title: shTRPS1_ctrl_MTA2_2 [ChIP-seq]

status: Public on Oct 21 2018

city: Boston

first: Kornelia

last: Polyak

state: MA

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description: ChIP-seq for MTA2 in HCC3153 cells in control condition.

data_processing:
RNA-Seq: Illumina Casava1.7 software used for basecalling.
RNA-seq: Quality check was performed using the Broad Firehose pipeline (screen data) and VIPER [https://bitbucket.org/cfce/viper/src/master/] (validation data).
RNA-Seq: The datasets were aligned to the human reference GRCh37/hg19 genome using the STAR RNA-Seq aligner in Firehose and VIPER using the default parameters.
RNA-Seq: The read counts for individual genes were generated using the 'RNASeqMetricsSetSummary' module of Firehose and VIPER using the default parameters and the hg19 Ensembl and RefSeq annotation files.
Genome_build: hg19
ChIP-Seq: Illumina Casava1.7 software used for basecalling
ChIP-Seq: Read quality check was performed using the chilin pipeline (https://github.com/cfce/chilin).
ChIP-Seq: Reads were aligned to GRCh37/hg19 using BWA in chilin.
ChIP-Seq: Peak calling was performed using MACS2 in chilin.
Supplementary_files_format_and_content: RNA-Seq: Tab-separated file of the raw read counts of the screened samples or each validation samples for each gene.
Supplementary_files_format_and_content: ChIP-Seq: Bigwig (bw) files generated using MACS2 in the chilin pipeline.

growth_protocol: HCC3153 cells were cultured in RPMI1640 supplemented with 10% FBS and 1% penicillin/streptomycin. MDA-IBC3 and SUM159 cells were cultured in a 1:1 mixture of DMEM/F12 supplemented with 10% FBS and 1% penicillin/streptomycin and Human Mammary Epithelial Cell Medium. For genomic profiling, 59 cell lines were grown in corresponding media described in Table S1.

extract_protocol:
For RNA-seq total RNA was extracted using the RNeasy Kit (Qiagen). For ChIP-seq 5-8 × 10^6 cells were fixed by adding 1:20 volume of fixing buffer (11% paraformaldehyde (Electron Microscopy Sciences, cat# 15714), 0.1M NaCl, 1mM EDTA pH 8.0, 50mM HEPES pH 8.0) directly to the tissue culture medium for 10 min at room temperature for histone modification ChIPs or at 37°C for transcription factor ChIPs and subsequently quenched by glycine. Cells were lysed in lysis buffer (50mM HEPES pH 8.0, 140mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, and 0.25% Triton X-100) for 10 min at 4°C. Nuclei were pelleted and washed in wash buffer (10mM Tris-HCl pH 8.0, 200mM NaCl, 1mM EDTA, 0.5mM EGTA) for 10 min at 4°C and then pelleted and resuspended shearing buffer (10mM Tris-HCl pH 7.4, 1mM EDTA, 0.1% SDS, 1% Triton X-100, 0.1% sodium deoxycholate, 0.25% sarkosyl, 1mM DTT) and sonicated in a Covaris sonicator. Debris was removed by centrifugation (5 min at 10,000g) and 970µl of the lysate was mixed with 30µl of 5M NaCl. Chromatin was pre-cleared for 1 hr at 4°C with 40µl of Dynabeads Protein G (LifeTechnologies, cat# 10003D) washed in 0.5% BSA in PBS. Lysates were then incubated with corresponding primary antibody overnight at 4°C. Complexes were precipitated by incubation with 40µl of washed Dynabeads Protein G for 2 hrs at 4°C, washed with low salt wash buffer (20mM Tris-HCl pH 8.0, 150mM NaCl, 2mM EDTA pH 8.0, 1% Triton X-100, 0.1% SDS), high salt wash buffer (20mM Tris-HCl pH 8.0, 500mM NaCl, 2mM EDTA pH 8.0, 1% Triton X-100, 0.1% SDS), LiCl wash buffer (10mM Tris-HCl pH 8.0, 250mM LiCl, 1mM EDTA pH 8.0, 1% NP40, 1% sodium deoxycholate), and twice with TE pH 8.0. DNA was eluted in elution buffer (100mM NaHCO3, 1% SDS) by incubating overnight at 65°C, followed by 30 min treatment with RNase A at 37°C and 2 hrs treatment with proteinase K at 55°C. DNA was purified with phenol-chloroform extraction and precipitated with isopropanol. For methylation analysis, DNA was isolated using QIAamp DNA Mini kit (QIAGEN, cat# 51304). DNA methylation profiling was carried out on Infinium HumanMethylation450K BeadChip arrays (Illumina, discontinued) at the Harvard Medical School-Partners HealthCare Center for Genetics and Genomics.
RNA-seq libraries were prepared using Illumina TruSeq Stranded mRNA sample preparation kits from 500 ng of purified total RNA according to the manufacturer’s protocol. The finished dsDNA libraries were quantified by Qubit fluorometer, Agilent TapeStation 2200, and RT-qPCR using the Kapa Biosystems library quantification kit according to manufacturer’s protocols. ChIP-seq libraries were prepared using the Rubicon ThruPLEX DNA-seq Kit from purified ChIP DNA or input DNA according to the manufacturer’s protocol.

treatment_protocol: Were indicated as "dox+", cells were treated with 100 ng/ml of doxycycline.

tag: hairpin

tag: antibody info

value: abcam, cat# ab8106, lot GR280090-7


title: J82C3

status: Public on Oct 22 2018

type: RNA

city: Madrid

first: Monica

last: Martinez-Fernandez

address: Avda Complutense 40

country: Spain

institute: CIEMAT

description: J82 cell line control 3

hyb_protocol: Following fragmentation, 5,5 ug of fragmented and labeled ss-DNA were hybridized for 16 hr at 45ºC at 60 rpm on Hybridization Oven 640 de Affymetrix. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneArray Scanner 7G de Affymetrix

data_processing: Expression data were normalized, background-and batch corrected using the Guanine Cytosine Count Normalization (GCCN) and Signal Space Transformation (SST), and prior to summarizing using the Robust Multi-Array Average (RMA) algorithm implemented in the Affymetrix Expression Console software. In order to combine the different microarray data sets, possible batch effects were corrected by using the Bioconductor Combat package in R environment (Johnson et al., 2007)

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: J82 cell line control

label_protocol: cRNA is converted to biotinylated sense-strand DNA prepared according to the standard Affymetrix protocol from 12 ngs total RNA (GeneChip Whole Trasncript WT Expression Arrays, Affymetrix).

growth_protocol: The bladder cancer cell lines were maintained in Dulbecco's Modified Eagle Medium GlutaMAX™ (Gibco-BRL Life Technologies) with 10% fetal bovine serum (Hyclone) and 1% antibiotic-antimycotic (Gibco-BRL Life Technologies) at 37°C in a humidified atmosphere of 5% CO2.

extract_protocol: Extraction of total RNA was performed using miRNeasy Mini Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Control (PBS-treated) and palbociclib-treated (IC50) RT112, J82 and 5637 cells, were analyzed. Cell pool transcriptomes were obtained from 3 different p100 dishes grown to 70-80% confluence.

tag: cell line

tag: cell type

value: Bladder cell line

tag: treated with

value: PBS (control)


title: pooled KD patient at convalescent phase 3

city: Kaohsiung

first: Sung-Chou

last: Li

state: Kaohsiung

address: No.386, Dazhong 1st Rd

department: Department of Medical Education and Research

country: Taiwan

institute: Kaohsiung Veterans General Hospital

hyb_protocol: Samples were hybridized with GeneChip Human Transcriptome 2.0 ST Arrays (Affymetrix) and scanned with the GeneChip Scanner 3000 7G in Genomics and Proteomics Core lab., Kaohsiung Chang Gung memorial Hospital, Taiwan.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing:
The raw data of HTA 2.0 chips were first subject to quality control examination as suggested by Affymetrix manuals. And, the chips passing the quality control criteria were then analyzed with Partek.
RNA expression value derived from Expression Console software; gene-level analysis

source_name: pooled sample

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT PLUS Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Whole blood samples were collected from the subjects, followed by red blood cell (RBC) lysis with RBC lysis buffer to enrich total white blood cells (WBCs).

extract_protocol: We used mirVanaTM miRNA Isolation Kit (Ambion, CA, USA) to extract RNA following the manufacturer’s protocols. The concentration of RNA was measured with NanoDrop 2000 spectrophotometer (Thermo scientific, MA, USA). All RNA samples passed the criterion of RIN≥ 7 assessed with Agilent 2100 Bioanalyzer (Agilent, CA, USA).

tag: disease state

value: convalescent-phase KD

value: white blood cell


title: pooled healthy control 3

value: control


title: shTRPS1_ctrl_MTA2_1 [ChIP-seq]

type: SRA

country: USA

library_source: genomic

molecule: genomic DNA

tag: antibody


title: pooled KD patient at convalescent phase 1


title: pooled KD patient at acute phase 3

value: acute-phase KD


title: pooled KD patient at acute phase 2


title: pooled KD patient at acute phase 1


title: J82C1

description: J82 cell line control 1


title: pooled healthy control 1


title: pooled KD patient at convalescent phase 2


title: shTRPS1_ctrl_HDAC2_2 [ChIP-seq]

description: ChIP-seq for HDAC2 in HCC3153 cells in control condition.


title: pooled healthy control 2


title: shTRPS1_ctrl_HDAC2_1 [ChIP-seq]


title: genomic DNA from total WBC of convalescent phase KD patient 9

type: genomic

description:
genomic DNA from total WBC of convalescent phase KD patient
200069280179_R03C02
KD09-conv

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
We had 36 DNA samples examined with M450K chips, including 12 HC, 12 KD at acute phase and 12 KD at convalescent phase samples. For each sample, the Grn.idat and Red.idat raw files were provided. In addition, the beta matrix table is also available. We included only the CpG markers with cg accession number, e.g. cg00000029, for analysis in our study.
The raw Gen.idat and Red.idat files were input into Illumina's GenomeStudio program to output the files specific for Partek. During this step, each CpG marker's intensity and Average Beta were generated, presented as log2 transfomed.

label: Cy5 and Cy3

source_name: convalescent phase KD patient 9

label_protocol: Standard Illumina Protocol

extract_protocol: We used QIAamp® DNA Blood Mini Kit (QIAGEN, CA, USA) to extract DNA following the manufacturer’s protocols.

treatment_protocol: The extracted DNA samples were bisulfite modified with EZ DNA Methylation-Lightning TM Kit (Zymo Research, Irvine, USA). Briefly, 0.5 ug of DNA was mixed with lightning conversion reagent, followed by the thermal-cycling condition: 98℃ for 8 min, 54℃ for 60 min and held at 4℃. Next, the DNA samples were loaded into spin column and mixed with M-binding buffer. After centrifuge, spin column was incubated with L-desulphonation buffer at room temperature. Finally, bisulfite modified DNA was eluted using M-elution buffer and stock at -80℃.

tag: gender

value: Female


title: genomic DNA from total WBC of convalescent phase KD patient 11

description:
genomic DNA from total WBC of convalescent phase KD patient
200069280179_R05C02
KD11-conv

source_name: convalescent phase KD patient 11


title: Prog_CM_HFN_2

city: Indianapolis

first: Keith

middle: M

last: Goldstein

state: IN

address: Lilly Corporate Center

department: Investigative Toxicology

institute: Eli Lilly & Co.

hyb_protocol: Affymetrix hyb protocol: EukGE-WS2v5_450

scan_protocol: Arrays were washed and stained with streptavidin-conjugated phycoerythrin on an Affymetrix FS450 Fluidics station. The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G.

data_processing: Data generated using Affymetrix GeneChip Command Console and Expression Console’s MAS 5.0 algorithm with all arrays scaled to 1500.

source_name: IPSC cardiomyocytes (Cellular Dynamics) cultured for 24hrs (progenitors)

label_protocol: 1ug of RNA was used for preparation of biotin-labeled targets (cRNA) using modified MessageAmp™ -based protocols (Ambion Inc.), fragmented, and hybridized to HG-U133_plus2 microarrays (Affymetrix) according to the manufacturer’s instructions (Affymetrix).

growth_protocol: iPSC progenitor and mature cells (hepatocytes and cardiomyocytes) were purchased from Cellular Dynamics Incorporated (Madison, WI).  Cells were seeded at 0.257x10^6 cells/mL in cell culture media provided by Cellular Dynamics Incorporated for each respective cell type (R1093 for iPSC progenitors and R1007 for cardiomyocytes).  Plates for iPSC progenitors were pre-coated with 5μg/mL fibronectin.  Plates utilized for iPSC mature cardiomyocytes were pre-coated with 0.1% gelatin. iPSC progenitors were treated 24 hours post-seeding while mature cardiomyocytes and hepatocytes were allowed to fully mature for two weeks with CDI maintenance media changes every 2-3 days.

extract_protocol: TRIzol reagent (Invitrogen) followed by purification over RNeasy columns (Qiagen)

treatment_protocol: Cells were treated with compound in DMSO (1% DMSO final concentration) for 24hrs.

