title: ttpA-D450trx_sample_4

source_name: strain AX3_ttpA-D450trx

growth_protocol: Amebae were grown under axenic conditions in growth medium until approximately 80% confluence was reached. They were then frozen until RNA extraction was performed.


title: nasopharyngeal gene expression of subject M118 at m12 [121150011182]

status: Public on Nov 24 2021

type: RNA

city: Utrecht

first: Wouter

last: de Steenhuijsen Piters

address: Heidelberglaan 100

country: Netherlands

institute: UMC Utrecht

hyb_protocol: Following fragmentation, cRNA were hybridized on Affymetrix Clariom S Human Pico arrays.

scan_protocol: GeneChips were scanned inhouse by Hologic Ltd. UK.

data_processing: The data were analyzed using R/Rstudio. Outliers were identified using raw intensity data using the arrayQualityMetrics package and removed from the dataset. RMA was performed to reduce the data from 300304 probe-level features to 27189 genes. After removing non-annotated genes/control probes, 18526 genes remained, which were for the conclusions in the paper.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: nasopharyngeal cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: N/A; study in human infants.

extract_protocol: RNA was extracted by a TRIzol reagent (Invitrogen)/chlorform method, cleaned using the RNAeasy Micro Kit (Qiagen) (OpenWetWare contributors, 2015)

treatment_protocol: Nasopharyngeal cells were collected in RNAprotect Cell Reagent (Qiagen) at -80 °C until extraction.

tag: subject

tag: time point

tag: age

tag: cell type

value: nasopharyngeal cells


title: nasopharyngeal gene expression of subject M116 at m12 [121150011162]


title: ttpA-D450trx_sample_3

type: SRA

city: Durham

first: Melissa

last: Wells

state: NC

address: 111 TW Alexander Drive

department: LST

country: USA

institute: NIEHS

library_source: transcriptomic

data_processing:
Base calling  and generation of FASTQ files was performed with Illumina bcl2fastq2
Read pairs were filtered to remove those where either mate's mean quality score fell below 20
Reads were aligned to D. discoideum reference assembly using STAR 2.6.0c
Counts per gene were determined using featureCounts 1.5.1 based on dictyBase.org gene annotations downloaded in March 2018
Normalized counts were determined using the estimateSizeFactors function
Genome_build: dictyBase.org D. discoideum Chromosomal DNA created 05-13-2009
Supplementary_files_format_and_content: tab-delimited text, raw and normalized read counts per gene

organism: Dictyostelium discoideum

extract_protocol:
RNA was purified using the Illustra RNAspin Kit (GE Healthcare Life Sciences) following the manufacturer’s protocol.
Total cellular RNA was quantitated with a Qubit fluorometer, and 250 ng of each sample was transcribed to generate cDNA libraries using the Illumina TruSeq RNA Kit (Illumina Inc, San Diego, CA) following the manufacturer's Low Sample (LS) protocol, with the following modifications:  2 minutes of centrifugation were used during the bead drying steps and 12 cycles were used to enrich DNA fragments.

tag: strain background

tag: genotype


title: 1HF250V

city: Lausanne

first: Ana

last: Rodriguez Sanchez-Archidona

state: Vaud

address: Genopode building - Quartier Sorge

department: CIG

country: Switzerland

institute: University of Lausanne

data_processing:
Reads were mapped and quantified with STAR-2.5.3a software (18) usingM.musculus-mm15 as reference genome and GRCm38.83 from ENSEMBL as the reference annotation index.
Counts were filtered, excluding those genes with less than one count per million in nine libraries, and normalized using trimmed mean normalization method (TMM) with 'edgeR'.
Genome_build: M.musculus-mm15 reference genome.
Supplementary_files_format_and_content: Normalized matrix in log2 were raw counts were filtered, excluding those genes with less than one count per million in nine libraries, and normalized using trimmed mean normalization method (TMM) with 'edgeR'.

organism: Mus musculus

source_name: Visceral adipose tissue

extract_protocol:
Total RNA from liver, soleus muscle and visceral adipose tissue was extracted using the RNeasy Plus micro kit (Qiagen, Hombrechtikon, Switzerland).
Integrity of RNA was verified on a Fragment Analyzer (Agilent Technologies, Inc., Santa Clara, CA 95051, USA) and all preparations had a RNA quality number (RQN) between 8.2 and 9.3. RNA-seq libraries were prepared using 250ng of total RNA and the Illumina TruSeq Stranded mRNA reagents (Illumina; San Diego, California, USA). Cluster generation was performed with the resulting libraries using the Illumina TruSeq SR Cluster Kit v4 reagents
Sequenced on the Illumina HiSeq 2500 using TruSeq SBS Kit v4 reagents. A sequencing depth of 27 to 46 million reads using 100bp single reads was used.

tag: strain

tag: diet

value: HFD

tag: time

tag: tissue

value: Visceral adipose tissue


title: 1HF250S

source_name: Soleus muscle

value: Soleus muscle


title: WT_sample 4

source_name: strain AX3_WT

value: WT


title: ttpA-D450trx_sample_1


title: ttpA-D450trx_sample_2


title: 1HF249S


title: WT_sample 3


title: nasopharyngeal gene expression of subject M122 at m12 [121150011222]


title: nasopharyngeal gene expression of subject M120 at m12 [121150011202]


title: nasopharyngeal gene expression of subject M111 at m12 [121150011112]


title: 1HF249V


title: WT_sample 2


title: 1HF250L

source_name: Liver

value: Liver


title: WT_sample 1


title: ttpA-Y242fsx_sample_4

source_name: strain AX3_ttpA-Y242fsx


title: ttpA-C240ins_LG_sample_2

source_name: strain AX3_ttpA-C240ins_liquid growth

growth_protocol: Amebae were grown under axenic conditions in growth medium until approximately 80% confluence was reached in the case of cells in surface cultures, or approximately 2 million cells/ml in the case of liquid cultures. They were then frozen until RNA extraction was performed.

tag: growth condition

value: liquid growth


title: ttpA-Y242fsx_sample_3


title: ttpA-Y242fsx_sample_2


title: 1HF249L


title: nasopharyngeal gene expression of subject M096 at m12 [121150010962]


title: nasopharyngeal gene expression of subject M105 at m12 [121150011052]


title: ttpA-Y242fsx_sample_1


title: nasopharyngeal gene expression of subject M108 at m12 [121150011082]


title: 1HF231V


title: nasopharyngeal gene expression of subject M098 at m12 [121150010982]


title: 1HF231S


title: nasopharyngeal gene expression of subject M100 at m12 [121150011002]


title: WT_sample_4


title: WT_sample_2


title: WT_sample_1


title: ttpA-E236fsx_sample_4

source_name: strain AX3_ttpA-E236fsx


title: nasopharyngeal gene expression of subject M094 at m12 [121150010942]


title: ttpA-E236fsx_sample_3


title: ttpA-E236fsx_sample_1


title: ttpA-E236fsx_sample_2


title: 1HF230S


title: 1HF230V


title: ttpA-C231S_sample_4

source_name: strain AX3_ttpA-C231S


title: 1HF231L


title: 1HF230L


title: ttpA-C231S_sample_3


title: nasopharyngeal gene expression of subject M078 at m12 [121150010782]


title: nasopharyngeal gene expression of subject M138 at m9 [121149011382]


