title: ISO-SP-10XTCR

city: Wuhan

first: Jie

last: Wu

state: Hubei

address: Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Jiefang Road 1277

department: Department of Cardiovascular Surgery

data_processing:
Library strategy: TCR-seq
We obtained H5 files after fastq files were processed by software Cell Ranger
Seruat (version 4.0.1) was used to filter the clusters
clusters were identified by characteristic genes combined with SingleR (version 1.4.1) annotation
CellChat (version 1.0.0) was used for cell communication analysis.
Genome_build: mm10
Supplementary_files_format_and_content: h5 (Filtered feature-barcode matrices HDF5)

extract_protocol:
Cardiac allografts normally arrest at day 7 after transplantation because of acute transplantation rejection. Therefore, we harvested spleens and cardiac allografts of allograft group recipients at day 6 before cardiac allografts arrest. At the same time, spleens and cardiac isografts of isograft group recipients were harvested. CD45+ cells were respectively isolated from cardiac allografts, allograft group recipients’ spleen, cardiac isografts and isograft group recipients’ spleen after digestion, centrifugation and flow sorting. In brief, cardiac grafts were cut into pieces and digested with 1 mg/mL of collagenase B (Roche 11088815001) in HEPES buffer for 45 min at 37°C. After digestion, cell suspensions were collected and filtered with 70-μm cell strainers (BIOFIL), Percoll (Beijing Solarbio Science & Technology Co., Ltd.) was used to purify mononuclear cells through density centrifugation with 600g 25min RT not-brake. Splenocytes were prepared through grinding, erythrocyte lysis, washing and centrifugation (600g, 3min). CD45+ live cells were then sorted by FACSAria flow cytometer after Cardiac graft infiltrating cells and splenocytes stained with CD45-APC (Biolegend 103112) and Zombie GreenTM Fixable Viability Kit (Biolegend 423112).
10X5'RNA-seq
10XTCR-seq

treatment_protocol: 8-10 weeks male C57BL/6 (H-2b) and BALB/c(H-2d) were purchased from Charles River (Beijing, China). All mice experiments were performed in a specific pathogen-free facility according to the guidelines of the animal care and use committee of Huazhong University of Science and Technology. We established the murine heterotopic heart transplantation model as previously described . Allograft group: BALB/c (H2d) hearts were transplanted into fully MHC-mismatched C57BL/6 (H2b) recipients. Isograft group: C57BL/6 (H2b) hearts were transplanted into MHC-matched C57BL/6 (H2b) recipients.

value: CD45+ cells  isolated from isograft group recipients' spleen


title: Input, 100 nM

status: Public on Sep 21 2022

type: SRA

city: Berkeley

first: Timothy

middle: J

last: Eisen

state: CALIFORNIA

address: Stanley Hall

country: USA

institute: UC Berkeley

description: mRNA display

library_source: transcriptomic

data_processing:
Alignment of paired-end FASTQ files using Kallisto (Bray et al., 2016).
Supplementary files format and content: Tab-delimited read count file, as output from the aligner.

molecule: total RNA

organism: Severe acute respiratory syndrome coronavirus 2

source_name: Sample 28

extract_protocol:
mRNA display was performed on a library of variants. Peptides were selected based on their ability to bind to a His6-tagged HR1 peptide, which was purified with Ni-NTA beads.
Peptide-mRNA fusions were reverse-transcribed using Superscript III (ThermoFisher) and oligo-dT(20-mer) as an RT primer. After precipitation, cDNA was PCR-amplified, agarose-gel purified, and sequenced.

tag: fraction

value: Input

tag: hr1 concentration


title: ARPE19 cancer cell progession line - T53D4 rep 1

city: Fort Collins

first: Erin

last: Osborne Nishimura

state: CO

address: 1870 Campus Delivery, 200 W. Lake St.

department: Biochemistry and Molecular Biology

institute: Colorado State University

data_processing:
Samples were assessed for quality and trimmed for adapter, primer, and polyX sequences by fastp (v 0.20.0) (Chen 2017; PMID: 30423086)
Trimmed reads were aligned separately to either the hg38 genome or to transgenic sequences using hisat2 (v 2.1.0) (Kim 2017; PMID: 31375807).
The number of reads associated with each gene model was tabulated for the human genome annotation (hg38_pc_20200113_UCSC_compatible.gtf.gz) using featureCounts (v 1.6.4) (Liao 2014; PMID: 24227677).
samtools (v 1.9) (Li 2009; PMID: 19505943), DeepTools (bamCoverage v 3.2.0) (Ramírez 2016; PMID: 27079975), and UCSC Kent Utilities were used to transform alignments into formats suitable for viewing on UCSC Genome Browser (Kent 2002; PMID: 12045153) or IGV (v 2.9.0) (Robinson 2011; PMID: 21221095).
RNA-seq count data were filtered for detected genes (> 10 counts across all samples) and analyzed using DESeq2 (v 1.28.1) (Love 2014; PMID: 25516281) with default settings in the R Environment (v 4.0.3, BiocManager, v 1.30.10).
The raw counts (210215_raw_counts.txt), normalized counts (210215_norm_counts.txt), and normalized/variance-stabilized/log-transformed counts (210215_RStabilized_log_counts.txt) are provided.
Genome_build: human genome, hg38
Supplementary_files_format_and_content: .bw files were generated using bamCoverage, part of the DeepTools package
Supplementary_files_format_and_content: merged.bw files were merged by replicate using UCSC Kent Utilities
Supplementary_files_format_and_content: counts tables were generated from featureCounts tabultion and then processed within DESeq2

molecule: polyA RNA

organism: Homo sapiens

source_name: Human retinal pigment epitheial cell line

growth_protocol: Cells were grown adherently in DMEM/F12 (Thermo 11330) supplemented with 10% FBS and antibiotic-antimycotic (Thermo 15240062)

extract_protocol:
Total RNA was extracted from ~2 million cells using an RNeasy mini kit (Qiagen 74104). Each replicate was isolated from a freshly thawed cryovial that had been passaged twice prior to extraction.
mRNA was prepared for sequencing using the NEB Next Ultra II Directional Library Prep Kit for Illumina (NEB E7760S) and Poly(A) Magnetic Isolation Module (NEB E7490S).
Libraries of a median 200 - 400 bp length were generated and sequenced at 2 x 150 bp on a NovaSeq 6000 to a read depth of roughly 50 – 100 million reads.

tag: transfection

value: pbabe-hTERT+p53DD (Addgene plasmid # 11128); pbabe-cyclinD1+CDK4R24C (Addgene plasmid # 11129)

tag: cell line pathway

value: T53D4 primed cell line

tag: disease state

value: not transformed


title: O3_DMSO_72_0

city: Perugia

first: Lorenzo

last: Brunetti

address: Piazzale Menghini 8/9

country: Italy

institute: University of Perugia

data_processing:
FastQ files were aligned to the hg19 genome using HISAT version 2.1.0
Quantification performed using Cufflinks
Genome_build: hg19
Supplementary_files_format_and_content: fpkm text file

source_name: OCI-AML3 cells

growth_protocol: OCI-AML3 cells were cultured in complete RPMI FBS 10%

extract_protocol:
RNA was purified using the Zymo Quick-RNA Microprep Kit
Illumina TruSeq stranded mRNA protocol

tag: cell ine

tag: tissue source

value: Blood and bone marrow

tag: cell type

value: AML cell line

tag: treatment

value: DMSO 72 hours


title: O3_330_24_1

value: Selinexor 24 hours


title: ARPE19 cancer cell progession line - RasV12 rep 1

value: pbabe-hTERT+p53DD (Addgene plasmid # 11128); pbabe-cyclinD1+CDK4R24C (Addgene plasmid # 11129); pWZL-H-RasV12 (Addgene plasmid # 18749)

value: RAS pathway

value: transformed


title: O3_330_24_0


title: HT-SP-10X5

country: China

institute: Union Hospital, Tongji Medical College, Huazhong University of Science and Technology

data_processing:
We obtained H5 files after fastq files were processed by software Cell Ranger
Seruat (version 4.0.1) was used to filter the clusters
clusters were identified by characteristic genes combined with SingleR (version 1.4.1) annotation
CellChat (version 1.0.0) was used for cell communication analysis.
Genome_build: mm10
Supplementary_files_format_and_content: h5 (Filtered feature-barcode matrices HDF5)

organism: Mus musculus

tag: strain

value: CD45+ cells  isolated from allograft group recipients' spleen


title: Input, 32 nM

description: mRNA display

source_name: Sample 19


title: ISO-SP-10X5


title: ARPE19 cancer cell progession line - ARPE19 rep 1

value: no transfection


title: HT-SP-10XTCR


title: ARPE19 cancer cell progession line - AKTmyr rep 1

value: pbabe-hTERT+p53DD (Addgene plasmid # 11128); pbabe-cyclinD1+CDK4R24C (Addgene plasmid # 11129); pBabe-myr-HA-Akt, (Addgene plasmid # 15294)

value: PI3K-AKT pathway


title: O3_DMSO_72_1


title: Input, 10 nM

description: mRNA display

source_name: Sample 10


title: O3_DMSO_24_1

value: DMSO 24 hours


title: E12.5_WT_H3K27me3_R1.fq.gz

city: Beijing

first: Zhang

last: shuangfeng

address: 1 Beichen West Road, Chaoyang District, Beijing 100101, P.R.China

institute: Institute of Zoology, Chinese Academy of Sciences

description: CUT&Tag

library_source: genomic

data_processing:
Library strategy: CUT&TAG
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Bowtie2 (v.2.4.1).
MACS2 (v.2.2.7.1) was used to call peaks (-g mm -q 0.01 -f BAM) relative to input sample. MAnorm (v.1.2.0) was then used for quantitative comparison of ChIP-Seq data.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample
Supplementary_files_format_and_content: wig files were generated using bamcoverage function of DeepTools (v.3.4.0).
Supplementary_files_format_and_content: tab-delimited text files. Peak annotation was performed using ChIPseeker (v.1.22.1) at gene level and promoter regions was defined as +/- 3000bp of TSS

molecule: genomic DNA

source_name: Forebrain tissue

extract_protocol: EED DNA libraries were prepared for sequencing using standard BGISEQ-500 protocols. Other DNA libraries were prepared from CUT&Tag protocol and using standard NovaSeq protocols.

tag: genotype

value: wild type

tag: tissue

value: forebrain

value: untreated


title: Eluate, 0 nM

description: mRNA display

source_name: Sample 37

value: Eluate


title: O3_330WO_72_0

value: Selinexor 72 hours short treatment


title: ARPE19 cancer cell progession line - MekDD rep 1

value: pbabe-hTERT+p53DD (Addgene plasmid # 11128); pbabe-cyclinD1+CDK4R24C (Addgene plasmid # 11129); pBabe-Puro-MEK-DD (Addgene plasmid # 15268)

value: MAPK pathway

value: weakly transformed


title: O3_DMSO_24_0

value: Blood and bone marrow

value: AML cell line


title: Heart-10XTCR

value: CD45+ cells  isolated from cardiac allografts


title: IP RNAPII Ctrl R3

city: Lyon

first: Cyril

middle: F

last: Bourgeois

address: 46 Allée d'Italie

department: LBMC

country: France

institute: ENS de Lyon

description: Replicate 3

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Sequence reads were mapped to reference genome hg19 using Bowtie 1.0.0 with the following parameters -m 1 --strata --best -y -S -l 40 -p 2.
Genome_build: hg19
Supplementary_files_format_and_content: Wig files were generated using with an in-house script (Variable step, span=25, reads were elongated to 200b).

source_name: Neuroblastoma SH-SY5Y cell line (ECACC)

growth_protocol: Cells were cultured in 4,5 g/L Glucose DMEM/F-12 (ThermoFischer Scientific) supplemented with 10% (v/v) fetal bovine serum (ThermoFischer Scientific), and 2 mM L-Glutamine (ThermoFischer Scientific) in 5% CO2 at 37°C.

extract_protocol:
Cells were cross-linked (1% formaldehyde), harvested, lysed and sonicated (Covaris S220 ultrasonicator). Chromatin (40 µg per antibody) was diluted and precleared on Protein A/G Dynabeads for 30 min at 4°C under rotation. Beads were removed and 1% of chromatin was taken apart as Input material. Antibodies were added to chromatin and incubated overnight at 4°C under constant mixing, before being bound to Protein A/G Dynabeads for 5h.   Immunoprecipitated material was washed once with Low Salt buffer, once with High Salt Buffer, once with LiCl Buffer and twice with Tris/EDTA buffer, before being eluted and reverse crossed-linked  overnight at 65°C on Thermomixer (Eppendorf) in the presence of 200 mM NaCl and 20 µg proteinase K (Roche). DNA was then purified by phenol extraction and ethanol precipitation, and quantified for library preparation.
ChIP samples were purified using Agencourt AMPure XP beads (Beckman Coulter) and quantified with the Qubit (Invitrogen). ChIP-seq libraries were prepared from 10 ng of double-stranded purified DNA using the MicroPlex Library Preparation kit v2 (C05010014, Diagenode s.a., Seraing, Belgium), according to manufacturer's instructions. In the first step, the DNA was repaired and yielded molecules with blunt ends. In the next step, stem-loop adaptors with blocked 5 prime ends were ligated to the 5 prime end of the genomic DNA, leaving a nick at the 3 prime end. The adaptors cannot ligate to each other and do not have single-strand tails, avoiding non-specific background. In the final step, the 3 prime ends of the genomic DNA were extended to complete library synthesis and Illumina compatible indexes were added through a PCR amplification (7 + --- cycles). Amplified libraries were purified and size-selected using Agencourt AMPure XP beads (Beckman Coulter) to remove unincorporated primers and other reagents.

