV2

tag: time post-infection

value: 48 hr


title: 293cyT (icSHAPE)

city: Qingdao

first: Lei

last: Sun

state: Shandong

address: Shandong street

institute: Shandong University

data_processing:
Library strategy: icSHAPE
remove duplicete reads as icshape pipeline
trimmed reads adaptor as icshape pipeline
mapping reads to human hg38 or mouse mm10 reference genome with bowtie2 as default parameters
calculate rpkm as icshape pipeline
calulate reverse transcript stop sites as icshape pipeline
calculate icSHAPE score as icshape pipeline
For irCLIP,Reads were mapped to mm10 assembly and PCR duplicates were removed using UMI-tools). Reproducible RT stops were identified using the FAST-iCLIP pipeline. Lin28a binding sites were called by Piranha with the parameter –s –b 50.
Genome_build: hg38 and mm10
Supplementary_files_format_and_content: tab-delimited text files for icshape files. First column is the Ensemble ID, second is gene length, third is RPKM, then every column is the nucleotide resolution icSHAPE score. NULL means no confident score. CLIP bed files are formatted as Piranha software. The first three columns are the peaks sites [chromosome, start sites, end sites], the fifth column means support reads of its peaks, the seventh is peaks confident P-value as Piranha.

source_name: HEK293 cell line

growth_protocol: Human HEK293 cells were cultured in DMEM supplemented with 10% FBS at 37°C with 5% CO2 in 15-cm plates. V6.5 mouse ES cells were cultured at 37°C with 5% CO2 in 15-cm plates coated with 0.2% gelatin, in knockout DMEM (Gibco) media supplemented with 15% FBS, 1% PenStrep, 1% MEM NEAA, 1% Glutamax, 0.2% beta-mercaptoethanol, and 0.01% LIF. Cells were cultured to 80~90% confluency, then rinsed, collected and treated with NAI-N3 as previously described by Flynn et. al. (2016).To carry out CLIP-seq experiments, mettl3 WT and KO mESCs9 were grown on gelatinized plates in Knockout DMEM media (Gibco) supplemented with 15% FBS, 1% penicillin-streptomycin (Gibco), glutamate, non-essential amino acids (NEAA), basal medium eagle (BME, Thermo Fischer Scientific), and ESGRO LIF (EMD Millipore).

extract_protocol:
The  RNA or modified RNA was extracted or cleaned up and eluted in RNase-free water by using RNeasy mini columns (Qiagen).
10 µg of RNA from each subcellular fraction for HEK293 cells was depleted of ribosomal RNA (rRNA) using the mouse/human ribominus kit (Invitrogen). About 500 ng RNA was recovered in the nucleoplasmic and cytoplasmic samples and about 2 µg RNA in the chromatin fractions. RNA from mES-cell fractions were depleted using the ribominus eukaryotic system v2 kit (Thermo Fischer Scientific). IcSHAPE sequencing libraries were then constructed from these RNA samples as icSHAPE protocol. Libraries of mES-cells were sequenced on the Hiseq 4000 and libraries of HEK293 cells were sequenced on the Hiseq 2500 to ~200 million reads per replicate.For irCLIP, RNA trimming, on-bead biochemistry, and library generation was performed as irCLIP protocol. Reverse transcription of LIN28 bound RNA was performed with SuperScript IV (Thermo Fischer Scientific) at 53°C for 30 minutes. Library amplification was done for a total of 14 cycles using Phusion HF polymerase master mix (NEB). Libraries were gel purified and submitted for sequencing. Libraries were sequenced on NextSeq 500 with custom sequencing primer P6_seq.

treatment_protocol: For in vivo treatment, cells was incubated with NAI-N3 at 37°C for 5min, then subcellular fractionatio was performed. For in vitro treatment, RNA was extracted by RNeasy mini columns (Qiagen) after subcellular fractionation.For refolding, purified RNA was first denatured at 95°C for 1 min, quickly cooled to 4°C, and then incubated for 5 min in the folding buffer with 100 mM HEPES, 6 mM MgCl2, and 100 mM NaCl. Samples were then respectively modified for 5 minutes at 37°C with the NAI-N3 reagent and DMSO as control. For irCLIP, cells were initially washed with ice-cold PBS, then crosslinked on ice with UV-C (254 nm) at 0.3 J/cm2 in a Stratalinker, washed again with ice-cold PBS (+10 mM EDTA) for 5 minutes, and removed from the plate. Immunoprecipitation of crosslinked protein-RNA complexes was performed with anti-LIN28 antibody (Abcam ab46030), the control samples with anti-GFP antibody (Abcam).

value: human embryonic kidney cells

tag: cellular compartment

value: cytoplasm (cy)

value: in vitro NAI-N3 treatment (T)


title: 293cyN (icSHAPE)

value: in vivo NAI-N3 treatment (N)


title: 293cyD (icSHAPE)

value: DMSO (D)


title: hTECs clone with refringent colony morphology, biological rep2


title: m19z CD4 CAR T cells, biological rep3 [RNA-seq]

source_name: m19z CD4 CAR T cells

tag: strain

value: Spleen T cells


title: multiplexed sample of single embryos, sample 2

city: Haifa

first: Harel

last: Zalts

state: Israel

address: Technion city

country: Israel

institute: Technion

description:
C japonica embryos, multiplexed sequencing file, Read 1. Read 1 includes the CEL-Seq barcode.
C japonica embryos, multiplexed sequencing file, Read 2. Read 2 includes the gene sequence.

data_processing:
Libraries were sequenced on the Illumina HiSeq2000 according to standard, paired-end sequencing, protocols. Primary analysis done in RTA 1.17.20,1.13.48
Conversion from BCL to FASTQ and deumltiplexing using CASAVA-1.8 (configureBclToFastq.pl--fastq-cluster-count 1234567890 --mismatches 0 --use-bases-mask Y15n,I6n,Y35n)
Filter and read trimming (barcode minimum quality of 10. trimming of read2 to 35 bases - not required).
CEL-Seq (Hashimshony, et al. 2012) demultiplexing of second mate, using first mate barcode, allowing no mismatches in barcode.
bowtie2, version 2.1.0, against C. japonica genome C_japonica-7.0.1
Read counting with htseq-count version 0.5.4p3. Using on WS230 annotations
Genome_build: C_japonica-7.0.1
Supplementary_files_format_and_content: [isoformUsage_cjap_new.csv] tabular Expression matrix for 46 samples (C. japonica Sample Names: jW_#)

molecule: polyA RNA

organism: Caenorhabditis japonica

source_name: multiplexed sample of single embryos

growth_protocol: Standard C. elegans techniques were followed to grow c japonica (Stiernagle 2006).

extract_protocol:
RNA was isolated using TRIzol as previously described (Levin et al., 2012).
The CEL-Seq protocol (Hashimshony, et al. 2012) was used to amplify and sequence. CEL-seq multiplexing barocdes were used.

treatment_protocol: For the embryo collection of all species adult hermaphrodites or females were collected and cut to obtain embryos. Embryos were washed with a bleach solution (70% DDW, 20% bleach, 10% 5M KOH) for 30 seconds and subsequently with a 5% BSA solution for 30 seconds. 4-cell embryos were collected,washed 4 times in clear DDW and incubated at 20°C for the appropriate time for each species to reach stages 1-10. After incubation embryos were frozen in liquid nitrogen and kept at -80°C until RNA extraction.

tag: time (minutes after 4-cell)

value: Single embryos, counting from the four cell stage:140 - 290 minutes at 10 minute intervals. Cel-Seq barcodes (from 2012 publication):16-1 (descending order), respectively.


title: multiplexed sample of single embryos, sample 1

value: single embryos, including 1-cell, 2- cell and 4-cell embryos, then counting from the four cell stage:10 - 130 minutes at 10 minute intervals. Cel-Seq barcodes (from 2012 publication):1-16, respectively.


title: m19z CD4 CAR T cells, biological rep1 [RNA-seq]


title: multiplexed sample of single embryos, sample 3

value: Single embryos, counting from the four cell stage:300-430 minutes at 10 minute intervals. Also includes two extra samples for 330 and 340 minutes. Cel-Seq barcodes (from 2012 publication):1-16, respectively.


title: hTECs clone with stratified colony morphology, biological rep3

description: Thy14 IV Cl42

value: female

tag: tissue

value: Thymus

value: cultivated Human Thymic Epithelial Cells (hTECs)


title: m19z CD4 CAR T cells, biological rep2 [RNA-seq]


title: m1928z CD4 CAR T cells, biological rep1 [RNA-seq]


title: Rap2.9 con2

description:
SAMPLE 2
252116913723_2
Gene expression in Rap2.9 overexpressing Arabidopsis leaves under control condition

source_name: 35S::Rap2.9-GFP, Arabidopsis leaf, replicate 2

value: 35S::Rap2.9-GFP transgenic line

value: leaf


title: Col-0 con3

description:
SAMPLE 3
252116913723_3
Gene expression in Col-0 leaves under control condition

source_name: wild-type Col-0, Arabidopsis leaf, replicate 3

value: wild-type


title: Col-0 con2

description:
SAMPLE 6
252116913727_2
Gene expression in Col-0 leaves under control condition

source_name: wild-type Col-0, Arabidopsis leaf, replicate 2


title: 293npT (icSHAPE)

value: nucleoplasm(np)


title: hTECs clone with stratified colony morphology, biological rep1

description: Thy14 IV Cl94


title: Col-0 con4

description:
SAMPLE 5
252116913727_1
Gene expression in Col-0 leaves under control condition

source_name: wild-type Col-0, Arabidopsis leaf, replicate 4


title: Col-0 con1

description:
SAMPLE 1
252116913723_1
Gene expression in Col-0 leaves under control condition

source_name: wild-type Col-0, Arabidopsis leaf, replicate 1


title: 293npD (icSHAPE)


title: 293chT (icSHAPE)

value: chromatin (ch)


title: BT474_shCon #2

source_name: Human mammary gland

tag: disease state

value: ductal carcinoma

value: shCon


title: Rap2.9 con4

description:
SAMPLE 4
252116913723_4
Gene expression in Rap2.9 overexpressing Arabidopsis leaves under control condition