title: ttpA-C231S_sample_2


title: WT_sample_3


title: 1HF227V


title: 1HF227S


title: ttpA-C231S_sample_1


title: WT_8h

city: Tian Jin

first: Zhang

last: Sissy

address: FuKang Road

country: China

institute: Nankai university

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
FPKM were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: NC_004431
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Escherichia coli CFT073

source_name: UPEC

extract_protocol:
bacterial were collected, frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with was used with 4 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: protocol

value: Cell


title: 21792_hpNPC_Tbr2

city: London

first: Marco

last: Trizzino

state: UK

address: Imperial College Road

department: Life Sciences

country: United Kingdom

institute: Imperial College London

library_source: genomic

data_processing:
ChIP-seq and ATAC-seq data were aligned to hg19 or panTro5 as appropriate using BWA-mem
RNA-seq data were analyzed with kallisto using hg19 or panTro5 as appropriate
ATAC-seq peaks were called with MACS2.
RNA-seq gene expression was quantified using Kallisto
For input bigwig was made with Deeptools
Genome_build: hg19 for Homo sapiens samples and panTro5 for Pan troglodytes samples.
Supplementary_files_format_and_content: peak text files (ChIP-seq, ATAC-seq), Kallisto quantification (spreadsheet) for RNA-seq. Bigwig for input of Chip-seq

molecule: genomic DNA

source_name: HS Rep 3 (21792 line)

growth_protocol: The iPSC lines were expanded in feeder-free, serum-free mTeSR™1 medium (STEMCELL Technologies). Cells were passaged ~1:10 at 80% confluency using ReLeSR (STEMCELL Technologies) and small cell clusters (50–200 cells) were subsequently plated on tissue culture dishes coated overnight with Geltrex™ LDEV-Free hESC-qualified Reduced Growth Factor Basement Membrane Matrix (Fisher-Scientific).

extract_protocol: Barcoded libraries were made with NEB ULTRA II DNA Library Prep Kit for Illumina, and sequenced on Illumina NovaSeq6000, producing 100x100 PE reads or the NextSeq500 producing 80x80 PE reads

treatment_protocol: The stem cells were treated with a previously published media for differentiation into hippocampal intermediate progenitors (Yu et al 2014). This consists of 1:1 DMEM/F12 supplemented with N2, B27, Noggin, Cyclopamine, DKK-1 and SB43154 and PennStrep antibiotic. The cells were exposed to this media for five days prior to collection.

tag: antibodies

value: TBR2/EOMES Abcam ab216870


title: GM238_hpNPC_Tbr2

source_name: HS Rep 2 (GM23716 line)


title: 1HF227L


title: 21792_hpNPC_d5

extract_protocol: 50000 cells per condition were processed as described in the original ATAC-seq protocol paper (Buenrostro et al 2013)


title: SV20_hpNPC_d5

source_name: HS Rep 1 (SV20 line)


title: nasopharyngeal gene expression of subject M133 at m9 [121149011332]


title: nasopharyngeal gene expression of subject M134 at m9 [121149011342]


title: GM238_hpNPC_d5


title: 1HF225V


title: 1HF225S


title: nasopharyngeal gene expression of subject M132 at m9 [121149011322]


title: nasopharyngeal gene expression of subject M135 at m9 [121149011352]


title: nasopharyngeal gene expression of subject M128 at m9 [121149011282]


title: 21792_hpNPCd5_RNA

extract_protocol:
Cells were lysed in Tri-reagent (Zymo research) and total RNA was extracted using Quick-RNA Miniprep kit (Zymo research).
RNA libraries were prepared using NEBNext® Poly(A) mRNA Magnetic Isolation Module, NEBNext® UltraTM II Directional RNA Library Prep Kit for Illumina® and NEBNext® UltraTM II DNA Library Prep Kit for Illumina® according to the manufacturer’s instructions (New England Biolabs). 1 μg of total RNA input was used for each library


title: GM238_hpNPCd5_RNA_REP


title: nasopharyngeal gene expression of subject M126 at m9 [121149011262]


title: 21792_hpNPCd5_RNA_REP


title: GM238_hpNPCd5_RNA


title: 1HF225Lb


title: WTLB

value: LB


title: 1HF225La


title: SV20_hpNPCd5_RNA


title: SV20_hpNPCd5_RNA_REP


title: 1HF225L


title: nasopharyngeal gene expression of subject M122 at m9 [121149011222]


title: nasopharyngeal gene expression of subject M119 at m9 [121149011192]


title: nasopharyngeal gene expression of subject M120 at m9 [121149011202]


title: nasopharyngeal gene expression of subject M118 at m9 [121149011182]


title: scBCR-Seq of tm8 decidual tissues

city: Changsha

first: Lei

last: Dai

state: Hunan

address: 87 Xiangya Road

institute: Xiangya Hospital, Central South University

description:
Single cell BCR
VDJ-seq

data_processing:
Library strategy: BCR-seq
bcl2fastq tools for base calling.
CellRanger software for single cell identifying.
PCA and UMAP/TSNE for dimensionality reduction.
Seurat for finding clusters.
Genome_build: GRCh38
Supplementary_files_format_and_content: filtered_matrix.mtx files contain genewise read counts for detected cells in a space-efficient matrix market format; filtered_genes.tsv files contain Ensembl IDs and gene symbols as tab-delimited text; filtered_barcode.tsv files contain the 10X barcodes used to identify cells.
Supplementary_files_format_and_content: clonotypes.csv files contain high-level descriptions of each clonotype.
Supplementary_files_format_and_content: filtered_contig_annotations.csv files contain high-level annotations of each high-confidence, cellular contig.

source_name: decidual tissues

extract_protocol:
The small tissue blocks were cut into pieces and processed with digestive enzyme. Then, the tissues were made into single-cell suspension using the gentleMACS Dissociator. Finally, the single cells were suspended in calcium- and magnesium-free PBS containing 0.04% weight/volume BSA.
cDNA libraries and TCR VDJ libraries were prepared using 10x Genomics Chromium Single Cell 5' Library Construction Kit (10x Genomics) and Chromium Single Cell V(D)J Enrichment Kit (10x Genomics), following the manufacturer’s instruction.

tag: patient

tag: gender

value: Female

tag: group

value: Non-labor

tag: gestational week

tag: delivery mode

value: Caesarean section

value: Decidual tissues


title: scTCR-Seq of tm8 decidual tissues

description:
Single cell TCR
VDJ-seq

data_processing:
Library strategy: TCR-seq
bcl2fastq tools for base calling.
CellRanger software for single cell identifying.
PCA and UMAP/TSNE for dimensionality reduction.
Seurat for finding clusters.
Genome_build: GRCh38
Supplementary_files_format_and_content: filtered_matrix.mtx files contain genewise read counts for detected cells in a space-efficient matrix market format; filtered_genes.tsv files contain Ensembl IDs and gene symbols as tab-delimited text; filtered_barcode.tsv files contain the 10X barcodes used to identify cells.
Supplementary_files_format_and_content: clonotypes.csv files contain high-level descriptions of each clonotype.
Supplementary_files_format_and_content: filtered_contig_annotations.csv files contain high-level annotations of each high-confidence, cellular contig.