value: Progenitor cardiomyocytes

tag: treatment

value: 0.1uM halifuginone


title: genomic DNA from total WBC of convalescent phase KD patient 8

description:
genomic DNA from total WBC of convalescent phase KD patient
200069280179_R02C02
KD08-conv

source_name: convalescent phase KD patient 8

value: Male


title: Prog_CM_HFN_3


title: genomic DNA from total WBC of convalescent phase KD patient 12

description:
genomic DNA from total WBC of convalescent phase KD patient
200069280179_R06C02
KD12-conv

source_name: convalescent phase KD patient 12


title: genomic DNA from total WBC of convalescent phase KD patient 4

description:
genomic DNA from total WBC of convalescent phase KD patient
200069280179_R03C01
KD04-conv

source_name: convalescent phase KD patient 4


title: genomic DNA from total WBC of convalescent phase KD patient 10

description:
genomic DNA from total WBC of convalescent phase KD patient
200069280179_R04C02
KD10-conv

source_name: convalescent phase KD patient 10


title: genomic DNA from total WBC of convalescent phase KD patient 6

description:
genomic DNA from total WBC of convalescent phase KD patient
200069280179_R05C01
KD06-conv

source_name: convalescent phase KD patient 6


title: genomic DNA from total WBC of convalescent phase KD patient 5

description:
genomic DNA from total WBC of convalescent phase KD patient
200069280179_R04C01
KD05-conv

source_name: convalescent phase KD patient 5


title: genomic DNA from total WBC of convalescent phase KD patient 3

description:
genomic DNA from total WBC of convalescent phase KD patient
200069280179_R02C01
KD03-conv

source_name: convalescent phase KD patient 3


title: Prog_CM_HFN_1


title: CM_mat_Tunic_3

source_name: IPSC cardiomyocytes (Cellular Dynamics) cultured for 2 weeks (mature)

value: Mature cardiomyocytes

value: 2uM tunicamycin


title: CM_mat_HFN_3


title: CM_mat_HFN_1


title: CM_mat_HFN_2


title: genomic DNA from total WBC of convalescent phase KD patient 7

description:
genomic DNA from total WBC of convalescent phase KD patient
200069280179_R06C01
KD07-conv

source_name: convalescent phase KD patient 7


title: genomic DNA from total WBC of acute phase KD patient 12

description:
genomic DNA from total WBC of acute phase KD patient
9376538079_R04C01
KD12-acute

source_name: acute phase KD patient 12


title: genomic DNA from total WBC of acute phase KD patient 6

description:
genomic DNA from total WBC of acute phase KD patient
9376538077_R01C02
KD06-acute

source_name: acute phase KD patient 6


title: genomic DNA from total WBC of convalescent phase KD patient 1

description:
genomic DNA from total WBC of convalescent phase KD patient
200069280179_R01C02
KD01-conv

source_name: convalescent phase KD patient 1


title: genomic DNA from total WBC of acute phase KD patient 10

description:
genomic DNA from total WBC of acute phase KD patient
9376538077_R06C02
KD10-acute

source_name: acute phase KD patient 10


title: genomic DNA from total WBC of acute phase KD patient 8

description:
genomic DNA from total WBC of acute phase KD patient
9376538077_R03C02
KD08-acute

source_name: acute phase KD patient 8


title: genomic DNA from total WBC of acute phase KD patient 4

description:
genomic DNA from total WBC of acute phase KD patient
9376538077_R05C01
KD04-acute

source_name: acute phase KD patient 4


title: CM_mat_Tunic_2


title: 16108_H1299-G1_S54_L999_R1_001

city: Duarte

first: keqiang

last: zhang

state: CA

address: 1500 East Duarte Road

department: Molecular Pharmacology

institute: City of Hope National Medical Center

description: Total RNA was extracted at 72h posttransfection of G9a siRNA 1

library_source: transcriptomic

data_processing:
Illumina Casava1.8 software used for basecalling. Raw short sequence fragments were accepted if they passed the quality filtering parameters used in the Illumina GA Pipeline GERALD stage.
Sequenced reads were mapped to hg19 whole genome using tophat-v2.0.8b
Aligned reads was normalized by edgeR bioconductor package and outputed as normalized counts file
Genome_build: Genome Reference Consortium GRCh37
Supplementary_files_format_and_content: text file with raw counts

source_name: Lung

growth_protocol: Cells were routinely cultured in DMEM/RPMI medium with 10% FBS and  1% PenStrep (100 U/mL )

extract_protocol:
RNA extracted with the RNeasy Mini Kit (Qiagen).
Transcriptome libraries were constructed with TruSeq RNA Sample Preparation Kit V2  (Illumia, San Diego, USA) with minor modifications.

treatment_protocol: LipofectaminE RNAiMAX reagent mediated siRNA transfection/RNA interference

value: Non-small cell lung cancer

tag: sirna knockdown


title: genomic DNA from total WBC of acute phase KD patient 11

description:
genomic DNA from total WBC of acute phase KD patient
9376538079_R02C01
KD11-acute

source_name: acute phase KD patient 11


title: 16106_H1299-C1_S52_L999_R1_001

description: Total RNA was extracted at 72h posttransfection of Control siRNA 1

value: Control


description:
genomic DNA from total WBC of convalescent phase KD patient
200069280179_R01C01
KD02-conv

source_name: convalescent phase KD patient 2


title: 4C_MEF2C_recVP2_SHSY5Y_rep2

city: Gent

first: Sarah

last: Vergult

address: Corneel Heymanslaan 10

department: Department of Biomolecular Medicine

country: Belgium

institute: Ghent University

data_processing:
Base-calling was performed on the NextSeq 500 system by RTA v2.
Sequencing libraries were demultiplexed based on the presence of the viewpoint-specific reading primer sequence, which precedes the captured DNA sequence.
Captured sequences were mapped to the hg19 reference genome using Bowtie2.
For the cis chromosome, mapped read counts were summarized per DpnII restriction fragment.
4C coverage profiles were obtained by normalizing the per fragment coverage to reads per million (RPM) on the cis chromosome and smoothing the normalized coverage using the rollmean function from the R ‘zoo’ package with a window size of 21 fragments.
Genome_build: hg19
Supplementary_files_format_and_content: 4C-seq interaction profiles in bedgraph format. The file contains the normalized counts per restriction fragment after rolling-mean smoothing.

source_name: SH-SY5Y cell line

growth_protocol: Cell lines were cultured in complete RPMI 1640 medium (10%FBS, 1%P/S, 1% glutamine, 1% kanamycine). Cells were passaged every 3-4 days. We allowed at least two passages before using cells in experiments.

extract_protocol:
4C templates were prepared according to the protocol by Van de Werken et al. (Methods Enzymol., 2012). In brief, for each template 1x10^7 cells were detached, counted, resuspended and crosslinked by incubating them with 2% formaldehyde for 10 min at room temperature. Following cell lysis, crosslinked DNA was digested with 400U of DpnII restriction enzyme (NEB #R0543L) and nearby DNA fragments were ligated using 50U of T4 DNA ligase (Roche #10799009001). Ligated DNA circles were de-crosslinked overnight using proteinase K and purified with NucleoMag P-Beads (Macherey-Nagel) to obtain an intermediate 3C template. A second round of digestion and ligation, using 50U of Csp6I restriction enzyme (Thermo Scientific #ER0211), resulted in 4C templates.
Adaptor-containing reading and non-reading primers, specific to the viewpoints of interest, were designed to amplify all captured, interacting DNA fragments. For each viewpoint, 16 PCR reactions, each using 200 ng of input 4C template, were pooled. Resulting 4C sequencing libraries were purified using High Pure PCR Product Purification kit (Roche #11732676001) and QIAquick PCR Purification kit (Qiagen #28106). Approximately 15-20 different 4C sequencing libraries were pooled and sequenced simultaneously on an Illumina NextSeq 500 (single-end, 75 nt, loading concentration 1.6 pM).

tag: 4c viewpoint (vp)

value: MEF2C reciprocal VP 2

tag: assay


title: 16109_H1299-G2_S42_L999_R1_001

description: Total RNA was extracted at 72h posttransfection of G9a siRNA 2


title: Prog_CM_Thaps_3

source_name: IPSC cardiomyocytes (Cellular Dynamics) cultured for 24hrs (progenitors)

value: 1uM thapsigargin


description:
genomic DNA from total WBC of acute phase KD patient
9376538077_R05C02
KD09-acute

source_name: acute phase KD patient 9


title: genomic DNA from total WBC of acute phase KD patient 5

description:
genomic DNA from total WBC of acute phase KD patient
9376538077_R06C01
KD05-acute

source_name: acute phase KD patient 5


title: 16105_A549-G2_S51_L999_R1_001

description: Total RNA was extracted at 72h posttransfection of G9a siRNA  2


title: CM_mat_Tunic_1


title: genomic DNA from total WBC of acute phase KD patient 7

description:
genomic DNA from total WBC of acute phase KD patient
9376538077_R02C02
KD07-acute

source_name: acute phase KD patient 7


title: 16107_H1299-C2_S53_L999_R1_001

description: Total RNA was extracted at 72h posttransfection of Control siRNA 2


title: 16104_A549-G1_S50_L999_R1_001


title: Prog_CM_Thaps_2


title: genomic DNA from total WBC of acute phase KD patient 1

description:
genomic DNA from total WBC of acute phase KD patient
9376538077_R01C01
KD01-acute

source_name: acute phase KD patient 1


title: genomic DNA from total WBC of acute phase KD patient 2

description:
genomic DNA from total WBC of acute phase KD patient
9376538077_R03C01
KD02-acute

source_name: acute phase KD patient 2


title: Prog_CM_Thaps_1


title: 16103_A549-C2_S49_L999_R1_001


title: 16102_A549-C1_S48_L999_R1_001


title: genomic DNA from total WBC of acute phase KD patient 3

description:
genomic DNA from total WBC of acute phase KD patient
9376538077_R04C01
KD03-acute

source_name: acute phase KD patient 3


title: Prog_CM_Tunic_3


title: 1316Stroma

city: Houston

first: Tsz-Lun

last: Yeung

state: TX

address: 1515 Holcombe Blvd. Unit 1362

department: Gynecologic Oncology and Reproductive Medicine

institute: University of Texas MD Anderson Cancer Center

description: Gene expression data from microdissected ovarian cancer stroma

hyb_protocol: For each sample, 15 microgram of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array

scan_protocol: GeneChip Scanner 3000 (Affymetrix) was used for array scanning and data collection

data_processing: Microarray data analysis software, GeneSpring V.14.9 (Agilent Technologies Inc.) was used to perform the primary data analysis. RMA summerization algorithm was used and baseline transformation to median of all samples were performed.

label: Biotin

source_name: Microdissected ovarian cancer stroma

label_protocol: RNA samples were amplified and labeled using the two-cycle amplification protocol (Affymetrix).

extract_protocol: Frozen sections were affixed onto FRAME slides (Leica, Wetzlar, Germany), fixed in 70% alcohol and stained by 1% methyl green. Air-dried tissue sections were then taken for microdissection using a MD LMD laser microdissecting microscope (Leica). Different types of tissues were dissected and harvested. Total RNA was isolated using the RNeasy Micro kit (Qiagen).

treatment_protocol: Cancer specimens were obtained from the primary tumors of previously untreated ovarian cancer patients. All specimens were collected under protocols approved by the institutional review boards.

tag: tissue

value: Human ovarian tissue


title: Prog_CM_Tunic_1


title: Prog_CM_Tunic_2


title: pDC PU.1 ChIP-seq Rep 2

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
FASTQ files were output using standard Illumina protocols and software at the Beijing Genomics Institute (BGI).
Reads were aligned to the mouse genome using Subread 1.4.4.
Reads were assigned to genomic windows using the R package csaw version 1.4.1. The window width was set to 10 with spacing of 50bp. Single-end reads were extended directionally to make up a fragment length of 170. Windows were filtered if their count was less than 3-fold higher than background, leaving 329996 windows.
Genome_build: mm10 (NCBI build 38.1)
Supplementary_files_format_and_content: The process files are tab-delimited text files with two columns representing the genomic window coordinates and the number of reads or DNA fragments overlapping that window. The supplementary file 'WindowCounts.tsv.gz' collates the counts for all five samples of this series into one file. The supplementary file 'GenomicWindows.bed.gz' gives the coordinates of each genomic window in BED format.

organism: Mus musculus

source_name: Plasmacytoid dentritic cells

growth_protocol: Dendritic cells were generated in Flt3L culture.

extract_protocol:
10^7 cells were crosslinked 1% paraformaldehyde (Sigma-Aldrich) in PBS then lysed (1%SDS + 1mM EDTA + proteases inhibitors). Cross-linked DNA was sonicated with the Bioruptor (Diagenode). Protein G Dynabeads (Invitrogen) were incubated with 20 μg of PU.1 antibody (Santa Cruz, T-20) according to the manufacturer’s protocol. Coupled antibody was added to 100 μg of chromatin and incubated overnight at 4°C. Unbound chromatin was removed using a series of four washes. Following elution, bound chromatin was reverse cross-linked and subjected phenol/chloroform immunoprecipitation.
Libraries were prepared at the Beijing Genomic Institute (BGI) according to Illumina's instructions and standard BGI ChIP-seq protocols.