source_name: 35S::Rap2.9-GFP, Arabidopsis leaf, replicate 4


title: hTECs clone with stratified colony morphology, biological rep2

tag: cell type


title: NUH_R016

description: Gene expression data of human gastric tumor

source_name: Human stomach

value: Gastric tumor


title: 293npN (icSHAPE)

value: human embryonic kidney cells

value: in vivo NAI-N3 treatment (N)


title: 293chN (icSHAPE)


title: TWEAK-siRNAs523629-24hr-B

city: Cambridge

first: Kejie

state: Massachusetts

address: 225 Binney Street

institute: Biogen

description: replicate B

data_processing:
Reads were aligned to reference genome (hg19) using STAR aligner
QC includes sequence quality, GC content, 5’-3’ gene body coverage (Supplementary Table S6)
Outlier detection absolute Z score > 2 was applied on overall sequencing quality score, 5 prime coverage, 3 prime coverage, mean_GC content, duplication rate, mean_ and mapped percentage. Sample with absolute Z score > 2 would be discarded, which did not apply to this study.
Aligned reads were counted against gene model annotation (Gencode v18) to obtain expression values by using FeatureCounts
DESeq2 was used for gene expression normalization
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each Sample:
DESeq2_normalized_count_matrix.txt: Count matrix for counts per gene, normalized for library size using DESeq2
DESeq2_regularized_log_transformed.txt: Made using the rlogTransformation function in DESeq2. This function transforms the count data to the log2 scale in a way which minimizes differences between samples for rows with small counts, and which normalizes with respect to library size. These are the values used to obtain clustering and PCA results.
QC_statistics_to_deliver.txt: Tot_reads(M)- Total number of reads in the sample, in millions  rRNA(%)- Percent of reads aligned to ribosomal RNA  Map(%)- Percent of reads which map to genome  UQ_map(%)- Percent of reads which map to only one locus on the genome  Gene_assn(%)- Of uniquely mapped reads, percentage which may be assigned to exons of genes by gene counting program featureCounts  Strand(%)- Percentage of reads which are reversely stranded. If unstranded protocol, this is not counted and listed as 0.  5prime_cov- Mean normalized coverage from Picard for percentiles 11-30 along gene body  3prime_cov- Mean normalized coverage from Picard for percentiles 71-90 along gene body  Mean_GC(%)- Mean GC content averaging GC content for each read across all reads  Dup(%)- Percentage of reads which were duplicates  Mean_inner_dist- Inner distance = Read 2 start - Read 1 end. Negative indicates overlap.  CDS, UTR, Intronic, and Intergenic(%)- Percentage of reads assigned to different regions of the genome. These four add up to 100%.  chrM(%)- For reads assigned to genes, percentage assigned to mitochondrial genes.  Top_ten(%)- For reads assigned to genes, percentage assigned to the top 10 most highly expressed genes.
featureCounts_count_matrix.txt: Raw count matrix with counts per gene as obtained by featureCounts
gene_annotation_info.txt: More info on the genes in the count matrices, such as gene coordinates, biotype (coding vs. noncoding), etc.
kallisto_TPM_matrix.txt: Per transcript in the annotation, the TPM (transcripts per million) value given by Kallisto. If this file is not present, then Kallisto was not run for this project.
kallisto_est_count_matrix.txt: Per transcript in the annotation, the estimated counts value given by Kallisto. If this file is not present, then Kallisto was not run for this project.

source_name: U2OS cell

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

value: TWEAK

tag: time


title: 293chD (icSHAPE)

value: DMSO (D)


title: TWEAK-NTsiRNA-24hr-B

description: replicate B

value: NTsiRNA


title: TWEAK-siRNAs523626-24hr-B

description: replicate B


title: UnStim-siRNAs523629-24hr-B

description: replicate B

value: UnStim


title: UnStim-siRNAs523626-24h-B

description: replicate B


title: UnStim-NTsiRNA-24hr-B

description: replicate B


title: TWEAK-siRNAs523629-4hr-B

description: replicate B


title: UnStim-siRNAs523629-4hr-B

description: replicate B


title: sigD_delete_1st

city: Kyoto

first: Masayuki

last: Inui

address: 9-2 Kizugawadai, Kizugawa

country: Japan

institute: Research institute of Innovative Technology for the Earth (RITE)

hyb_protocol: Labeled cDNA (4.5 μg each) are mixed with 1 × hybridization buffer (6 × SSC, 0.2% SDS, 5 × Denhardt’s solution, 0.1 mg/ml denatured salmon sperm DNA) in a total volume of 340 μl, and denatured at 95˚C for 2 min. The hybridization mixture was hybridized to a microarray in an Agilent Technologies Microarray chamber at 60˚C for 17 h in a rotating Agilent hybridization oven. After hybridization, microarrays were washed for 5 minutes with wash buffer 1 (2x SSC, 0.2% SDS) at room temperature , 5 minutes with wash buffer 2 (0.2x SSC, 0.2% SDS) at 60˚C, and 5 minutes with wash buffer 3 (0.2x SSC) at room temperature.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) at a resolution of 5 µm. PMT is set to 100% for Cy3 and Cy5 channels.

data_processing: The scanned images were analyzed quantified with Feature Extraction Software 10.5.5.1 (Agilent) using default parameters (protocol GE2-NonAT_105_Dec08). Feature extracted data were analyzed using GeneSpring GX v 13.1 software from Agilent. Normalization of the data was done in GeneSpring GX using the Lowess normalization algorithm without baseline transformation.

organism: Corynebacterium glutamicum R

source_name: WT_exponential phase

label_protocol: The cDNAs were synthesized from RNA by using reverse transcriptase from 10 μg of total RNAs and labeled with cyanine 3 (Cy3) or cyanine 5 (Cy5) using the SuperScript Indirect cDNA Labeling system (Life Technologies).

growth_protocol: C. glutamicum strains are grown in 100 ml of nutrient rich A medium containing 1% glucose in  500 ml flask at 33˚C

extract_protocol: Total RNA was extracted from C. glutamicum cells using NucleoSpin RNA II kit (Macherey-Nagel, Germany) according to the manufacture's manual.

tag: genotype/variation

value: wild type

tag: growth phase

value: exponential phase

source_name: sigD mutant_exponential phase

value: sigD mutant


title: vector_control_2nd

description:
vector_control_2nd
IPTG was added at the final concentration of 0.5 mM during the exponential phase of growth

data_processing: The scanned images were analyzed quantified with Feature Extraction Software 10.5.5.1 (Agilent) using default parameters (protocol GE2-NonAT_105_Dec08). Feature extracted data were analyzed using GeneSpring GX v 12.5 software from Agilent. Normalization of the data was done in GeneSpring GX using the Lowess normalization algorithm without baseline transformation.

source_name: WT carrying the vacant vector before IPTG induction

treatment_protocol: To induce sigD overexpression, isopropyl-β-d-thiogalactopyranoside (IPTG) was added at the final concentration of 0.5 mM to exponentially-growing culture. After 15 min, 1 ml of culture was mixed with 1 ml bacterial RNA protect reagent (Qiagen) for RNA stabilization.

value: carrying the empty vector in WT background

tag: plasmid

tag: time point

value: before IPTG induction

source_name: WT carrying the vacant vector after 15 min of IPTG induction

value: after 15 min of IPTG induction


title: UnStim-siRNAs523626-4hr-B

description: replicate B


title: vector_control_1st

description:
vector_control_1st
IPTG was added at the final concentration of 0.5 mM during the exponential phase of growth


title: TWEAK-NTsiRNA-4hr-B

description: replicate B


title: sigD_delete_2nd


title: sigD_delete_3rd


title: rsdA_delete_2nd

source_name: rsdA mutant_exponential phase

value: rsdA mutant


title: vector_control_3rd

description:
vector_control_3rd
IPTG was added at the final concentration of 0.5 mM during the exponential phase of growth


title: sigD_overexpress_3rd

description:
sigD_ox_3rd
IPTG was added at the final concentration of 0.5 mM during the exponential phase of growth

source_name: WT carrying the sigD overexpressing plasmid before IPTG induction

value: carrying the sigD overexpressing plasmid in WT background

source_name: WT carrying the sigD overexpressing plasmid after 15 min of IPTG induction


title: sigD_overexpress_4th

description:
sigD_ox_4th
IPTG was added at the final concentration of 0.5 mM during the exponential phase of growth


title: UnStim-NTsiRNA-4hr-B

description: replicate B


title: TWEAK-siRNAs523629-24hr-A

description: replicate A


title: UnStim-siRNAs523629-24hr-A

description: replicate A


title: rsdA_delete_1st


title: TWEAK-siRNAs523626-24hr-A

description: replicate A


title: UnStim-NTsiRNA-24hr-A

description: replicate A


title: TWEAK-siRNAs523626-4hr-B

description: replicate B


title: UnStim-siRNAs523626-24hr-A

description: replicate A


title: TWEAK-NTsiRNA-24hr-A

description: replicate A


title: sigD_overexpress_1st

description:
sigD_ox_1st
IPTG was added at the final concentration of 0.5 mM during the exponential phase of growth


title: sigD_overexpress_2nd

description:
sigD_ox_2nd
IPTG was added at the final concentration of 0.5 mM during the exponential phase of growth


title: TWEAK-siRNAs523629-4hr-A

description: replicate A


title: the rsdA mutant1 at the exponential phase_2nd

hyb_protocol: Hybridization was performed using Gene Expression Hybridization Kit according to the manufacture’s manual (Agilent). The labeled cDNA was hybridized to microarrays in an Agilent Technologies Microarray chamber at 65˚C for 17 h in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent), and 1 minute with 37˚C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) at a resolution of 5 µm using single color scan setting for 4x44k array slides. PMT is set to 100% for Cy3 channels.

data_processing: The scanned images were analyzed quantified with Feature Extraction Software 10.5.5.1 (Agilent) using default parameters (protocol GE1_105_Dec08). Feature extracted data were analyzed using GeneSpring GX v 13.1 software from Agilent. Normalization of the data was done in GeneSpring GX using the recommended Percentile shift normalization (50th percentile) and baseilne was transformed to median of all samples.