title: nasopharyngeal gene expression of subject M117 at m9 [121149011172]

tag: subject

tag: time point


title: 1HF209V


title: 1HF209S


title: nasopharyngeal gene expression of subject M116 at m9 [121149011162]

tag: age

tag: cell type


title: scRNA-Seq of tm8 decidual tissues

description: Single cell RNA

data_processing:
bcl2fastq tools for base calling.
CellRanger software for single cell identifying.
PCA and UMAP/TSNE for dimensionality reduction.
Seurat for finding clusters.
Genome_build: GRCh38
Supplementary_files_format_and_content: filtered_matrix.mtx files contain genewise read counts for detected cells in a space-efficient matrix market format; filtered_genes.tsv files contain Ensembl IDs and gene symbols as tab-delimited text; filtered_barcode.tsv files contain the 10X barcodes used to identify cells.
Supplementary_files_format_and_content: clonotypes.csv files contain high-level descriptions of each clonotype.
Supplementary_files_format_and_content: filtered_contig_annotations.csv files contain high-level annotations of each high-confidence, cellular contig.


title: scBCR-Seq of tm4 decidual tissues

description:
Single cell BCR
VDJ-seq


title: scBCR-Seq of tm7 decidual tissues

description:
Single cell BCR
VDJ-seq

value: Labor onset

value: Vaginal delivery


title: scTCR-Seq of tm3 decidual tissues

description:
Single cell TCR
VDJ-seq


title: scTCR-Seq of tm7 decidual tissues

description:
Single cell TCR
VDJ-seq


title: Pancreatic islets, 3RC274

data_processing:
Reads were mapped with STAR-2.5.3a software to M.musculus-mm15 reference genome.
Read counts for each gene were generated with HTSeq-0.9.1 software using as reference the annotation index GRCm38.83 from ENSEMBL.
Counts were filtered, excluding those genes with less than one count per million in two libraries, and normalized using trimmed mean normalization method (TMM) with 'edgeR'.
3 clear outliers (1RC274, 2HF270, 2RC275), as determined by PCA and hierarchical clustering, were discarded.
Genome_build: M.musculus-mm15 reference genome.
Supplementary_files_format_and_content: Normalized matrix in log2 were raw counts were filtered, excluding those genes with less than one count per million in two libraries, and normalized using trimmed mean normalization method (TMM) with 'edgeR'.

source_name: Pancreatic islets

growth_protocol: Islets from 8 week-old male mice were isolated by hand-picking following pancreata digestion by Liberase. After overnight recovery in cell culture medium, RNA was extracted on batches of 120-150 islets per mouse.

extract_protocol:
Total RNA from islets was extracted using the RNeasy Plus micro kit (Qiagen, Hombrechtikon, Switzerland).
Integrity of islet RNA was verified on a Fragment Analyzer (Agilent Technologies, Inc., Santa Clara, CA 95051, USA) and all preparations had a RNA quality number (RQN) between 8.2 and 9.3. RNA-seq libraries were prepared using 250ng of total RNA and the Illumina TruSeq Stranded mRNA reagents (Illumina; San Diego, California, USA). Cluster generation was performed with the resulting libraries using the Illumina TruSeq SR Cluster Kit v4 reagents
Sequenced on the Illumina HiSeq 2500 using TruSeq SBS Kit v4 reagents. A sequencing depth of 31 to 46 million reads using 125bp single-end reads was used.

value: BALB/cJ

value: RC

tag: day


title: scRNA-Seq of tm4 decidual tissues

description: Single cell RNA


title: scRNA-Seq of tm3 decidual tissues

description: Single cell RNA


title: 1HF209L

tag: strain

value: HFD


title: Pancreatic islets, 3RC275

tag: diet


title: scTCR-Seq of tm2 decidual tissues

description:
Single cell TCR
VDJ-seq


title: Pancreatic islets, 3RC273


title: scRNA-Seq of tm7 decidual tissues

description: Single cell RNA


title: scBCR-Seq of tm3 decidual tissues

description:
Single cell BCR
VDJ-seq


title: nasopharyngeal gene expression of subject M109 at m9 [121149011092]

value: nasopharyngeal cells


title: nasopharyngeal gene expression of subject M114 at m9 [121149011142]


title: scRNA-Seq of tm2 decidual tissues

description: Single cell RNA


title: nasopharyngeal gene expression of subject M108 at m9 [121149011082]


title: scTCR-Seq of tm4 decidual tissues

description:
Single cell TCR
VDJ-seq


title: Pancreatic islets, 3RC272


title: scTCR-Seq of tm1 decidual tissues

description:
Single cell TCR
VDJ-seq


title: scBCR-Seq of tm2 decidual tissues

description:
Single cell BCR
VDJ-seq


title: nasopharyngeal gene expression of subject M102 at m9 [121149011022]


title: Pancreatic islets, 3HF275


title: Pancreatic islets, 3HF276


title: nasopharyngeal gene expression of subject M101 at m9 [121149011012]


title: nasopharyngeal gene expression of subject M111 at m9 [121149011112]


title: skin fibroblasts, siM_P_4

city: Charleston

first: Carol

last: Feghali-Bostwick

state: SC

address: 96 Johnathan Lucas St Suite 816 MSC 637

department: Medicine - Rheumatology

institute: Medical University of South Carolina

description:
siM_P_4
res_DESeq2_combat_PDGFBB_siMCHR1_vs_ctrl
res_DESeq2_combat_siRNA_PDGFBB_vs_veh
counts_PDGFBB_siRNA_vs_cont_COMBAT
counts_siRNA_PDGFBB_vs_veh_COMBAT

data_processing:
Novogene: Original image data file from HTS platforms is transformed to sequenced reads ( Raw Data or Raw Reads) by CASAVA base recognition (Base Calling).
Raw data are stored in FASTQ(fq) format files, which contain sequences of reads and corresponding base quality.
STAR software is used to accomplish the mapping. The alignment by STAR precisely and effectively performs positioning junction reads for RNA sequencing data analysis.
Gene expression level is calculated by the number of mapped reads with FeatureCounts. Read counts is proportional to gene expression level, gene length and sequencing depth, and is used for DE analysis.
Gene-level count data were generated by HTSeq and FeatureCounts and normalized by ComBat-seq (Zhang et al., 2020). DE analysis of two conditions/groups was performed using the DESeq2 R package (Anders et al., 2010). Significance criteria q-value<0.1.
Genome_build: Homo Sapiens(GRCh38/hg38)
Supplementary_files_format_and_content: tab-delimited .txt files include DESEQ2 output for each Comparison ...

source_name: primary human skin fibroblasts

growth_protocol: skin fibroblasts were maintained in DMEM media with 10%FBS, 1X ab/am

extract_protocol:
total RNA was extracted with trizol method
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA library prep kit for Illumina (NEB, USA).

treatment_protocol: A mixture of 100 nM of each RNAi and Lipofectamine®2000 was added to cells, and cells were cultured for 72 h. Fibroblasts were serum-starved at least 2 h before further stimulation. MCHR1 silenced or controlled fibroblasts were treated with 40 ng/mL PDGF-BB (R&D) and harvested 24hrs after stimulation.