value: Plasmacytoid dentritic cells

tag: strain

tag: chip antibody

value: PU.1 antibody


title: cDC PU.1 ChIP-seq Rep 2

source_name: Conventional dendritic cells

value: Conventional dendritic cells


title: pDC PU.1 ChIP-seq Rep 1


title: genomic DNA from total WBC of healthy control 9

description:
genomic DNA from total WBC of healthy control subject
9376537157_R03C02
HC09

source_name: healthy control 9

value: white blood cell


title: CM_mat_veh_3

source_name: IPSC cardiomyocytes (Cellular Dynamics) cultured for 2 weeks (mature)

value: vehicle


title: CM_mat_Thaps_2


title: genomic DNA from total WBC of healthy control 8

description:
genomic DNA from total WBC of healthy control subject
9376537157_R02C02
HC08

source_name: healthy control 8

value: control


title: Prog_CM_Veh_3


title: Prog_CM_Veh_1


title: CM_mat_Thaps_1


title: Prog_CM_Veh_2


title: genomic DNA from total WBC of healthy control 10

description:
genomic DNA from total WBC of healthy control subject
9376537157_R04C02
HC10

source_name: healthy control 10


title: Input DNA


title: CM_mat_veh_2


title: cDC PU.1 ChIP-seq Rep 1


title: CM_mat_Thaps_3


title: MB6

status: Public on Oct 20 2018

city: Los Angeles

first: Rosane

last: Teles

state: California

address: 10833 Le Conte Ave, CHS 52-121

department: Medicine

institute: UCLA

data_processing:
Sequenced reads were demultiplexed and aligned to the human reference genome hg19 (UCSC) using TopHat (version 2.0.6) and Bowtie2 (version 2.0.2).
The HTseq package was then used to assign uniquely mapped reads to exons and genes using the gene annotation file for build hg19 from Ensembl in order to generate raw count data.
Once raw count data was generated, data normalization (RPKM) and differential expression analysis using a negative binomial model was performed in the R statistical programming environment using the DESeq (version 1.5) Bioconductor package.
Genome_build: hg19
Supplementary_files_format_and_content: 1 csv file  of RPKM values  and another csv file  for raw counts from all samples

source_name: peripheral whole blood

growth_protocol: whole blood of leprosy patients from venepuncture was collected in PAXgene® blood collection tubes (stored at -80°C)

extract_protocol:
Total RNA from whole blood was extracted and purified using the PAXgene® blood RNA kit (BD Biosciences) including on-column DNase digestion according to the manufacturers’ protocol.
Extracted RNA was quantified with Quant-iT RiboGreen RNA Assay Kit (Invitrogen) and RNA quality was assessed using the Agilent 2200 Tapestation. Total RNA was subjected to poly-A-selection to purify messenger RNA, then fragmented and converted into double stranded cDNA. Library construction was then done using TruSeq Sample Preparation Kit (Illumina) according to manufacturer’s instructions. This included the ligation of sequencing adapters containing 7 nucleotide indexes for multiplexing. Libraries were quantified using PicoGreen (Invitrogen) and quality was assessed using the Agilent 2200 Tapestation.
Library samples were pooled (6 per lane) at equimolar quantities (10uM each library) and sequenced on a HiSeq 2000 sequencer (Illumina) with 100bp single-end protocol.

treatment_protocol: whole blood of leprosy patients were collected at the time of leprosy diagnosis and/or during the first reactional episode and reaction treatment

value: whole blood

tag: donors

value: leprosy patient

tag: clinical form

value: MB


title: MB7


title: MB5


title: MB2


title: PDX D

city: Halifax

first: Paola

last: Marcato

state: Nova Scotia

address: PO Box 15000

department: Pathology

country: Canada

institute: Dalhousie University

hyb_protocol: as described in Illumina protocol

scan_protocol: as described in Illumina protocol

data_processing: Genome studio

label: Cy3, Cy5

source_name: patient-derived xenograft, human cells

label_protocol: as described in Illumina protocol

growth_protocol: In vivo: female NOD-scid mice

extract_protocol: PureLink genomic DNA kit

value: female


title: MB1


title: genomic DNA from total WBC of healthy control 12

description:
genomic DNA from total WBC of healthy control subject
9376537157_R06C02
HC12

source_name: healthy control 12

value: Male


title: PB8

value: PB


title: PB7


title: PB5


title: MB3


title: PB4


title: PB3


title: genomic DNA from total WBC of healthy control 7

description:
genomic DNA from total WBC of healthy control subject
9376537157_R01C02
HC07

source_name: healthy control 7

value: Female


title: genomic DNA from total WBC of healthy control 5

description:
genomic DNA from total WBC of healthy control subject
9376537157_R05C01
HC05

source_name: healthy control 5


title: PDX C


title: genomic DNA from total WBC of healthy control 11

description:
genomic DNA from total WBC of healthy control subject
9376537157_R05C02
HC11

source_name: healthy control 11


title: DD -9

value: Treatment


title: PB2


title: DD -7

value: Type 1 R


title: CM_mat_veh_1

value: Mature cardiomyocytes


title: genomic DNA from total WBC of healthy control 3

description:
genomic DNA from total WBC of healthy control subject
9376537157_R03C01
HC03

source_name: healthy control 3


title: DD -4


title: BM-046-4


title: BMS-MB-38-9


title: genomic DNA from total WBC of healthy control 1

description:
genomic DNA from total WBC of healthy control subject
9376537157_R01C01
HC01

source_name: healthy control 1


title: BMS-MB-36-7


title: BMS-MB-36-9


title: BMS-MB-81-7

value: Type 2 R


title: BMS-MB-38-7


title: PB6


title: MGL-02-MB-006-9


title: MGL-02-MB-006-7


title: MGL-02-MB-042-9


title: BMS-MB-81-4


title: MGL-02-MB-032-7


title: BMS-MB-36-4


title: BMS-MB-38-4


title: MGL-02-MB-042-7


title: MGL-02-MB-003-7


title: genomic DNA from total WBC of healthy control 4

description:
genomic DNA from total WBC of healthy control subject
9376537157_R04C01
HC04

source_name: healthy control 4


title: MB4


title: genomic DNA from total WBC of healthy control 2

description:
genomic DNA from total WBC of healthy control subject
9376537157_R02C01
HC02

source_name: healthy control 2


title: BMS-MB-81-9


title: genomic DNA from total WBC of healthy control 6

description:
genomic DNA from total WBC of healthy control subject
9376537157_R06C01
HC06

source_name: healthy control 6


title: MGL-02-MB-042-4


title: MGL-02-MB-032-4


title: MGL-02-MB-006-4


title: MB8


title: MGL-02-MB-003-9


title: MGL-02-MB-032-9


title: MGL-01-Rx-038-9


title: MGL-01-Rx-034-9


title: MGL-01-Rx-029-9


title: MGL-01-Rx-022-9


title: MGL-01-Rx-013-9


title: MGL-01-Rx-038-7


title: MGL-01-Rx-022-7


title: MGL-01-Rx-013-7


title: MGL-01-Rx-029-7


title: MGL-01-MB-034-4


title: MGL-01-MB-029-4


title: MGL-01-MB-022-4


title: MGL-01-MB-038-4


title: MGL-01-MB-013-4


title: MGL-02-MB-003-4


title: BM-046-9


title: MGL-01-Rx-034-7


title: FERS105_Wfdc1

city: Baltimore

first: Amir

last: Rattner

state: MD - Maryland

address: 725 North Wolfe St.

institute: Johns Hopkins University

description: polysomes ~50ug, bait ~5ml

data_processing:
Library strategy: ACAP-seq
RNAseq reads were aligned to the GRCm38/mm10 mouse genome using the RSEM-1.3.0 program with the command ~/RSEM-1.3.0/rsem-calculate-expression -p 20 --bowtie2 --bowtie2-path ~/bowtie2-2.2.9 --estimate-rspd --append-names --output-genome-bam --sort-bam-by-coordinate
Bigwig files for visualization on the IGV browser were produced using the DeepTool program bamCoverage, with the command bamCoverage -p 20 -bs 1 —normalizeUsingRPKM
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

source_name: polysomal RNA

growth_protocol: mice were housed in our animal facility with 12 h light/dark cycles and food ab libitum. Animals were used for analysis in accordance with protocols approved by the Institutional Animal Care and Use Committee

extract_protocol:
Polysomes were extracted from frozen post natal day 1 mouse brain or from testis and purified on a sucrose density shelf.
Polysomes were captured with bait-decorated magnetic beads. Captured RNA was extracted and used for sequencing library preparation.
Bar-coded libraries for NextGen sequencing (Illumina) were prepared using the Ovation Single Cell RNAseq Library Kit (NuGen).

value: brain

tag: age

tag: bait


title: ARAC1_Vsig1

description: polysomes ~50ug, bait ~5ml


title: ARAC3_Vstm4

description: polysomes ~50ug, bait ~5ml


title: FERS11_Vegf-Fc

description: polysomes ~50ug, bait ~5ml

value: Vegf-Fc


title: ARAC9_Fc-VEGF

description: polysomes ~50ug, bait ~5ml

value: Fc-VEGF


title: FERS74_testis_input

description: polysomes ~50ug

value: testis

value: adult


title: ARAC14_brain_input

description: polysomes ~50ug


title: ARAC6_Vsig10

description: polysomes ~50ug, bait ~5ml


title: FERS104_Sparc

description: polysomes ~50ug, bait ~5ml

value: Sparc-Fc


title: XPRS40_Unc5a

description: polysomes ~50ug, bait ~5ml


title: ARAC8_Tigit

description: polysomes ~50ug, bait ~5ml

value: Tigit-Fc


title: FERS1_Vegf-Fc

description: polysomes ~50ug, bait ~5ml


title: ARAC4_Vsig8

description: polysomes ~50ug, bait ~5ml


title: ARAC5_Visir

description: polysomes ~50ug, bait ~5ml

value: Visir-Fc


title: ARAC16_brain_input

description: polysomes ~50ug


title: XPRS39_Sema4b

description: polysomes ~50ug, bait ~5ml


title: FERS64_Sost

description: polysomes ~50ug, bait ~5ml

value: Sost-Fc


title: FERS10_Pdgfb

description: polysomes ~50ug, bait ~5ml

value: Pdgfb-Fc


title: XPRS41_Plxnd1

description: polysomes ~50ug, bait ~5ml


title: FERS101_Ptprg

description: polysomes ~50ug, bait ~5ml

value: Ptprg-Fc


title: FERS54_Pvrl2

description: polysomes ~50ug, bait ~5ml


title: XPRS46_Sdk2

description: polysomes ~50ug, bait ~5ml


title: FERS67_Pcsk9

description: polysomes ~50ug, bait ~5ml


title: FERS16_Sema3a

description: polysomes ~50ug, bait ~5ml


title: BM-046-7

value: whole blood

value: leprosy patient


title: PB1

value: PB


title: XPRS53_Pcdh9

description: polysomes ~50ug, bait ~5ml


title: FERS5_Optc

description: polysomes ~50ug, bait ~5ml

value: Optc-Fc


title: FERS70_Sostdc1

description: polysomes ~50ug, bait ~5ml


title: FERS92_Ocm

description: polysomes ~50ug, bait ~5ml

value: Ocm-Fc


title: FERS93_Nrn1

description: polysomes ~50ug, bait ~5ml


title: FERS95_Nrnl1

description: polysomes ~50ug, bait ~5ml


title: FERS51_Nlgn2(-)

description: polysomes ~50ug, bait ~5ml


title: XPRS45_Neo1

description: polysomes ~50ug, bait ~5ml


title: FERS56_Necl2

description: polysomes ~50ug, bait ~5ml


title: FERS48_Nlgn1(A)

description: polysomes ~50ug, bait ~5ml


title: FERS55_Necl1

description: polysomes ~50ug, bait ~5ml


title: XPRS42_Nrp2.3

description: polysomes ~50ug, bait ~5ml


title: FERS99_Ly75

description: polysomes ~50ug, bait ~5ml


title: FERS49_Nlgn1(B)

description: polysomes ~50ug, bait ~5ml


title: FERS50_Nlgn1(AB)

description: polysomes ~50ug, bait ~5ml


title: FERS47_Nlgn1(-)

description: polysomes ~50ug, bait ~5ml


title: XPRS1_Lypd6

description: polysomes ~50ug, bait ~5ml


title: FERS52_Nlgn2(A)

description: polysomes ~50ug, bait ~5ml


title: FERS3_Lrtm2

description: polysomes ~50ug, bait ~5ml


title: FERS45_Lphn1

description: polysomes ~50ug, bait ~5ml


title: XPRS31_Lsr

description: polysomes ~50ug, bait ~5ml

value: Lsr-Fc


title: XPRS30_Lsamp

description: polysomes ~50ug, bait ~5ml

value: brain

value: Lsamp-Fc


title: FERS71_Ldlr

description: polysomes ~50ug, bait ~5ml

value: Ldlr-Fc


title: FERS46_Lphn3

description: polysomes ~50ug, bait ~5ml


title: FERS107_Ly75

description: polysomes ~50ug, bait ~5ml


title: FERS79_Jam3

description: polysomes ~50ug, bait ~5ml


title: FERS77_Jam1

description: polysomes ~50ug, bait ~5ml


title: XPRS32_Mog

description: polysomes ~50ug, bait ~5ml

value: Mog-Fc


title: FERS96_Ism1

description: polysomes ~50ug, bait ~5ml


title: ARAC11_Madcam1

description: polysomes ~50ug, bait ~5ml


title: FERS78_Jam2

description: polysomes ~50ug, bait ~5ml


title: XPRS22_Intectin

description: polysomes ~50ug, bait ~5ml

value: Intectin-Fc


title: XPRS28_Igsf11

description: polysomes ~50ug, bait ~5ml


title: XPRS44_Islr2.b

description: polysomes ~50ug, bait ~5ml


title: XPRS27_Hepacam2

description: polysomes ~50ug, bait ~5ml


title: FERS58_Flrt3

description: polysomes ~50ug, bait ~5ml


title: FERS62_Flrt1

description: polysomes ~50ug, bait ~5ml


title: FERS9_Fgf21

description: polysomes ~50ug, bait ~5ml


title: FERS57_Flrt2

description: polysomes ~50ug, bait ~5ml


title: FERS102_Gpr116

description: polysomes ~50ug, bait ~5ml


title: sams-1 37 rep 2

city: Worcester

first: Amy

last: Walker

address: 373 Plantation Street

department: Program in Molecular Medicine

institute: UMASS Medical School

description:
SAMS1.37.4
processed data files:
sams.15.37.xlsx
37.control.sams.xlsx

data_processing:
Raw sequencing reads were processed using an in-house RNA-Seq data processing software Dolphin at University of Massachusetts Medical School.
The raw read pairs first were aligned to C. elegans reference genome with ws245 annotation.
The RSEM method was used to quantify the expression levels of genes (Li & Dewey, 2011, PMID: 21816040)
Deseq was used to generate differental expression files for each data pair.
Genome_build: ws245
Supplementary_files_format_and_content: the processed data files contain normalized reads from individual replicates supplied by Dolphin, as well as the the padj, log2FoldChange, pvalue, foldChange, and log10padj for the samples listed in the name of the file.