label_protocol: The cDNAs were synthesized from RNA by using reverse transcriptase from 10 μg of total RNAs and labeled with cyanine 3 (Cy3) using the SuperScript Indirect cDNA Labeling system (Life Technologies).


title: the sigD mutant1 at the exponential phase_2nd [Agilent-025748]

value: sigD deletant


title: UnStim-siRNAs523629-4hr-A

description: replicate A


title: TWEAK-NTsiRNA-4hr-A

description: replicate A


title: UnStim-siRNAs523626-4hr-A

description: replicate A


title: TWEAK-siRNAs523626-4hr-A

description: replicate A


title: wt at the exponential phase_2nd [Agilent-025748]


title: wt at the exponential phase_1st [Agilent-025748]


title: TGFbeta_2APB-1

city: Grand Forks

first: Archana

last: Dhasarathy

state: North Dakota

address: 501 N Columbia Rd.

institute: University of North Dakota

data_processing:
Preliminary quality control perfomed using FastQC v0.11.2
Reads were aligned to mouse genome (mm10) using TopHat v2.0.13
Read counts were summarized at the gene-level using Rsubread v1.16.1
Differential expression analysis performed using DESeq2 v1.6.1
Genome_build: mm10
Supplementary_files_format_and_content: Comma separated text file of count abundance data for all samples

source_name: NMuMG cells

extract_protocol:
Total RNA was extracted using Qiagen's RNeasy kit
RNA libraries were prepared for sequencing using standard Illumina protocols


title: UnStim-NTsiRNA-4hr-A

description: replicate A


title: TWEAK-BIO032202-24hr-B

description: replicate B


title: the sigD mutant1 at the exponential phase_1st [Agilent-025748]


title: TGFbeta-1

value: TGFbeta


title: TGFbeta_2APB-2


title: TGFbeta-2


title: TWEAK-BIO0919278-24hr-B

description: replicate B


title: UnStim-BIO032202-24hr-B

description: replicate B


title: wt at the exponential phase_2nd


title: UnStim-BIO0919278-24hr-B

description: replicate B


title: TWEAK-BIO0702697-24hr-B

description: replicate B


title: UnStim-BIO0702697-24hr-B

description: replicate B


title: DMSO-2

value: Control


title: DMSO-1


title: TWEAK-BIO032202-4hr-B

description: replicate B


title: SigD-ChIP_2nd

type: genomic

hyb_protocol: Hybridization was performed using Agilent Oligo aCGH Hybridization kit according to the manufacture’s manual (Agilent). Equal amount (2.5 μg) of each labeled DNA were mixed and hybridized to microarrays in an Agilent Technologies Microarray chamber at 65˚C for 24 h in a rotating Agilent hybridization oven at 20 rpm. After hybridization, microarrays were washed 5 min at room temperature with Oligo aCGH/ChIP-on-chip Wash Buffer 1 (Agilent), 5 min with 31˚C Oligo aCGH/ChIP-on-chip Wash buffer 2 (Agilent Technologies), 10 sec with acetonitrile, and 30 sec with Stabilization and Drying Solution (Agilent) at room temperature.

scan_protocol: Slides were scanned immediately after washing and placement within an Agilent Ozone Barrier Slide cover (Agilent) the Agilent DNA Microarray Scanner (G2505C) using two color scan setting for 4x44k array Scan resolution 5 microns. Scanning was done in both channels and PMT is set to 100% for both Cy3\cy5 channels.

data_processing: Feature extraction software provided by Agilent (version 10.5.1.1, Agilent Technologies, Palo Alto, CA, USA) was used to quantify the intensity of the fluorescent images and to normalize the results by subtracting local background fluorescence, according to the manufacturer’s instructions.

molecule: genomic DNA

source_name: SigD-FLAG ChIP DNA_C. glutamicum WT_exponential phase

label_protocol: DNA samples were blunted with T4 DNA polymerase, ligated to linkers, and amplified by PCR. Amplified DNA from reference DNA and immunoprecipitated DNA were differentially labeled with Cy3 and Cy5, respectively, by using CGH labeling kit (Invitrogen) according to the manufacture’s instruction.

growth_protocol: C. glutamicum is grown in 100 ml of nutrient rich A medium containing 1% glucose in  500 ml flask at 33˚C

extract_protocol: C. glutamicum cultures at the late exponential phase (at the OD610 of up to 2.5) were treated with formaldehyde (at the final concentration of 1%) and incubate for 20 min at room temperature. The cross-linking was quenched by addition of glycine (at the final concentration of 125 mM) and incubation for 10 min at room temperature. Cells were then collected by centrifugation, washed twice with Tris-buffered saline (20 mM Tris-HCl pH 7.5, 150 mM NaCl) and stored at -80˚C. Pellets were resuspended in 2 ml IP buffer (50 mM HEPES-KOH pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS, Roche Antiprotease mini). The cells were mechanically disrupted for nine cycles of 25 s at a speed rating of 6.5 with a FastPrep™ FP120 (BIO 101, Thermo Savant) at room temperature with intermittent cooling on ice for 5 min. The supernatant after centrifugation was sonicated on ice to shear DNA to an average size to 600-1,000 bp. A 50 μl fraction of the supernatant was saved for later analysis (reference DNA). The remainder was subjected to immunoprecipitation with 100μl of magnetic beads coated with Protein G (Invitrogen), which was coupled to the monoclonal anti-FLAG-tag antibody (Sigma). The mixture was incubated overnight on a rotating platform at 4˚C. The beads were washed once with IP buffer, twice with IP buffer containing 400 mM NaCl, eight times with RIPA buffer (50 mM HEPES pH7.6, 500 mM LiCl, 1 mM EDTA, 1% NP-40, 0.7% Sodium deoxycholate), and twice with TE buffer with 50 mM NaCl. Immunoprecipitated complexes were eluted from the beads by treatment with 210 μl elution buffer (50 mM Tris-HCl pH8.0, 10 mM EDTA, 1% SDS) at 65˚C for 20 min. Cross-links of immunoprecipitated samples and of total DNA samples were reversed by incubation overnight at 65˚C. Samples were then treated with RNase A and proteinase K for 2 h at 55˚C. DNA was extracted with phenol-chloroform and purified with QIAquick PCR purification mini Elute kit (Qiagen).

value: expressing the FLAG-tagged SigD in WT background

source_name: Reference genomic DNA, no IP treatment control

value: stationary phase


title: TWEAK-DMSO-24hr-B

description: replicate B

value: TWEAK

value: DMSO


title: the rsdA mutant1 at the exponential phase_1st


title: UnStim-DMSO-24hr-B

description: replicate B


title: TWEAK-BIO0919278-4hr-B

description: replicate B


title: UnStim-BIO0702697-4hr-B

description: replicate B


title: TWEAK-DMSO-4hr-B

description: replicate B


title: wt at the exponential phase_1st


title: TWEAK-BIO032202-24hr-A

description: replicate A


title: SigD-ChIP_1st


title: UnStim-BIO032202-4hr-B

description: replicate B


title: TWEAK-BIO0702697-4hr-B

description: replicate B


title: UnStim-DMSO-4hr-B

description: replicate B


title: TWEAK-BIO0919278-24hr-A

description: replicate A


title: UnStim-BIO032202-24hr-A

description: replicate A


title: UnStim-BIO0919278-24hr-A

description: replicate A


title: TWEAK-BIO0702697-24hr-A

description: replicate A


title: TWEAK-BIO032202-4hr-A

description: replicate A


title: UnStim-DMSO-24hr-A

description: replicate A


title: TWEAK-DMSO-24hr-A

description: replicate A


title: UnStim-BIO032202-4hr-A

description: replicate A


title: TWEAK-BIO0702697-4hr-A

description: replicate A


title: UnStim-BIO0702697-4hr-A

description: replicate A


title: T16 9

city: Barcelona

first: Bruno

last: Campos

address: jordi girona, 18, 18

department: Environmental Chemistry

country: Spain

institute: IDAEA-CSIC

hyb_protocol: according to manufacturer protocols

scan_protocol: according to manufacturer protocols

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5 (Agilent) using default parameters (protocol GE1-v1_91 and Grid:079797)to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Daphnia magna

source_name: Full organism, 4 days old.

label_protocol: according to manufacturer protocols Low input Quick Amp labeling

growth_protocol: daphnias were cultured and grown according to Barata and Baird, 200

extract_protocol: Total RNA was extracted using Trizol according to Soetaert et al. 2007

value: Clone 16 -/-

value: all body

tag: age

value: 5 days

tag: Sex

value: female


title: T17 9

value: Clone 17 -/-


title: T17 3


title: UnStim-BIO0919278-4hr-A

description: replicate A

tag: stimulation

value: UnStim


title: UnStim-BIO0919278-4hr-B

description: replicate B

tag: cell line


title: T17 5


title: UnStim-BIO0702697-24hr-A

description: replicate A

tag: treatment


title: T16 5


title: UnStim-DMSO-4hr-A

description: replicate A


title: T17 7


title: T13 7

value: Clone 13 +/-


title: T16 7


title: T13 9


title: T13 5


title: TWEAK-BIO0919278-4hr-A

description: replicate A


title: RNA-Seq of Treeshrew ZIKV-infected PBMC +6dpi, 2

city: Suzhou

first: feng

last: ma

state: Jiangsu

address: 218 Xinghu Street, B5-527

department: Suzhou Institute of Systems Medicine

institute: CAMS

data_processing:
bcl2fastq(v 2.17) software was used to base-calling
trimmomatic was used to remove illumina sequencing adapters within raw reads of every sample, trim low quality bases of both read ends
clean reads were mapped to Chinese_treeshrew_KIZv2.gtf by using HISAT (v2.0.4 ), reference genome could be downloaded in website http://www.treeshrewdb.org/
DESeq2 was used to identify DEGs (p<=0.05, FC>=2) based on raw reads counts.
Genome_build: treeshrewdb
Supplementary_files_format_and_content: xls files include reads counts for each Sample

organism: Tupaia chinensis

source_name: #2 treeshrew

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) from 0, 2 and 6 dpi (two for each group) were isolated using Ficoll-Hypaque and total RNA were extracted by RNeasy mini kit (Qiagen, German) for global transcriptome analysis.
RNA libraries were constructed using a TruSeq Stranded mRNA Sample Prep Kit (RS-122-2001, Illumina) according to the manufacturer’s guideline.