value: skin fibroblast

tag: transfection

tag: treatment

value: PDGFBB


title: skin fibroblasts, siM_P_3

description:
siM_P_3
res_DESeq2_combat_PDGFBB_siMCHR1_vs_ctrl
res_DESeq2_combat_siRNA_PDGFBB_vs_veh
counts_PDGFBB_siRNA_vs_cont_COMBAT
counts_siRNA_PDGFBB_vs_veh_COMBAT


title: nasopharyngeal gene expression of subject M100 at m9 [121149011002]


title: skin fibroblasts, siM_P_1

description:
siM_P_1
res_DESeq2_combat_PDGFBB_siMCHR1_vs_ctrl
res_DESeq2_combat_siRNA_PDGFBB_vs_veh
counts_PDGFBB_siRNA_vs_cont_COMBAT
counts_siRNA_PDGFBB_vs_veh_COMBAT


title: skin fibroblasts, Cont_P_3

description:
Cont_P_3
res_DESeq2_combat_PDGFBB_siMCHR1_vs_ctrl
res_DESeq2_combat_control_PDGFBB_vs_veh
counts_PDGFBB_siRNA_vs_cont_COMBAT
counts_cont_PDGFBB_vs_veh_COMBAT

value: siRNA-scramble


title: scBCR-Seq of tm1 decidual tissues

description:
Single cell BCR
VDJ-seq

tag: tissue


title: skin fibroblasts, Cont_P_1

description:
Cont_P_1
res_DESeq2_combat_PDGFBB_siMCHR1_vs_ctrl
res_DESeq2_combat_control_PDGFBB_vs_veh
counts_PDGFBB_siRNA_vs_cont_COMBAT
counts_cont_PDGFBB_vs_veh_COMBAT


title: skin fibroblasts, Cont_P_4

description:
Cont_P_4
res_DESeq2_combat_PDGFBB_siMCHR1_vs_ctrl
res_DESeq2_combat_control_PDGFBB_vs_veh
counts_PDGFBB_siRNA_vs_cont_COMBAT
counts_cont_PDGFBB_vs_veh_COMBAT


title: Pancreatic islets, 3HF273


title: scRNA-Seq of tm1 decidual tissues

description: Single cell RNA


title: skin fibroblasts, siM_V_3

description:
siM_V_3
res_DESeq2_combat_siRNA_PDGFBB_vs_veh
counts_siRNA_PDGFBB_vs_veh_COMBAT

value: vehicle


title: Pancreatic islets, 3RC289


title: skin fibroblasts, siM_V_4

description:
siM_V_4
res_DESeq2_combat_siRNA_PDGFBB_vs_veh
counts_siRNA_PDGFBB_vs_veh_COMBAT


title: skin fibroblasts, Cont_V_4

description:
Cont_V_4
res_DESeq2_combat_control_PDGFBB_vs_veh
counts_cont_PDGFBB_vs_veh_COMBAT


title: nasopharyngeal gene expression of subject M098 at m9 [121149010982]


title: nasopharyngeal gene expression of subject M090 at m9 [121149010902]


title: skin fibroblasts, Cont_V_3

description:
Cont_V_3
res_DESeq2_combat_control_PDGFBB_vs_veh
counts_cont_PDGFBB_vs_veh_COMBAT


title: skin fibroblasts, siM_V_1

description:
siM_V_1
res_DESeq2_combat_siRNA_PDGFBB_vs_veh
counts_siRNA_PDGFBB_vs_veh_COMBAT


title: Pancreatic islets, 3RC282


title: nasopharyngeal gene expression of subject M094 at m9 [121149010942]


title: Pancreatic islets, 3RC281


title: nasopharyngeal gene expression of subject M097 at m9 [121149010972]


title: nasopharyngeal gene expression of subject M080 at m9 [121149010802]


title: Pancreatic islets, 3RC280


title: Pancreatic islets, 3HF282


title: Pancreatic islets, 3HF290


title: Pancreatic islets, 3HF281


title: Pancreatic islets, 3HF291


title: NCI-N87 KRT17-KO2 rep2

city: Hangzhou

first: Mengjie

last: Li

address: NO.866 Yuhangtang Road

institute: Zhejiang University

description: Gene expression of NC-N87 KRT17 knockout cells

data_processing:
Clean reads were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: NCI-N87 KRT17 knockout cells

extract_protocol:
Total RNA was extracted from each cell sample using the Trizol  method
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Gastric cancer

tag: cell line

tag: genotype

value: KRT17 knockout


title: NCI-N87 KRT17-KO2 rep1


title: NCI-N87 KRT17-KO1 rep2


title: nasopharyngeal gene expression of subject M071 at m9 [121149010712]

source_name: nasopharyngeal cells


title: nasopharyngeal gene expression of subject M078 at m9 [121149010782]


title: nasopharyngeal gene expression of subject M133 at m6 [121148011332]


title: NCI-N87 KRT17-KO1 rep1


title: nasopharyngeal gene expression of subject M134 at m6 [121148011342]


title: skin fibroblasts, Cont_V_1

description:
Cont_V_1
res_DESeq2_combat_control_PDGFBB_vs_veh
counts_cont_PDGFBB_vs_veh_COMBAT


title: Pancreatic islets, 3RC286


title: NCI-N87 WT rep1

description: Gene expression of NCI-N87 wild type cells

source_name: NCI-N87 wild type cells

value: wild type


title: N_M9_output_rep1

city: Würzburg

first: Falk

last: Ponath

address: Josef-Schneider-Straße 2

country: Germany

institute: Helmholtz Institute for RNA-based Infection Research (HIRI)

description:
Around 30,000 transformants/library were obtained and pooled in 10 ml 1×PBS. Cells were washed twice on fresh 1×PBS prior to inoculation on the selective (M9+succinate) and non-selective (LB) media. The turbidity of the transformants suspension was measured and 4 ODs were stored as ‘input’. Next, 2 ODs were inoculated in 50 ml of either M9+succinate or LB in a 250 ml flask and incubated without aeration for 22h at 37°C. From the resulting cultures, 4 ODs were collected and considered ‘output’. Plasmid content from ‘input’ and ‘output’ was extracted by Nucleospin Mini plasmid kit (Macherey-Nagel) and used as template for library preparation for deep sequencing
Mutational Scanning - Results.xlsx

data_processing:
The reads were used input for Enrich2 to determine enrichment of point mutations. For this, Enrich2 settings were set to include reads with an average read quality above 20 and up to 50 mismatches to the ProQ sequence. These results were then subsetted to only include the occurences of single point mutations.
Genome_build: NC_016810.1
Supplementary_files_format_and_content: Mutational Scanning: counts of individual mutant (.xlsx); CoIP: coverage files (.wig)

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

source_name: German Collection of Microorganisms and Cell Cultures GmbH

extract_protocol: Library preparation was carried out by using 50 ng of plasmid as template from the ‘input’ and ‘output’. For each library LIB1 (1-81 aa), LIB2 (73-155 aa) and LIB3 (155-227 aa), same region subjected to mutagenesis was amplified by PCR with specific primers that incorporated Nextera adapters: i) JVO18138/JVO18139 for LIB1, ii) JVO18140/JVO18141 for LIB2 and iii) JVO18142/JVO18143 for LIB3. The distribution of the library and concentration of library DNA was determined by DNA bioanalyzer and a DNA Qubit measurement respectively. Amplified DNAs from different libraries were pooled and sequenced on an Illumina MiSeq 2 x 300 bp at the next generation sequencing core unit of the Helmholtz Centre for Infection Biology (HZI).