organism: Caenorhabditis elegans

source_name: sams-1_37_whole animal RNA

growth_protocol: C. elegans were grown on stated RNAi from hatching

extract_protocol:
RNA was extracted by trireagent and purified by RNAeasy (Qiagen).
Library was constructed by BGI

treatment_protocol: young adult C. elegans were shifted from 15°C to 37°C for 90 minutes

tag: strain background

tag: RNAi

tag: stress

value: whole worm


title: sams-1 37 rep 1

description:
SAMS1.37.1
processed data files:
sams.15.37.xlsx
37.control.sams.xlsx


title: set-2 37 rep 2

description:
SET2.37.4
processed data files:
set2.15.37.xlsx
37.control.set2.xlsx

source_name: set-2_37_whole animal RNA


title: Control 37 rep 1

description:
EV37.1
processed data files:
control.15.37.xlsx
37.control.sams.xlsx
37.control.set2.xlsx
37.control.set16.xlsx

source_name: Control_37_whole animal RNA

value: control


title: FERS8_Fgf19

description: polysomes ~50ug, bait ~5ml


title: Control 37 rep 2

description:
EV.37.4
processed data files:
control.15.37.xlsx
37.control.sams.xlsx
37.control.set2.xlsx
37.control.set16.xlsx


title: Testis-Azin2WT-rep2

city: Murcia

first: Ana

last: Lambertos

address: Campus Espinardo

institute: Universidad de Murcia

description: Gene expression data from testis expressing AZIN2

hyb_protocol: Hybridization was performed using the Affymetrix GeneAtlas Hybridization, Wash and Stain Kit for WT Array Strips.

scan_protocol: Affymetrix Mouse Gene 1.1 ST Array Strip was finally scanned using GeneAtlas Scanner.

data_processing: Affymetrix CEL files were imported into Partek 6.13.1224 for data visualization and statistical testing. Background correction was conducted using Robust Multi-strip Average (RMA) (Irizarry et al, 2003) to remove noise from auto fluorescence. After background correction, normalization was conducted using Quantiles normalization (Bolstad et al, 2003) to normalize the distribution of probe intensities among different microarray chips. Subsequently, a summarization step was conducted using a linear median polish algorithm to integrate probe intensities in order to compute the expression levels for each gene transcript.

source_name: pool of three testis fron Azin2 WT mice

label_protocol: Biotinylated cRNA were prepared according to the standard GeneAtlas 3’IVT Express Kit protocol from  total RNA.  Agilent 2100 Bioanalyzer was used to determine the cRNA concentration/quality as well as to optimize the cRNA fragmentation.

growth_protocol: Animals were maintained under standard conditions at the Service of Laboratory Animals (University of Murcia)

extract_protocol: Testes were homogenized in Trizol and total RNA was extracted with Pure Link RNA Mini Kit (Life Technologies) following the manufacturer’s instructions

tag: genotype

value: Azin2 Wild type

value: testis


title: set-16 15 rep1

description:
SET16.15.1
processed data files:
set16.15.37.xlsx
15.control.set16.xlsx

source_name: set-16_15_whole animal RNA


title: set-16 37 rep2

description:
SET16.37.4
processed data files:
set16.15.37.xlsx
37.control.set16.xlsx

source_name: set-16_37_whole animal RNA


title: set-2 15 rep 2

description:
SET2.15.4
processed data files:
set2.15.37.xlsx
15.control.set2.xlsx

source_name: set-2_15_whole animal RNA


title: set-2 37 rep 1

description:
SET2.37.1
processed data files:
set2.15.37.xlsx
37.control.set2.xlsx


title: Testis-Azin2KO-rep2

description: Gene expression data from testis lacking AZIN2

source_name: pool of three testis fron Azin2 KO mice

value: Azin2 Knock out


title: Testis-Azin2WT-rep1


title: set-2 15 rep 1

description:
SET2.15.1
processed data files:
set2.15.37.xlsx
15.control.set2.xlsx


title: FERS27_Gpr124

description: polysomes ~50ug, bait ~5ml


title: set-16 37 rep1

description:
SET16.37.1
processed data files:
set16.15.37.xlsx
37.control.set16.xlsx


title: SH_RA_differentiated_2

city: San Francisco

first: Charles

last: Chiu

address: 185 Berry Street, Box 0134

department: Laboratory Medicine

institute: University of California, San Francisco

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using STAR v3.12.2 with parameters --outFilterIntronMotifs RemoveNoncanonical --outSAMstrandField intronMotif
output bam file from STAR is used for counting reads that map to each gene using HTSeq v0.60
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include raw read counts for each Sample.

source_name: neuroblastoma cells

growth_protocol: SH-SY5Y cells were plated in 24-well plates at a concentration of 2 × 105 per well and infected with different ZIKV strains at a multiplicity of infection (MOI) of  1, for one hour, followed by washing twice, and then kept in MEM and 1% FBS media.

extract_protocol:
RNA was extracted with the Direct-zol RNA MiniPrep Kit (Zymo Research) according to the manufacturer instructions.
The Ovation Human Blood RNA-Seq Kit (NuGEN Technologies Inc., San Carlos, CA) was used to generate strand-specific RNA-seq libraries. Libraries were sequenced as 100 base pair (bp) paired-end runs on a HiSeq. 2500 instrument (Illumina, San Diego, CA).

treatment_protocol: We use a protocol for differentiation of SH-SY5Y cells, which includes retinoic acid (RA). We use 10µM RA for 2 days. In parallele we had control cells which were not exposed to RA. We collect cell samples by triplicate, and mix with three volumes of trizol. and libraries wree prepared with Nugen Ovation kit.

tag: cell type

value: SH-SY5Y  neuroblastoma cells

tag: passage

value: retionic acid 10µM


title: SH_RA_differentiated_3

tag: treatment


title: FERS94_Esm1

description: polysomes ~50ug, bait ~5ml


title: sams-1 15 rep 2

description:
SAMS1.15.4
processed data files:
sams.15.37.xlsx
15.control.sams.xlsx

source_name: sams-1_15_whole animal RNA


title: set-16 15 rep2

description:
SET16.15.4
processed data files:
set16.15.37.xlsx
15.control.set16.xlsx


title: SH_RA_differentiated_1


title: sams-1 15 rep 1

description:
SAMS1.15-.1
processed data files:
sams.15.37.xlsx
15.control.sams.xlsx


title: FERS7_Epo

description: polysomes ~50ug, bait ~5ml

value: Epo-Fc


title: Control 15 rep 2

description:
EV.15.4
processed data files:
control.15.37.xlsx
15.control.sams.xlsx
15.control.set2.xlsx
15.control.set16.xlsx

source_name: Control_15_whole animal RNA


title: SH_undifferentiated_3


title: Control 15 rep 1

description:
EV15.1
processed data files:
control.15.37.xlsx
15.control.sams.xlsx
15.control.set2.xlsx
15.control.set16.xlsx


title: FERS13_EphB1

description: polysomes ~50ug, bait ~5ml


title: set-2 R24 rep 1

description:
RW_s2_1a
processed data files:
set2.DMSO.R24.out.csv
R24.control.set2.out.csv

source_name: set-2_R24_whole animal RNA

treatment_protocol: young adult C. elegans were shifted to DMSO or R24


title: FERS72_Eng

description: polysomes ~50ug, bait ~5ml

value: Eng-Fc


title: SH_undifferentiated_1


title: Control R24 rep 1

description:
RW_C_1a
processed data files:
control.DMSO.R24.out.csv
R24.control.sams.out.csv
R24.control.set2.out.csv
R24.control.set16.out.csv

source_name: Control_R24_whole animal RNA


title: Control R24 rep 2

description:
RW_C_2a
processed data files:
control.DMSO.R24.out.csv
R24.control.sams.out.csv
R24.control.set2.out.csv
R24.control.set16.out.csv


title: sams-1 R24 rep 2

description:
RW_sams_2a
processed data files:
sams.DMSO.R24.out.csv
R24.control.sams.out.csv

source_name: sams-1_R24_whole animal RNA


title: FERS14_Elfn1

description: polysomes ~50ug, bait ~5ml


title: set-16 R24 rep1

description:
RW_s16_1a
processed data files:
set16.DMSO.R24.out.csv
R24.control.set16.out.csv

source_name: set-16_R24_whole animal RNA


title: FERS76_Eltd1

description: polysomes ~50ug, bait ~5ml


title: FERS15_Elfn2

description: polysomes ~50ug, bait ~5ml


title: set-16 DMSO rep1

description:
DMSO_s16_1a
processed data files:
set16.DMSO.R24.out.csv
DMSO.control.set16.out.csv

source_name: set-16_DMSO_whole animal RNA

value: DMSO


title: Testis-Azin2KO-rep1


title: XPRSE5_Efna1

description: polysomes ~50ug, bait ~5ml

source_name: polysomal RNA


title: XPRSE54_Efna1

description: polysomes ~50ug, bait ~5ml


title: set-2 DMSO rep 2

description:
DMSO_s2_2a
processed data files:
set2.DMSO.R24.out.csv
DMSO.control.set2.out.csv

source_name: set-2_DMSO_whole animal RNA


title: sams-1 DMSO rep 1

description:
DMSO_sams_1a
processed data files:
sams.DMSO.R24.out.csv
DMSO.control.sams.out.csv

source_name: sams-1_DMSO_whole animal RNA


title: sams-1 DMSO rep 2

description:
DMSO_sams_2a
processed data files:
sams.DMSO.R24.out.csv
DMSO.control.sams.out.csv


title: XPRSE3_Efna1

description: polysomes ~50ug, bait ~5ml


title: set-16 R24 rep2

description:
RW_s16_2a
processed data files:
set16.DMSO.R24.out.csv
R24.control.set16.out.csv


title: sams-1 R24 rep 1

description:
RW_sams_1a
processed data files:
sams.DMSO.R24.out.csv
R24.control.sams.out.csv


title: set-2 DMSO rep 1

description:
DMSO_s2_1a
processed data files:
set2.DMSO.R24.out.csv
DMSO.control.set2.out.csv


title: set-2 R24 rep 2

description:
RW_s2_2a
processed data files:
set2.DMSO.R24.out.csv
R24.control.set2.out.csv


title: set-16 PA14 rep1

description:
PA14_s16_1a
processed data files:
set16.OP50.PA14.out.csv
PA14.control.set16.out.csv

source_name: set-16 PA14_whole animal RNA

treatment_protocol: young adult C. elegans were shifted to OP50 (E. coli) or Pa14 (Pseudomonas aeruginosa) for 6 hours and then harvested


title: SH_undifferentiated_2


title: Control DMSO rep 1

description:
DMSO_C_1a
processed data files:
control.DMSO.R24.out.csv
DMSO.control.sams.out.csv
DMSO.control.set2.out.csv
DMSO.control.set16.out.csv

source_name: Control_DMSO_whole animal RNA


title: set-16 DMSO rep2

description:
DMSO_s16_2a
processed data files:
set16.DMSO.R24.out.csv
DMSO.control.set16.out.csv


title: set-2 PA14 rep 2

description:
PA14_s2_2a
processed data files:
set2.OP50.PA14.out.csv
PA14.control.set2.out.csv

source_name: set-2 PA14_whole animal RNA


title: FERS83_Efna1

description: polysomes ~50ug, bait ~5ml


title: FERS97_Efna1

description: polysomes ~50ug, bait ~5ml


title: Control PA14 rep 2

description:
PA14_C_2a
processed data files:
control.OP50.PA14.out.csv
PA14.control.sams.out.csv
PA14.control.set2.out.csv
PA14.control.set16.out.csv

source_name: Control PA14_whole animal RNA


title: FERS63_Efna1

description: polysomes ~50ug, bait ~5ml


title: set-16 OP50 rep1

description:
OP50_s16_1a
processed data files:
set16.OP50.PA14.out.csv
Op50.control.set16.out.csv

source_name: set-16 OP50_whole animal RNA

value: E. coli


title: FERS53_Efna1

description: polysomes ~50ug, bait ~5ml


title: set-2 OP50 rep 1

description:
OP50_s2_1a
processed data files:
set2.OP50.PA14.out.csv
OP50.control.set2.out.csv

source_name: set-2 OP50_whole animal RNA


title: set-2 PA14 rep 1

description:
PA14_s2_1a
processed data files:
set2.OP50.PA14.out.csv
PA14.control.set2.out.csv


title: sams-1 PA14 rep 2

description:
PA14_sams_2a
processed data files:
sams.OP50.PA14.out.csv
PA14.control.sams.out.csv

source_name: sams-1 PA14_whole animal RNA


title: sams-1 PA14 rep 1

description:
PA14_sams_1a
processed data files:
sams.OP50.PA14.out.csv
PA14.control.sams.out.csv


title: Tibetan group

city: Beijing

first: Liping

last: Sun

address: No. 28, Fuxing Rd

country: China

institute: Chinese PLA General Hospital

data_processing:
The raw reads were subjected to the Illumina pipeline filter (Solexa 0.3), and the dataset was further processed with an in-house program, ACGT101-miR (LC Sciences, Texas, USA), to remove adapter dimers, junk, low complexity molecules, common RNA families (rRNA, tRNA, snRNA, and snoRNA) and repeats.
Unique sequences with 18-26 nucleotides in length were mapped to specific species precursors in miRBase 20.0 using a BLAST search to identify known miRNAs.
miRNA differential expression based on normalized deep-sequencing counts was analyzed by selectively using Fisher’s exact test, the Chi-squared 2X2 test, the Chi-squared nXn test, Student’s t-test, and ANOVA depending on the experimental design.
miRNAs with markedly altered expression levels between two groups were identified using fold change and p-value cutoffs of 2 and 0.05 for each test, respectively.
Genome_build: human ensembl genome Build 38
Supplementary_files_format_and_content: xls files include normalized values for each Sample.