treatment_protocol: Cells were transfected for 48h with siRNAs at a final concentration of 20 nM with lipofectamine RNAimax (ThermoFischer Scientific).

tag: transfected sirna

value: Negative control siRNA anti-luciferase

tag: extract

value: RNA Pol II IP (F12 antibody)


title: Input, 0 nM

description: mRNA display

source_name: Sample 1

value: Input


title: HC3

status: Public on Sep 20 2022

city: Jena

first: Yu-Heng

last: Tseng

state: Thuringia

address: Dornburgerstr. 159

department: Plant Physiology

country: Germany

institute: Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich-Schiller University Jena

data_processing:
Raw reads were mapped to TAIR10 reference genome with STAR (v. 2.7.10a).
Readcounts were generated from the mapped bam files with featureCount (v. 2.0.1).
DESeq2 (v. 1.34.0) was applied to calculate the fold change and statistics for each mapped gene.
Supplementary_files_format_and_content: csv files containng the statistics of each mapped genes following DESEq2 analysis

organism: Arabidopsis thaliana

source_name: Root

growth_protocol: Arabidopsis seedlings were grown on MS media for 10 days, then transferred to PNM medium with nylon membrane for 1 day before treatment.

extract_protocol: Total RNA was extracted with Trizol reagent. DNA was digested with TURBO Dnase.

treatment_protocol: 1 mL of water or 10 µM cellotriose was applied to roots  of 8 seedlings on  single petri dish. Two petri dishes (16 seedlings) were used per treatment.

value: 10 uM cellotriose

value: Homozygous mutant


title: Heart-10X5


title: HC1


title: SC3

value: Segregate wild-type


title: HW2

value: water


title: HC2


title: SC2


title: HCT116_PJ-34/5-aza-dC/TSA_rep1

type: RNA

city: Nagasaki

first: Mitsuko

last: Masutani

state: Nagasaki

address: 1-12-4 Sakamoto

department: Department of Molecular and Genomic Biomedicine

country: Japan

institute: Nagasaki University

hyb_protocol: Target cRNA preparation from total RNA, hybridization to the microarray, washing and staining with a Single Stain procedure and scanning were all carried out according to the manufacturer’s instructions.

scan_protocol: GeneChips were scanned using the GeneArray scanner GA2500 (Agilent).

data_processing: The expression value (Signal) of each probe set was calculated using GeneChip Operating Software (GCOS) ver. 1.3 (Affymetrix), so that the mean of expression values in each experiment was set at 100 to adjust for minor differences between experiments.

label: phycoerythrin

source_name: Cells, 3 days treatment

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (GeneChip Expression Analysis Technical Manual, rev 1, Affymetrix).

growth_protocol: Cells were grown with medium containing 10% FBS and penicilline-streptomycin.

extract_protocol: Isogen (Nippon Gene) extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Cells were treated with control or drugs for 3 days.

tag: cell line


title: SC1


title: HW1


title: HW3


title: HCT116_PJ-34_rep1


title: RKO_5-aza-dC_rep1

value: RKO


title: SW3


title: HCT116_Control_rep1

value: control


title: HCT116_5-aza-dC_rep1


title: HCT116_PJ-34/TSA_rep1


title: HCT116_PJ-34/5-aza-dC_rep1


title: RKO_5-aza-dC/TSA_rep1


title: RKO_PJ-34/5-aza-dC_rep1


title: RKO_PJ-34/TSA_rep1


title: HCT116_5-aza-dC/TSA_rep1


title: SW2


title: RKO_Control_rep1


title: RKO_PJ-34/5-aza-dC/TSA_rep1


title: 19_5_3

city: Stillwater,

first: Khursheed

last: Iqbal

state: OK

address: 310 N Monroe St,

institute: Oklahoma state university

library_source: transcriptomic single cell

data_processing:
The Cell Ranger Single-Cell Software Suite (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger) was used to perform sample demultiplexing, barcode processing, and single-cell 3' gene counting. The reads were aligned to the rn6 reference genome. BAM files produced by the 10x Genomics/Cell Ranger pipeline
Assembly: rn6
Supplementary files format and content:  Genes.tsv, Barcodes.tsv, Matrix.mtx

organism: Rattus norvegicus

source_name: rat 19.5 uterine-placental interface

extract_protocol: Single cells were captured into droplets using 10x chromium device followed by preparation of single-cell cDNA libraries with the 10x protocol.

value: uterine-placental interface

tag: age


title: 19_5_2


title: HCT116_TSA_rep1

value: TSA


title: SW1


title: RKO_TSA_rep1


title: 15_5_3

source_name: rat 15.5 uterine-placental interface


title: 19_5_1


title: 15_5_2


title: RKO_PJ-34_rep1


title: Chronic12

city: Philadelphia

first: Benjamin

middle: C.

last: Reiner

state: PA

address: 125 S 31st St

institute: University of Pennsylvania

data_processing:
10x Genomics Cell Ranger v3.1
Genome_build: Reference created from Ensembl Rattus_norvegicus.Rnor_6.0.101
Supplementary_files_format_and_content: Cell Ranger raw feature barcode matrix

source_name: nucleus accumbens

extract_protocol:
Nuclei were captured with the 10x Genomics Chromium controller for 3' gene expression assay (v3.1) according to manufacturer protocols
Libraries were prepared according to 10x Genomics manufacturer protocols

value: Brown Norway Rat

value: frozen postmortem brain

tag: brain region

value: nucleus accumbens

tag: Sex

value: Male

value: Morphine self-administration

tag: molecule subtype

value: nuclear mRNA


title: Chronic10


title: Chronic08


title: Low protein sperm and normal protein seminal plasma (LN) replicate 4

city: Nottingham

first: Marios

last: Georgiou

address: Queen's Medical Centre

department: School of Life Sciences

country: United Kingdom

institute: University of Nottingham

description:
LN6 - M
Adult mouse liver gene expression data derived from offspring of dietary manipulated fathers.

hyb_protocol: Hybridized to Affymetrix

scan_protocol: GeneChips were scanned using the GeneChip™ Scanner 3000 7G System.

data_processing: The data were analyzed with Partek® Genomics Suite® analysis software and global scaling as normalization method.

label: Biotin

source_name: Adult mouse liver

label_protocol:
First-strand cDNA was synthesised from 10 ug RNA and converted to double-stranded cDNA using the GeneChip™ WT PLUS Reagent Kit.
Biotinylated cRNA were prepared according to the standard GeneChip Wt PLUS Reagent Kit User Guide (Catalog Numbers 902280 and 902281 Publication Number MAN0018137).

extract_protocol: Total RNA extracted using Qiagen's RNeasy kit following manufacturer's instructions.

treatment_protocol: Offspring mice were generated using sperm and seminal plasma from males fed either a normal protein diet (termed NN, the first letter denotes the diet of the sperm and the second denoted the diet of the seminal plasma), males fed a low protein diet (termed LL), sperm from normal protein diet males but seminal plasma from low protein diet males (NL) or sperm from low protein diet fed males and seminal plasma from normal protein diet fed males (termed LN). At 16 weeks of age, offspring were culled and the livers snap frozen for subsequent RNA isolation.

value: 16 weeks

value: male

value: liver

tag: paternal diet

value: LN


title: Low protein sperm and normal protein seminal plasma (LN) replicate 5

description:
LN7 - M
Adult mouse liver gene expression data derived from offspring of dietary manipulated fathers.


title: Low protein sperm and normal protein seminal plasma (LN) replicate 3

description:
LN4 - F
Adult mouse liver gene expression data derived from offspring of dietary manipulated fathers.

value: female


title: 15_5_1


title: Normal protein sperm and low protein seminal plasma (NL) replicate 6

description:
NL9 - M
Adult mouse liver gene expression data derived from offspring of dietary manipulated fathers.

value: NL


title: Low protein sperm and normal protein seminal plasma (LN) replicate 1

description:
LN1 - F
Adult mouse liver gene expression data derived from offspring of dietary manipulated fathers.


title: Low protein sperm and normal protein seminal plasma (LN) replicate 2

description:
LN2 - F
Adult mouse liver gene expression data derived from offspring of dietary manipulated fathers.


title: Chronic06


title: Low protein sperm and normal protein seminal plasma (LN) replicate 6

description:
LN9 - M
Adult mouse liver gene expression data derived from offspring of dietary manipulated fathers.


title: Low protein sperm and normal protein seminal plasma (LN) replicate 7

description:
LN10 - M
Adult mouse liver gene expression data derived from offspring of dietary manipulated fathers.


title: Normal protein sperm and low protein seminal plasma (NL) replicate 7

description:
NL10 - M
Adult mouse liver gene expression data derived from offspring of dietary manipulated fathers.


title: Normal protein sperm and low protein seminal plasma (NL) replicate 3

description:
NL5 - F
Adult mouse liver gene expression data derived from offspring of dietary manipulated fathers.


title: Eluate, 32 nM

description: mRNA display

source_name: Sample 55

tag: fraction

value: Eluate

tag: hr1 concentration


title: Chronic02


title: Chronic04


title: Normal protein sperm and low protein seminal plasma (NL) replicate 2

description:
NL4 - F
Adult mouse liver gene expression data derived from offspring of dietary manipulated fathers.


title: Low protein sperm and low protein seminal plasma (LL) replicate 9

description:
LL10 - M
Adult mouse liver gene expression data derived from offspring of dietary manipulated fathers.

value: LL


title: Low protein sperm and low protein seminal plasma (LL) replicate 8

description:
LL9 - M
Adult mouse liver gene expression data derived from offspring of dietary manipulated fathers.


title: Acute09

value: Morphine injection


title: Normal protein sperm and low protein seminal plasma (NL) replicate 1

description:
NL2 - F
Adult mouse liver gene expression data derived from offspring of dietary manipulated fathers.


title: Normal protein sperm and low protein seminal plasma (NL) replicate 5

description:
NL8 - M
Adult mouse liver gene expression data derived from offspring of dietary manipulated fathers.


title: Low protein sperm and low protein seminal plasma (LL) replicate 4

description:
LL4 - F
Adult mouse liver gene expression data derived from offspring of dietary manipulated fathers.


title: Low protein sperm and low protein seminal plasma (LL) replicate 6

description:
LL6 - M
Adult mouse liver gene expression data derived from offspring of dietary manipulated fathers.


title: Low protein sperm and low protein seminal plasma (LL) replicate 2

description:
LL2 - F
Adult mouse liver gene expression data derived from offspring of dietary manipulated fathers.


title: Normal protein sperm and low protein seminal plasma (NL) replicate 4

description:
NL7 - M
Adult mouse liver gene expression data derived from offspring of dietary manipulated fathers.


title: HCT116_Aspirin+Ticagrelor_C

city: Yuseong-gu

first: Seung Woo

last: Baek

state: Daejeon

address: Gwahak-ro 125

country: South Korea

institute: Korea Research Institute Biology & Biotechnology

description: replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Quantile normalization of raw data and subsequent data processing were performed using the R software package.

label: biotin

source_name: HCT116 Aspirin+Ticagrelor  uM 24h - 4

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with RNAiso reagent, followed by clean-up and with QIAGEN Rneasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with illumina.

value: Colon cancer

tag: agent

value: Aspirin+Ticagrelor


title: HCT116_Aspirin+Prasugrel_C

description: replicate 3

source_name: HCT116 Aspirin+Prasugrel  uM 24h - 5

value: Aspirin+Prasugrel


title: Acute07

value: Brown Norway Rat

value: frozen postmortem brain


title: HCT116_Ticagrelor_C

description: replicate 3

source_name: HCT116 Ticagrelor 20 uM 24h - 5

value: Ticagrelor


title: Low protein sperm and low protein seminal plasma (LL) replicate 7

description:
LL8 - M
Adult mouse liver gene expression data derived from offspring of dietary manipulated fathers.


title: Low protein sperm and low protein seminal plasma (LL) replicate 3

description:
LL3 - F
Adult mouse liver gene expression data derived from offspring of dietary manipulated fathers.


title: HCT116_Aspirin+Clopidogrel_C

description: replicate 3

source_name: HCT116 Aspirin+Clopidogrel  uM 24h - 5

value: Aspirin+Clopidogrel


title: HCT116_DMSO_C

description: replicate 3

source_name: HCT116 DMSO 24h - 5

value: DMSO


title: Low protein sperm and low protein seminal plasma (LL) replicate 5

description:
LL5 - F
Adult mouse liver gene expression data derived from offspring of dietary manipulated fathers.

value: 16 weeks


title: HCT116_Clopidogrel_C

description: replicate 3

source_name: HCT116 Clopidogrel 100 uM 24h - 5

value: Clopidogrel


title: HCT116_Aspirin_C

description: replicate 3

source_name: HCT116 Aspirin 1000 uM 24h - 5

value: Aspirin


title: Low protein sperm and low protein seminal plasma (LL) replicate 1

description:
LL1 - F
Adult mouse liver gene expression data derived from offspring of dietary manipulated fathers.

value: liver


title: HCT116_Aspirin+Clopidogrel_B

description: replicate 2

source_name: HCT116 Aspirin+Clopidogrel  uM 24h - 2


title: HCT116_Ticagrelor_B

description: replicate 2

source_name: HCT116 Ticagrelor 20 uM 24h - 4


title: Normal protein diet sperm and seminal plasma (NN) replicate 7

description:
NN10 - M
Adult mouse liver gene expression data derived from offspring of dietary manipulated fathers.