tag: sample type

value: output for mutational scanning - M9 media - replicate 1


title: Pancreatic islets, 3RC283


title: NCI-N87 WT rep2


title: Pancreatic islets, 3RC285


title: nasopharyngeal gene expression of subject M131 at m6 [121148011312]


title: nasopharyngeal gene expression of subject M129 at m6 [121148011292]


title: Pancreatic islets, 3RC287


title: N_M9_input_rep2

data_processing:
The reads were used input for Enrich2 to determine enrichment of point mutations. For this, Enrich2 settings were set to include reads with an average read quality above 20 and up to 50 mismatches to the ProQ sequence. These results were then subsetted to
Genome_build: NC_016810.1
Supplementary_files_format_and_content: Mutational Scanning: counts of individual mutant (.xlsx); CoIP: coverage files (.wig)

value: input for mutational scanning - M9 media - replicate 2


title: NB3: BE2N infected with Dn-hTERT for 55 days

city: New York

first: Neal

last: Lue

state: New York

address: 1300 York Ave.

institute: Weill Cornell Medicine

data_processing:
The samples were sequenced using Illumina NovaSeq6000 sequencer with paired-end 50 bps reads. The raw sequencing reads in BCL format were processed through bcl2fastq 2.19 (Illumina) for FASTQ conversion and demultiplexing.
The RNA reads were aligned and mapped to the GRCh37 human reference genome by STAR (Version2.5.2).
The transcriptome reconstruction was performed by Cufflinks (Version 2.1.1). The abundance of transcripts was measured with Cufflinks in Fragments Per Kilobase of exon model per Million mapped reads (FPKM).
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text file include normalized abundance measurements(FPKM) at gene level for each samples

source_name: cultured neuroblastoma cell

growth_protocol: Cells were cultured in RPMI-1640 medium (CORING) supplemented with 10% fetal bovine serum (FBS) (GEMINI) and 1% penicillin/streptomycin (Pen/Strep) (Gibco).

extract_protocol:
Cells were harvested and total RNA was isolated using the RNeasy Mini Kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Amphotropic retroviruses were generated in Phoenix packaging cells by Ca2PO4 transfection of the retroviral vectors (20 μg each) . Transfection efficiency was monitored based on GFP expression. At 48 hr post-transfection, the viral supernatants were filtered through a 0.45 μm filter and used to infect BE2N cells with the addition of 4 μg/ml polybrene. Cells were infected twice for 6 ~ 8 hr, and were selected with puromycin (0.9 μg/ml) at 48 hr post-infection. Cells were passaged in media for up to 100 days and harvested at different time points for RNA-seq analysis.

value: cultured neuroblastoma cell

value: MYCN-amplified

value: Dn-hTERT, 55 days


title: NB4: BE2N infected with Dn-hTERT for 82 days

value: Dn-hTERT, 82 days


title: nasopharyngeal gene expression of subject M128 at m6 [121148011282]


title: nasopharyngeal gene expression of subject M127 at m6 [121148011272]


title: Pancreatic islets, 3HF287

value: BALB/cJ


title: N_M9_output_rep2

value: output for mutational scanning - M9 media - replicate 2


title: N_M9_input_rep1

value: input for mutational scanning - M9 media - replicate 1


title: nasopharyngeal gene expression of subject M136 at m6 [121148011362]

value: nasopharyngeal cells


title: NB2: BE2N infected with Dn-hTERT for 33 days

value: Dn-hTERT, 33 days


title: Pancreatic islets, 3HF284

value: HFD


title: NB1: Parental BE2N

value: DMSO


title: nasopharyngeal gene expression of subject M120 at m6 [121148011202]


title: Pancreatic islets, 3HF283


title: N_LB_input

value: input for mutational scanning - LB


title: N_LB_output

value: output for mutational scanning - LB


title: Pancreatic islets, 2RC275

value: RC


title: Pancreatic islets, 3HF288


title: nasopharyngeal gene expression of subject M123 at m6 [121148011232]


title: L_M9_output_rep2


title: BE2N5: BE2N treated with BrdU for 26 days

value: BrdU


title: nasopharyngeal gene expression of subject M119 at m6 [121148011192]


title: L_M9_output_rep1

value: output for mutational scanning - M9 media - replicate 1


title: BE2N4: BE2N treated with BrdU for 20 days


title: nasopharyngeal gene expression of subject M115 at m6 [121148011152]


title: nasopharyngeal gene expression of subject M117 at m6 [121148011172]


title: L_M9_inut_rep2

value: input for mutational scanning - M9 media - replicate 2


title: Pancreatic islets, 2RC273


title: BE2N3: BE2N treated with BrdU for 11 days

value: cultured neuroblastoma cell


title: Pancreatic islets, 2RC274


title: Pancreatic islets, 2RC272


title: BE2N2: BE2N treated with BrdU for 5 days

value: MYCN-amplified


title: BE2N1: BE2N treated with DMSO


title: nasopharyngeal gene expression of subject M114 at m6 [121148011142]


title: nasopharyngeal gene expression of subject M108 at m6 [121148011082]


title: L_LB_output


title: Pancreatic islets, 2HF275


title: Pancreatic islets, 2HF274


title: L_LB_input


title: Pancreatic islets, 2HF272


title: C_M9_output_rep2


title: Pancreatic islets, 2HF273


title: nasopharyngeal gene expression of subject M109 at m6 [121148011092]


title: Pancreatic islets, 2RC271


title: C_M9_input_rep2


title: nasopharyngeal gene expression of subject M106 at m6 [121148011062]


title: nasopharyngeal gene expression of subject M107 at m6 [121148011072]


title: C_M9_input_rep1


title: nasopharyngeal gene expression of subject M104 at m6 [121148011042]


title: Pancreatic islets, 2RC268


title: Pancreatic islets, 2RC267


title: L_M9_input_rep1


title: Pancreatic islets, 2RC266


title: C_LB_output


title: C_LB_input


title: nasopharyngeal gene expression of subject M100 at m6 [121148011002]


title: Pancreatic islets, 2HF269


title: C_M9_output_rep1


title: nasopharyngeal gene expression of subject M098 at m6 [121148010982]


title: nasopharyngeal gene expression of subject M126 at m6 [121148011262]


title: Pancreatic islets, 2HF267


title: nasopharyngeal gene expression of subject M090 at m6 [121148010902]


title: nasopharyngeal gene expression of subject M138 at m4 [121147011382]


title: SCC1_Control_1

city: Ariel

first: Santosh

last: Kumar

state: Ariel

address: RamatHa Golan Street 65'

department: Molecular Biology

country: Israel

institute: Ariel University

description: Naïve_parental_line_10nM treamtment

data_processing:
Reads were trimmed and clipped for quality control in trim_galore (v0.5.0).
Read quality was checked for each sample using FastQC (v0.11.7).
Reads were taken to Hisat2 (v2.1.0) for alignment using hg38, GRch38.97
High-quality reads were then imported into samtools (v1.9 using htslib 1.9) for conversion of SAM files to BAM file.
Gene-count summaries were generated with featureCounts (v1.6.3): A numeric matrix of raw read counts was generated, with genes in rows and samples in columns, and used for differential gene expression analysis with the Bioconductor Limma package.
Genome_build: hg38, GRch38.97
Supplementary_files_format_and_content: featureCounts.txt :Combined Tab-delimited text file includes count for all samples.
Supplementary_files_format_and_content: Avg_exp.csv: Pre-processing of data containing average expression of genes in the samples
Supplementary_files_format_and_content: Normalised_count.csv: Normalized data for counts among samples.
Supplementary_files_format_and_content: MSC1vsControl.xlsx: List of differentially expressed genes in MSC1 compared to SCC1_control.
Supplementary_files_format_and_content: MSC2vsControl.xlsx: List of differentially expressed genes in MSC2 compared to SCC1_control.
Supplementary_files_format_and_content: MSC3vsControl.xlsx: List of differentially expressed genes in MSC3 compared to SCC1_control.