source_name: 12 native Tibetans who resided in Lhasa (Tibetan), a city in the Tibet Autonomous Region located at an altitude of 3658 m.

extract_protocol:
Whole blood was centrifuged for 5 min at 2500 rpm. The plasma and buffy coat layers were aspirated for initial removal of plasma, leukocytes and platelets. Mature RBCs were then passed through filter membranes for leukocyte removal and washed three times with phosphate-buffered saline (PBS) to obtain purified mature RBCs.Total RNA was extracted from 100 µl purified RBCs of each sample using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. The Quantity and purity of the total RNA were measured using an RNA 6000 Nano Lab Chip Kit and Bioanalyzer 2100 (Agilent, CA, USA).
Approximately 1 μg of total RNA was used to prepare a small RNA library according to the TruSeq Small RNA Sample Prep Kit protocol (Illumina, CA, USA), and single-end sequencing (36 bp) was performed on an Illumina HiSeq 2500 at LC-BIO (Hangzhou, China) according to the manufacturer’s recommended guideline.

value: whole blood

value: red blood cell

tag: altitude

tag: race

value: Tibetan individuals


title: sams-1 OP50 rep 2

description:
OP50_sams_2a
processed data files:
sams.OP50.PA14.out.csv
Op50.control.sams.out.csv

source_name: sams-1 OP50_whole animal RNA


title: sams-1 OP50 rep 1

description:
OP50_sams_1a
processed data files:
sams.OP50.PA14.out.csv
Op50.control.sams.out.csv


title: Control OP50 rep 2

description:
OP50_C_2a
processed data files:
control.OP50.PA14.out.csv
Op50.control.sams.out.csv
OP50.control.set2.out.csv
Op50.control.set16.out.csv

source_name: Control OP50_whole animal RNA


title: FERS2_Efna1

description: polysomes ~50ug, bait ~5ml

value: brain


title: set-16 PA14 rep2

description:
PA14_s16_2a
processed data files:
set16.OP50.PA14.out.csv
PA14.control.set16.out.csv


title: Control DMSO rep 2

description:
DMSO_C_2a
processed data files:
control.DMSO.R24.out.csv
DMSO.control.sams.out.csv
DMSO.control.set2.out.csv
DMSO.control.set16.out.csv


title: Control OP50 rep 1

description:
OP50_C_1a
processed data files:
control.OP50.PA14.out.csv
Op50.control.sams.out.csv
OP50.control.set2.out.csv
Op50.control.set16.out.csv


title: Tibet Han group

source_name: 10 ethnic Han Chinese who migrated approximately 15 years ago from the plains to Lhasa (Tibet Han).

value: Han individuals


title: FERS25_Efna1

description: polysomes 100ug, bait 0.4ml


title: set-2 OP50 rep 2

description:
OP50_s2_2a
processed data files:
set2.OP50.PA14.out.csv
OP50.control.set2.out.csv


title: Sichuan Han group

source_name: 20 Han Chinese residing in Chengdu, Sichuan Province (Sichuan Han) at an altitude of 500 m.


title: XPRSE4_Efna1

description: polysomes ~50ug, bait ~5ml


title: XPRSE2_Efna1

description: polysomes ~50ug, bait ~5ml


title: set-16 OP50 rep2

description:
OP50_s16_2a
processed data files:
set16.OP50.PA14.out.csv
Op50.control.set16.out.csv


title: C57/Bl6J_control

city: Durham

first: Yasuhito

last: Yahara

state: NC

address: Duke Hospital South, 200 Trent Drive, Orange Zone 5th floor

institute: Duke Univ

data_processing:
Alignment, counting, filtering, of single cell RNA-Seq of C57/Bl6J_control and C57/Bl6J_20HC_treated, using 10X Cellranger v2.1.1 with default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: matrix.mtx:  Gene-barcode matrix in Market Exchange Format (MEX) for Mus musculus C57/Bl6J_control and Mus musculus C57/Bl6J_20HC_treatment SVZ-derived neural stem cells. Columns correspond to individual cells(barcodes), while rows correspond to genes.
Supplementary_files_format_and_content: genes.tsv: Genes corresponding to row indices in matrix.mtx. Gene ID and gene name are stored in the first and second column.
Supplementary_files_format_and_content: barcodes.tsv: Barcode sequences that correspond to column indices in matrix.mtx.

source_name: C57/Bl6J SVZ-derived neural stem cells

extract_protocol:
Cell were prepared for 10X Genomics Single Cell RNA-Seq using Chromium Single Cell 3′ Library & Gel Bead Kit v1.
10X Single Cell 3'

treatment_protocol: 3 days treatment with 1uM 20HC

value: neural stem cells


title: C57/Bl6J_20HC_treated


title: FERS73_Efna1

description: polysomes ~50ug, bait ~5ml


title: Control PA14 rep 1

description:
PA14_C_1a
processed data files:
control.OP50.PA14.out.csv
PA14.control.sams.out.csv
PA14.control.set2.out.csv
PA14.control.set16.out.csv

value: whole worm


title: Taxus cuspidata rep2

city: hangzhou

first: chengchao

address: Xuelin Street No.16

institute: Hangzhou Normal University

data_processing:
The paired-end sequencing was performed on an Illumina Hiseq 2500 or  4000 platform
The reads containing adaptor, low quality bases and undetermined bases were  removed
The transcriptome from each species was processed using software Trinity 2.4.0
Genome_build: de novo assembly. FASTA files with transcript sequences are available on the series record.
Supplementary_files_format_and_content: txt file with count and TPM

organism: Taxus cuspidata

source_name: fresh twigs

growth_protocol: The growth conditions were set at 25 ± 1°C with a light/dark cycle of 12/12 h and a 60%–70% relative humidity

extract_protocol:
For RNA sequencing, total RNAs were extracted using an RNeasy plant mini kit (Qiagen, Hilden, Germany) according to the manufacturer’s manual. DNA contamination was removed by adding DNaseI and checked using a NanoPhotometer® spectrophotometer (Implem, Schatzboge, Germany) and 1% agarose gel electrophoresis.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: three years

value: twigs (wood and needles)


title: 5A-NG4-input1: Drosophila 5A-NG4 total extract (replicate 1)

city: Montreal

first: Eric

last: Lecuyer

state: Quebec

address: 110 Pine Ave W

department: RNA biology

institute: IRCM

data_processing:
Read quality was assessed with FastQC
Read alignment was performed with TopHat on dm3
Featurecount was used to extract read counts
The count files were used with DESeq for differential expression
Genome_build: dm3
Supplementary_files_format_and_content: tab-delimited files include normalized read counts for each sample

organism: Drosophila melanogaster

source_name: Total 5A-NG4 ovary extract

growth_protocol: Fruit flies (Drosophila melanogaster) were grown under standard lab conditions.

extract_protocol:
15 mg of ovaries were homogenized using a Dounce in 10% w/v polysome buffer (50 mM Tris, pH 7.5, 100 mM KCl, 12 mM MgCl2, 1% NP-40, 1 mM DTT, 1 mg/mL heparin, 200 U/mL RNaseOut RNase inhibitor, protease inhibitors and 100 mg/mL cycloheximide) and centrifuged at 10,000 rpm for 10 min.
paired-end 50 rRNA-depleted stranded

treatment_protocol: Ovaries were dissected from 5-10 day old female flies in PBST (PBS with 0.3% Triton-100) and transferred to ice immediately. Ovary lysis was made based on the extract protocol.

value: ovary

tag: genotype/variation

value: RpS5a knocked down by RNAi


title: 5A-NG4-input3: Drosophila 5A-NG4 total extract (replicate 1)

tag: tissue


title: 5A-NG4-input2: Drosophila 5A-NG4 total extract (replicate 1)


title: FERS22_Efna1

description: polysomes 100ug, bait 10ml

source_name: polysomal RNA


title: Taxus cuspidata rep3


title: 5A-NG4-IP3-5A: Drosophila 5A-NG4 immunoprecipitation of 5A (replicate 3)

source_name: Total 5A-NG4 IP5A ovary extract


title: FERS23_Efna1

description: polysomes 100ug, bait 10ml


title: Taxus cuspidata rep1


title: 5A-NG4-IP1-5A: Drosophila 5A-NG4 immunoprecipitation of 5A (replicate 1)


title: FERS19_Efna1

description: polysomes 100ug, bait 10ml


title: FERS24_Efna1

description: polysomes 100ug, bait 2ml


title: FERS21_Efna1

description: polysomes 4ug, bait 10ml


title: 5A-NG4-IP2-5A: Drosophila 5A-NG4 immunoprecipitation of 5A (replicate 2)


title: FERS20_Efna1

description: polysomes 20ug, bait 10ml


title: 5A-NG4-IP3-5B: Drosophila 5A-NG4 immunoprecipitation of 5B (replicate 3)

source_name: Total 5A-NG4 IP5B ovary extract


title: cortex [cortexC2]

first: Katleen

last: De Preter

department: Center for Medical Genetics

description:
cortexC2
SAMPLE 116

data_processing: Raw Cq values were calculated using the SDS software version 2.1 applying automatic baseline settings and a threshold of 0.05. For further data analysis, only those miRNAs with a Cq value equal to or below 35 (representing single molecule template detection) were taken into account. For NB tumor samples all 448 miRNAs and small RNA controls were profiled. RT-qPCR assays were spread across two 384-well plates. Inter-run variation was accounted for by equalizing the mean Cq-value of the 18 small RNA controls that were profiled in both plates. For the remaining samples 366 miRNAs and 18 small RNA controls were profiled in a single 384-well plate.

label: TaqMan

source_name: Ghent

label_protocol: 20 ng of total RNA was reverse transcribed using the Megaplex RT stem-loop primer pool (Applied Biosystems, Foster City, CA, USA), enabling miRNA specific cDNA synthesis for 430 different human miRNAs and 18 small RNA controls. Subsequently, Megaplex RT product was pre-amplified by means of a 14-cycle PCR reaction with a miRNA specific forward primer and universal reverse primer to increase detection sensitivity. Finally, a 1,600-fold dilution of pre-amplified miRNA cDNA was used as input for a 40-cycle qPCR reaction with miRNA specific hydrolysis probes and primers (Applied Biosystems). All reactions were performed on the 7900 HT (Applied Biosystems) using the gene maximization strategy.

extract_protocol: Total RNA was isolated using the miRNAeasy kit (Qiagen, Valencia, CA, USA) according to the manufacturer's instructions.

tag: Stage

value: cortex


title: FERS12_Efna1

description: polysomes ~50ug, bait ~5ml


title: ARAC12_Efna1

description: polysomes ~50ug, bait ~5ml


title: cortex [cortexB]

description:
cortexB
SAMPLE 113


title: cortex [cortexA2]

description:
cortexA2
SAMPLE 114


title: neuroblast [neuroblastA]

description:
neuroblastA
SAMPLE 118

value: neuroblast


title: neuroblast [neuroblastC2]

description:
neuroblastC2
SAMPLE 115


title: 5A-NG4-IP2-5B: Drosophila 5A-NG4 immunoprecipitation of 5B (replicate 2)


title: FERS87_Efna1_testis

description: polysomes ~50ug, bait ~5ml

value: testis

value: adult


title: cortex [cortexA]

description:
cortexA
SAMPLE 112


title: neuroblast [neuroblastA2]

description:
neuroblastA2
SAMPLE 111


title: cortex [cortexC]

description:
cortexC
SAMPLE 110


title: 5A-NG4-IP1-5B: Drosophila 5A-NG4 immunoprecipitation of 5B (replicate 1)


title: neuroblast [neuroblastC]

description:
neuroblastC
SAMPLE 109


title: 5Bko-input3: Drosophila 5B knock out total extract (replicate 3)

source_name: Total 5Bko ovary extract


title: neuroblast [neuroblastB]

description:
neuroblastB
SAMPLE 117


title: FERS60_Dkk4

description: polysomes ~50ug, bait ~5ml


title: 5Bko-input2: Drosophila 5B knock out total extract (replicate 2)


title: cortex [cortexD2]

description:
cortexD2
SAMPLE 108


title: cortex [cortexD]

description:
cortexD
SAMPLE 107


title: FERS59_Dkk1

description: polysomes ~50ug, bait ~5ml


title: 5Bko-IP2-5A: Drosophila 5B knock out immunoprecipitation of 5A (replicate 2)

source_name: Total 5Bko IP5A ovary extract


title: 5Bko-IP3-5A: Drosophila 5B knock out immunoprecipitation of 5A (replicate 3)


title: ESClineVUB [RNA3929]

description:
RNA3929
SAMPLE 104

source_name: Brussels

tag: cell line

value: ESClineVUB


title: XPRS14_Cntn4.2

description: polysomes ~50ug, bait ~5ml


title: ESClineVUB [RNA3926]