treatment_protocol: Two treeshreews (duplicated) infected with10^5 PFU of ZIKV(GZ01 strain) by the subcutaneous (s.c.) route.

value: PBMC

tag: culture

value: in vivo

tag: agent

value: ZIKV


title: RNA-Seq of Treeshrew ZIKV-infected PBMC +2dpi, 1

source_name: #1 treeshrew


title: T16 3


title: T13 3


title: F 9


title: F 3


title: FaDOF2 Control R2

city: CÓRDOBA

first: Francisco

middle: Javier

last: Molina-Hidalgo

state: Cordoba

address: Edif. Severo Ochoa (C6.) Planta Baja-Ala Norte Campus de Rabanales

department: Biochemistry and molecular biology

institute: University of Cordoba

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: Data analysis of the microarray expression studies was performed with the software for gene expression analysis Array Star (DNASTAR). The moderated t-test and FDR (Benjamini and Hochberg, 1995) for multiple testing corrections were used, with a confidence p-value < 0.05 in order to statistically identify significant differences.

organism: Fragaria x ananassa

source_name: Strawberry fruit agroinjected with the empty vector Replicate 2

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Strawberry plants (F. x ananassa) used for agro-infiltration were grown in plant chamber at 25 ºC, 10.000 lux and 80% humidity and afterwards maintained in a greenhouse.

extract_protocol: Total RNA was isolated from independent strawberry fruits as stated by Asif et al. (2000). The total RNA obtained was treated with DNase I (RNase free) (Invitrogen), in accordance with the manufacturer's instructions, to remove genomic DNA contamination, after which it was purified by using the RNeasy Mini kit (Qiagen).

treatment_protocol: The A. tumefaciens strain AGL0 (Lazo et al., 1991), containing the pFRN-FaDOF2 was used to inject the strawberry fruit receptacles (Fragaria × ananassa), according to Hoffmann et al. (2006). A total of 15-25 strawberry plants and 30-40 agroinfiltrated fruits were inoculated and analysed, respectively. As control, fruits agroinfiltrated with the empty pFRN vector were used.

value: fruit

tag: phenotype

value: Normal


title: FaDOF2-RNAi R3

source_name: Strawberry fruit agroinjected with the FaDOF2-RNAi construct Replicate 3

value: Low level of eugenol


title: FaDOF2-RNAi R2

source_name: Strawberry fruit agroinjected with the FaDOF2-RNAi construct Replicate 2


title: F 7


title: TWEAK-DMSO-4hr-A

description: replicate A

source_name: U2OS cell


title: RNA-Seq of Treeshrew ZIKV-infected PBMC +6dpi, 1


title: RNA-Seq of Treeshrew ZIKV-infected PBMC -2dpi, 1


title: RNA-Seq of Treeshrew ZIKV-infected PBMC +2dpi, 2


title: RNA-Seq of Treeshrew ZIKV-infected PBMC -2dpi, 2


title: FaDOF2 Control R1

source_name: Strawberry fruit agroinjected with the empty vector Replicate 1


title: FaDOF2 Control R3

source_name: Strawberry fruit agroinjected with the empty vector Replicate 3


title: FaDOF2-RNAi R1

source_name: Strawberry fruit agroinjected with the FaDOF2-RNAi construct Replicate 1


title: Tp30_Rep2_GFP: Pulse-seq T=30 days, Rep2, basal lineage-positive GFP+

status: Public on Jul 30 2018

city: Boston

first: Adam

last: Haber

address: 665 Huntington Ave, HSPH Building 1, Room 305

institute: Harvard T. H. Chan School of Public Health

description: 3' RNAseq reads aligned to mm10

data_processing:
3' polyA RNA-seq
CellRanger 1.0
PCA (prcomp in R)
kNN-based graph clustering (R code)
Genome_build: mm10
Supplementary_files_format_and_content: 10X genomics CellRanger output: UMI count expression values for each gene (rows) in each cell (columns)

source_name: Pulse-seq reporter mouse tracheal epithelial cells

extract_protocol:
3' polyA RNA seq
10X Genomics Chromium Prep

tag: strain

value: trachea epithelium

tag: genotype

value: 30 days after tamoxifen induction


title: Tp30_Rep1_GFP: Pulse-seq T=30 days, Rep1, basal lineage-positive GFP+

description: 3' RNAseq reads aligned to mm10

tag: tissue


title: Tp60_Rep2_GFP: Pulse-seq T=60 days, Rep2, basal lineage-positive GFP+

description: 3' RNAseq reads aligned to mm10

value: 60 days after tamoxifen induction


title: Tp30_Rep1_Tom: Pulse-seq T=30 days, Rep1, basal lineage-negative tdTomato+

description: 3' RNAseq reads aligned to mm10


title: Tp60_Rep3_Tom: Pulse-seq T=60 days, Rep3, basal lineage-negative tdTomato+

description: 3' RNAseq reads aligned to mm10


title: Tp60_Rep1_Tom: Pulse-seq T=60 days, Rep1, basal lineage-negative tdTomato+

description: 3' RNAseq reads aligned to mm10


title: Tp60_Rep1_GFP: Pulse-seq T=60 days, Rep1, basal lineage-positive GFP+

description: 3' RNAseq reads aligned to mm10


title: Tp60_Rep3_GFP: Pulse-seq T=60 days, Rep3, basal lineage-positive GFP+

description: 3' RNAseq reads aligned to mm10


title: Tp0_Rep3_Tom: Pulse-seq T=0 days, Rep3, basal lineage-negative tdTomato+

description: 3' RNAseq reads aligned to mm10

value: 0 days after tamoxifen induction


title: Tp30_Rep2_Tom: Pulse-seq T=30 days, Rep2, basal lineage-negative tdTomato+

description: 3' RNAseq reads aligned to mm10


title: Tp0_Rep3_GFP: Pulse-seq T=0 days, Rep3, basal lineage-positive GFP+

description: 3' RNAseq reads aligned to mm10


title: Tp0_Rep2_Tom: Pulse-seq T=0 days, Rep2, basal lineage-negative tdTomato+

description: 3' RNAseq reads aligned to mm10


title: Tp0_Rep1_Tom: Pulse-seq T=0 days, Rep1, basal lineage-negative tdTomato+

description: 3' RNAseq reads aligned to mm10


title: Tp0_Rep2_GFP: Pulse-seq T=0 days, Rep2, basal lineage-positive GFP+

description: 3' RNAseq reads aligned to mm10


title: Tp0_Rep1_GFP: Pulse-seq T=0 days, Rep1, basal lineage-positive GFP+

description: 3' RNAseq reads aligned to mm10


title: Tp30_Rep3_Tom: Pulse-seq T=30 days, Rep3, basal lineage-negative tdTomato+

description: 3' RNAseq reads aligned to mm10


title: 38_KO.stim

city: Münster

first: Luisa

last: Klotz

address: Albert-Schweitzer-Campus 1, A1

institute: Universitätsklinikum Münster

data_processing:
Trimming: Trimmomatic 0.36 (Parameter: SE -phred33, ILLUMINACLIP:adapters/NEB-SE.fa:2:30:10, LEADING:3 TRAILING:3 MINLEN:15)
Alignment: hisat 2.1.0 (Parameter: default)
Sorting: samtools sort names (Version: Version: 1.2-25-gf995b71-dirty using htslib 1.2.1-39-g5ffc4a2-dirty)
Counting: htseq-count 0.9.1 (Parameter: --minaqual 0,  --stranded reverse)
Differential Expression Analysis inside R: R version 3.4.4 (2018-03-15) plus Bioconductor BiocInstaller_1.28.0 using Platform: x86_64-w64-mingw32/x64 (64-bit) and Running under: Windows 10 x64 (build 9200), used R-packages: DESeq2_1.18.1
Visualization of significant Genes: pathview_1.18.2, gplots version 3.0.1, ggplot2_2.2.1, ggbiplot_0.55
Preparation for Gene Set Enrichment Analysis on DAVID inside R using the following packages: AnnotationDbi_1.40.0, org.Mm.eg.db_3.5.0
Gene Set Enrichment Analysis was performed using DAVID-Online tool Version 6.8 (https://david.ncifcrf.gov/summary.jsp)
Genome_build: mm10
Supplementary_files_format_and_content: The count files (Output of htseq-count) are tab-separated plain-text files: 1. column gene name, 2. column read count

source_name: spleen, inguinal and axillary lymph node

extract_protocol:
CD4 positive T cells were isolated from spleen and lymph nodes and subsequently stimulated with aCD3 and aCD28 for 12h. RNA was isolated using RNeasy Mini Kit (Qiagen) with an integrated DNA digestion on the column using RNase-Free DNase Set (Qiagen) according to manufacturer’s instruction.
quality checked (Bioanalyzer RIN value) total RNA was enriched for Poly(A) RNA (NEBNext Poly(A) Isolation Module, NEB) and used for directional RNA library preparation (NEBNext Ultra RNA II directional, NEB) according to manufacturer´s instructions

value: stimulated


title: 37_KO.unstim

value: spleen, inguinal and axillary lymph node

value: control


title: F 5

value: all body

value: 5 days

value: female


title: 39_KO.stim_Inh1

value: stimulated + Inhibitor 1 [XCT790, 10microgram/ml]


title: 40_KO.stim_Inh2

value: stimulated + Inhibitor 2 [Compound A (CompA), 10micorgram/ml]