value: male

value: NN


title: HCT116_Clopidogrel_B

description: replicate 2

source_name: HCT116 Clopidogrel 100 uM 24h - 2


title: HCT116_Aspirin_B

description: replicate 2

source_name: HCT116 Aspirin 1000 uM 24h - 3


title: HCT116_Prasugrel_B

description: replicate 2

source_name: HCT116 Prasugrel 100 uM 24h - 3

value: Prasugrel


title: HCT116_DMSO_B

description: replicate 2

source_name: HCT116 DMSO 24h - 3


title: Normal protein diet sperm and seminal plasma (NN) replicate 6

description:
NN9 - M
Adult mouse liver gene expression data derived from offspring of dietary manipulated fathers.


title: HCT116_Aspirin+Ticagrelor_A

description: replicate 1

source_name: HCT116 Aspirin+Ticagrelor  uM 24h - 1


title: Acute05

source_name: nucleus accumbens

value: nucleus accumbens

value: Male

value: nuclear mRNA


title: HCT116_Aspirin+Ticagrelor_B

description: replicate 2

source_name: HCT116 Aspirin+Ticagrelor  uM 24h - 2

value: Colon cancer

value: Aspirin+Ticagrelor


title: Mouse-AS-2

city: Kanazawa City

first: Tsuyoshi

last: Hattori

state: Ishikawa

address: 13-1 Takara-Machi

department: Department of Neuroanatomy

institute: Kanazawa University

data_processing:
Base-calling were performed using Illumina HiSeq Control Software 2.2.38
Demultiplexing and trimming adapters from sequenced reads were performed by  bcl2fastq 2.17
Reads were aligned to genome assembly MusPutFur1 and GRCm38 using STAR 2.7.0f
Fragments Per Kilobase of exon per Million mapped reads (FPKM) ware calculated using cufflinks 2.2.1
Assembly: MusPutFur1, GRCm38
Supplementary files format and content: tab-delimited text files include FPKM values for every gene

source_name: astrocytes

growth_protocol: Astrocyte cultures were prepared from the cerebral cortices of P1 to P3 neonatal mice and P1 ferrets. Cerebral cortices were digested at 37 °C in Hanks' Balanced Salt Solution with 2 mg/mL Dispase II. Cells were plated on poly-D-lysine-coated T75 flasks and cultured in Dulbecco's modified Eagle’s medium supplemented with 10% fetal bovine serum. After 14 days of cultivation, the culture flasks were shaken at 200 rpm for 12 hs and the supernatant was discarded. The astrocytes were detached using 0.05% trypsin-EDTA and plated at 1 × 105 cells/cm2 density.

extract_protocol:
RNA was extracted using RNA Basic Kit (FastGene #FG-8025).
Libraries were prepared using TruSeq Stranded mRNA Sample Preparation Kit (20020594, Illumina, Inc.), with polyA selection for ribosomal RNA depletion.

value: P1 to P3

value: cerebral cortex

value: primary astrocytes

value: ICR


title: Normal protein diet sperm and seminal plasma (NN) replicate 5

description:
NN8 - M
Adult mouse liver gene expression data derived from offspring of dietary manipulated fathers.

source_name: Adult mouse liver


title: Mouse-AS-1


title: HCT116_Aspirin+Prasugrel_A

description: replicate 1

source_name: HCT116 Aspirin+Prasugrel  uM 24h - 1

value: Aspirin+Prasugrel


title: HCT116_Aspirin+Clopidogrel_A

description: replicate 1

source_name: HCT116 Aspirin+Clopidogrel  uM 24h - 1

value: Aspirin+Clopidogrel


title: Acute03

value: Brown Norway Rat

value: frozen postmortem brain

value: Morphine injection


title: Acute01


title: Ferret-AS-2

organism: Mustela putorius furo


title: Stomach Mutant 3 (SM3)

city: Tuskegee

first: Pawan

last: Puri

state: Alabama

address: 1200 W Montgomery Road

department: Biomedical Sciences

institute: Tuskegee University

data_processing:
Original image data file from high-throughput sequencing Illumina platform was transformed to sequenced reads by CASAVA base recognition.
Raw data of FASTQ format were firstly processed through fastp. In this step, clean data (clean reads) were obtained by removing reads containing adapter sequences and reads with low quality. All the downstream analyses were based on clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly.
Genome_build: Indexes of the reference genome were built using STAR and paired-end clean reads were aligned to the reference genome using STAR (v2.5).  FeatureCounts was used to count the read numbers mapped of each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for all gene and each sample …
Supplementary_files_format_and_content: tab-delimited text files include readcounts values for all gene and each sample …

source_name: Stomach Corpus region

growth_protocol: Animals used in these studies were maintained and euthanized according to the principles and procedures described in the NIH Guide for the Care and Use of Laboratory Animals. These studies were approved by the Tuskegee University Institutional Animal Care and Use Committee.

extract_protocol:
Corpus region of the stomach was removed and collected in RNAlater solution (Cat # AM7020Thermo Fisher Scientific) and  RNA was harvested using Trizol reagent.
Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations.

treatment_protocol: No treatment was administered to control or mutant mice

tag: background strain

value: Mixed (C57BL/6  X CD1)

value: Six2-Cre+/- PKAcaR fl/wt


title: Ferret-AS-1

tag: cell type


title: HCT116_Prasugrel_A

description: replicate 1

source_name: HCT116 Prasugrel 100 uM 24h - 2

value: Prasugrel


title: Stomach Mutant 1 (SM1)


title: Normal protein diet sperm and seminal plasma (NN) replicate 3

description:
NN4 - F
Adult mouse liver gene expression data derived from offspring of dietary manipulated fathers.

value: 16 weeks

value: female

value: liver

value: NN


title: HCT116_Clopidogrel_A

description: replicate 1

source_name: HCT116 Clopidogrel 100 uM 24h - 1

value: Colon cancer

value: Clopidogrel


title: Stomach Mutant 2 (SM2)


title: Stomach Control 3 (SC3)

value: Six2-Cre+/- PKAcaR wt/wt


title: Stomach Control 4 (SC4)


title: Normal protein diet sperm and seminal plasma (NN) replicate 2

description:
NN3 - F
Adult mouse liver gene expression data derived from offspring of dietary manipulated fathers.


title: HCT116_Aspirin_A

description: replicate 1

source_name: HCT116 Aspirin 1000 uM 24h - 1

value: Aspirin


title: Ts66_hippo_2599

city: ILLKIRCH

first: Yann

last: HERAULT

address: 1 rue Laurent Fries

institute: IGBMC/PHENOMIN-ICS

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
The "Ts66Dn_ento_subSeries_DESeq2_normalization_matrix" was obtained by using DESeq2 normalization of raw data from entorhinal cortices
The "Ts66Dn_ento_subSeries_FCROS_results_matrix" was obtained by using FCROS normalization of raw data from entorhinal cortices
the " Ts66Dn_hippo_subSeries_DESeq2_normalization_matrix" was obtained by using DESeq2 normalization of raw data from hippocampus
The "Ts66Dn_hippo_subSeries_FCROS_results_matrix" was obtained by using FCROS normalization of raw data from hippocampus
Assembly: mm10
Supplementary files format and content: counts, log2FoldChange

source_name: Hippocampus

extract_protocol:
RNA was extracted with the qiagen RNeasy plus kit (gDNA exclusion step, then RNA separation).
RNA-Seq libraries were generated from 1000 ng of total RNA using TruSeq Stranded mRNA Library Prep Kit and TruSeq RNA Single Indexes kits A and B (Illumina, San Diego, CA), according to manufacturer's instructions. Briefly, following purification with poly-T oligo attached magnetic beads, the mRNA was fragmented using divalent cations at 94oC for 2 minutes. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity was achieved by replacing dTTP with dUTP during second strand cDNA synthesis using DNA Polymerase I and RNase H. Following addition of a single 'A' base and subsequent ligation of the adapter on double stranded cDNA fragments, the products were purified and enriched with PCR (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC) to create the cDNA library. Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.

value: male

tag: model

value: Hippocampus


title: Ts66_EntCortex_2599

source_name: Entorhinal cortex

value: Entorhinal cortex


title: Normal protein diet sperm and seminal plasma (NN) replicate 1

description:
NN2 - F
Adult mouse liver gene expression data derived from offspring of dietary manipulated fathers.

tag: strain


title: HCT116_DMSO_A

description: replicate 1

source_name: HCT116 DMSO 24h - 1

value: DMSO


title: Normal protein diet sperm and seminal plasma (NN) replicate 4

description:
NN6 - M
Adult mouse liver gene expression data derived from offspring of dietary manipulated fathers.


title: Ts66_EntCortex_2598


title: Stomach Control 1 (SC1)

tag: genotype


title: Adult NSCs treated with  PluriSIn#2 rep3

city: Shanghai

first: Qin

last: shangyao

address: Xiangyin Road 800

department: Institute of Neuroscience

institute: Second Military Medical University

data_processing:
After low complexity reads were filtered out, remaining reads were aligned to Mouse genome (mm10) using STAR with default parameters. The aligned reads were then provided as an input to HTSeq-count utility (HTSeq package) and the obtained raw read count files were then processed for differential expression using DESeq package.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Adult NSCs

growth_protocol: Wild type cells were grown as previously described (Guo, W. et al. 2012)

extract_protocol:
RNA was extracted using Rneasy kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Primary adult NSCs cultured in medium containing FGF2 and EGF (both at 20 ng/ml, Invitrogen), which was changed after 24 h and cells were treated  for 3 days with 20 μM PluriSIn#2 or DMSO as a control

value: post natal day 60

value: SVZ-derived neural stem cells

tag: treatment

value: treated with PluriSIn#4


title: Stomach Mutant 4 (SM4)

value: Mixed (C57BL/6  X CD1)

value: Six2-Cre+/- PKAcaR fl/wt


title: Adult NSCs treated with  PluriSIn#2 rep2

value: treated with PluriSIn#3


title: Ts66_hippo_2598

tag: tissue


title: Adult NSCs treated with  PluriSIn#2 rep1

value: treated with PluriSIn#2


title: Adult_D_Stromal_rep2

city: Amsterdam

first: Renee

last: van Amerongen

address: Science Park 904

department: Swammerdam Institute for Life Sciences

country: Netherlands

institute: University of Amsterdam

description:
X4070_32_D_2.Stromal_GCCAATA
readcounts_adult.txt
readcounts_adult_normalized_10mil.txt

data_processing:
RNA sequencing was performed on a HiSeq2500 (Illumina) system at the NKI Genomics core facility. The puberty samples and the adult samples were sequenced in two different runs (months apart in 2016 and 2017), resulting in two different count tables (readcounts_puberty.txt and readcounts_adult.txt)
For both the puberty and the adult sequencing run, single-end reads (65 bp) were aligned to the refrence sequence GRCm38/mm10 with Tophat version 2.1 and Bowtie version 1.1.0.
Expression values were determined by HTSeq-count.
Assembly: mm10
Supplementary files format and content: readcounts_puberty.txt
Supplementary files format and content: readcounts_puberty_normalized_10mil.txt
Supplementary files format and content: readcounts_adult.txt
Supplementary files format and content: readcounts_adult_normalized_10mil.txt

source_name: mammary gland

growth_protocol: Wildtype FVB/N mice used in this study were purchased from Envigo. All mice were maintained under standard housing conditions in open cages, with 12 hour light/dark cycle and ad libitum access to food and water.

extract_protocol:
The 3rd and 4th mammary glands were isolated, minced and enzymatically digested as described in the materials and methods of the accompanying paper. Cell populations were isolated as described in the materials and methods of the accompanying paper. Cells were lysed in TRIzol LS. RNA was extracted and purified using the Qiagen RNeasy column purification kit.
RNA quality was checked with a Bioanalyzer (Agilent), after which polyA+ stranded RNA library preparation was performed using the Illumina TruSeq stranded RNA prep kit. RNA sequencing was performed on a HiSeq2500 (Illumina) system at the NKI Genomics core facility.

treatment_protocol: Pubertal mice of 34-36 days old were used and for each day 4 mice from 3 different litters were pooled to obtain sufficient cells for RNA sequencing. Adult mice of 14-16 weeks old were sacrificed at the appropriate time point in the estrous cycle.

value: mammary gland

value: FVB/N

value: stromal

value: wildtype


title: Adult_D_Luminal_rep2

description:
X4070_31_D_2.Luminal_ACAGTGA
readcounts_adult.txt
readcounts_adult_normalized_10mil.txt

value: luminal


title: Adult_D_Fat_rep2

description:
X4070_29_D_2.Fat_CGATGTA
readcounts_adult.txt
readcounts_adult_normalized_10mil.txt

value: fat


title: Stomach Control 2 (SC2)

value: Six2-Cre+/- PKAcaR wt/wt


title: Ts66_EntCortex_2613

value: male


title: Adult_D_Fat_rep1

description:
X4070_25_D_1.Fat_CGTACGT
readcounts_adult.txt
readcounts_adult_normalized_10mil.txt


title: HCT116_Ticagrelor_A

description: replicate 1

source_name: HCT116 Ticagrelor 20 uM 24h - 2

value: Colon cancer

value: Ticagrelor


title: Adult NSCs - TOP2a_IP

data_processing:
ChIP-seq reads were mapped to mouse mm10 reference genome using bwa program with default parameters.  Aligned ChIP-seq reads were remove duplicate with samtools rmdup package.The characteristic peaks of TOP2a on chromatins were found by peak calling using the software MACS2 software. Threshold for the peaks called is q-value < 0.05.
Genome_build: mm10
Supplementary_files_format_and_content: bw file were generated using bamCoverage program in deepTools
Supplementary_files_format_and_content: peak text files called with MACS2

source_name: Adult Neural stem cells

extract_protocol:
Library construction from the TOP2a ChIP-seq samples and sequencing of paired-end 150bps long reads by the Illumina HiSeq 2000.
Libraries were prepared according to Illumina's instructions.