description:
RNA3926
SAMPLE 102


title: neuroblast [neuroblastD]

description:
neuroblastD
SAMPLE 105


title: neuroblast [neuroblastD2]

description:
neuroblastD2
SAMPLE 106


title: 5Bko-input1: Drosophila 5B knock out total extract (replicate 1)


title: ESClineVUB [RNA3922]

description:
RNA3922
SAMPLE 99


title: ESClineVUB [RNA3921]

description:
RNA3921
SAMPLE 98


title: XPRS13_Cntn3

description: polysomes ~50ug, bait ~5ml


title: ESClineVUB [RNA3924]

description:
RNA3924
SAMPLE 101


title: 5Bko-IP1-5A: Drosophila 5B knock out immunoprecipitation of 5A (replicate 1)


title: WT-input3: Drosophila Wild Type total extract (replicate 1)

source_name: Total WT ovary extract

value: wildtype


title: FERS61_Dkk3

description: polysomes ~50ug, bait ~5ml


title: ESClineVUB [RNA3389]

description:
RNA3389
SAMPLE 97


title: NBtumor [nrc4099]

description:
nrc4099
SAMPLE 95

source_name: Essen

value: NBtumor


title: NBtumor [nrc4098]

description:
nrc4098
SAMPLE 94


title: XPRS16_Cntn6

description: polysomes ~50ug, bait ~5ml


title: XPRS48_Clstn3

description: polysomes ~50ug, bait ~5ml


title: XPRS10_Cecam20

description: polysomes ~50ug, bait ~5ml


title: WT-input1: Drosophila Wild Type total extract (replicate 1)


title: NBtumor [nrc4097]

description:
nrc4097
SAMPLE 93


title: WT-input2: Drosophila Wild Type total extract (replicate 1)


title: ESClineVUB [RNA3923]

description:
RNA3923
SAMPLE 100


title: NBtumor [nrc4096]

description:
nrc4096
SAMPLE 92


title: ESClineVUB [RNA3927]

description:
RNA3927
SAMPLE 103


title: WT-IP3-5A: Drosophila Wild Type immunoprecipitation of 5A (replicate 3)

source_name: Total IP5A ovary  extract


title: XPRS5_Cecam19

description: polysomes ~50ug, bait ~5ml


title: XPRS3_Ceacam18

description: polysomes ~50ug, bait ~5ml


title: NBtumor [nrc4095]

description:
nrc4095
SAMPLE 91


title: WT-IP2-5A: Drosophila Wild Type immunoprecipitation of 5A (replicate 2)


title: NBtumor [nrc4092]

description:
nrc4092
SAMPLE 88


title: NBtumor [nrc4093]

description:
nrc4093
SAMPLE 89


title: WT-IP1-5A: Drosophila Wild Type immunoprecipitation of 5A (replicate 1)

source_name: Total IP5A ovary extract


title: XPRS2_Ceacam1

description: polysomes ~50ug, bait ~5ml


title: NBtumor [nrc4009]

description:
nrc4009
SAMPLE 86


title: NBtumor [nrc4088]

description:
nrc4088
SAMPLE 84


title: XPRS52_Cdh8

description: polysomes ~50ug, bait ~5ml


title: FERS100_Cd93

description: polysomes ~50ug, bait ~5ml


title: XPRS11_Cntn1

description: polysomes ~50ug, bait ~5ml


title: WT-IP2-5B: Drosophila Wild Type immunoprecipitation of 5B (replicate 2)

source_name: Total IP5B ovary extract


title: FERS98_Cd40

description: polysomes ~50ug, bait ~5ml


title: NBtumor [nrc4094]

description:
nrc4094
SAMPLE 90


title: WT-IP3-5B: Drosophila Wild Type immunoprecipitation of 5B (replicate 3)


title: NBtumor [nrc4090]

description:
nrc4090
SAMPLE 87


title: ARAC7_CD200r1

description: polysomes ~50ug, bait ~5ml


title: FERS106_AU021092

description: polysomes ~50ug, bait ~5ml


title: NBtumor [nrc4089]

description:
nrc4089
SAMPLE 85


title: XPRS26_Cadm3

description: polysomes ~50ug, bait ~5ml


title: NBtumor [nrc4087]

description:
nrc4087
SAMPLE 83


title: FERS66_Astn2

description: polysomes ~50ug, bait ~5ml


title: NBtumor [nrc4080]

description:
nrc4080
SAMPLE 78


title: NBtumor [nrc4077]

description:
nrc4077
SAMPLE 74


title: NBtumor [nrc4079]

description:
nrc4079
SAMPLE 76


title: NBtumor [nrc4008]

description:
nrc4008
SAMPLE 77


title: NBtumor [nrc4081]

description:
nrc4081
SAMPLE 79


title: NBtumor [nrc4084]

description:
nrc4084
SAMPLE 82


title: NBtumor [nrc4083]

description:
nrc4083
SAMPLE 81


title: NBtumor [nrc4082]

description:
nrc4082
SAMPLE 80


title: NBtumor [nrc4078]

description:
nrc4078
SAMPLE 75


title: WT-IP1-5B: Drosophila Wild Type immunoprecipitation of 5B (replicate 1)


title: NBtumor [nrc4076]

description:
nrc4076
SAMPLE 73


title: FERS65_Astn1

description: polysomes ~50ug, bait ~5ml


title: NBtumor [nrc4074]

description:
nrc4074
SAMPLE 71


title: NBtumor [nrc4072]

description:
nrc4072
SAMPLE 70


title: NBtumor [nrc4075]

description:
nrc4075
SAMPLE 72


title: NBtumor [nrc4071]

description:
nrc4071
SAMPLE 69


title: FERS68_App

description: polysomes ~50ug, bait ~5ml

value: App-Fc


title: NBtumor [nrc4070]

description:
nrc4070
SAMPLE 68


title: NBtumor [nrc4007]

description:
nrc4007
SAMPLE 67


title: FERS69_Aplp2

description: polysomes ~50ug, bait ~5ml


title: NBtumor [nrc4069]

description:
nrc4069
SAMPLE 66


title: NBtumor [nrc4068]

description:
nrc4068
SAMPLE 65


title: NBtumor [nrc4067]

description:
nrc4067
SAMPLE 64


title: FERS6_Ager

description: polysomes ~50ug, bait ~5ml

value: Ager-Fc


title: NBtumor [nrc4065]

description:
nrc4065
SAMPLE 62


title: ALS4: sporadic amyotrophic lateral sclerosis

city: Fujisawa

first: Kentaro

last: Otake

state: Kanagawa

address: 26-1, Muraoka-Higashi 2-Chome

department: Neuroscience Drug Discovery Unit

country: Japan

institute: Takeda Pharmaceutical Company Limited

data_processing:
Base Calls were performed in NextSeq 500 sequencing system.
Mapping to genome and counting the reads were performed by RNA-seq pipeline implemented in Omicsoft Array Studio (QIAGEN).
Count per million mapped reads (CPM) was calculated.
Row count data was normalized by logarithm of geometric mean and size factor was calculated.
Differentially expressed genes between normal healthy condition and ALS were analyzed by DESeq2 function in Omicsoft Array Studio (QIAGEN).
Genome_build: B37.3
Supplementary_files_format_and_content: Tab-delimited text files representing raw counts and the result of DESeq2.

source_name: exosomes from cerebrospinal fluid (CSF)

extract_protocol:
Up to 1 mL of human CSF was centrifuged at 2,000 x g for 5 min and 10, 000 x g for 20 min. Supernatant from final centrifugation was applied to exoRNeasy spin column and RNA was extracted.
Whole cDNA amplification was performed with SMART-seq v4 Ultra Low Input RNA Kit. Illumina library was constructed with Nextera XT DNA Library Prep Kit.

tag: diagnosis

value: sporadic amyotrophic lateral sclerosis

tag: Sex

value: Male

value: exosomes from cerebrospinal fluid (CSF)


title: ALS3: sporadic amyotrophic lateral sclerosis

tag: age


title: ALS1: sporadic amyotrophic lateral sclerosis


title: ALS2: sporadic amyotrophic lateral sclerosis


title: NBtumor [nrc4066]

description:
nrc4066
SAMPLE 63


title: NH4: normal healthy condition

value: normal healthy condition


title: NBtumor [nrc4064]

description:
nrc4064
SAMPLE 61


title: NBtumor [nrc4061]

description:
nrc4061
SAMPLE 58


title: NBtumor [nrc4054]

description:
nrc4054
SAMPLE 53


title: NBtumor [nrc4060]

description:
nrc4060
SAMPLE 57


title: NBtumor [nrc4006]

description:
nrc4006
SAMPLE 56


title: NBtumor [nrc4059]

description:
nrc4059
SAMPLE 55


title: NBtumor [nrc4055]

description:
nrc4055
SAMPLE 54


title: NBtumor [nrc4063]

description:
nrc4063
SAMPLE 60


title: NBtumor [nrc4053]

description:
nrc4053
SAMPLE 52


title: NH2: normal healthy condition


title: NH1: normal healthy condition


title: NBtumor [nrc4051]

description:
nrc4051
SAMPLE 51


title: NBtumor [nrc4047]

description:
nrc4047
SAMPLE 48


title: NBtumor [nrc4046]

description:
nrc4046
SAMPLE 47


title: NBtumor [nrc4048]

description:
nrc4048
SAMPLE 49


title: NBtumor [nrc4062]

description:
nrc4062
SAMPLE 59


title: NBtumor [nrc4045]

description:
nrc4045
SAMPLE 46


title: NBtumor [nrc4044]

description:
nrc4044
SAMPLE 45


title: NBtumor [nrc4043]

description:
nrc4043
SAMPLE 44

source_name: Spain


title: NH3: normal healthy condition


title: NBtumor [nrc4042]

description:
nrc4042
SAMPLE 43


title: pDC.ko.2

data_processing:
FASTQ files were output using standard Illumina protocols and software.
Reads were aligned to the mouse genome by Subread 1.4.6
Read counts were summarized by Entrez Gene ID using the featureCounts function of the Rsubread package version 1.16.1 and Rsubread's built-in NCBI annotation. The supplementary file GenewiseCounts.tsv provides the gene-level counts for all the samples.
Genome_build: mm10 (NCBI build 38.1)
Supplementary_files_format_and_content: tab-delimited text files; columns represent Entrez Gene ID, total gene length and the number of reads mapping to that gene.

source_name: Plasmacytoid dentritic cells

extract_protocol:
RNA was isolated with the RNeasy Plus Mini Kit (Qiagen).
mRNA reverse transcription cDNA libraries were prepared using the TruSeq RNA Sample Preparation Kit (Illumina) following the manufacturer’s instructions.

tag: background strain

value: Spleen

tag: library prepation protocol

value: TruSeq


title: cDC.ko.1

source_name: Conventional dendritic cells


title: cDC.ko.2


title: NBtumor [nrc4039]

description:
nrc4039
SAMPLE 41


title: NBtumor [nrc4040]

description:
nrc4040
SAMPLE 42


title: pDC.het.2


title: cDC.het.2


title: NBtumor [nrc4005]

description:
nrc4005
SAMPLE 50


title: cDC.het.1


title: NBtumor [nrc4038]

description:
nrc4038
SAMPLE 40


title: pDC.het.1


title: NBtumor [nrc4031]

description:
nrc4031
SAMPLE 34


title: NBtumor [nrc4033]

description:
nrc4033
SAMPLE 36


title: NBtumor [nrc4030]

description:
nrc4030
SAMPLE 33


title: NBtumor [nrc4036]

description:
nrc4036
SAMPLE 38


title: NBtumor [nrc4037]

description:
nrc4037
SAMPLE 39


title: NBtumor [nrc4032]

description:
nrc4032
SAMPLE 35


title: pDC.wt.2

value: Wild type


title: pDC.ko.1


title: NBtumor [nrc4028]

description:
nrc4028
SAMPLE 31


title: NBtumor [nrc4029]

description:
nrc4029
SAMPLE 32


title: NBtumor [nrc4026]

description:
nrc4026
SAMPLE 29


title: KFSY S phase

city: Stanford

first: David

last: Kingsley

address: 279 Campus Drive

department: Developmental Biology

institute: Stanford University

data_processing:
Library strategy: Repli-seq
Reads were adapter trimmed and aligned to the reference stickleback genome (version gasAcu1) using Burrows-Wheeler Aligner’s Smith-Waterman Alignment.
Read depth was extracted for each base in the genome, and bases mapping more than 3 standard deviations over the mean read depth were discarded from subsequent analysis.
Each individual G0/G1-phase and S-phase library read depth was normalized to its own mean depth, then all 9 populations’ G0/G1-phase normalized depths were combined into a single G0/G1-phase dataset, and all 9 populations’ S-phase normalized depths were combined into a single S-phase dataset.
The S/G depth ratio was calculated using the combined normalized read depth from these datasets over a 50 kb sliding window with 25 kb step.
Genome_build: gasAcu1
Supplementary_files_format_and_content: Tab-delimited file columns: position, S:G read depth ratio, normalized combined G-phase read depth, normalized combined S-phase read depth. Files are split by chromosome.

organism: Gasterosteus aculeatus

source_name: Kalifonsky lake embryos, S-phase cells

growth_protocol: Stickleback clutches of ~50-100 embryos from 9 different populations (BDGB, RABS, JADE, BOOT, BEPA, KFSY, LSHP, ORPH, BOUL) of wild-caught fish were grown for ~10 days at 16°C until they reached Swarup developmental stages 24-26.