title: 35_KO.stim_Inh1


title: 33_KO.unstim


title: Tp30_Rep3_GFP: Pulse-seq T=30 days, Rep3, basal lineage-positive GFP+

description: 3' RNAseq reads aligned to mm10


title: 32_KO.stim_Inh2


title: 31_KO.stim_Inh1


title: 30_KO.stim


title: 29_KO.unstim


title: 34_KO.stim


title: 10_WT.stim

value: WT


title: 13_WT.unstim


title: 7_WT.stim_Inh1


title: 28_KO.stim_Inh2


title: 6_WT.stim


title: 12_WT.stim_Inh2


title: 5_WT.unstim


title: 8_WT.stim_Inh2


title: 27_KO.stim_Inh1


title: 16_WT.stim_Inh2


title: 11_WT.stim_Inh1


title: 26_KO.stim


title: 25_KO.unstim


title: 15_WT.stim_Inh1


title: 14_WT.stim


title: 1_WT.unstim


title: 2_WT.stim


title: 4_WT.stim_Inh2


title: 3_WT.stim_Inh1


title: Trachea epithelial single cell 300

description:
This sample represents a single cell processed with the SMART-Seq2 protocol.
Full-length RNAseq (SMART-Seq2). The expression levels for each gene (rows) in each single cell (column) in transcripts per million (TPM) as calculated using RSEM. Each column header provides the sequencing batch id, the cell identifier, the region of origin (proximal or distal trachea), and the cell type as identified by cluster analysis. Each ID is seperated by '_'
processed data file:
Trachea_fullLength_TPM.txt

data_processing:
Full-length RNAseq (SMART-Seq2)
Tophat
Bowtie
RSEM
PCA (prcomp in R)
kNN-based graph clustering (R code)
genome build: mm10
processed data files format and content: Transcripts per million (TPM) expression values (derived from RSEM  for each gene (rows) in each cell (columns)

source_name: WT Mouse airway (trachea) epithelial cells

extract_protocol:
Smart-seq2 method described by Picelli et al. (Nature Protocols 2014)
Nextera XT DNA Library Preperation Kit (Illumina)

tag: trachea region

value: proximal

tag: cell phenotype

value: Club

value: Wild type


title: Trachea epithelial single cell 297


title: Trachea epithelial single cell 301

value: Ionocyte


title: 9_WT.unstim


title: Trachea epithelial single cell 299

value: trachea epithelium

value: Basal


title: Trachea epithelial single cell 298


title: Trachea epithelial single cell 296


title: Trachea epithelial single cell 294


title: Trachea epithelial single cell 292

value: Neuroendocrine


title: Trachea epithelial single cell 281


title: Trachea epithelial single cell 288


title: Trachea epithelial single cell 287


title: Trachea epithelial single cell 289


title: Trachea epithelial single cell 285


title: Trachea epithelial single cell 286


title: Trachea epithelial single cell 293


title: Trachea epithelial single cell 279


title: Trachea epithelial single cell 291


title: Trachea epithelial single cell 290


title: Trachea epithelial single cell 276


title: Trachea epithelial single cell 282


title: Trachea epithelial single cell 280


title: Trachea epithelial single cell 284


title: Trachea epithelial single cell 275


title: Trachea epithelial single cell 283

value: Tuft


title: Trachea epithelial single cell 277


title: Trachea epithelial single cell 273


title: Trachea epithelial single cell 271


title: Trachea epithelial single cell 270


title: Trachea epithelial single cell 272


title: Trachea epithelial single cell 295


title: Trachea epithelial single cell 268


title: Trachea epithelial single cell 269


title: Trachea epithelial single cell 278


title: Trachea epithelial single cell 267

value: Ciliated


title: Trachea epithelial single cell 266


title: Trachea epithelial single cell 263


title: Trachea epithelial single cell 265


title: Trachea epithelial single cell 261


title: Trachea epithelial single cell 262


title: Trachea epithelial single cell 259


title: Trachea epithelial single cell 255


title: Trachea epithelial single cell 260


title: Trachea epithelial single cell 274


title: Trachea epithelial single cell 257


title: Trachea epithelial single cell 256


title: Trachea epithelial single cell 258


title: Trachea epithelial single cell 254


title: Trachea epithelial single cell 250


title: Trachea epithelial single cell 251


title: Trachea epithelial single cell 253


title: Trachea epithelial single cell 252


title: Trachea epithelial single cell 249


title: Trachea epithelial single cell 248


title: Trachea epithelial single cell 246

value: distal


title: Trachea epithelial single cell 247


title: Trachea epithelial single cell 244


title: Trachea epithelial single cell 243


title: Trachea epithelial single cell 242


title: Trachea epithelial single cell 264


title: Trachea epithelial single cell 241


title: Tp60_Rep2_Tom: Pulse-seq T=60 days, Rep2, basal lineage-negative tdTomato+