value: SVZ-derived adult Neural stem cells

tag: chip antibody

value: TOP2a (Abcam, ab52934, EP1102Y)

value: untreated


title: Ts66_hippo_2612

value: Hippocampus


title: Ts66_EntCortex_2611

value: Entorhinal cortex


title: Ts66_EntCortex_2612


title: Ts66_hippo_2613


title: Adult_D_Basal_rep2

description:
X4070_30_D_2.Basal_TGACCAA
readcounts_adult.txt
readcounts_adult_normalized_10mil.txt

value: basal


title: Ts66_hippo_2611


title: Adult_D_Basal_rep1

description:
X4070_26_D_1.Basal_GAGTGGA
readcounts_adult.txt
readcounts_adult_normalized_10mil.txt


title: Adult_M_Fat_rep2

description:
X4070_21_M_2.Fat_TAGCTTA
readcounts_adult.txt
readcounts_adult_normalized_10mil.txt


title: Adult NSCs treated with DMSO rep3

value: post natal day 60

tag: cell line

value: SVZ-derived neural stem cells

value: treated with DMSO


title: Adult_D_Stromal_rep1

description:
X4070_28_D_1.Stromal_ATTCCTT
readcounts_adult.txt
readcounts_adult_normalized_10mil.txt

value: mammary gland

value: FVB/N

value: stromal


title: cord blood E3637-750knsp

type: genomic

city: Fuzhou

first: Xiaoqing

last: Wu

address: 18 daoshan road, Gulou district

institute: Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University

description: Hybridized to 750K_Nsp

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
The array image was acquired using Affymetrix GeneChip® Operating Software (ChAS 4.0). Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using GTYPE 4.1 and Affymetrix Copy Number Analysis Tool (CNAT 4.0.1) softwares. Genomic Smoothing analysis was performed by using the smoothing window of 0 Mb, and inferred copy number states were derived from a Hidden Markov Model (HMM) based algorithm implemented in CNAT 4.0.1. Circular Binary Segmentation (Ohlsen et al., 2004) was applied using DNAcopy package for R Bioconductor on raw data.
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

source_name: cord blood E3637

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Cell were grown according to standard conditions.

extract_protocol: Genomic DNA was extracted from uncultured amniotic fluid, fetal cord blood using a QIAGEN kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions.

value: cord blood

tag: ultrasound abnormality classification

value: Isolated FGR

tag: obstruction level classification

value: FGR


title: cord blood E3027-750knsp

description: Hybridized to 750K_Nsp

source_name: cord blood E3027

value: Nonisolated FGR

value: FGR, Increased nuchal translucency


title: cord blood E2835-750knsp

description: Hybridized to 750K_Nsp

source_name: cord blood E2835

value: FGR, echogenic intracardiac focus


title: Adult_D_Luminal_rep1

description:
X4070_27_D_1.Luminal_ACTGATA
readcounts_adult.txt
readcounts_adult_normalized_10mil.txt

value: luminal

value: wildtype


title: amniotic fluid S47-750knsp

description: Hybridized to 750K_Nsp

source_name: amniotic fluid S47

value: amniotic fluid

value: FGR, Single umbilical artery, oligohydramnios


title: HCT116_Prasugrel_C

description: replicate 3

source_name: HCT116 Prasugrel 100 uM 24h - 5

value: Colon cancer

value: Prasugrel


title: cord blood E3049-750knsp

description: Hybridized to 750K_Nsp

source_name: cord blood E3049


title: Adult NSCs - Input

value: SVZ-derived adult Neural stem cells

value: TOP2a (Abcam, ab52934, EP1102Y)

value: untreated


title: amniotic fluid S144-750knsp

description: Hybridized to 750K_Nsp

source_name: amniotic fluid S144


title: Adult_M_Luminal_rep2

description:
X4070_23_M_2.Luminal_GTGGCCT
readcounts_adult.txt
readcounts_adult_normalized_10mil.txt

value: mammary gland

value: FVB/N


title: Adult NSCs treated with DMSO rep1

tag: age

value: post natal day 60

value: SVZ-derived neural stem cells

value: treated with DMSO


title: cord blood E3659-750knsp

description: Hybridized to 750K_Nsp

source_name: cord blood E3659

value: cord blood

value: Isolated FGR

value: FGR


title: amniotic fluid R2462-750knsp

description: Hybridized to 750K_Nsp

source_name: amniotic fluid R2462


title: cord blood E2639-750knsp

description: Hybridized to 750K_Nsp

source_name: cord blood E2639

value: Nonisolated FGR

value: FGR, Echogenic bowel,


title: amniotic fluid S131-750knsp

description: Hybridized to 750K_Nsp

source_name: amniotic fluid S131

value: amniotic fluid


title: Ts66_EntCortex_2610

source_name: Entorhinal cortex

tag: Sex

value: male

value: Entorhinal cortex


title: Adult_M_Stromal_rep2

description:
X4070_24_M_2.Stromal_GTTTCGG
readcounts_adult.txt
readcounts_adult_normalized_10mil.txt

value: stromal

value: wildtype


title: Ts66_hippo_2610

source_name: Hippocampus

value: Hippocampus


title: cord blood E2301-750knsp

description: Hybridized to 750K_Nsp

source_name: cord blood E2301

value: FGR, increased nuchal fold


title: cord blood E2380-750knsp

description: Hybridized to 750K_Nsp

source_name: cord blood E2380


title: wt_hippo_2609

value: wt


title: wt_EntCortex_2609


title: amniotic fluid P4317-750knsp

description: Hybridized to 750K_Nsp

source_name: amniotic fluid P4317

value: FGR, increased nuchal fold, aberrant right subclavian artery


title: Adult_M_Basal_rep2

description:
X4070_22_M_2.Basal_GGCTACA
readcounts_adult.txt
readcounts_adult_normalized_10mil.txt

source_name: mammary gland

value: mammary gland

value: FVB/N

value: basal


title: amniotic fluid G9468-750knsp

description: Hybridized to 750K_Nsp

source_name: amniotic fluid G9468


title: Adult_M_Stromal_rep1

description:
X4070_20_M_1.Stromal_GATCAGA
readcounts_adult.txt
readcounts_adult_normalized_10mil.txt


title: wt_EntCortex_2608


title: cord blood E2248-750knsp

description: Hybridized to 750K_Nsp

source_name: cord blood E2248

value: cord blood

value: FGR, high risk of NIPT


title: Adult_M_Fat_rep1

description:
X4070_17_M_1.Fat_ATCACGA
readcounts_adult.txt
readcounts_adult_normalized_10mil.txt

value: fat


title: amniotic fluid R3122-750knsp

description: Hybridized to 750K_Nsp

source_name: amniotic fluid R3122

value: Nonisolated FGR

value: FGR, tricuspid regurgitation,


title: Adult_M_Luminal_rep1

description:
X4070_19_M_1.Luminal_ACTTGAA
readcounts_adult.txt
readcounts_adult_normalized_10mil.txt

value: luminal


title: amniotic fluid P8799-750knsp

description: Hybridized to 750K_Nsp

source_name: amniotic fluid P8799

value: amniotic fluid

value: Isolated FGR

value: FGR


title: amniotic fluid P9003-750knsp

description: Hybridized to 750K_Nsp

source_name: amniotic fluid P9003


title: wt_EntCortex_2593

value: male

value: Entorhinal cortex


title: amniotic fluid P2340-750knsp

description: Hybridized to 750K_Nsp

source_name: amniotic fluid P2340

value: FGR, increased nuchal fold


title: amniotic fluid P2341-750knsp

description: Hybridized to 750K_Nsp

source_name: amniotic fluid P2341

value: FGR,  tricuspid regurgitation,


title: amniotic fluid P4534-750knsp

description: Hybridized to 750K_Nsp

source_name: amniotic fluid P4534

value: FGR,Ventriculomegaly, persistent left superior vena cava, Single umbilical artery, Echogenic bowel, echogenic intracardiac focus,


title: Adult_E_Fat_rep2

description:
X4070_13_E_2.Fat_ATGTCAG
readcounts_adult.txt
readcounts_adult_normalized_10mil.txt

value: mammary gland

value: wildtype


title: wt_hippo_2593

value: wt

value: Hippocampus


title: Adult_M_Basal_rep1

description:
X4070_18_M_1.Basal_TTAGGCA
readcounts_adult.txt
readcounts_adult_normalized_10mil.txt

value: FVB/N

value: basal


title: HCT116_Aspirin+Prasugrel_B

description: replicate 2

source_name: HCT116 Aspirin+Prasugrel  uM 24h - 2

value: Colon cancer

value: Aspirin+Prasugrel


title: Adult_E_Stromal_rep2

description:
X4070_16_E_2.Stromal_GTGAAAC
readcounts_adult.txt
readcounts_adult_normalized_10mil.txt

value: stromal


title: wt_EntCortex_2594


title: wt_hippo_2594


title: Adult NSCs treated with DMSO rep2

source_name: Adult NSCs

value: post natal day 60

value: SVZ-derived neural stem cells

value: treated with DMSO


title: amniotic fluid P2758-750knsp

description: Hybridized to 750K_Nsp

source_name: amniotic fluid P2758

value: amniotic fluid

value: Nonisolated FGR

value: FGR, Echogenic bowel, tricuspid regurgitation, oligohydramnios


title: amniotic fluid P8139-750knsp

description: Hybridized to 750K_Nsp

source_name: amniotic fluid P8139

value: FGR, Echogenic bowel, tricuspid regurgitation,


title: amniotic fluid P3780-750knsp

description: Hybridized to 750K_Nsp

source_name: amniotic fluid P3780

value: FGR, increased nuchal fold


title: Adult_E_Luminal_rep2

description:
X4070_15_E_2.Luminal_GTCCGCA
readcounts_adult.txt
readcounts_adult_normalized_10mil.txt

value: mammary gland

value: luminal


title: wt_hippo_2608

source_name: Hippocampus

value: male

value: wt


title: wt_EntCortex_2642

source_name: Entorhinal cortex

value: Entorhinal cortex


title: amniotic fluid R3068-750knsp

description: Hybridized to 750K_Nsp

source_name: amniotic fluid R3068

value: FGR, echogenic intracardiac focus,


title: amniotic fluid P1957-750knsp

description: Hybridized to 750K_Nsp

source_name: amniotic fluid P1957

value: Isolated FGR

value: FGR, high risk of NIPT


title: wt_hippo_2642

value: Hippocampus


title: Adult_E_Basal_rep2

description:
X4070_14_E_2.Basal_CCGTCCC
readcounts_adult.txt
readcounts_adult_normalized_10mil.txt

source_name: mammary gland

value: FVB/N

value: basal

value: wildtype


title: amniotic fluid R2590-750knsp

description: Hybridized to 750K_Nsp

source_name: amniotic fluid R2590

value: amniotic fluid

value: FGR


title: Adult_E_Fat_rep1

description:
X4070_9_E_1.Fat_CAGATCA
readcounts_adult.txt
readcounts_adult_normalized_10mil.txt

value: fat


title: amniotic fluid P9449-750knsp

description: Hybridized to 750K_Nsp

source_name: amniotic fluid P9449

value: Nonisolated FGR

value: FGR, increased nuchal fold, Echogenic bowel, Nasal bone dysplasia


title: Adult_E_Stromal_rep1

description:
X4070_12_E_1.Stromal_AGTTCCG
readcounts_adult.txt
readcounts_adult_normalized_10mil.txt

value: mammary gland

value: stromal


title: amniotic fluid R4569-750knsp

description: Hybridized to 750K_Nsp

source_name: amniotic fluid R4569


title: ts65DnxCEntho_4796 CE

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
The "Ts65Dn_ento_subSeries_DESeq2_normalization_matrix" was obtained by using DESeq2 normalization of raw data from entorhinal cortices
The "Ts65Dn_ento_subSeries_FCROS_results_matrix" was obtained by using FCROS normalization of raw data from entorhinal cortices
the " Ts65Dn_hippo_subSeries_DESeq2_normalization_matrix" was obtained by using DESeq2 normalization of raw data from hippocampus
The "Ts65Dn_hippo_subSeries_FCROS_results_matrix" was obtained by using FCROS normalization of raw data from hippocampus
Assembly: mm10
Supplementary files format and content: counts, log2FoldChange

value: male


title: ts65Dnxhipp_4796 H


title: amniotic fluid R3940-750knsp

description: Hybridized to 750K_Nsp

source_name: amniotic fluid R3940


title: Adult_E_Luminal_rep1

description:
X4070_11_E_1.Luminal_AGTCAAC
readcounts_adult.txt
readcounts_adult_normalized_10mil.txt

value: luminal


title: Adult_E_Basal_rep1

description:
X4070_10_E_1.Basal_CTTGTAA
readcounts_adult.txt
readcounts_adult_normalized_10mil.txt


title: ts65Dnxhipp_4780 H


title: microglia, mafba, rep3

city: Hong Kong

first: LIANG

last: LOU

address: HKUST

department: LIFS

institute: HKUST

description:
Smart-seq2 oligodT captured
mafba_c

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using TrimGalore with parameters trim_galore -q 20 --phred33 --stringency 5 --length 20 -e 0.1 --paired
Trimed reads were mapped to GRCz11.94 (danRer11) genome using STAR
Mapped reads (Bam) were quantified using Rsubred package
Assembly: GRCz11.94 (danRer11)
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Danio rerio