growth_protocol: Cell lines were obtained from the ATCC. HCT116 cells (ATCC Cat# CCL-247, RRID:CVCL_0291) were cultured in McCoy's 5A Medium supplemented 10% FBS, 4mM L-glutamine (Cat#03-020-1B, BI-Biologicals), 2mM L-alanyl-L-glutamine (Cat#03-022-1B, BI-Biologicals), 1% penstrep (Cat#03-031-1B, BI-Biologicals), and were grown in a humidified incubator at 37°C and 5% CO2 (43). Cell cultures were checked for mycoplasma contamination routinely at six-week intervals by PCR using EZ-PCR™ Mycoplasma Detection Kit (Biological Industries, Israel) and confirmed to be mycoplasma-free. Irinotecan was purchased from Sigma-Aldrich (MO, USA). Cell was cloned using single cell cloning to obtain homogenetic population.

extract_protocol:
Total RNA was isolated from cells using Qiagen RNeasy Plus Mini kit (Cat. #74134;GmbH) as per manufacturer protocol.
RNA was extracted from cells using the RNeasy Mini kit (Cat#74104, Qiagen). Library preparation strategy (BGISEQ-500, RRID:SCR_017979) was adopted and performed by BGI, China. Briefly, mRNA molecules were purified from total RNA using oligo(dT) attached magnetic beads and fragmented into small pieces using fragmentation reagent after reaction a certain period at proper temperature. First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second strand cDNA synthesis. The synthesized cDNA was subjected to end-repair and then was 3’ adenylated. Adapters were ligated to the ends of these 3’ adenylated cDNA fragments. This process amplified the cDNA fragments with adapters from previous step. PCR products were purified with Ampure XP Beads (AGENCOURT), and dissolved in EB solution. Library was validated on the Agilent Technologies 2100 bioanalyzer (2100 Bioanalyzer Instrument, RRID:SCR_018043). The double stranded PCR products were heat denatured and circularized by the splint oligo sequence. The single strand circle DNA (ssCir DNA) were formatted as the final library. The library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular. The DNBs were load into the patterned nanoarray and single end 50 (pair end 100) bases reads were generated in the way of sequenced by synthesis.

treatment_protocol: Cells were barcoded with individual barcodes using Cellecta's 50M barcode library, Further were treated and adapted to Irinotecan through several escalated doses ranging from 1nM to 40nM. Once the cell population were resistant to highest dose, cells were re-cloned and three resitant-subclones were isolated. Their clonality was checked through sequencing the individual barcodes. These three barcoded resistant subclones along with the parental line SCC1 (Single cell clone-1) were treated with 10nM irinotecan for 24 hours followed by total RNA isolation and transcriptome sequencing was performed as customer services at BGI, China.

value: Colon cancer cell line

value: Treated with Irinotecan (10nM)


title: SCC1_Control_2

description: Naïve_parental_line_10nM treamtment


title: nasopharyngeal gene expression of subject M134 at m4 [121147011342]


title: Pancreatic islets, 2HF266


title: Pancreatic islets, 2RC283


title: MSC2_2

description: Resistant mutant sub-clone (10nM treatment)


title: Pancreatic islets, 2HF270


title: MSC2_1


title: SKNAS-RBM39KD-190-001

city: Memphis

first: Hongjian

last: Jin

state: TN

address: 262 Danny Thomas Place

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hospital

data_processing:
Total stranded RNA sequencing data were processed by  the internal AutoMapper pipeline.First the raw reads were firs trimmed (Trim-Galore version 0.60),  mapped to human genome assembly (GRCh38) (STAR v2.7) and then the gene level values were quantified (RSEM v1.31) based on GENCODE annotation (v31) .
After mapping RNA-seq data, rMATS v4.1.0 was used for RNA alternative splicing analysis by using the mapped BAM files as input.
For stranded RNA-seq data, the argument “--libType fr-firststrand” was applied. To process reads with variable lengths, the argument “--variable-read-length” was also used for rMATS.
To select statistically significantly differential splicing events, the following thresholds were used: FDR <0.05 and the absolute value of IncLevelDifference > 0.1.
Genome_build: hg38
Supplementary_files_format_and_content: rMATS tsv tables, gene-level RSEM raw count, TPM, FPKM txt files

source_name: cell line

growth_protocol: BE2C (100,000 per well) and SKNAS cells (150,000) were plated in 6-well plate in RPMI-1640 media (supplemented with 10% FBS and 1% Pen/strep). SIMA (5 million per flank) and SKNAS cells (5 million per flank) were injected into (4-6 weeks old) NSG mice.

extract_protocol:
RNA was isolated from the cells using RNAeasy mini kit (Qiagen) according to manufacturer’s protocol. Tumor tissues were cut into 1-2mm pieces and sonicated with lysis buffer using RNeasy mini kit (Qiagen) and RNA was isolated according to the manufacturer's protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols at the St. Jude Hartwell Center.

treatment_protocol: Cells were treated either with DMSO (vehicle) or with 250 nM of Indisulam (Cayman chemical, catalog number: 22759) for 72 hours. Tumors were let grown to be palpable and then mice were treated with vehicle or Indisulam (25mg/kg). After termination of the treatment, mice were sacfificed and tumor tissues were isolated.

value: SKNAS


title: nasopharyngeal gene expression of subject M132 at m4 [121147011322]


title: nasopharyngeal gene expression of subject M130 at m4 [121147011302]


title: nasopharyngeal gene expression of subject M133 at m4 [121147011332]


title: SKNAS-RBM39KD-190-002


title: Pancreatic islets, 2RC282


title: MSC1_2


title: SKNAS-RBM39KD-188-002


title: MSC3_2


title: Pancreatic islets, 2RC281


title: nasopharyngeal gene expression of subject M128 at m4 [121147011282]


title: MSC1_1


title: SKNAS-RBM39KD-188-001


title: MSC3_1


title: Pancreatic islets, 2HF284


title: Pancreatic islets, 2RC284


title: KO2

city: Birmingham

first: Jianmei

middle: Wu

last: Leavenworth

state: AL

address: 1600 6th Ave South

department: Neurosurgery, Microbiology

institute: University of Alabama at Birmingham

description:
3 μL of Reporter CodeSet and 2 μL Capture ProbeSet
B2

hyb_protocol: Samples were processed on the NanoString nCounter Flex System per manufacturer instructions

scan_protocol: using the nCounter Mouse PanCancer Immune Profiling panel

data_processing: Within nSolver (4.0) the nCounter Advanced Analysis (version 2.0.134) was run using the raw data in order to predict the best housekeeping genes to use (based on the gnorm program). 17 housekeeping genes were used (discarded G6pdx, Polr1b, Polr2a). Differentially expressed genes were identified as genes with a p value of less than 0.05 versus the respective baseline control.

label: Nanostring

source_name: CD45-tumor cells

label_protocol: 100 ng of purified RNA was added to 3 μL of Reporter CodeSet and 2 μL Capture ProbeSet using an nCounter master kit as recommended (NanoString Technologies)

extract_protocol: Total RNA was extracted using a QIAshredder kit (QIAGEN) and an RNeasy Plus Micro Kit (QIAGEN) according to the manufacturer’s protocol.