description: 3' RNAseq reads aligned to mm10

value: 60 days after tamoxifen induction


title: Trachea epithelial single cell 240


title: Trachea epithelial single cell 239


title: Trachea epithelial single cell 237


title: Trachea epithelial single cell 238


title: Trachea epithelial single cell 235


title: Trachea epithelial single cell 233


title: Trachea epithelial single cell 231


title: Trachea epithelial single cell 234


title: Trachea epithelial single cell 232


title: Trachea epithelial single cell 226


title: Trachea epithelial single cell 227


title: Trachea epithelial single cell 229


title: Trachea epithelial single cell 225


title: Trachea epithelial single cell 224


title: Trachea epithelial single cell 245


title: Trachea epithelial single cell 228


title: Trachea epithelial single cell 223


title: Trachea epithelial single cell 221


title: Trachea epithelial single cell 217


title: Trachea epithelial single cell 214


title: Trachea epithelial single cell 215


title: Trachea epithelial single cell 236


title: Trachea epithelial single cell 218


title: Trachea epithelial single cell 209


title: Trachea epithelial single cell 216


title: Trachea epithelial single cell 220


title: Trachea epithelial single cell 219


title: Trachea epithelial single cell 205


title: Trachea epithelial single cell 212


title: Trachea epithelial single cell 204


title: Trachea epithelial single cell 230


title: Trachea epithelial single cell 211


title: Trachea epithelial single cell 213


title: Trachea epithelial single cell 210


title: Trachea epithelial single cell 202


title: Trachea epithelial single cell 208


title: Trachea epithelial single cell 207


title: Trachea epithelial single cell 197


title: Trachea epithelial single cell 198


title: Trachea epithelial single cell 206


title: Trachea epithelial single cell 222


title: Trachea epithelial single cell 199


title: Trachea epithelial single cell 200


title: Trachea epithelial single cell 192


title: Trachea epithelial single cell 193


title: Trachea epithelial single cell 191


title: Trachea epithelial single cell 190


title: 36_KO.stim_Inh2

value: spleen, inguinal and axillary lymph node


title: Trachea epithelial single cell 203


title: Trachea epithelial single cell 187


title: Trachea epithelial single cell 201


title: Trachea epithelial single cell 186


title: Trachea epithelial single cell 196


title: Trachea epithelial single cell 184


title: Trachea epithelial single cell 183


title: Trachea epithelial single cell 181


title: Trachea epithelial single cell 195


title: Trachea epithelial single cell 185


title: Trachea epithelial single cell 194


title: Trachea epithelial single cell 179


title: Trachea epithelial single cell 177


title: Trachea epithelial single cell 176


title: Trachea epithelial single cell 175


title: Trachea epithelial single cell 180


title: Trachea epithelial single cell 178


title: Trachea epithelial single cell 182


title: Trachea epithelial single cell 174


title: Trachea epithelial single cell 171


title: Trachea epithelial single cell 173


title: Trachea epithelial single cell 172


title: Trachea epithelial single cell 170


title: Trachea epithelial single cell 169


title: Trachea epithelial single cell 189


title: Trachea epithelial single cell 168


title: Trachea epithelial single cell 188


title: Trachea epithelial single cell 167


title: Trachea epithelial single cell 166


title: Trachea epithelial single cell 163


title: Trachea epithelial single cell 164


title: Trachea epithelial single cell 165


title: Trachea epithelial single cell 162


title: Trachea epithelial single cell 161


title: Trachea epithelial single cell 160


title: Trachea epithelial single cell 159


title: Trachea epithelial single cell 158


title: Trachea epithelial single cell 153


title: Trachea epithelial single cell 156


title: Trachea epithelial single cell 152


title: Trachea epithelial single cell 154


title: Trachea epithelial single cell 149


title: Trachea epithelial single cell 151


title: Trachea epithelial single cell 150


title: Trachea epithelial single cell 148


title: Trachea epithelial single cell 155


title: Trachea epithelial single cell 146


title: Trachea epithelial single cell 147


title: Trachea epithelial single cell 145


title: Trachea epithelial single cell 143


title: Trachea epithelial single cell 141


title: Trachea epithelial single cell 140


title: Trachea epithelial single cell 139


title: Trachea epithelial single cell 138


title: Trachea epithelial single cell 137


title: Trachea epithelial single cell 136


title: Trachea epithelial single cell 134


title: Trachea epithelial single cell 135


title: Trachea epithelial single cell 133


title: Trachea epithelial single cell 132


title: Trachea epithelial single cell 157


title: Trachea epithelial single cell 131


title: Trachea epithelial single cell 130


title: Trachea epithelial single cell 129


title: Trachea epithelial single cell 128


title: Trachea epithelial single cell 127


title: Trachea epithelial single cell 124


title: Trachea epithelial single cell 125


title: Trachea epithelial single cell 122


title: Trachea epithelial single cell 123


title: Trachea epithelial single cell 120


title: Trachea epithelial single cell 121


title: Trachea epithelial single cell 118


title: Trachea epithelial single cell 117


title: Trachea epithelial single cell 126


title: Trachea epithelial single cell 142


title: Trachea epithelial single cell 115


title: Trachea epithelial single cell 119


title: Trachea epithelial single cell 113


title: Trachea epithelial single cell 116


title: Trachea epithelial single cell 114


title: Trachea epithelial single cell 111


title: Trachea epithelial single cell 110


title: Trachea epithelial single cell 109


title: Trachea epithelial single cell 112


title: Trachea epithelial single cell 108


title: Trachea epithelial single cell 104


title: Trachea epithelial single cell 105


title: Trachea epithelial single cell 144


title: Trachea epithelial single cell 99


title: Trachea epithelial single cell 102


title: Trachea epithelial single cell 103


title: Trachea epithelial single cell 95


title: Trachea epithelial single cell 96


title: Trachea epithelial single cell 97


title: Trachea epithelial single cell 101


title: Trachea epithelial single cell 98


title: Trachea epithelial single cell 93


title: Trachea epithelial single cell 91


title: Trachea epithelial single cell 94


title: Trachea epithelial single cell 92


title: Trachea epithelial single cell 90


title: Trachea epithelial single cell 88


title: Trachea epithelial single cell 89


title: Trachea epithelial single cell 86


title: Trachea epithelial single cell 84


title: Trachea epithelial single cell 107


title: Trachea epithelial single cell 106


title: Trachea epithelial single cell 85


title: Trachea epithelial single cell 83


title: Trachea epithelial single cell 82


title: Trachea epithelial single cell 81


title: Trachea epithelial single cell 80


title: Trachea epithelial single cell 78


title: Trachea epithelial single cell 100


title: Trachea epithelial single cell 77


title: Trachea epithelial single cell 76


title: Trachea epithelial single cell 74


title: Trachea epithelial single cell 73


title: Trachea epithelial single cell 79


title: Trachea epithelial single cell 70


title: Trachea epithelial single cell 68


title: Trachea epithelial single cell 72


title: Trachea epithelial single cell 66


title: Trachea epithelial single cell 63


title: Trachea epithelial single cell 60


title: Trachea epithelial single cell 61


title: Trachea epithelial single cell 62


title: Trachea epithelial single cell 64


title: Trachea epithelial single cell 59


title: Trachea epithelial single cell 69


title: Trachea epithelial single cell 57


title: Trachea epithelial single cell 58


title: Trachea epithelial single cell 53


title: Trachea epithelial single cell 56


title: Trachea epithelial single cell 54


title: Trachea epithelial single cell 55


title: Trachea epithelial single cell 51


title: Trachea epithelial single cell 52


title: Trachea epithelial single cell 50


title: Trachea epithelial single cell 75


title: Trachea epithelial single cell 49


title: Trachea epithelial single cell 71


title: Trachea epithelial single cell 65


title: Trachea epithelial single cell 42


title: Trachea epithelial single cell 41


title: Trachea epithelial single cell 46


title: Trachea epithelial single cell 45


title: Trachea epithelial single cell 47


title: Trachea epithelial single cell 48


title: Trachea epithelial single cell 43


title: Trachea epithelial single cell 44


title: Trachea epithelial single cell 34


title: Trachea epithelial single cell 40


title: Trachea epithelial single cell 25


title: Trachea epithelial single cell 28


title: Trachea epithelial single cell 20


title: Trachea epithelial single cell 19


title: Trachea epithelial single cell 37


title: Trachea epithelial single cell 24


title: Trachea epithelial single cell 33


title: Trachea epithelial single cell 38


title: Trachea epithelial single cell 23


title: Trachea epithelial single cell 39


title: Trachea epithelial single cell 22


title: Trachea epithelial single cell 35


title: Trachea epithelial single cell 36


title: Trachea epithelial single cell 32


title: Trachea epithelial single cell 26


title: Trachea epithelial single cell 29


title: Trachea epithelial single cell 31


title: Trachea epithelial single cell 17


title: Trachea epithelial single cell 30


title: Trachea epithelial single cell 18


title: Trachea epithelial single cell 27


title: Trachea epithelial single cell 21


title: Trachea epithelial single cell 14


title: Trachea epithelial single cell 16


title: Trachea epithelial single cell 13


title: Trachea epithelial single cell 15


title: Trachea epithelial single cell 11


title: Trachea epithelial single cell 10


title: Trachea epithelial single cell 9


title: Trachea epithelial single cell 12


title: Trachea epithelial single cell 8


title: Trachea epithelial single cell 4


title: Trachea epithelial single cell 6


title: Trachea epithelial single cell 1


title: Trachea epithelial single cell 7


title: Trachea epithelial single cell 2


title: Trachea epithelial single cell 5


title: Trachea epithelial single cell 3


title: DCM_458

city: Tokyo

first: Seitaro

last: Nomura

state: Select a State or Province

address: 7-3-1, Hongo, Bunkyo-ku

department: Department of Cardiovascular Medicine

institute: The University of Tokyo

data_processing:
For human single-cardiomyocyte RNA-seq, reads were mapped to the human genome (hg19) using Bowtie (version 1.1.1) with the parameters “-S -m 1 -l 36 -n 2 hg19”.
RPKM was calculated with reads mapped to the nuclear genome using DEGseq (version 1.8.0).
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files including RPKM values for each sample

source_name: Cardiomyocytes

extract_protocol:
All experiments were approved by the ethics committee of the University of Tokyo. All procedures were conducted according to the Declaration of Helsinki, and all patients gave written informed consent before taking part in the study. Heart samples from normal subjects and patients with DCM (n = 10) were used. Heart tissues were obtained immediately after death due to non-cardiac causes (normal cardiac function) or during left ventricular assist device (LVAD) surgery, respectively. Immediately after the collection of the heart tissue, rod-shaped live cardiomyocytes were isolated, as previously described previously, and then incubated in lysis buffer.
Single-cell cDNA libraries were generated using the Smart-seq2 protocol.

tag: cell type

value: Cardiomyocytes

tag: disease

value: patients with dilated cardiomyopathy

tag: single cell or bulk

value: single cell


title: DCM_456


title: DCM_466


title: DCM_469


title: DCM_467


title: DCM_465


title: DCM_463


title: DCM_470


title: DCM_468


title: DCM_464


title: DCM_461


title: DCM_460


title: DCM_457


title: DCM_459


title: DCM_462


title: DCM_454


title: DCM_455


title: DCM_453


title: DCM_452


title: H7 organoid

city: Cleveland

first: Paul

last: Tesar

state: Ohio

address: 10900 Euclid Ave.

department: Genetics & Genome Sciences

institute: Case Western Reserve University

data_processing:
Raw reads were processed through 10x Genomics Cell Ranger pipeline version 2.1.0 ( https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Cell Ranger Pipeline Command --cellranger mkfastq performs 10x barcode aware demultiplexing from BCL to FASTQ.
Cell Ranger Pipeline Command -- cellranger count performs transcriptome alignment with STAR, processes barcodes, counts genes, and produces a gene/cell matrix.
Cell ranger pipeline counts only unique UMIs and selects cells with a total UMI count of greater than or equal to 10% of the 99th percentile of the expected recovered cells and provides a filted gene barcode matrix of these cells.
Genome_build: hg19
Supplementary_files_format_and_content: A gene/barcode matrix containing UMI counts.

source_name: H7 organoid

extract_protocol:
Ten week 12 organoids were pooled and dissociated uisng the Worthington Papain dissociation system according to manufacturers instructions (Worthington Biochemical Corp., Lakewood NJ, Cat#: LK003150). Single cells were generated on a 10x Chromium according to manufacturers instructions (https://support.10xgenomics.com/single-cell-gene-expression/sample-prep/doc/demonstrated-protocol-single-cell-protocols-cell-preparation-guide)
Library was constructed using 10x Genomics Single Cell 3' Reagents Kits v2 according to manufacturers instructions (https://support.10xgenomics.com/single-cell-gene-expression/library-prep/doc/user-guide-chromium-single-cell-3-reagent-kit-v2-chemistry).

tag: source (es cell line)