extract_protocol:
Genomic DNA was isolated by phenol:chloroform extraction with 1-2 chloroform washes and ethanol precipitation.
Sequencing libraries were prepared using the Nextera DNA Library Preparation Kit (Illumina) according to manufacturer’s instructions, except we increased Tagmentation time to 10 minutes from 5 minutes, and we used 50 uL of AMPure XP beads instead of 30 uL for PCR cleanup.  G0/G1-phase DNA and S-phase DNA were separately barcoded during library preparation and sequenced together in one lane (per population) on the Illumina HiSeq 2000 platform with single-end 101 bp runs.

treatment_protocol: Each clutch was then dissociated into single cells using the Worthington Papain Dissociation System according to manufacturer’s instructions with ~40 minutes incubation in papain solution.  Single cells were resuspended in 3 mL cold PBS with 1% FBS, and 7 mL of cold 100% ethanol was added slowly while swirling to fix the cells.  Fixed cells were stored at –20°C.  Ethanol fixed cells were spun down and resuspended in 50 ug/mL propidium iodide, 250 ug/mL RNaseA, in PBS with 1% FBS to stain for DNA content.  Cells were filtered through a 70 um nylon cell strainer before sorting on a BD FACS Aria by propidium iodide.  Although traditional replication timing strategies collect an early S-phase and a late S-phase population, we collected just one mid S-phase population, due to the limiting number of cells undergoing DNA replication in developing embryos.  Sorting continued until ~2,000,000 G0/G1-phase cells and ~250,000 S-phase cells were collected.  Another 200 ug of glycogen was added to the collected cells along with ~3-5 volumes of 100% ethanol, and then cells were precipitated by centrifugation at 300 g for 5 min.  The pellet was resuspended in 600 uL of 10 mM Tris pH 8.0, 100 mM NaCl, 10 mM EDTA, 0.5% SDS, and 333 ng/uL Proteinase K, and incubated overnight at 55°C.

tag: cell-cycle phase

value: S

tag: population

value: Kalifonsky lake

tag: developmental stage

value: Whole embryo Swarup stage 24-26


title: NBtumor [nrc4027]

description:
nrc4027
SAMPLE 30

tag: cell type


title: NBtumor [nrc4025]

description:
nrc4025
SAMPLE 28


title: NBtumor [nrc4034]

description:
nrc4034
SAMPLE 37


title: cDC.wt.2


title: NBtumor [nrc4024]

description:
nrc4024
SAMPLE 27


title: NBtumor [nrc4023]

description:
nrc4023
SAMPLE 26


title: JADE S phase

source_name: Jade lake embryos, S-phase cells

value: Jade lake


title: cDC.wt.1


title: pDC.wt.1


title: KFSY G phase

source_name: Kalifonsky lake embryos, G0/G1-phase cells


title: NBtumor [nrc4022]

description:
nrc4022
SAMPLE 25


title: NBtumor [nrc4020]

description:
nrc4020
SAMPLE 23


title: NBtumor [nrc4021]

description:
nrc4021
SAMPLE 24


title: BOOT S phase

source_name: Boot lake embryos, S-phase cells

value: Boot lake


title: BOOT G phase

source_name: Boot lake embryos, G0/G1-phase cells


title: JADE G phase

source_name: Jade lake embryos, G0/G1-phase cells


title: NBtumor [nrc4016]

description:
nrc4016
SAMPLE 18


title: NBtumor [nrc4002]

description:
nrc4002
SAMPLE 22


title: NBtumor [nrc4017]

description:
nrc4017
SAMPLE 19

source_name: Ghent


title: NBtumor [nrc4018]

description:
nrc4018
SAMPLE 20


title: ORPH G phase

source_name: Orphea lake embryos, G0/G1-phase cells

value: Orphea lake


title: NBtumor [nrc4015]

description:
nrc4015
SAMPLE 17


title: QJSB group 3

city: Shanghai

first: ai

middle: ping

last: jiang

address: No.151, Libing Rd., Zhangjiang Hi-tech Park, Pudong

institute: Shanghai Biotechnology Corporation

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Hisat2.
Fragments Per Kilobase of exon model per Million mapped reads (FPKM) were calculated for normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: Bone marrow cells

extract_protocol:
Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea, CA,USA)and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).
Strand-specific libraries were prepared using the VAHTS Total RNA-Seq Library PrepKit for Illumina (Vazyme, China) following the manufacturer’s instructions. Using Ribo-Zero rRNA removal beads, ribosomal RNA was removed from total RNA. Following purification, the mRNA is fragmented into small pieces using divalent cations under 94°C for 8 min. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then go through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products are then purified and enriched with PCR to create the final cDNA library. Purified libraries were quantified by Qubit® 2.0 Fluorometer (Life Technologies, USA) and validated by Agilent 2100 bioanalyzer (Agilent Technologies, USA) to confirm the insert size and calculate the mole concentration. Cluster was generated by cBot with the library diluted to 10 pM and then were sequenced on the Illumina HiSeq 2500 (Illumina, USA).

value: Total bone marrow cells in femur

tag: strain

value: ICR


title: LSHP S phase

source_name: L-shaped lake embryos, S-phase cells

value: L-shaped


title: leucogen group 3


title: QJSB group 2


title: leucogen group 2


title: LSHP G phase

source_name: L-shaped lake embryos, G0/G1-phase cells


title: leucogen group 1


title: NBtumor [nrc4014]

description:
nrc4014
SAMPLE 16

value: NBtumor


title: NBtumor [nrc4019]

description:
nrc4019
SAMPLE 21


title: NBtumor [nrc4013]

description:
nrc4013
SAMPLE 15


title: ORPH S phase

source_name: Orphea lake embryos, S-phase cells


title: BOUL S phase

source_name: Boulton lake embryos, S-phase cells

value: Boulton lake


title: QJSB group 1


title: NBtumor [nrc4012]

description:
nrc4012
SAMPLE 14


title: BOUL G phase

source_name: Boulton lake embryos, G0/G1-phase cells


title: model group 3


title: NBtumor [nrc4011]

description:
nrc4011
SAMPLE 13


title: model group 2


title: BEPA S phase

source_name: Bear Paw lake embryos, S-phase cells

value: Bear Paw


title: Atrial at T3, biological rep3

first: 唐

last: 伟评

address: 2 Anzhen Rd, Chaoyang District,

institute: Beijing Institute of Heart Lung and Blood Vessel Diseases

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

scan_protocol: Genechips were scanned by GeneChip® Scanner 3000.

data_processing:
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0
affymetrix-array-type = Clariom_S_Mouse
program-name = Expression Console
program-version = 1.4.1.46

source_name: Mouse atrial Angiotensin II treated for 3weeks

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1-8 ug total RNA

growth_protocol: Eight to ten-week-old C57BL/6 male mice were kept at least 1 wk at 22°C and 55% relative humidity in a 12-h day/night lighting environment with free access to food and water.

extract_protocol: All mice were euthanized by an overdose of pentobarbital on days 1, 3 and 7 of Ang II treatment. Total RNA was isolated with TRIzol (Invitrogen) from atrials (n=4 per group) at each time point according to manufacturer’s instructions.

treatment_protocol: Mice were implanted with osmotic pumps (Alzet Model 1007D; Cupertino, CA,USA) and infused with Angiotensin II at 2000ng/kg/min in Ringer's solution (0.01mmol/L acetic acid in saline) for 1, 2, and 3 weeks . Systolic blood pressure was measured by the tail-cuff method before starting treatment and again every day after Angiotensin II infusion.

value: 8-10 weeks

value: male

tag: treatment

value: Angiotensin II for 3 wks

value: atrials


title: NBtumor [nrc4109]

address: Corneel Heymanslaan 10

institute: Ghent University

description:
nrc4109
SAMPLE 12

source_name: Essen


title: BEPA G phase

source_name: Bear Paw lake embryos, G0/G1-phase cells


title: normal group 3


title: model group 1


title: Atrial at T3, biological rep2


title: normal group 2


title: NBtumor [nrc4108]

description:
nrc4108
SAMPLE 11


title: RABS S phase

source_name: Rabbit Slough embryos, S-phase cells

value: Rabbit Slough


title: normal group 1


title: NBtumor [nrc4107]

description:
nrc4107
SAMPLE 10


title: RABS G phase

source_name: Rabbit Slough embryos, G0/G1-phase cells


title: Atrial at T3, biological rep4


title: BDGB S phase

source_name: Bodega Bay embryos, S-phase cells

value: S

value: Bodega Bay


title: NBtumor [nrc4106]

description:
nrc4106
SAMPLE 9


title: Atrial at T2, biological rep4

source_name: Mouse atrial Angiotensin II treated for 2weeks

value: Angiotensin II for 2 wks


title: Atrial at T3, biological rep1


title: Atrial at T2, biological rep3


title: BDGB G phase

source_name: Bodega Bay embryos, G0/G1-phase cells

value: Whole embryo Swarup stage 24-26


title: NBtumor [nrc4104]

description:
nrc4104
SAMPLE 7


title: HFD+EGCG_female

city: Soraku-gun

first: Mikiko

last: Yamanaka

state: Kyoto

address: 8-1-1, Seikadai, Seika-cho

department: research institute

institute: Suntory Global Innovation Center

data_processing:
Illumina CASAVA ver 1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Drosophila whole genome(dmel-all-chromosome-r6.12.fasta) using TopHat V2.1.1.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using Cuffdiff v2.2.1.
Genome_build: Drosophila whole genome (dmel-all-chromosome-r6.12.fasta)

source_name: body without wings or legs

extract_protocol:
Total RNA was extracted from 15-day-old adults using Isogen. Sureselect strand specific RNA Library Prep Kit was used.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Flies were reared in ND, HFD, HFD+QG or HFD+EGCG for 7days. After tha treatments, the flies were in the standard diet for 2 hours to let them excrete undigested foods from their guts. After that, the flies were collected and rinse them with PBS containing 1% Triton X-100. Wings and legs were removed.

value: adult

value: Canton S

tag: diet

value: HFD+EGCG

tag: gender

value: female

value: body without wings or legs


title: HFD+QG_female

value: HFD+QG


title: Taxus media rep3

last: zhang

organism: Taxus x media

source_name: fresh twigs

value: three years

value: twigs (wood and needles)


title: HFD_female

value: HFD


title: Atrial at T2, biological rep2

value: 8-10 weeks

value: male


title: Taxus media rep2


title: Atrial at T1, biological rep4

source_name: Mouse atrial Angiotensin II treated for 1weeks

value: Angiotensin II for 1 wk

value: atrials


title: Atrial at T1, biological rep3


title: NBtumor [nrc4103]

city: Gent

description:
nrc4103
SAMPLE 6

value: NBtumor


title: ND_female

value: ND


title: Atrial at T2, biological rep1

value: Angiotensin II for 2 wks


title: NBtumor [nrc4102]

description:
nrc4102
SAMPLE 5


title: HFD+EGCG_male


title: Taxus media rep1


title: NBtumor [nrc4105]

description:
nrc4105
SAMPLE 8


title: Atrial at T1, biological rep2


title: Atrial at T1, biological rep1


title: Atrial at T0, biological rep4

source_name: Mouse atrial with no Angiotensin II  treatmeant


title: NBtumor [nrc4101]

description:
nrc4101
SAMPLE 4


title: HFD+QG_male


title: NBtumor [nrc4100]

description:
nrc4100
SAMPLE 3


title: Taxus mairei rep2

organism: Taxus mairei


title: Taxus mairei rep3


title: HFD_male


title: Taxus mairei rep1


title: ND_male


title: 100EGF_100IGF___rep1

status: Public on Oct 19 2018

first: Dmitry

last: Kuchenov

address: 1700 4th Street

institute: Gladstone Institutes

description: HJHT3BGX2_DK_12_1_16s008381-1-1_Kuchenov_lane116s008381

data_processing:
RNA-seq reads were aligned with salmon version 0.8.2 (Patro, 2017) to the Human Reference Genome GRCh38 obtained from Ensembl (http://www.ensembl.org). The assigned read counts were normalized in the Bioconductor package “DESeq2”.
Genome_build: Human Reference Genome GRCh38
Supplementary_files_format_and_content: normalized counts

source_name: HeLa Kyoto_100EGF_100IGF

growth_protocol: HeLa Kyoto cells were maintained in low glucose DMEM (Life Technologies) supplemented with 10 % FBS and with 100 µg/mL of primocin (Invivogen).

extract_protocol:
We lysed cells by the direct addition of 3 ml of TRIzol (Life Technologies) after media removal according to the manufacturer’s instructions. For RNA extraction lysates were treated with 0.6 ml chloroform (Sigma-Aldrich) for 3 min and centrifuged at 12,500 g for 15 min at 4 °C. Aqueous supernatant was collected and diluted 1:1 with 70% ethanol. Total RNA was extracted from solution using RNeasy Mini Kit (Qiagen), following the manufacturer’s instructions and quantified using the NanoDrop spectrophotometer. RNA was used with A(260/280) nm ≥ 1.8 and A(260/230) nm ≥ 2.0. RNA quality was assessed using RNA 6000 Nano chips on the Agilent 2100 Bioanalyzer. The library preparation and RNA sequencing were performed by a Genomics Core Facility at EMBL.
RNA libraries were prepared for sequencing using standard Illumina protocols by a Genomics Core Facility at EMBL

treatment_protocol: HeLa cells were seeded in 60 mm dishes pre-coated with gelatin to reproduce conditions similar to microarrays. Prior to stimulation cells were starved in the absence of serum overnight. Afterwards, cells were incubated with GFs for four hours.