value: Prdm1fl/flFoxP3YFP-Cre (KO)

value: Tumor

tag: tumor stage

value: less than or equal to 1.5 cm3


title: nasopharyngeal gene expression of subject M120 at m4 [121147011202]

data_processing: The data were analyzed using R/Rstudio. Outliers were identified using raw intensity data using the arrayQualityMetrics package and removed from the dataset. RMA was performed to reduce the data from 300304 probe-level features to 27189 genes. After removing non-annotated genes/control probes, 18526 genes remained, which were for the conclusions in the paper.

value: nasopharyngeal cells


title: Pancreatic islets, 2HF283

value: HFD


title: KO1

description:
3 μL of Reporter CodeSet and 2 μL Capture ProbeSet
B1


title: nasopharyngeal gene expression of subject M117 at m4 [121147011172]


title: SKNAS-Ctrl-001

value: shRNA-ctrl


title: nasopharyngeal gene expression of subject M119 at m4 [121147011192]


title: WT3

description:
3 μL of Reporter CodeSet and 2 μL Capture ProbeSet
A3

value: FoxP3YFP-Cre (WT)


title: nasopharyngeal gene expression of subject M122 at m4 [121147011222]


title: BE2C-RBM39KD-190-002


title: BE2C-RBM39KD-190-001


title: nasopharyngeal gene expression of subject M127 at m4 [121147011272]


title: Pancreatic islets, 1RC277


title: WT2

description:
3 μL of Reporter CodeSet and 2 μL Capture ProbeSet
A2


title: Pancreatic islets, 2HF285


title: Pancreatic islets, 3HF274

value: BALB/cJ


title: WT1

description:
3 μL of Reporter CodeSet and 2 μL Capture ProbeSet
A1


title: Pancreatic islets, 1RC274

value: RC


title: SKNAS-Ctrl-002


title: BE2C-RBM39KD-188-001


title: Pancreatic islets, 1RC273


title: Pancreatic islets, 2HF281


title: nasopharyngeal gene expression of subject M110 at m4 [121147011102]


title: BE2C-Ctrl-002


title: nasopharyngeal gene expression of subject M109 at m4 [121147011092]


title: Pancreatic islets, 1RC272


title: BE2C-Ctrl-001


title: BE2C-RBM39KD-188-002


title: Pancreatic islets, 1HF274


title: BE2C-WT-ISM-001

value: indisulam


title: BE2C-WT-ISM-002


title: nasopharyngeal gene expression of subject M115 at m4 [121147011152]


title: nasopharyngeal gene expression of subject M116 at m4 [121147011162]


title: Pancreatic islets, 1HF273


title: Pancreatic islets, 1HF272


title: nasopharyngeal gene expression of subject M107 at m4 [121147011072]


title: nasopharyngeal gene expression of subject M108 at m4 [121147011082]


title: BE2C-WT-Ctrl-002

value: 0.1% DMSO


title: nasopharyngeal gene expression of subject M114 at m4 [121147011142]


title: BE2C-WT-Ctrl-001


title: nasopharyngeal gene expression of subject M105 at m4 [121147011052]


title: HCN-2 cells transfected with scrambled control mimic 2

city: Kaohsiung

first: Sung-Chou

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 Clariom D Arrays (Affymetrix) and scanned at the Kaohsiung Chang Gung Memorial Hospital Microarray Core Facility.

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

data_processing:
RMA expression value derived from Expression Console software; core-exon analysis
Raw data were processed with the Exon Array Computational Tool (ExACT) (Affymetrix) for background correction and normalization. Data analysis was conducted with Partek.

source_name: HCN-2 cell

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

growth_protocol: Human Cortical Neuronal cells (HCN-2, CRL-10742, ATCC) were cultured in Dulbecco's modified Eagle's medium (DMEM, Gibco 11965092) supplemented with 4 mM L-glutamine (Gibco 25030149), 1.5 g/L sodium bicarbonate, 4.5 g/L glucose, and 10% fetal bovine serum (Gibco 10437028).

extract_protocol: RNA was isolated from cell lysate of HCN-2 cells with the RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions. Inclusion of 10 mL/L of the RNase inhibitor NucleoGuard (AmpTec) in the lysis buffer improved RNA yield and recoveries of long transcripts. All samples were treated with TURBO DNA-free (Ambion) to remove trace amounts of genomic DNA. A 2-round amplification was performed with the ExpressArt TRinucleotide mRNA Amplification Kit (AmpTec) according to the manufacturer’s instructions.

treatment_protocol: MiRNA mimics for hsa‐miR-126‐5p (YM00470487), hsa‐miR-140‐3p (YM00470393), hsa‐miR-30e-5p (YM00470246), and scramble control (YM00479903) were obtained from QIAGEN. For miRNA mimic transfection, 2 × 105 HCN-2 cells were first seeded on a 24‐well plate and each well contained 500 μL of culture medium. After 24 hr, 3 μL of miRNA mimic (20 μM) and 6 μL of HiPerFect transfection reagent (QIAGENT) were mixed in 200 μL of culture medium without fetal bovine serum (FBS). After 6 hr, 600 μL of culture medium were added into the 24‐well plate and the cells were cultured.

value: scrambled control


title: Pancreatic islets, 1RC284


title: nasopharyngeal gene expression of subject M102 at m4 [121147011022]

extract_protocol: RNA was extracted by a TRIzol reagent (Invitrogen)/chlorform method, cleaned using the RNAeasy Micro Kit (Qiagen) (OpenWetWare contributors, 2015)


title: HCN-2 cells transfected with scrambled control mimic 3


title: Pancreatic islets, 1HF277


title: HCN-2 cells transfected with miR-140-3p mimic 2


title: nasopharyngeal gene expression of subject M097 at m4 [121147010972]


title: HCN-2 cells transfected with miR-140-3p mimic 1


title: HCN-2 cells transfected with miR-140-3p mimic 3


title: Pancreatic islets, 1RC282


title: Pancreatic islets, 1RC281


title: HCN-2 cells transfected with scrambled control mimic 1


title: Sal_3

city: Jingzhou

first: Min

last: Yao

address: Jingmi Road #266

institute: Yangtze University

description: Salmonella treated

data_processing:
Illumina Casava1.7 software used for basecalling.
RNA-Seq reads were mapped to Mouse reference mRNA using the Bowtie software
Using R version 3.4.2 software to find differential genes
Genome_build: Sus_scrofa.Sscrofa11.1
Supplementary_files_format_and_content: Reads count (tab deli text)

organism: Sus scrofa

source_name: PBMC

extract_protocol:
Total RNA were extrated by PAXgene RNA kit using the standard protocols.All samples were quantified using a NanoDrop 2000 (Thermo-Fisher Scientific, Waltham, MA, USA), and assessed with an Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA). The RNA integrity number (RIN) of each sample was >8.
RNA libraries were prepared for sequencing with an Illumina Truseq RNA sample preparation kit according to the manufacturer’s protocol (Illumina, San Diego, CA, USA).