title: DCM_448


title: DCM_450


title: DCM_447


title: DCM_449


title: DCM_444


title: DCM_442


title: DCM_446


title: DCM_441


title: DCM_440


title: DCM_445


title: DCM_443


title: DCM_437


title: DCM_433


title: DCM_435


title: DCM_432


title: DCM_434


title: DCM_436


title: DCM_431


title: DCM_430


title: DCM_429


title: DCM_451


title: DCM_426


title: DCM_427


title: DCM_428


title: DCM_438


title: DCM_425


title: DCM_439


title: DCM_422


title: DCM_421


title: DCM_423


title: DCM_418


title: DCM_417


title: DCM_420


title: Trachea epithelial single cell 87


title: DCM_419


title: DCM_414


title: DCM_413


title: DCM_412


title: DCM_424


title: DCM_415


title: DCM_410


title: DCM_406


title: DCM_411


title: DCM_409


title: DCM_408


title: DCM_405


title: Trachea epithelial single cell 67


title: DCM_416


title: DCM_404


title: DCM_403


title: DCM_399


title: DCM_401


title: DCM_402


title: DCM_398


title: DCM_400


title: DCM_397


title: DCM_407


title: DCM_396


title: DCM_394


title: DCM_390


title: DCM_392


title: DCM_388


title: DCM_386


title: DCM_391


title: DCM_389


title: DCM_387


title: DCM_385


title: DCM_381


title: DCM_382


title: DCM_383


title: DCM_378


title: DCM_379


title: DCM_380


title: DCM_395


title: DCM_393


title: DCM_384


title: DCM_377


title: DCM_376


title: DCM_487


title: DCM_479


title: DCM_480


title: DCM_478


title: DCM_485


title: DCM_486


title: DCM_483


title: DCM_481


title: DCM_477


title: DCM_488


title: DCM_484


title: DCM_482


title: Control_71

value: healthy subject


title: DCM_472


title: DCM_474


title: DCM_475


title: Control_68


title: Control_70


title: Control_69


title: Control_65


title: Control_64


title: Control_63


title: DCM_476


title: DCM_473


title: DCM_471


title: Control_62


title: Control_61


title: Control_60


title: Control_67


title: Control_66


title: Control_58


title: Control_59


title: Control_57


title: Control_50


title: Control_54


title: Control_51


title: Control_45


title: Control_52


title: Control_48


title: Control_46


title: Control_43


title: Control_41


title: Control_42


title: Control_44


title: Control_47


title: Control_38


title: Control_53


title: Control_39


title: Control_40


title: Control_37


title: Control_35


title: Control_34


title: Control_33


title: Control_49


title: Control_31


title: Control_56


title: Control_55


title: Control_30


title: Control_29


title: Control_28


title: Control_27


title: Control_36


title: Control_19


title: Control_21


title: Control_22


title: Control_25


title: Control_26


title: Control_20


title: Control_18


title: Control_24


title: Control_15


title: Control_13


title: Control_14


title: Control_23


title: Control_12


title: Control_11


title: Control_16


title: Control_10


title: Control_9


title: Control_8


title: Control_7


title: Control_4


title: Control_2


title: Control_6


title: Control_5


title: Control_3


title: Control_1


title: Control_17


title: DCM_190


title: DCM_181


title: DCM_189


title: DCM_188


title: DCM_187


title: DCM_186


title: DCM_183


title: DCM_180


title: DCM_177


title: DCM_184


title: DCM_176


title: DCM_179


title: DCM_173


title: DCM_185


title: DCM_174


title: DCM_175


title: DCM_172


title: DCM_178


title: DCM_170


title: DCM_171


title: DCM_169


title: DCM_166


title: DCM_167


title: DCM_168


title: DCM_165


title: DCM_164


title: DCM_182


title: Control_32


title: DCM_162


title: DCM_161


title: DCM_160


title: DCM_158


title: DCM_154


title: DCM_159


title: DCM_155


title: DCM_150


title: DCM_146


title: DCM_148


title: DCM_149


title: DCM_163


title: DCM_144


title: DCM_153


title: DCM_142


title: DCM_152


title: DCM_141


title: DCM_139


title: DCM_140


title: DCM_145


title: DCM_147


title: DCM_137


title: DCM_143


title: DCM_138


title: DCM_151


title: DCM_136


title: DCM_156


title: DCM_157


title: DCM_133


title: DCM_134


title: DCM_135


title: DCM_132


title: DCM_129


title: DCM_130


title: DCM_128


title: DCM_127


title: DCM_121


title: DCM_126


title: DCM_125


title: DCM_122


title: DCM_120


title: DCM_124


title: DCM_118


title: DCM_119


title: DCM_131


title: DCM_117


title: DCM_114


title: DCM_110


title: DCM_109


title: DCM_112


title: DCM_115


title: DCM_116


title: DCM_111


title: DCM_107


title: DCM_108


title: DCM_106


title: DCM_105


title: DCM_103


title: DCM_123


title: DCM_113


title: DCM_104


title: DCM_102


title: DCM_100


title: DCM_101


title: DCM_373


title: DCM_98


title: DCM_97


title: DCM_99


title: DCM_374


title: DCM_371


title: DCM_370


title: DCM_362


title: DCM_361


title: DCM_363


title: DCM_365


title: DCM_368


title: DCM_372


title: DCM_369


title: DCM_367


title: DCM_366


title: DCM_358


title: DCM_357


title: DCM_359


title: DCM_355


title: DCM_360


title: DCM_354


title: DCM_353


title: DCM_356


title: DCM_375


title: DCM_364


title: DCM_352


title: DCM_349


title: DCM_350


title: DCM_351


title: DCM_348


title: DCM_347


title: DCM_345


title: DCM_343


title: DCM_344


title: DCM_335


title: DCM_341


title: DCM_340


title: DCM_337


title: DCM_339


title: DCM_336


title: DCM_331


title: DCM_328


title: DCM_333


title: DCM_330


title: DCM_338


title: DCM_334


title: DCM_342


title: DCM_329


title: DCM_327


title: DCM_332


title: Jurkat chromatin run-on 1 [ChRO-seq]

city: Ithaca

first: Charles

middle: G

last: Danko

address: Hungerford Hill Rd

department: Baker Institute

institute: Cornell University

description:
Nascent RNA
Jurkat chromatin run-on

data_processing:
Library strategy: ChRO-seq
Data was aligned to the reference genome using scripts here: https://github.com/Danko-Lab/utils/tree/master/proseq
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *bw: Mapped reads are provided in bigWig format.

source_name: Jurkat T-cells

extract_protocol:
T-cells were grown in RPMI-1640 media. Nuclei were extracted as described (Danko et. al. (2015) Nature Methods). Chromatin was extracted as described (Chu et. al. (2018) Nature Genetics).
We prepared PRO-seq libraries as described in Kwak et. al. (2013) Science.

value: Jurkat

value: T cells

tag: genotype/variation

tag: batch


title: Jurkat chromatin run-on 2 [ChRO-seq]

description:
Nascent RNA
Jurkat chromatin run-on


title: Jurkat chromatin length-extension run-on [leChRO-seq]

description:
Nascent RNA
Jurkat chromatin length-extension run-on

data_processing:
Library strategy: leChRO-seq
Data was aligned to the reference genome using scripts here: https://github.com/Danko-Lab/utils/tree/master/proseq
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *bw: Mapped reads are provided in bigWig format.


title: DCM_326


title: DCM_346


title: Jurkat Nuclei [PRO-seq]

description:
Nascent RNA
Jurkat nuclei

data_processing:
Library strategy: PRO-seq
Data was aligned to the reference genome using scripts here: https://github.com/Danko-Lab/utils/tree/master/proseq
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *bw: Mapped reads are provided in bigWig format.


title: DCM_325


title: DCM_323


title: DCM_322


title: DCM_324


title: DCM_320


title: DCM_319


title: DCM_318


title: DCM_315


title: DCM_313


title: DCM_309


title: DCM_312


title: DCM_307


title: DCM_305


title: DCM_304


title: DCM_316


title: DCM_317


title: DCM_314


title: DCM_303


title: DCM_311


title: DCM_302


title: DCM_308


title: DCM_310


title: DCM_306


title: DCM_299


title: DCM_300


title: LP4

city: Newcastle upon Tyne

first: Meng

address: Ellison Place

department: Applied Sciences

institute: Northumbria University

description: Biological 2, techinical 2

data_processing:
MiSeq for base calling
The quality of sequencing data was assessed using FastQC, (V11.2) before the reads were trimmed using Trimmomatic (V0.33).
The trimmed reads were aligned against E. 149 coli MG1655 (GenBank: U00096.3) using bowtie2 (Version 2.2.4)
The counts of reads 150 aligning to genomic features were obtained using the 'feaureCounts' function from the R package 'Rsubread'
Gene annotation was obtained from the EcoCyc E. coli Database (https://ecocyc.org/).
The R package 'DESeq2' (Version 1.12.4) was used to calculate differential gene expression between the LP group and the HP group.
Genome_build: U00096.3
Supplementary_files_format_and_content: Table of read counts with genes as  rows and samples as columns.

organism: Escherichia coli str. K-12 substr. MG1655

source_name: bacterial cells

growth_protocol: E. coli K-12 MG 1655 was grown  in LB-Miller broth at 37°C ,160rpm to  an O.D.600 nm of 0. 7

extract_protocol:
Total RNAs from two biological replicate, each with two technical replicates were extracted using the Total RNA Purification Kit (Norgen Biotek, UK) according to the manufacturer’s protocol with the addition of 1 mg/ml lysozyme for cell lysis.
The lysates were applied to gDNA removal columns and rRNA was removed from total RNA using a Ribo-Zero rRNA removal kit (Illumina, UK) following the manufacture’s instruction for Gram-positive bacteria. The sequencing libraries were prepared from the enriched mRNA using the NEBNext Ultra RNA library prep kit (NEB, UK), and independently indexed using NEBNext multi-plex oligos for Illumina (NEB, UK). The libraries were pooled at equimolar ratios before they were sequenced using MiSeq Reagent Kit v3 600 cycles (Illumina,UK).

treatment_protocol: 1 ml aliquot of culture was transferred to pressure vessel and pressurized at 1MPa for 15 min

value: K-12 substr. MG1655

value: bacterial cells

tag: stimulus

value: Control


title: DCM_321


title: DCM_297


title: DCM_298


title: DCM_301


title: DCM_295


title: LP1

description: Biological 1, technical 1


title: LP2

description: Biological 1, technical 2


title: HP4

description: Biological 2, techinical 2

value: 1 MPa for 15 min


title: HP3

description: Biological 2, techinical 1


title: DCM_293


title: DCM_292


title: DCM_291


title: DCM_290


title: HP2

description: Biological 1, technical 2


title: DCM_289


title: LP3

description: Biological 2, techinical 1


title: DCM_288


title: DCM_286


title: DCM_287


title: DCM_296


title: H2

city: Ribeirão Preto

first: Ana

middle: Lucia

last: Fachin

state: SP

address: Av. Costabile Romano, 2201

department: Biotechonology  Unit

country: Brazil

institute: Unaerp

description:
HaCat cell line - control, replicate II
geneCounts_hg19_H.txt
DESeq_hg19_CO_vs_H.csv

data_processing:
FastQC v0.11.2 was used to visualize the libraries quality before and after trimming.
FASTX-Tookit (fastq_quality_filter) was used to remove poor quality sequences, such that remaining sequences had a minimum quality score of 20 with a minimum of 50% of bases within a read meeting this quality score requirement.
Filtered reads were mapped onto the T. rubrum genome using the Bowtie2 v2.1.0.
Reads were assigned to annotated genes and counted using the "summarizeOverlaps" function from the GenomicRanges Bioconductor package.
The data were analyzed using the R package DESeq version 1.28.0. The samples were normalized, and the dispersions were estimated using the default DESeq settings. DESeq was then used to identify differentially expressed genes for each pairwise comparison of interest. Genes with an adjusted P value of < 0.05 and a log2(foldchange) > 1.0 (upregulation) or < -1.0 (downregulation) were called as differentially expressed.
Genome_build: Broad T. rubrum strain CBS118892 genome
Supplementary_files_format_and_content: tab-delimited text files include reads count values for each sample and DESeq output in CSV format containing mean expression, fold changes and p value.

source_name: HaCat cell line - control

growth_protocol: The Trichophyton rubrum strain CBS 118892 was cultured on Sabouraud dextrose agar  for 15 days at 28ºC. Keratinocytes were cultured in RPMI medium)supplemented with 10% fetal bovine serum (FBS) at 37ºC in a humidified atmosphere containing 5% CO2.

extract_protocol:
RNA extraction of T. rubrum and HaCat cell were performed using an Illustra RNAspin Mini RNA Isolation according to GE Healthcare guidelines.
RNA libraries were prepared for sequencing according to Illumina guidelines.