source_name: brain

extract_protocol:
After brains from around ten 3-dpf embryos were dissected and dissociated, three DsRed+ cells were manually picked with micromanipulator system (NT-88-V3; Nikon) under Nikon inverted microscopy, then washed with RNase-free PBS containing 2% BSA once, and finally transferred into 4.4ul lysis buffer (0.2% Triton X-100 solution) in one 200µl RNase-free tube. Three tubes (three cells in one tube) were prepared for each genotype. The smart-seq2 protocol was used for whole transcriptome amplification.
cDNA libraries were prepared for sequencing using standard Illumina protocols

value: brain

value: microglia

tag: cell subtype

value: immune cell

value: mafba mutant

tag: development stage

value: 3 dpf

value: manually picking


title: microglia, mafbb, rep2

description:
Smart-seq2 oligodT captured
mafbb_b

value: mafbb mutant


title: microglia, mafbb, rep1

description:
Smart-seq2 oligodT captured
mafbb_a


title: microglia, DMut, rep2

description:
Smart-seq2 oligodT captured
DMut_b

value: DMut


title: microglia, DMut, rep1

description:
Smart-seq2 oligodT captured
DMut_a


title: amniotic fluid P2393-750knsp

description: Hybridized to 750K_Nsp

source_name: amniotic fluid P2393

value: amniotic fluid

value: Isolated FGR

value: FGR, high risk of maternal serum screen


title: microglia, mafba, rep2

description:
Smart-seq2 oligodT captured
mafba_b


title: ts65Dnxhipp_4778 H

value: Hippocampus


title: microglia, mafbb, rep3

description:
Smart-seq2 oligodT captured
mafbb_c


title: ts65DnxCEntho_4778 CE

value: Entorhinal cortex


title: Adult_P_Fat_rep2

description:
X4070_5_P_2.Fat_CGATGTA
readcounts_adult.txt
readcounts_adult_normalized_10mil.txt

value: mammary gland

value: FVB/N

value: fat

value: wildtype


title: microglia, DMut, rep3

description:
Smart-seq2 oligodT captured
DMut_c

value: brain


title: Adult_P_Basal_rep2

description:
X4070_6_P_2.Basal_TGACCAA
readcounts_adult.txt
readcounts_adult_normalized_10mil.txt

value: basal


title: microglia, sib, rep3

description:
Smart-seq2 oligodT captured
sib_c

value: microglia

value: immune cell

value: siblings


title: microglia, sib, rep2

description:
Smart-seq2 oligodT captured
sib_b

value: 3 dpf

value: manually picking


title: microglia, sib, rep1

description:
Smart-seq2 oligodT captured
sib_a


title: ts65DnxCEntho_4780 CE

value: male


title: microglia, mafba, rep1

description:
Smart-seq2 oligodT captured
mafba_a

value: mafba mutant


title: ts65Dnxhipp_4742 H


title: Adult_P_Luminal_rep2

description:
X4070_7_P_2.Luminal_ACAGTGA
readcounts_adult.txt
readcounts_adult_normalized_10mil.txt

value: luminal


title: Adult_P_Fat_rep1

description:
X4070_1_P_1.Fat_CGTACGT
readcounts_adult.txt
readcounts_adult_normalized_10mil.txt


title: Adult_P_Stromal_rep2

description:
X4070_8_P_2.Stromal_GCCAATA
readcounts_adult.txt
readcounts_adult_normalized_10mil.txt

value: stromal


title: SPBC530.07c_H10_rep4

city: Mainz

first: Falk

last: Butter

state: Germany

address: Ackermannweg 4

department: Quantitative Proteomics

institute: Institute of Molecular Biology gGmbH

description:
Knock-out strain
3' mRNA-Seq

data_processing:
Sequencing raw files were analyzed using the “NGSpipe2go” RNA-seq pipeline (https://github.com/imbforge/NGSpipe2go). Version of the tools used were: R (3.5.1), FastQC (0.11.8), STAR (2.6.1b), SAMtools (1.5), HTSeq (0.9.0), Subread (1.6.2), BEDTools (2.27.1), Picard (2.17.6), RSeQC (3.0.0), Qualimap (2.2.1), KentUtils (v365), rMATS (4.0.2), FastQScreen (0.12.2), deepTools (3.1.0), BamUtil (1.0.13), and STAR-Fusion (0.8.0). The default RPKM calculation was replaced with CPM (counts per million) as 3’-end sequencing was performed. “ASM294v2.40.gtf” was used as the gene model, and “ASM294v2.dna.toplevel.fa” was used as the genome for S. pombe. “rld” transformation of the data from the “DE_Seq” part of the pipeline was replaced with “vst” transformation due to the high number of samples being processed.
Alignment was done with STAR (2.6.1b).
Read count per gene was done with Subread (1.6.2).
DESeq2 R-package was used for calculating CPM values and statistics of differential regulation.
Genome_build: ASM294v2.dna.toplevel.fa
Supplementary_files_format_and_content: allSamples.CPM.csv: Processed data file is a semicolon-separated text file and includes CPM (counts per million) values for all gene models established in ASM294v2.40.gtf in all conditions.

organism: Schizosaccharomyces pombe

source_name: cell culture

growth_protocol: S. pombe knockout library (Bioneer, version M-3030H) was grown in YES medium (5 g l-1 yeast extract, 30 g l-1 D-glucose, supplemented with 225 mg l-1 adenine, L-histidine, L-leucine, uracil and L-lysine each f.c.) at 32 ºC shaking at 160 rpm for 2 days. A second inoculation was performed with 5 µl of the initial culture in a 96-deepwell plate filled with 2 ml YES media, and grown for another 12-14 hours.

extract_protocol:
Total RNA extraction was performed according to [A rapid and simple method for preparation of RNA from Saccharomyces cerevisiae, Mark E.Schmitt, NAR, 1990] and the RNA pellet was resuspended in 87ul of RNase free water. DNA was digested using 3ul of DNase (Qiagen) and 10ul RDD DNase buffer at 37ºC for 30 minutes. RNA cleanup was performed with the Purelink RNA Mini kit (Thermo Scientific) according to the manufacturer's instructions. RNA integrity was measured on a Bioanalyzer 2100 system (Agilent).
NGS library prep was performed with Lexogen 3´mRNA-Seq Library Prep Kit FWD HT following Lexogens standard protocol (015UG110V0110). Libraries were prepared with a starting amount of 338ng and amplified in 13 PCR cycles. Libraries were profiled using a High Sensitivity DNA chip on a 2100 Bioanalyzer (Agilent) and quantified using the Qubit dsDNA HS Assay Kit in a Qubit 2.0 Fluorometer (Life Technologies). 2x192 libraries were pooled together in equimolar ratio and sequenced in single-end mode on 2 NextSeq 500 High-output flowcells, for 1x75 cycles plus 2x8 cycles for the dual index read.

tag: replicate


title: SPBC660.11_H12_rep4

description:
Knock-out strain
3' mRNA-Seq


title: ts65Dnxhipp_4575 H

value: Hippocampus


title: Adult_P_Stromal_rep1

description:
X4070_4_P_1.Stromal_ATTCCTT
readcounts_adult.txt
readcounts_adult_normalized_10mil.txt


title: SPCC5E4.07_H9_rep4

description:
Knock-out strain
3' mRNA-Seq


title: SPAC3A12.13c_H8_rep4

description:
Knock-out strain
3' mRNA-Seq


title: SPAC22F3.09c_H11_rep4

description:
Knock-out strain
3' mRNA-Seq


title: ts65DnxCEntho_4742 CE

value: Entorhinal cortex


title: SPCC4G3.11_H4_rep4

description:
Knock-out strain
3' mRNA-Seq


title: SPAC4G9.16c_H7_rep4

description:
Knock-out strain
3' mRNA-Seq


title: ts65DnxCEntho_4575 CE


title: SPAC29B12.04_H6_rep4

description:
Knock-out strain
3' mRNA-Seq


title: SPCC320.12_H5_rep4

description:
Knock-out strain
3' mRNA-Seq


title: ts65Dnxhipp_4574 H


title: ts65DnxCEntho_4574 CE


title: Adult_P_Luminal_rep1

description:
X4070_3_P_1.Luminal_ACTGATA
readcounts_adult.txt
readcounts_adult_normalized_10mil.txt

value: mammary gland


title: Puberty_Fat_rep2

description:
X3828_16_Pool_Fat_sample_12_ACTTGAA
readcounts_puberty.txt
readcounts_puberty_normalized_10mil.txt

value: FVB/N


title: SPBPB10D8.06c_H3_rep4

description:
Knock-out strain
3' mRNA-Seq


title: Puberty_Stromal_rep2

description:
X3828_15_Pool_Stromal_sample_7_CAGATCA
readcounts_puberty.txt
readcounts_puberty_normalized_10mil.txt


title: SPCC594.05c_H2_rep4

description:
Knock-out strain
3' mRNA-Seq


title: Adult_P_Basal_rep1

description:
X4070_2_P_1.Basal_GAGTGGA
readcounts_adult.txt
readcounts_adult_normalized_10mil.txt


title: Puberty_Luminal_rep2

description:
X3828_14_Pool_Luminal_sample_6_GCCAATA
readcounts_puberty.txt
readcounts_puberty_normalized_10mil.txt


title: wtxCEntho_4981 CE

value: wt


title: wtxHipp_4981 H


title: wtxHipp_4923 H


title: Puberty_Basal_rep2

description:
X3828_13_Pool_Basal_sample_5_ACAGTGA
readcounts_puberty.txt
readcounts_puberty_normalized_10mil.txt

value: wildtype


title: Puberty_Fat_rep1

description:
X3828_12_Pool_Fat_sample_4_TGACCAA
readcounts_puberty.txt
readcounts_puberty_normalized_10mil.txt

value: fat


title: SPCC1259.01c_H1_rep4

description:
Knock-out strain
3' mRNA-Seq


title: wtxCEntho_4923 CE


title: wtxCEntho_4791 CE


title: wtxHipp_4791 H


title: wtxHipp_4790 H


title: wtxCEntho_4790 CE


title: skin fibroblasts, caNrf2_3

city: Zurich

first: Paul

last: Hiebert

address: Otto-Stern-Weg 7

country: Switzerland

institute: ETH Zurich

data_processing:
Base calling was performed with CASAVA v.1.8 and further data processing was performed using the miARma-seq tool and accompanying software (Andrés-León et al, 2018).
Adapter sequences were removed using Cutadapt and default parameters.
Sequences were mapped to the mm10 whole genome using Bowtie1. Maximum number mismatches in seed alignment in bowtie analysis=0. Length of the seed substrings to align during multiseed alignment=19. The following bowtie parameters were used: --best --nomaqround.
Read counts were generated using featureCounts and default parameters.
Differential expression was determined using EdgeR and the following parameters: filter=yes, cpmvalue=2, repthreshold=1, edger_normethod=TMM, replicates=yes.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files of raw read counts

source_name: skin of newborn transgenic mice with Cre-recombinase expressed in fibroblasts

extract_protocol:
Total RNA was isolated using Trizol reagent (Life technologies) according to the manufacturer's protocol.
Small RNA libraries were prepared for sequencing using standard Illumina protocols

value: Primary dermal fibroblasts

tag: passages


title: wtxHipp_4582 H


title: skin fibroblasts, caNrf2_2

value: skin of newborn transgenic mice with Cre-recombinase expressed in fibroblasts


title: SPBC365.03c_F10_rep4

description:
Knock-out strain
3' mRNA-Seq


title: SPAC22H12.02_G1_rep4

description:
Knock-out strain
3' mRNA-Seq


title: SPCC285.09c_G11_rep4

description:
Knock-out strain
3' mRNA-Seq


title: SPBC1105.14_G3_rep4

description:
Knock-out strain
3' mRNA-Seq


title: SPAC18G6.10_F12_rep4

description:
Knock-out strain
3' mRNA-Seq


title: SPAC20G4.07c_G12_rep4

description:
Knock-out strain
3' mRNA-Seq


title: SPAPB2B4.04c_G2_rep4

description:
Knock-out strain
3' mRNA-Seq


title: Puberty_Stromal_rep1

description:
X3828_11_Pool_Stromal_sample_3_TTAGGCA
readcounts_puberty.txt
readcounts_puberty_normalized_10mil.txt


title: Puberty_Basal_rep1

description:
X3828_9_Pool_Basal_sample_1_ATCACGA
readcounts_puberty.txt
readcounts_puberty_normalized_10mil.txt

value: basal


title: SPBC16C6.11_G4_rep4

description:
Knock-out strain
3' mRNA-Seq


title: SPBC543.07_G8_rep4

description:
Knock-out strain
3' mRNA-Seq


title: SPBC354.03_G5_rep4

description:
Knock-out strain
3' mRNA-Seq


title: SPBC3E7.05c_G6_rep4

description:
Knock-out strain
3' mRNA-Seq


title: SPCC1672.12c_G10_rep4

description:
Knock-out strain
3' mRNA-Seq


title: SPBC887.02_F11_rep4

description:
Knock-out strain
3' mRNA-Seq


title: wtxCEntho_4582 CE


title: wtxHipp_4560 H


title: wtxCEntho_4560 CE


title: SPBC3H7.03c_G9_rep4

description:
Knock-out strain
3' mRNA-Seq


title: SPBC405.07_G7_rep4

description:
Knock-out strain
3' mRNA-Seq


title: Puberty_Luminal_rep1

description:
X3828_10_Pool_Luminal_sample_2_CGATGTA
readcounts_puberty.txt
readcounts_puberty_normalized_10mil.txt