value: HeLa Kyoto cells

value: 100 ng/ml EGF+100 ng/ml IGF

tag: time

value: 4 hours


title: 100EGF_100IGF___rep3

description: HJH2HBGX2_DK_12_3_16s008441-1-1_Kuchenov_lane116s008441


title: 100IGF___rep2

description: HJCFCBGX2_DK_11_2_16s008428-1-1_Kuchenov_lane116s008428

source_name: HeLa Kyoto_100IGF

value: 100 ng/ml IGF


title: Atrial at T0, biological rep3

tag: tissue


title: 100IGF___rep1

description: HJHT3BGX2_DK_11_1_16s008380-1-1_Kuchenov_lane116s008380


title: 100EGF_100IGF___rep2

description: HJCFCBGX2_DK_12_2_16s008429-1-1_Kuchenov_lane116s008429


title: NBtumor [nrc4001]

description:
nrc4001
SAMPLE 1

source_name: Ghent

tag: Stage


title: 100EGF___rep1

description: HJHT3BGX2_DK_10_1_16s008379-1-1_Kuchenov_lane116s008379

source_name: HeLa Kyoto_100EGF

value: 100 ng/ml EGF


title: 100EGF___rep3

description: HJH2HBGX2_DK_10_3_16s008439-1-1_Kuchenov_lane116s008439


title: 100EGF___rep2

description: HJCFCBGX2_DK_10_2_16s008427-1-1_Kuchenov_lane116s008427


title: Atrial at T0, biological rep1


title: Atrial at T0, biological rep2


title: 6.25EGF_100IGF___rep3

description: HJH2HBGX2_DK_9_3_16s008438-1-1_Kuchenov_lane116s008438

source_name: HeLa Kyoto_6.25EGF_100IGF

value: 6.25 ng/ml EGF+100 ng/ml IGF


title: 100EGF_6.25IGF___rep2

description: HJCFCBGX2_DK_8_2_16s008425-1-1_Kuchenov_lane116s008425

source_name: HeLa Kyoto_100EGF_6.25IGF

value: 100 ng/ml EGF+6.25 ng/ml IGF


title: 12.5EGF_12.5IGF___rep4

description: HJH2HBGX2_DK_7_3_16s008436-1-1_Kuchenov_lane116s008436

source_name: HeLa Kyoto_12.5EGF_12.5IGF

value: 12.5 ng/ml EGF+12.5 ng/ml IGF


title: 6.25EGF_100IGF___rep1

description: HJHT3BGX2_DK_9_1_16s008378-1-1_Kuchenov_lane116s008378


title: 100EGF_6.25IGF___rep3

description: HJH2HBGX2_DK_8_3_16s008437-1-1_Kuchenov_lane116s008437


title: 12.5EGF_12.5IGF___rep3

description: HJCFCBGX2_DK_7_2_16s008424-1-1_Kuchenov_lane116s008424


title: NBtumor [nrc4010]

description:
nrc4010
SAMPLE 2


title: 12.5EGF_12.5IGF___rep1

description: HJHT3BGX2_DK_7_1_16s008376-1-1_Kuchenov_lane116s008376


title: 12.5IGF___rep4

description: HJH2HBGX2_DK_6_3_16s008435-1-1_Kuchenov_lane116s008435

source_name: HeLa Kyoto_12.5IGF

value: 12.5 ng/ml IGF


title: 12.5IGF___rep1

description: HJHT3BGX2_DK_6_1_16s008375-1-1_Kuchenov_lane116s008375


title: 12.5IGF___rep3

description: HJCFCBGX2_DK_6_2_16s008423-1-1_Kuchenov_lane116s008423


title: 12.5EGF___rep2

description: HJCFCBGX2_DK_5_2_16s008422-1-1_Kuchenov_lane116s008422

source_name: HeLa Kyoto_12.5EGF

value: 12.5 ng/ml EGF


title: 100IGF___rep3

description: HJH2HBGX2_DK_11_3_16s008440-1-1_Kuchenov_lane116s008440


title: 12.5EGF___rep1

description: HJHT3BGX2_DK_5_1_16s008374-1-1_Kuchenov_lane116s008374


title: 6.25IGF___rep2

description: HJCFCBGX2_DK_4_2_16s008421-1-1_Kuchenov_lane116s008421

source_name: HeLa Kyoto_6.25IGF

value: 6.25 ng/ml IGF


title: Mock___rep3

description: HJH2HBGX2_DK_2_3_16s008430-1-1_Kuchenov_lane116s008430

source_name: HeLa Kyoto_Mock

value: Mock


title: 6.25EGF___rep3

description: HJH2HBGX2_DK_3_3_16s008432-1-1_Kuchenov_lane116s008432

source_name: HeLa Kyoto_6.25EGF

value: 6.25 ng/ml EGF


title: Mock___rep2

description: HJCFCBGX2_DK_2_2_16s008419-1-1_Kuchenov_lane116s008419


title: 6.25IGF___rep1

description: HJHT3BGX2_DK_4_1_16s008373-1-1_Kuchenov_lane116s008373


title: Mock___rep1

description: HFKFMBGX2_DK_2_1_16s008371-1-1_Kuchenov_lane116s008371


title: 100EGF_6.25IGF___rep1

description: HJHT3BGX2_DK_8_1_16s008377-1-1_Kuchenov_lane116s008377


title: 6.25EGF___rep1

description: HJHT3BGX2_DK_3_1_16s008372-1-1_Kuchenov_lane116s008372


title: 6.25EGF___rep2

description: HJCFCBGX2_DK_3_2_16s008420-1-1_Kuchenov_lane116s008420


title: Mock___rep4

description: HJH2HBGX2_DK_2_4_16s008431-1-1_Kuchenov_lane116s008431


title: 6.25EGF_100IGF___rep2

description: HJCFCBGX2_DK_9_2_16s008426-1-1_Kuchenov_lane116s008426


title: 12.5EGF___rep3

description: HJH2HBGX2_DK_5_3_16s008434-1-1_Kuchenov_lane116s008434


title: T47D_Her2pos_populations.Rescue.seq.HER2.mut.Jan17_3_S180 [S180_L869R.Fulv+Palbo]

city: Cambridge

first: Ofir

last: Cohen

state: Massachusetts

address: 415 Main St, Cambridge, MA 02142

department: Cancer Program

institute: Broad Institute

description: Parental cell line with HER2 L869R over-expression treated with 1µM Fulv + 10µM Palbo

data_processing:
Library strategy: Smart-seq 2
mRNA-seq libraries were sequenced on an Illumina NextSeq 500 sequencer, V2 75 cycle kits
Reads were mapped with STAR aligner (Dobin et al. 2013)
Genome_build: hg19 of the human genome and build 12 of the GENCODE human genome annotation
Supplementary_files_format_and_content: rpkm and read counts

source_name: Breast Cancer

growth_protocol: T47D cells were infected de novo with lentivirus encoding HER2 mutants and controls (GFP, wild-type HER2, kinase-dead HER2, and ESR1 Y537S) in the pLX307 plasmid. Upon completion of selection with Puromycin, the cells were plated in 96-well plates in RPMI supplemented with 10% CSS for 48 hours.

extract_protocol: Plates with cell lysates were thawed and purified with 2.2x RNAClean SPRI beads (Beckman Coulter Genomics). The RNA captured beads were air-dried and processed immediately for RNA secondary structure denaturation (72˚C for three minutes) and cDNA synthesis. We performed SMART-Seq2 following the published protocol66

treatment_protocol: Cell were then treated with DMSO, 1μM fulvestrant, 1μM neratinib, 10μM palbociclib, 1μM fulvestrant + 1μM neratinib, or 1μM fulvestrant + 10μM palbociclib for 24 hours.

tag: cell line

tag: genotype/variation

value: HER2 L869R over-expression

tag: agent

value: 1microM Fulv + 10microM Palbo


title: T47D_Her2pos_populations.Rescue.seq.HER2.mut.Jan17_3_S192 [S192_ESR1.Fulv+Palbo]

description: Parental cell line with ESR1 Y537S over-expression treated with 1µM Fulv + 10µM Palbo

value: ESR1 Y537S over-expression


title: T47D_Her2pos_populations.Rescue.seq.HER2.mut.Jan17_3_S96 [S96_ESR1.Fulv+Palbo]


title: T47D_Her2pos_populations.Rescue.seq.HER2.mut.Jan17_3_S204 [S204_GFP.Fulv+Palbo]

description: Parental cell line with GFP over-expression treated with 1µM Fulv + 10µM Palbo

value: GFP over-expression


title: T47D_Her2pos_populations.Rescue.seq.HER2.mut.Jan17_3_S84 [S84_L869R.Fulv+Palbo]


title: T47D_Her2pos_populations.Rescue.seq.HER2.mut.Jan17_3_S228 [S228_D845A.Fulv+Palbo]

description: Parental cell line with HER2 D845A over-expression treated with 1µM Fulv + 10µM Palbo

value: HER2 D845A over-expression


title: T47D_Her2pos_populations.Rescue.seq.HER2.mut.Jan17_3_S60 [S60_L755S.Fulv+Palbo]

description: Parental cell line with HER2 L755S over-expression treated with 1µM Fulv + 10µM Palbo

value: HER2 L755S over-expression


title: 6.25IGF___rep3

description: HJH2HBGX2_DK_4_3_16s008433-1-1_Kuchenov_lane116s008433

value: HeLa Kyoto cells

value: 4 hours


title: T47D_Her2pos_populations.Rescue.seq.HER2.mut.Jan17_3_S240 [S240_S653C.Fulv+Palbo]

description: Parental cell line with HER2 S653C over-expression treated with 1µM Fulv + 10µM Palbo

value: HER2 S653C over-expression


title: T47D_Her2pos_populations.Rescue.seq.HER2.mut.Jan17_3_S120 [S120_wt.Fulv+Palbo]

description: Parental cell line with HER2 wt over-expression treated with 1µM Fulv + 10µM Palbo

value: HER2 wt over-expression


title: T47D_Her2pos_populations.Rescue.seq.HER2.mut.Jan17_3_S276 [S276_L869R.Fulv+Palbo]


title: T47D_Her2pos_populations.Rescue.seq.HER2.mut.Jan17_3_S252 [S252_L755S.Fulv+Palbo]


title: T47D_Her2pos_populations.Rescue.seq.HER2.mut.Jan17_3_S36 [S36_D845A.Fulv+Palbo]


title: T47D_Her2pos_populations.Rescue.seq.HER2.mut.Jan17_3_S24 [S24_wt.Fulv+Palbo]


title: T47D_Her2pos_populations.Rescue.seq.HER2.mut.Jan17_3_S48 [S48_S653C.Fulv+Palbo]


title: T47D_Her2pos_populations.Rescue.seq.HER2.mut.Jan17_3_S156 [S156_L755S.Fulv+Palbo]


title: T47D_Her2pos_populations.Rescue.seq.HER2.mut.Jan17_3_S132 [S132_D845A.Fulv+Palbo]


title: T47D_Her2pos_populations.Rescue.seq.HER2.mut.Jan17_3_S288 [S288_ESR1.Fulv+Palbo]


title: T47D_Her2pos_populations.Rescue.seq.HER2.mut.Jan17_3_S12 [S12_GFP.Fulv+Palbo]


title: T47D_Her2pos_populations.Rescue.seq.HER2.mut.Jan17_3_S216 [S216_wt.Fulv+Palbo]


title: T47D_Her2pos_populations.Rescue.seq.HER2.mut.Jan17_3_S108 [S108_GFP.Fulv+Palbo]


title: T47D_Her2pos_populations.Rescue.seq.HER2.mut.Jan17_3_S264 [S264_V777L.Fulv+Palbo]

description: Parental cell line with HER2 V777L over-expression treated with 1µM Fulv + 10µM Palbo

value: HER2 V777L over-expression


title: T47D_Her2pos_populations.Rescue.seq.HER2.mut.Jan17_3_S144 [S144_S653C.Fulv+Palbo]


title: T47D_Her2pos_populations.Rescue.seq.HER2.mut.Jan17_3_S83 [S83_L869R.Fulv+Palbo]


title: T47D_Her2pos_populations.Rescue.seq.HER2.mut.Jan17_3_S71 [S71_V777L.Fulv+Palbo]


title: T47D_Her2pos_populations.Rescue.seq.HER2.mut.Jan17_3_S107 [S107_GFP.Fulv+Palbo]


title: T47D_Her2pos_populations.Rescue.seq.HER2.mut.Jan17_3_S119 [S119_wt.Fulv+Palbo]


title: T47D_Her2pos_populations.Rescue.seq.HER2.mut.Jan17_3_S179 [S179_L869R.Fulv+Palbo]


title: T47D_Her2pos_populations.Rescue.seq.HER2.mut.Jan17_3_S275 [S275_L869R.Fulv+Palbo]


title: T47D_Her2pos_populations.Rescue.seq.HER2.mut.Jan17_3_S203 [S203_GFP.Fulv+Palbo]


title: T47D_Her2pos_populations.Rescue.seq.HER2.mut.Jan17_3_S167 [S167_V777L.Fulv+Palbo]


title: T47D_Her2pos_populations.Rescue.seq.HER2.mut.Jan17_3_S191 [S191_ESR1.Fulv+Palbo]


title: T47D_Her2pos_populations.Rescue.seq.HER2.mut.Jan17_3_S131 [S131_D845A.Fulv+Palbo]


title: T47D_Her2pos_populations.Rescue.seq.HER2.mut.Jan17_3_S59 [S59_L755S.Fulv+Palbo]


title: T47D_Her2pos_populations.Rescue.seq.HER2.mut.Jan17_3_S287 [S287_ESR1.Fulv+Palbo]