treatment_protocol: Pre-cultured conidia of T. rubrum were added to HaCat cell line and the co-culture was incubated for 24 h  at 37ºC in a humidified atmosphere containing 5% CO2.

value: HaCat cell line - control


title: H3

description:
HaCat cell line - control, replicate III
geneCounts_hg19_H.txt
DESeq_hg19_CO_vs_H.csv


title: DCM_285


title: DCM_294


title: DCM_284


title: DCM_283


title: DCM_282


title: DCM_279


title: HP1

description: Biological 1, technical 1


title: mimic-1825 5

city: Ulm

first: Axel

last: Freischmidt

address: Albert-Einstein-Allee 11

department: Neurology

institute: Ulm University

description:
transcriptome of HEK293 cells after transfection of miR-1825-mimic
m5_mimic-5

hyb_protocol: according to Affymetrix Whole Transcript (WT) Sense Target Labeling Assay

scan_protocol: according to Affymetrix protocols using a GeneChip 3000 Scanner

data_processing: Affymetrix® Expression Console™ Software 1.4.1.46 for feature extraction and normalization, BRB Array Tools for statistical analysis

growth_protocol: HEK293 cells were grown under standard conditions (37° C; 5% CO2) in DMEM (Thermo Fisher Scientifc #41965039) supplemented with 10% fetal bovine serum.

extract_protocol: Isolation of total RNA was performed with the RNeasy Plus Mini Kit (Qiagen) as specified by the manufacturer.

treatment_protocol: For transfections of AllStars Negative Control siRNA (Qiagen #1027280) or Syn-hsa-miR-1825 (Qiagen #MSY0006765) in a concentration of 5 nM we used the HiPerfect transfection reagent (Qiagen). 24 h post-transfection, the cells were washed twice with PBS followed by RNA extraction.

tag: cell line

tag: transfection


title: DCM_278


title: RAW264.7_scramble siRNA transfected

city: Kumamoto

first: Masaya

last: Baba

state: Kumamoto

address: 1-1-1 Honjo, Chuo-ku

department: Urology

institute: Kumamoto University

description: Gene expression data from scramble siRNA transfected RAW264.7 cells

hyb_protocol: 10 micrograms of fragmented cRNA were hybridised (45 degrees Celsius, 16 hours). Hybridization was controlled by use of the GeneChip Eukaryotic Hybridization Control Kit (Affymetrix). Washing and staining were performed in a Fluidics Station 450 (Affymetrix) using the protocol EukGE-WS2v4.

scan_protocol: Scanning was performed in an Affymetrix GeneChip scanner 3000 7G.

data_processing: Affymetrix GeneChip Operating Software (GCOS) Version 1.0. with target intensity=100.

source_name: Raw264.7 cells, transfected with scramble siRNA

label_protocol: In vitro transcription was performed on 1 microgram of cDNA using the Enzo BioArray High Yield RNA transcript labelling kit (Enzo Diagnostics). The cRNA was cleaned using RNeasy clean-up columns (Qiagen). The cRNA was fragmented by heating in 40 mM Tris-acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc.

growth_protocol: Raw264.7 cells were cultured with RPMI-1640 supplemented with 10% FCS, 100 U/ml penicillin, 100 microg/ml streptomycin.

extract_protocol: Total RNA was collected and purified using the RNeasy Micro kit.RNA according to manufacturer's instructions.

treatment_protocol: Raw264.7 cells were transfected with scramble or Flcn targeted siRNA, followed by a medium change to MEM containing 10% FCS at 24hr after transfection. Cells were cultured for an additional 48hr.

value: Raw264.7 cells

tag: treatment

value: scramble siRNA transfected


title: mimic-1825 6

description:
transcriptome of HEK293 cells after transfection of miR-1825-mimic
m6_mimic-6

label_protocol: Whole Transcript (WT) Sense Target Labeling Assay


title: mimic-1825 4

description:
transcriptome of HEK293 cells after transfection of miR-1825-mimic
m4_mimic-4


title: DCM_276


title: RAW264.7_Flcn targeted siRNA transfected

description: Gene expression data from Flcn targeted siRNA transfected RAW264.7 cells

source_name: Raw264.7 cells, transfected with Flcn targeted siRNA

value: Flcn targeted siRNA transfected


title: DCM_281


title: DCM_275


title: DCM_273


title: mimic-1825 1

description:
transcriptome of HEK293 cells after transfection of miR-1825-mimic
m1_mimic-1


title: mimic-1825 3

description:
transcriptome of HEK293 cells after transfection of miR-1825-mimic
m3_mimic-3


title: DCM_274


title: DCM_280


title: DCM_272


title: control 4

description:
transcriptome of HEK293 cells after transfection of a control RNA
a4_allstar-4

source_name: control

value: control RNA


title: DCM_268


title: DCM_269


title: DCM_270


title: mimic-1825 2

description:
transcriptome of HEK293 cells after transfection of miR-1825-mimic
m2_mimic-2


title: DCM_267


title: control 6

description:
transcriptome of HEK293 cells after transfection of a control RNA
a6_allstar-6


title: DCM_277


title: control 2

description:
transcriptome of HEK293 cells after transfection of a control RNA
a2_allstar-2


title: control 3

description:
transcriptome of HEK293 cells after transfection of a control RNA
a3_allstar-3


title: control 1

description:
transcriptome of HEK293 cells after transfection of a control RNA
a1_allstar-1


title: DCM_271


title: DCM_265


title: DCM_264


title: DCM_263


title: DCM_262


title: control 5

description:
transcriptome of HEK293 cells after transfection of a control RNA
a5_allstar-5


title: DCM_259


title: DCM_258


title: DCM_257


title: DCM_260


title: DCM_250


title: DCM_253


title: DCM_256


title: DCM_252


title: DCM_251


title: DCM_249


title: DCM_254


title: DCM_247


title: DCM_266


title: DCM_246


title: DCM_248


title: DCM_245


title: DCM_244


title: DCM_261


title: DCM_255


title: DCM_242


title: DCM_239


title: DCM_238


title: DCM_241


title: DCM_237


title: DCM_236


title: DCM_234


title: DCM_232


title: DCM_231


title: DCM_229


title: DCM_230


title: DCM_243


title: DCM_228


title: DCM_226


title: DCM_227


title: DCM_221


title: DCM_240


title: DCM_222


title: DCM_219


title: DCM_224


title: DCM_225


title: DCM_223


title: DCM_220


title: DCM_214


title: DCM_213


title: DCM_216


title: DCM_215


title: DCM_233


title: DCM_235


title: DCM_210


title: DCM_211


title: DCM_208


title: DCM_209


title: DCM_207


title: DCM_204


title: DCM_203


title: DCM_202


title: DCM_217


title: DCM_201


title: DCM_218


title: DCM_200


title: DCM_199


title: DCM_196


title: DCM_193


title: DCM_192


title: DCM_195


title: DCM_198


title: DCM_194


title: DCM_212


title: DCM_4


title: DCM_197


title: DCM_6


title: DCM_2


title: DCM_191


title: DCM_7


title: DCM_5


title: DCM_3


title: DCM_48


title: DCM_46


title: DCM_205


title: DCM_47


title: DCM_45


title: DCM_43


title: DCM_44


title: DCM_42


title: DCM_41


title: DCM_40


title: DCM_38


title: DCM_39


title: DCM_37


title: DCM_1


title: DCM_35


title: DCM_33


title: DCM_32


title: DCM_30


title: DCM_36


title: DCM_31


title: DCM_96


title: DCM_27


title: DCM_25


title: DCM_28


title: DCM_94


title: DCM_92


title: DCM_26


title: DCM_91


title: DCM_29


title: DCM_95


title: DCM_93


title: DCM_90


title: DCM_89


title: DCM_87


title: DCM_88


title: DCM_86


title: DCM_85


title: DCM_34


title: DCM_83


title: DCM_82


title: DCM_81


title: DCM_80


title: DCM_78


title: DCM_77


title: DCM_79


title: DCM_76


title: DCM_74


title: DCM_66


title: DCM_65


title: DCM_72


title: DCM_69


title: DCM_68


title: DCM_71


title: DCM_70


title: DCM_67


title: DCM_63


title: DCM_64


title: DCM_59


title: DCM_62


title: DCM_58


title: DCM_57


title: DCM_84


title: DCM_54


title: DCM_206


title: DCM_61


title: DCM_75


title: DCM_56


title: DCM_60


title: DCM_73


title: DCM_52


title: DCM_53


title: DCM_49


title: DCM_51


title: DCM_24


title: DCM_50


title: DCM_23


title: DCM_20


title: DCM_22


title: DCM_21


title: DCM_17


title: DCM_15


title: DCM_19


title: DCM_16


title: DCM_18


title: DCM_12


title: DCM_14


title: DCM_13


title: DCM_10


title: DCM_55


title: DCM_9


title: DCM_8


title: H9-d94-T3

description: Cortical spheroids grown with modified method with application of PDGF-AA/IGF-1 between day 50 and 60 and T3 between days 62 and 70. Analysed week 14.

data_processing:
Reads were aligned to the hg19 genome using TopHat v2.0.6 without providing a reference transcriptome.
Abundance of transcripts from the iGenomes hg19 RefSeq reference were measured using Cufflinks v2.0.2.
FPKMs were quantile normalized.
Genome_build: hg19
Supplementary_files_format_and_content: genes.fpkm_tracking files from cufflinks v2.0.2

source_name: oligo-cortical spheroids

extract_protocol:
Four spheroids per line were collected in Tri Reagent (Zymo Research #R2050-1-200) and RNA was extracted as per manufacturer’s instructions. RNA was further purified using a Qiagen RNeasy Plus Mini kit (Qiagen, #73404).
Illumina libraries were prepared and sequenced in 50bp paired end mode on a HiSeq 2500 instrument at the CWRU Genomics Core facility.

tag: source esc line


title: H7-d92-none

description: Cortical spheroids grown using protocol from Pasca et al. 2013. Analysed week 14.

source_name: neuro-cortical spheroids