title: NIH3T3-No_Stim-Rep_3

city: Chicago

first: Savas

last: Tay

state: IL

address: 5640 South Ellis Avenue, Chicago, IL 60637

department: PME

institute: University of Chicago

data_processing:
Basecalls performed using CASAVA
Sequenced reads were trimmed for adaptor sequence and aligned using STAR aligner with default settings
Transcript abundance was calculated using featureCounts
Genome_build: mm10
Supplementary_files_format_and_content: featureCounts object with counts and annotations

source_name: NIH3T3 immortalized MEFs

growth_protocol: Cells were cultured in growth media and passaged at confluency for no more than 20 passages before use in a T25

extract_protocol:
Cells were detached with TrypLE, placed in 0.1% Triton-X 100 to lyse, and extraction-free RT and 10 cycles of pre-amplification performed using Superscript ii and KAPA HiFi respectively
cDNA libraries were prepared for sequencing using standard Illumina protocols from NexteraXT kit

treatment_protocol: Cells were loaded into custom microfluidic devices, stimulated with the indicated dose of TNF originating from a point source for four hours

value: RelA-/- Rela-DsRed 3T3s

value: Media


title: SUM 159 PTX Resistant expreriment #2

city: Ioannina

first: Angeliki

last: Magklara

address: Panepistimioupoli Ioanninon

department: Department of Medicine/Department of Biomedical Research (Ioannina) Foundation for Research & Technology-Hellas

country: Greece

institute: University of Ioannina/nstitute of Molecular Biology & Biotechnology

description:
Sample 4
SUM 159 Parental vs SUM 159 PTX Resistant analyzed data.txt

data_processing:
Quality Control was performed for the fastq raw data files using the “FASTQC” software
FastQ files were aligned to the human genome (hg19) using HISAT2
Counts were defined using HTSeq htseq-count command with the “intersection non empty” option . The count files were used as input for DESeq2
Normalization was performed with the estimate size factor function followed by Differentially Expressed Genes Analysis.
Assembly: human genome (hg19)
Supplementary files format and content: Text files include reads per gene for each sample (#1, #2, #3, #4)
Supplementary files format and content: Text file for the comparison of PTX resistant vs. parental cells with the following information: Gene name; baseMean; log2foldChange; lfcSE; stat; pvalue; padj.

source_name: Generation of PTX resistant cell line

growth_protocol: The SUM 159 human breast cancer cell line was cultured in Ham’s F12, supplemented with 5% fetal bovine serum, 1% penicillin/streptomycin, 5 μg/ml insulin and 1 μg/ml hydrocortisone in a humidified atmosphere of 5% CO2 at 37 °C. Cells were routinely passaged every 2 or 3 days and tested for mycoplasma. Paclitaxel (PTX)-resistant SUM159 cells were generated by exposure to twenty-five cycles of treatments with escalating doses of Paclitaxel (0,005 uM – 1 uM)

extract_protocol:
For total RNA extraction the RNeasy Kit (Qiagen) was used. Total RNA concentration and purity was measured with NanoDropTM 2000.
RNA-sequencing libraries were prepared with the illumina TruSeq RNA v2 kit using 1 μg of total RNA. The libraries were checked with the Agilent bioanalyzer (DNA1000 chip), quantitated with the qubit HS spectrophotometric method and pooled in equimolar amounts for sequencing. Approximately 25 million, 75 bp long, single-end reads were generated for each sample on an Illumina NextSeq500 sequenc-er.

value: Breast cancer cells

value: SUM 159

tag: phenotype

value: Chemoresistant


title: NIH3T3-100ng/mL TNF-α-Far-Rep_3

tag: cell type

value: 100 ng/mL TNF-alpha (source)


title: NIH3T3-No_Stim-Rep_2


title: NIH3T3-No_Stim-Rep_1


title: SPCC1393.05_F8_rep4

description:
Knock-out strain
3' mRNA-Seq


title: SPBC25H2.11c_F7_rep4

description:
Knock-out strain
3' mRNA-Seq


title: SPBC29A10.16c_F9_rep4

description:
Knock-out strain
3' mRNA-Seq


title: SUM 159 Parental experiment #2

description:
Sample 3
SUM 159 Parental vs SUM 159 PTX Resistant analyzed data.txt

source_name: Parental cells

value: Parental


title: SUM 159 PTX Resistant expreriment #1

description:
Sample 2
SUM 159 Parental vs SUM 159 PTX Resistant analyzed data.txt


title: NIH3T3-100ng/mL TNF-α-Far-Rep_2


title: SUM 159 Parental experiment #1

description:
Sample 1
SUM 159 Parental vs SUM 159 PTX Resistant analyzed data.txt


title: skin fibroblasts, caNrf2_1


title: skin fibroblasts, ctrl_3


title: skin fibroblasts, ctrl_1


title: skin fibroblasts, ctrl_2


title: SPBC21C3.12c_E11_rep4

description:
Knock-out strain
3' mRNA-Seq


title: SPAC1952.05_F2_rep4

description:
Knock-out strain
3' mRNA-Seq


title: SPBC4F6.10_F5_rep4

description:
Knock-out strain
3' mRNA-Seq


title: SPCC576.12c_F3_rep4

description:
Knock-out strain
3' mRNA-Seq


title: SPBC23E6.01c_E12_rep4

description:
Knock-out strain
3' mRNA-Seq


title: SPAC3H5.10_F6_rep4

description:
Knock-out strain
3' mRNA-Seq


title: SPAC9E9.09c_E9_rep4

description:
Knock-out strain
3' mRNA-Seq


title: SPAPB1E7.02c_E10_rep4

description:
Knock-out strain
3' mRNA-Seq


title: SPAC31A2.13c_F4_rep4

description:
Knock-out strain
3' mRNA-Seq


title: SPBC839.13c_E7_rep4

description:
Knock-out strain
3' mRNA-Seq


title: SPAC17A5.02c_F1_rep4

description:
Knock-out strain
3' mRNA-Seq


title: SPCC24B10.14c_E8_rep4

description:
Knock-out strain
3' mRNA-Seq


title: SPBC25H2.15_E2_rep4

description:
Knock-out strain
3' mRNA-Seq


title: SPBC3E7.15c_D11_rep4

description:
Knock-out strain
3' mRNA-Seq


title: SPBC3B9.13c_E5_rep4

description:
Knock-out strain
3' mRNA-Seq


title: SPCC757.09c_E3_rep4

description:
Knock-out strain
3' mRNA-Seq


title: SPAC4A8.09c_E4_rep4

description:
Knock-out strain
3' mRNA-Seq


title: SPBC14C8.17c_E1_rep4

description:
Knock-out strain
3' mRNA-Seq


title: SPAC8E11.10_D9_rep4

description:
Knock-out strain
3' mRNA-Seq


title: SPBC28F2.10c_D10_rep4

description:
Knock-out strain
3' mRNA-Seq


title: SPCC613.06_D12_rep4

description:
Knock-out strain
3' mRNA-Seq


title: SPBC577.15c_E6_rep4

description:
Knock-out strain
3' mRNA-Seq


title: NIH3T3-100ng/mL TNF-α-Mid-Rep_2


title: NIH3T3-100ng/mL TNF-α-Near-Rep_3


title: NIH3T3-100ng/mL TNF-α-Mid-Rep_3


title: NIH3T3-100ng/mL TNF-α-Mid-Rep_1


title: NIH3T3-100ng/mL TNF-α-Far-Rep_1


title: NIH3T3-100ng/mL TNF-α-Near-Rep_2


title: NIH3T3-30ng/mL TNF-α-Far-Rep_3

value: 30 ng/mL TNF-alpha (source)


title: NIH3T3-100ng/mL TNF-α-Near-Rep_1


title: NIH3T3-30ng/mL TNF-α-Far-Rep_1


title: High ERN2, stress rep03

city: Boston

first: Michael

last: Grey

state: MA

address: 300 Longwood Avenue, Enders 606

department: Gastroenterology, Hepatology, and Nutrition

institute: Boston Children's Hospital

description: Column 19

data_processing:
Data were processed using the Visualization Pipeline for RNAseq (VIPER) (Cornwell M, Vangala M, Taing L, Herbert Z, Köster J, Li B, et al. VIPER: Visualization Pipeline for RNA-seq, a Snakemake workflow for efficient and complete RNA-seq analysis. BMC Bioinformatics. 2018;19(1):135.).
Sequence reads were aligned using STAR (Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics (Oxford, England). 2013;29(1):15-21.)
Raw gene counts were used to calculate differential expression (log2 [Group1/Group2]) between groups with DESeq2 (Love MI, Huber W, and Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome biology. 2014;15(12):550.)
Assembly: hg38
Supplementary files format and content: tab-delimited text files include read counts per gene for each Sample

growth_protocol: HEK293doxERN cell line (Grey MJ, Cloots E, Simpson MS, et al. J Cell Biol 2020 219(2):e201904048) was maintained in DMEM with 10% FBS. Expression of FLAG-ERN2 was induced by treatment with 0, 10, or 100 ng/mL doxycycline for 24 hr.

extract_protocol:
Total RNA was extract from colon crypt epithelial cells using Qiagen RNeasy Mini Kit with on-column DNase treatment.
Total RNA quality and concentration were measured using Aligent Bioanalyzer and RNA libraries were prepared using KAPA stranded mRNA HyperPrep kits.

treatment_protocol: Cells were treated with 200 nM thapsigargin or equivalent volume of DMSO as control for 3 hr.

value: HEK293 cell line with dox-inducible FLAG-ERN2 transgene

value: 100 ng/mL doxycyclin 24 hr, 200 nM thapsigargin 3 hr


title: High ERN2, stress rep02

description: Column 18


title: High ERN2, stress rep01

description: Column 17


title: NIH3T3-30ng/mL TNF-α-Far-Rep_2


title: High ERN2, control rep03

description: Column 16

value: 100 ng/mL doxycyclin 24 hr, control


title: SPBC15D4.10c_D1_rep4

description:
Knock-out strain
3' mRNA-Seq


title: SPCC736.08_C10_rep4

description:
Knock-out strain
3' mRNA-Seq


title: SPCC663.04_C9_rep4

description:
Knock-out strain
3' mRNA-Seq


title: SPBC947.02_D2_rep4

description:
Knock-out strain
3' mRNA-Seq


title: SPBC776.01_C6_rep4

description:
Knock-out strain
3' mRNA-Seq


title: SPAC3A11.07_D3_rep4

description:
Knock-out strain
3' mRNA-Seq


title: SPAC1783.07c_C11_rep4

description:
Knock-out strain
3' mRNA-Seq


title: SPCC24B10.08c_C8_rep4

description:
Knock-out strain
3' mRNA-Seq


title: SPAC8C9.06c_C12_rep4

description:
Knock-out strain
3' mRNA-Seq


title: SPBP35G2.08c_D5_rep4

description:
Knock-out strain
3' mRNA-Seq


title: NIH3T3-30ng/mL TNF-α-Mid-Rep_3


title: NIH3T3-30ng/mL TNF-α-Mid-Rep_2


title: SPAC29A4.20_D8_rep4

description:
Knock-out strain
3' mRNA-Seq


title: SPBC713.07c_D4_rep4

description:
Knock-out strain
3' mRNA-Seq


title: SPAC17A2.13c_D6_rep4

description:
Knock-out strain
3' mRNA-Seq


title: SPAC17H9.19c_D7_rep4

description:
Knock-out strain
3' mRNA-Seq


title: SPBC24C6.11_C1_rep4

description:
Knock-out strain
3' mRNA-Seq


title: SPBC2F12.11c_C3_rep4

description:
Knock-out strain
3' mRNA-Seq


title: SPBC365.10_C5_rep4

description:
Knock-out strain
3' mRNA-Seq


title: SPBC2F12.12c_C4_rep4

description:
Knock-out strain
3' mRNA-Seq


title: SPBC28E12.06c_C2_rep4

description:
Knock-out strain
3' mRNA-Seq


title: SPBC776.17_C7_rep4

description:
Knock-out strain
3' mRNA-Seq


title: OVCAR-3

city: Taipei

first: YuAn

last: Chen

address: No.1, Sec. 1, Jen Ai Rd., Taipei Taiwan

country: Taiwan

institute: College of Medicine, National Taiwan University

data_processing:
The sequence was determined using Illumina's sequencing-by-synthesis (SBS) technology (Illumina, USA). Sequencing data (FASTQ reads) were generated using Welgene Biotech's pipeline based on Illumina's basecalling program bcl2fastq v2.20.
Illumina's official basecalling program, the  bcl2fastq conversion software v2.20, was used to convert BCL files from all Illumina sequencing platforms into FASTQ reads.
Adaptor clipping and sequence quality trimming were performed using Trimmomatic v0.36 with a sliding-window approach.
Assembly: Alignment Tool: HISAT2
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

growth_protocol: iOVCAR-3-OSKM cells were cultured in Primate ES cell medium (ESRC) (Reprocell, Beltsville, MD, USA) containing 10 ng/ml bFGF (Sigma–Aldrich, St. Louis, MO, USA).

extract_protocol:
Total RNA was extracted with TRIzol reagent (Invitrogen) and isolated using the RNeasy Plus Mini Kit (QIAGEN, Hilden, Germany) following the manufacturer's instructions.
SureSelect XT HS2 mRNA Library Preparation kit (Agilent, USA) was used for library construction followed by AMPure XP beads (Beckman Coulter, USA) size selection.

treatment_protocol: The CytoTune™-iPS 2.0 Sendai Reprogramming Kit was used for the generation of iOCICs via transduction of Yamanaka factors following the manufacturer's protocol (Invitrogen).

value: HGSOC


title: OVCAR-3 side population

source_name: OVCAR-3 side population

value: OVCAR-3 side population

value: side population of ovarian cancer cell line

value: sorting through dye-efflux activity assay


title: iOVCAR-3-OSKM

value: induced ovarian cancer initiating cell

value: OCT4, SOX2, KLF4 and MYC (OSKM) transduction


title: High ERN2, control rep01

description: Column 14


title: High ERN2, control rep02

description: Column 15


title: SPBC17A3.06_B10_rep4

description:
Knock-out strain
3' mRNA-Seq


title: SPBC21B10.03c_B12_rep4

description:
Knock-out strain
3' mRNA-Seq


title: SPBC19G7.10c_B11_rep4

description:
Knock-out strain
3' mRNA-Seq


title: BTY25 Dasatinib+Paclitaxel treated replicate 5

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

institute: Koch Institute

description:
BJ50.PD.5
ikohale_intCt.txt.gz
ikohale_l2cpm.txt.gz

data_processing:
NextSeq 500 using v3 chemistry. Software: Control v4.0.0.19, RTA 2.11.3. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch.
3’ DGE FASTQ sequencing reads were collapsed to one representative read per unique molecular identifier using a custom python script.
Gene expression was quantified using salmon version 1.1.0 (Patro et al. 2017) using a transcriptome prepared from the human hg38 primary genome assembly using the ensembl version 98 annotation.  The resulting counts were summarized to the gene level using R version 3.6.2 (R Core Team 2021) running tximport version 1.12.3 (Soneson, Love, and Robinson 2015) and counts per million (cpm) were calculated using utilities implement in edgeR version 3.26.8 (Robinson, McCarthy, and Smyth 2010; McCarthy, Chen, and Smyth 2012). The cpm values with a +1 offset were transformed to log2 space.
Assembly: hg38 with ensembl v98 annotation
Supplementary files format and content: ikohale_intCt.txt.gz is a tab delimited text file of integer count data
Supplementary files format and content: ikohale_l2cpm.txt.gz is a tab delimited text file of log2 counts (with a +1 offset) per million

source_name: Patient derived xenograft

growth_protocol: Early passage PDX tumor samples were collected after euthanization of the tumor bearing mice with carbon dioxide. Fresh tumor fragments were implanted subcutaneously in 6 to 8 week-old female NSG (NOD.Cg-Prkdc scid Il2rg tm1Wjl/SzJ) mice for drug treatments.

extract_protocol:
Pulverized frozen tissues were homogenized in TRIzol reagent, and RNA was extracted using Direct-zol-96 RNA kit (Zymo Research) according to manufacturer’s protocol.
High Throughput 3'DGE

treatment_protocol: Once the tumors were palpable and reached approximately 3mm in diameter, mice were randomized into four groups and treated with either vehicle control, paclitaxel (12.5 mg/kg, i.p. twice a week), dasatinib (12.5mg/kg, i.p. 5 days/week), or in combination for three weeks. Tumor growth was monitored by measuring with a caliper twice weekly. Mice were euthanized when met the euthanization criteria. Tumors were resected and flash frozen in liquid nitrogen and stored at -80C.

value: Patient derived xenograft

value: Primary triple negative breast cancer

value: Dasatinib+Paclitaxel


title: No ERN2, control rep03

description: Column 4

value: No doxycyline, control


title: No ERN2, control rep02

description: Column 3


title: Low ERN2, stress rep03

description: Column 13

value: 10 ng/mL doxycyclin 24 hr, 200 nM thapsigargin 3 hr


title: Low ERN2, control rep03

description: Column 10

value: 10 ng/mL doxycyclin 24 hr, control


title: Low ERN2, control rep02

description: Column 9


title: No ERN2, stress rep01

description: Column 5

value: No doxycyline, 200 nM thapsigargin 3 hr


title: No ERN2, stress rep03

description: Column 7


title: Low ERN2, control rep01

description: Column 8


title: Low ERN2, stress rep01

description: Column 11


title: Low ERN2, stress rep02

description: Column 12


title: No ERN2, stress rep02

description: Column 6


title: BTY25 Dasatinib+Paclitaxel treated replicate 4

description:
BJ50.PD.4
ikohale_intCt.txt.gz
ikohale_l2cpm.txt.gz


title: SPBC1685.01_B7_rep4

description:
Knock-out strain
3' mRNA-Seq


title: SPBC16A3.17c_B8_rep4

description:
Knock-out strain
3' mRNA-Seq


title: SPAC664.15_B5_rep4

description:
Knock-out strain
3' mRNA-Seq


title: SPBC16C6.02c_B9_rep4

description:
Knock-out strain
3' mRNA-Seq


title: SPBC1604.08c_B6_rep4

description:
Knock-out strain
3' mRNA-Seq


title: No ERN2, control rep01

description: Column 2


title: NIH3T3-30ng/mL TNF-α-Mid-Rep_1

value: RelA-/- Rela-DsRed 3T3s

value: 30 ng/mL TNF-alpha (source)


title: NIH3T3-30ng/mL TNF-α-Near-Rep_2


title: NIH3T3-30ng/mL TNF-α-Near-Rep_3


title: NIH3T3-30ng/mL TNF-α-Near-Rep_1


title: SPAC637.07_B4_rep4

description:
Knock-out strain
3' mRNA-Seq


title: SPBP22H7.08_A11_rep4

description:
Knock-out strain
3' mRNA-Seq


title: SPAC57A7.12_B3_rep4

description:
Knock-out strain
3' mRNA-Seq


title: SPAC22F8.11_A12_rep4

description:
Knock-out strain
3' mRNA-Seq


title: SPAC3H5.12c_B2_rep4

description:
Knock-out strain
3' mRNA-Seq


title: SPAC23A1.07_B1_rep4

description:
Knock-out strain
3' mRNA-Seq


title: CPT_5

city: Hunan

first: Yang

last: Ge

address: No. 86, Ziyuan Road, Changsha City, Hunan Province

institute: Hunan Children’s Hospital, Hunan

data_processing:
StringTie was adopted to assess expression levels for mRNAs and lncRNAs by calculating FPKM.
|log2(fold change)|≥1 with p value<0.05 were considered the differentially expressed mRNAs and lncRNAs by R package edgeR (bioconductor.org/packages/release/bioc/html/edgeR.html/) or DESeq2(www.bioconductor.org/packages/release/bioc/html/DESeq2.html).
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample, or tab-delimited text files include FPKM values for each Sample

source_name: periosteal-derived mesenchymal stromal cells

growth_protocol: The cells were cultured in DMEM medium supplement with 10% fetal bovine serum and maintained in a condition of 37˚C and 5% CO2.

extract_protocol:
Trizol reagent (Invitrogen, Carlsbad, CA, USA) were used to extract total RNA from cells according the instruction.
Ten sample’s Libraries were sequenced with on an Illumina HiSeq4000 with 2×75bp paired end reads.

treatment_protocol: untreated

value: mesenchymal stromal cells

value: CPT

value: untreated


title: CPT_4

value: periosteal-derived mesenchymal stromal cells


title: CPT_3


title: CPT_2


title: BTY25 Dasatinib+Paclitaxel treated replicate 3

description:
BJ50.PD.3
ikohale_intCt.txt.gz
ikohale_l2cpm.txt.gz


title: SPBC577.02_A10_rep4

description:
Knock-out strain
3' mRNA-Seq


title: SPBC11C11.07_A9_rep4

description:
Knock-out strain
3' mRNA-Seq


title: SPAPB17E12.05_A8_rep4

description:
Knock-out strain
3' mRNA-Seq


title: SPAC25G10.06_A6_rep4

description:
Knock-out strain
3' mRNA-Seq


title: CPT_1


title: SPAC3G6.02_A7_rep4

description:
Knock-out strain
3' mRNA-Seq


title: BTY25 Dasatinib+Paclitaxel treated replicate 2

description:
BJ50.PD.2
ikohale_intCt.txt.gz
ikohale_l2cpm.txt.gz


title: BTY25 Dasatinib+Paclitaxel treated replicate 1

description:
BJ50.PD.1
ikohale_intCt.txt.gz
ikohale_l2cpm.txt.gz


title: Control_5

value: Control


title: Control_4


title: BTY25 Paclitaxel treated replicate 2

description:
BJ50.P.2
ikohale_intCt.txt.gz
ikohale_l2cpm.txt.gz

value: Paclitaxel


title: BTY25 Paclitaxel treated replicate 3

description:
BJ50.P.3
ikohale_intCt.txt.gz
ikohale_l2cpm.txt.gz


title: BTY25 Paclitaxel treated replicate 1

description:
BJ50.P.1
ikohale_intCt.txt.gz
ikohale_l2cpm.txt.gz


title: Control_2


title: SPBC660.11_H12_rep3

description:
Knock-out strain
3' mRNA-Seq


title: SPAC23A1.11_A5_rep4

description:
Knock-out strain
3' mRNA-Seq


title: BTY25 Dasatinib treated replicate 5

description:
BJ50.D.5
ikohale_intCt.txt.gz
ikohale_l2cpm.txt.gz

value: Dasatinib


title: SPAC14C4.16_A3_rep4

description:
Knock-out strain
3' mRNA-Seq


title: SPAC1527.02_A4_rep4

description:
Knock-out strain
3' mRNA-Seq


title: wt1_A1_rep4

description:
Knock-out strain
3' mRNA-Seq


title: Control_3


title: BTY25 Dasatinib treated replicate 4

description:
BJ50.D.4
ikohale_intCt.txt.gz
ikohale_l2cpm.txt.gz


title: SPAC22F3.09c_H11_rep3

description:
Knock-out strain
3' mRNA-Seq


title: SPBC530.07c_H10_rep3

description:
Knock-out strain
3' mRNA-Seq


title: Control_1


title: SPAC3A12.13c_H8_rep3

description:
Knock-out strain
3' mRNA-Seq


title: SPAC4G9.16c_H7_rep3

description:
Knock-out strain
3' mRNA-Seq


title: wt2_A2_rep4

description:
Knock-out strain
3' mRNA-Seq


title: SPCC5E4.07_H9_rep3

description:
Knock-out strain
3' mRNA-Seq


title: BTY25 Dasatinib treated replicate 3

description:
BJ50.D.3
ikohale_intCt.txt.gz
ikohale_l2cpm.txt.gz


title: BTY25 Dasatinib treated replicate 2

description:
BJ50.D.2
ikohale_intCt.txt.gz
ikohale_l2cpm.txt.gz


title: BTY25 Vehicle treated replicate 4

description:
BJ50.C.4
ikohale_intCt.txt.gz
ikohale_l2cpm.txt.gz

value: Vehicle


title: BTY25 Vehicle treated replicate 5

description:
BJ50.C.5
ikohale_intCt.txt.gz
ikohale_l2cpm.txt.gz

value: Patient derived xenograft


title: SPCC594.05c_H2_rep3

description:
Knock-out strain
3' mRNA-Seq


title: SPBPB10D8.06c_H3_rep3

description:
Knock-out strain
3' mRNA-Seq


title: SPCC285.09c_G11_rep3

description:
Knock-out strain
3' mRNA-Seq


title: SPCC4G3.11_H4_rep3

description:
Knock-out strain
3' mRNA-Seq


title: SPAC29B12.04_H6_rep3

description:
Knock-out strain
3' mRNA-Seq


title: SPAC20G4.07c_G12_rep3

description:
Knock-out strain
3' mRNA-Seq


title: SPCC320.12_H5_rep3

description:
Knock-out strain
3' mRNA-Seq


title: BTY25 Vehicle treated replicate 3

description:
BJ50.C.3
ikohale_intCt.txt.gz
ikohale_l2cpm.txt.gz

value: Primary triple negative breast cancer


title: BTY25 Vehicle treated replicate 2

description:
BJ50.C.2
ikohale_intCt.txt.gz
ikohale_l2cpm.txt.gz


title: BTY25 Vehicle treated replicate 1

description:
BJ50.C.1
ikohale_intCt.txt.gz
ikohale_l2cpm.txt.gz


title: BTY25 Dasatinib treated replicate 1

description:
BJ50.D.1
ikohale_intCt.txt.gz
ikohale_l2cpm.txt.gz


title: SPCC1259.01c_H1_rep3

description:
Knock-out strain
3' mRNA-Seq


title: BTY10 Dasatinib+Paclitaxel treated replicate 4

description:
BJ41.PD.4
ikohale_intCt.txt.gz
ikohale_l2cpm.txt.gz

value: Dasatinib+Paclitaxel


title: BTY10 Dasatinib+Paclitaxel treated replicate 3

description:
BJ41.PD.3
ikohale_intCt.txt.gz
ikohale_l2cpm.txt.gz


title: BTY10 Dasatinib+Paclitaxel treated replicate 1

description:
BJ41.PD.1
ikohale_intCt.txt.gz
ikohale_l2cpm.txt.gz


title: BTY10 Dasatinib+Paclitaxel treated replicate 2

description:
BJ41.PD.2
ikohale_intCt.txt.gz
ikohale_l2cpm.txt.gz


title: BTY10 Paclitaxel treated replicate 4

description:
BJ41.P.4
ikohale_intCt.txt.gz
ikohale_l2cpm.txt.gz


title: SPAC3H5.10_F6_rep3

description:
Knock-out strain
3' mRNA-Seq


title: SPAC31A2.13c_F4_rep3

description:
Knock-out strain
3' mRNA-Seq


title: SPBC4F6.10_F5_rep3

description:
Knock-out strain
3' mRNA-Seq


title: SPCC576.12c_F3_rep3

description:
Knock-out strain
3' mRNA-Seq


title: BTY10 Paclitaxel treated replicate 3

description:
BJ41.P.3
ikohale_intCt.txt.gz
ikohale_l2cpm.txt.gz


title: SPAC17A5.02c_F1_rep3

description:
Knock-out strain
3' mRNA-Seq


title: SPAC1952.05_F2_rep3

description:
Knock-out strain
3' mRNA-Seq


title: BTY10 Paclitaxel treated replicate 2

description:
BJ41.P.2
ikohale_intCt.txt.gz
ikohale_l2cpm.txt.gz


title: BTY10 Dasatinib treated replicate 4

description:
BJ41.D.4
ikohale_intCt.txt.gz
ikohale_l2cpm.txt.gz


title: BTY10 Dasatinib treated replicate 3

description:
BJ41.D.3
ikohale_intCt.txt.gz
ikohale_l2cpm.txt.gz


title: BTY10 Dasatinib treated replicate 2

description:
BJ41.D.2
ikohale_intCt.txt.gz
ikohale_l2cpm.txt.gz


title: SPAC18G6.10_F12_rep3

description:
Knock-out strain
3' mRNA-Seq


title: SPBC887.02_F11_rep3

description:
Knock-out strain
3' mRNA-Seq


title: SPBC25H2.11c_F7_rep3

description:
Knock-out strain
3' mRNA-Seq


title: SPBC3E7.05c_G6_rep3

description:
Knock-out strain
3' mRNA-Seq


title: SPCC1393.05_F8_rep3

description:
Knock-out strain
3' mRNA-Seq


title: SPBC365.03c_F10_rep3

description:
Knock-out strain
3' mRNA-Seq


title: SPBC354.03_G5_rep3

description:
Knock-out strain
3' mRNA-Seq


title: SPBC29A10.16c_F9_rep3

description:
Knock-out strain
3' mRNA-Seq


title: SPBC1105.14_G3_rep3

description:
Knock-out strain
3' mRNA-Seq


title: SPBC543.07_G8_rep3

description:
Knock-out strain
3' mRNA-Seq


title: SPAPB2B4.04c_G2_rep3

description:
Knock-out strain
3' mRNA-Seq


title: SPCC1672.12c_G10_rep3

description:
Knock-out strain
3' mRNA-Seq


title: SPBC3H7.03c_G9_rep3

description:
Knock-out strain
3' mRNA-Seq


title: SPBC405.07_G7_rep3

description:
Knock-out strain
3' mRNA-Seq


title: SPBC16C6.11_G4_rep3

description:
Knock-out strain
3' mRNA-Seq


title: BTY10 Paclitaxel treated replicate 1

description:
BJ41.P.1
ikohale_intCt.txt.gz
ikohale_l2cpm.txt.gz


title: BTY10 Dasatinib treated replicate 1

description:
BJ41.D.1
ikohale_intCt.txt.gz
ikohale_l2cpm.txt.gz


title: SPBC21C3.12c_E11_rep3

description:
Knock-out strain
3' mRNA-Seq


title: SPAC9E9.09c_E9_rep3

description:
Knock-out strain
3' mRNA-Seq


title: SPCC24B10.14c_E8_rep3

description:
Knock-out strain
3' mRNA-Seq


title: SPBC23E6.01c_E12_rep3

description:
Knock-out strain
3' mRNA-Seq


title: SPAPB1E7.02c_E10_rep3

description:
Knock-out strain
3' mRNA-Seq


title: BTY10 Dasatinib+Paclitaxel treated replicate 5

description:
BJ41.PD.5
ikohale_intCt.txt.gz
ikohale_l2cpm.txt.gz


title: SPAC22H12.02_G1_rep3

description:
Knock-out strain
3' mRNA-Seq


title: BTY10 Vehicle treated replicate 1

description:
BJ41.C.1
ikohale_intCt.txt.gz
ikohale_l2cpm.txt.gz


title: BTY10 Vehicle treated replicate 4

description:
BJ41.C.4
ikohale_intCt.txt.gz
ikohale_l2cpm.txt.gz


title: BTY10 Vehicle treated replicate 2

description:
BJ41.C.2
ikohale_intCt.txt.gz
ikohale_l2cpm.txt.gz


title: BTY10 Vehicle treated replicate 5

description:
BJ41.C.5
ikohale_intCt.txt.gz
ikohale_l2cpm.txt.gz


title: BTY10 Vehicle treated replicate 3

description:
BJ41.C.3
ikohale_intCt.txt.gz
ikohale_l2cpm.txt.gz


title: BTY09 Dasatinib+Paclitaxel treated replicate 2

description:
BJ08.PD.2
ikohale_intCt.txt.gz
ikohale_l2cpm.txt.gz


title: BTY09 Dasatinib+Paclitaxel treated replicate 4

description:
BJ08.PD.4
ikohale_intCt.txt.gz
ikohale_l2cpm.txt.gz


title: BTY09 Dasatinib+Paclitaxel treated replicate 3

description:
BJ08.PD.3
ikohale_intCt.txt.gz
ikohale_l2cpm.txt.gz


title: SPBC15D4.10c_D1_rep3

description:
Knock-out strain
3' mRNA-Seq


title: SPBC25H2.15_E2_rep3

description:
Knock-out strain
3' mRNA-Seq


title: SPBC14C8.17c_E1_rep3

description:
Knock-out strain
3' mRNA-Seq


title: SPAC8C9.06c_C12_rep3

description:
Knock-out strain
3' mRNA-Seq


title: SPAC17A2.13c_D6_rep3

description:
Knock-out strain
3' mRNA-Seq


title: SPCC757.09c_E3_rep3

description:
Knock-out strain
3' mRNA-Seq


title: SPAC1783.07c_C11_rep3

description:
Knock-out strain
3' mRNA-Seq


title: SPCC736.08_C10_rep3

description:
Knock-out strain
3' mRNA-Seq


title: SPAC8E11.10_D9_rep3

description:
Knock-out strain
3' mRNA-Seq


title: SPCC613.06_D12_rep3

description:
Knock-out strain
3' mRNA-Seq


title: SPBC3B9.13c_E5_rep3

description:
Knock-out strain
3' mRNA-Seq


title: SPBP35G2.08c_D5_rep3

description:
Knock-out strain
3' mRNA-Seq


title: SPBC947.02_D2_rep3

description:
Knock-out strain
3' mRNA-Seq


title: SPBC839.13c_E7_rep3

description:
Knock-out strain
3' mRNA-Seq


title: SPBC3E7.15c_D11_rep3

description:
Knock-out strain
3' mRNA-Seq


title: SPBC577.15c_E6_rep3

description:
Knock-out strain
3' mRNA-Seq


title: SPAC4A8.09c_E4_rep3

description:
Knock-out strain
3' mRNA-Seq


title: SPBC713.07c_D4_rep3

description:
Knock-out strain
3' mRNA-Seq


title: SPAC3A11.07_D3_rep3

description:
Knock-out strain
3' mRNA-Seq


title: SPBC28F2.10c_D10_rep3

description:
Knock-out strain
3' mRNA-Seq


title: SPAC29A4.20_D8_rep3

description:
Knock-out strain
3' mRNA-Seq


title: SPAC17H9.19c_D7_rep3

description:
Knock-out strain
3' mRNA-Seq


title: BTY09 Dasatinib+Paclitaxel treated replicate 1

description:
BJ08.PD.1
ikohale_intCt.txt.gz
ikohale_l2cpm.txt.gz


title: SPCC663.04_C9_rep3

description:
Knock-out strain
3' mRNA-Seq


title: Nov16Batch, WT, GM_p49, NSC

first: Serkan

last: Erdin

address: 185 Cambridge Street

department: Center for Genomic Medicine

institute: Massachusetts General Hospital

description:
batch Nov16
16p11.2_KCTD13_cellLines_counts.txt.gz

data_processing:
Each bulk RNAseq library of mouse sample was aligned to mouse reference genome GRCm38 version 83 using STAR aligner. Expression counts for each sample was also generated by STAR aligner.
Differential expression analysis was performed by DESeq2 + SVA pipeline, whereas co-expression analysis was performed by WGCNA.
Each bulk RNAseq library of human cell line sample was aligned to human reference genome GRCh37 version 75 using STAR aligner. Expression counts for each sample was also generated by STAR aligner.
For scRNA, raw paired-end reads were aligned by Cellranger (v3.0.2) against human transcriptome GRCh38.92.
For each scRNA sample, its feature list, barcode list and count matrix were then read by Seurat (v4.0.3) into matrix. Cells with top and bottom 2.5% number of RNA molecules were filtered out.
All scRNA samples were then merged into one matrix using "merge" function in Seurat.
Assembly: single cell human reference genome GRCh38 v92; mouse reference genome for bulk RNAseq GRCm38 v83. human reference genome for bulk RNAseq GRCh37 v75.
Supplementary files format and content: "rawCounts_merged_16p_Organoid_GM08330.txt.gz" - gzipped text file for raw counts of scRNA data. Each row represents a gene while each column represents a cell. Outlier cells have been filtered out and not included.
Supplementary files format and content: "16p11.2_KCTD13_cellLines_counts.txt.gz" - gzipped tab delimited text file for raw counts of human cell line bulk RNAseq data including 16p11.2 deletion, 16p11.2 duplication and 16p11.2 wild-type NSCs and iNeurons as well as KCTD13 het del and KCTD13 wild-type iNeurons
Supplementary files format and content: "16p11.2_KCTD13_cellLines_metadata.txt" - metadata of bulk RNAseq data from human cell lines
Supplementary files format and content: "metaData_SCT_merged_16p_Organoid_GM08330.txt" - text file for scRNA meta-data.
Supplementary files format and content: "16p11.2_mouse_counts.txt.gz" - tab delimited text file for raw counts of mouse bulk RNAseq data.

growth_protocol: NSCs were maintained in PSC Neural Expansion Medium (ThermoFisher, A1647801) in humidified atmosphere with 5% CO2 at 37C; iNs were maintained in Neural Maintenance Media (Shi et al., 2012) supplemented with BDNF and NT-3 in humidified atmosphere with 5% CO2 at 37C; cerebral organoids were maintained in organoid medium (Lancaster et al., 2014) supplemented with BDNF in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
All RNA samples were extracted with Trizol reagent according to the manufacturer’s instruction (Invitrogen).
Mouse and human cell RNASeq libraries were prepared with customized version of strand specific dUTP method and TruSeq Stranded mRNA Library Kit (Illumina); scRNA-seq libraries were prepared using the Chromium Single Cell 3’ Library & Gel Bead Kit v3 (PN-1000075) according to manufacturer’s instructions (CG000183) using a Chromium Single Cell B Chip (PN-1000073) for a targeted cell recovery of 5,000 cells.
RNAseq for mouse tissues and human NSCs and iNs; single-cell RNAseq for cerebral organoids

treatment_protocol: For all CRISPR lines, Passage 7 stage NSCs were dissociated for RNA-seq; iNs were dissociated for RNA-seq on Day 24 of differentiation; For single-cell suspensions of cerebral organoids, organoids at 6 months were prepared using the Worthington Papain Dissociation System (Worthington Biochemical, LK003153).

value: NSC

value: WT

value: M


title: Nov16Batch, WT, GM_p46, NSC


title: BTY09 Dasatinib treated replicate 3

description:
BJ08.D.3
ikohale_intCt.txt.gz
ikohale_l2cpm.txt.gz


title: BTY09 Vehicle treated replicate 4

description:
BJ08.C.4
ikohale_intCt.txt.gz
ikohale_l2cpm.txt.gz


title: Nov16Batch, WT, GM_p44, iNeuron

value: Induced neuron


title: BTY09 Dasatinib treated replicate 2

description:
BJ08.D.2
ikohale_intCt.txt.gz
ikohale_l2cpm.txt.gz


title: Nov16Batch, WT, GM_FACS3, NSC


title: Nov16Batch, WT, GM_p46, iNeuron


title: BTY09 Dasatinib treated replicate 1

description:
BJ08.D.1
ikohale_intCt.txt.gz
ikohale_l2cpm.txt.gz


title: Nov16Batch, WT, GM_p44, NSC


title: BTY09 Dasatinib treated replicate 4

description:
BJ08.D.4
ikohale_intCt.txt.gz
ikohale_l2cpm.txt.gz


title: Nov16Batch, WT, GM_p49, iNeuron


title: BTY09 Vehicle treated replicate 3

description:
BJ08.C.3
ikohale_intCt.txt.gz
ikohale_l2cpm.txt.gz


title: BTY09 Vehicle treated replicate 2

description:
BJ08.C.2
ikohale_intCt.txt.gz
ikohale_l2cpm.txt.gz


title: BTY09 Vehicle treated replicate 1

description:
BJ08.C.1
ikohale_intCt.txt.gz
ikohale_l2cpm.txt.gz


title: Nov16Batch, WT, GM_FACS2, NSC


title: Nov16Batch, WT, GM_FACS2_iNeuron


title: SPBC365.10_C5_rep3

description:
Knock-out strain
3' mRNA-Seq


title: SPBC776.01_C6_rep3

description:
Knock-out strain
3' mRNA-Seq


title: SPCC24B10.08c_C8_rep3

description:
Knock-out strain
3' mRNA-Seq


title: SPBC776.17_C7_rep3

description:
Knock-out strain
3' mRNA-Seq


title: BTY14 Dasatinib+Paclitaxel treated replicate 3

description:
BJ02.PD.3
ikohale_intCt.txt.gz
ikohale_l2cpm.txt.gz