tag: breed

value: Duroc x Landrace x Yorkshire

value: PBMC

value: Salmonella treated


title: Sal_2

description: Salmonella treated


title: Pancreatic islets, 1RC283


title: HCN-2 cells transfected with miR-126-5p mimic 2


title: Sal_1

description: Salmonella treated


title: HCN-2 cells transfected with miR-126-5p mimic 3


title: Pancreatic islets, 1HF284


title: Pancreatic islets, 1HF283


title: nasopharyngeal gene expression of subject M094 at m4 [121147010942]


title: miR-124+Sa_4

description: miR-124 sponge and Salmonella treated

value: miR-124 sponge and Salmonella treated


title: Sal_4

description: Salmonella treated


title: Pancreatic islets, 1HF281


title: HCN-2 cells transfected with miR-126-5p mimic 1


title: miR-124+Sa_3

description: miR-124 sponge and Salmonella treated


title: nasopharyngeal gene expression of subject M080 at m4 [121147010802]


title: nasopharyngeal gene expression of subject M100 at m4 [121147011002]


title: Pancreatic islets, 1RC290


title: nasopharyngeal gene expression of subject M078 at m4 [121147010782]


title: nasopharyngeal gene expression of subject M096 at m4 [121147010962]


title: Pancreatic islets, 1HF280


title: miR-124+Sa_2

description: miR-124 sponge and Salmonella treated


title: miR-124+Sa_1

description: miR-124 sponge and Salmonella treated


title: Pancreatic islets, 1RC289


title: Control_4

description: Non-treated control samples

value: Control


title: nasopharyngeal gene expression of subject M138 at m3 [121146011382]


title: nasopharyngeal gene expression of subject M139 at m3 [121146011392]


title: Pancreatic islets, 1RC287


title: nasopharyngeal gene expression of subject M134 at m3 [121146011342]


title: Control_3

description: Non-treated control samples


title: Pancreatic islets, 1HF265


title: Control_2

description: Non-treated control samples


title: Control_1

description: Non-treated control samples


title: Pancreatic islets, 1RC288


title: Pancreatic islets, 1HF261


title: Pancreatic islets, 1HF264


title: Pancreatic islets, 1HF260


title: nasopharyngeal gene expression of subject M132 at m3 [121146011322]


title: nasopharyngeal gene expression of subject M102 at m6 [121148011022]


title: nasopharyngeal gene expression of subject M130 at m3 [121146011302]


title: nasopharyngeal gene expression of subject M129 at m3 [121146011292]


title: nasopharyngeal gene expression of subject M123 at m3 [121146011232]


title: nasopharyngeal gene expression of subject M071 at m4 [121147010712]


title: nasopharyngeal gene expression of subject M126 at m3 [121146011262]


title: nasopharyngeal gene expression of subject M120 at m3 [121146011202]


title: nasopharyngeal gene expression of subject M122 at m3 [121146011222]


title: nasopharyngeal gene expression of subject M119 at m3 [121146011192]


title: CKD TRF 4

city: Seoul

first: Yina

last: Fang

address: 64, Goryeodae-ro 17ga-gil, Seongbuk-gu

country: South Korea

institute: Korea University Anam Hospital

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(using fastx_trimmer), then mapped to mm10 (UCSC) whole genome using Bowtie2
Read count extraction using bedtools.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: Kidney

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

value: Kidney

tag: group

value: CKD TRF 4


title: CKD TRF 3

value: CKD TRF 3


title: LPS+L 2_NSCs

city: Tsukuba

first: Mariem

last: Achour

state: Ibaraki

address: 1-1-1 Tennodai

country: Japan

institute: Alliance for Research on the Mediterranean and North Africa

hyb_protocol: Following fragmentation, 100 ng of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome Array (MG-430). GeneChips were washed and stained in the Gene Atlas Fluidics Station 400

scan_protocol: GeneChips were scanned using the GeneAtlas Imaging Station

data_processing: The raw data were normalized using Expression Console Software provided by the Affymetrix following robust multichip average (RMA) algorithm (http://www.affymetrix.com). Subsequent analysis of the gene expression data was carried out in the freely available Transcriptome Analysis Console (TAC) version 4 (Thermofisher inc.). Further analysis was conducted using an online data mining tool DAVID (Database for Annotation, Visualization and Integrated Discovery, ver. 6.8). We used 'Functional Annotation' tool of DAVID to identify the most relevant biological terms, including gene ontology (GO) terms, biological pathways.

source_name: NSCs isolated from LPS depression induced mouse model treated with luteolin , replicate2

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 9.4 ug total RNA

extract_protocol: The total RNA was extracted from the cells using ISOGEN kit (Nippon Gene Co. Ltd., Japan) following the manufacturer’s instructions. Total RNA was purified using chloroform and Isopropanol (Wako, Japan) and quantified and assessed for quality with a NanoDrop 2000 spectrophotometer (Thermo Scientific, Wilmington, DE, USA).

treatment_protocol: Healthy adult male ICR mice (21 weeks old, weighting between 33 and 46g) were used for animal experiments. All animals were purchased from Charles River Laboratories JAPAN Inc., Kanagawa, Japan and were housed individually at controlled temperature (25°C), with a 12/12 h light/dark cycle, and had access to food and water ad libitum. After acclimatization, the mice were randomly assigned into four experimental groups (n = 6/group): Control group (PBS), the depression model group: lipopolysaccharide group (LPS), control group treated with Luteolin (PBS+L) and lipopolysaccharide group treated with Luteolin (LPS+L). All experimental animals were maintained in accordance with the Guide for the Care and Use of Laboratory Animals, and the protocol was approved by the Animal Ethics Committee of the University of Tsukuba, Japan . At day 1 and prior to depression induction by LPS, the behavioral test: Tail Suspension Test (TST) was performed to all mice to screen their initial stress status. The TST methodology used in our study was as described by Steru (Steru, Chermat et al. 1985). Briefly, the duration of the test was 6 min and the immobility time was measured on the last 4 min of the test. The mouse was considered immobile only when it is hanged passively, showing no resistance to the stress applied by the test. The experiment was recorded using a camera and scored by videos observations. Immediately after performing the TST test, LPS (850µg/kg) was injected via the intraperitoneal route (i.p.) to the LPS and LPS+L groups and PBS was injected by the same route to the PBS and PBS+L groups. Starting from Day 2 and during eight consecutive days, luteolin (10mg/kg) and PBS were orally administrated to mice once per day. Luteolin (10mg/kg) was administrated to the LPS+L and PBS+ L groups and PBS to both PBS and LPS groups. At day 9, mice were sacrified. Two mice brains were used to isolate mice NSCs using the Anti-Prominin-1 MicroBeads kits (Miltenyi Biotec Inc., CA, USA, order no. 130-092-333).

value: Mouse Neural Stem Cells


title: nasopharyngeal gene expression of subject M118 at m3 [121146011182]

city: Utrecht

first: Wouter

address: Heidelberglaan 100

institute: UMC Utrecht

value: nasopharyngeal cells


title: LPS+L 1_NSCs

source_name: NSCs isolated from LPS depression induced mouse model treated with luteolin, replicate1


title: CKD TRF 2

value: CKD TRF 2


title: CKD TRF 1

value: CKD TRF 1


title: nasopharyngeal gene expression of subject M116 at m3 [121146011162]


title: CKD 4

value: CKD 4


title: nasopharyngeal gene expression of subject M117 at m3 [121146011172]


title: PBS+L2_NSCs

source_name: NSCs isolated from normal mouse treated with luteolin mouse , replicate2

value: PBS mouse treated with luteolin


title: nasopharyngeal gene expression of subject M114 at m3 [121146011142]


title: PBS+L1_NSCs

source_name: NSCs isolated from normal mouse treated with luteolin mouse , replicate1


title: LPS 1_NSCs

source_name: NSCs isolated from LPS depression induced mouse model , replicate1

value: LPS depression induced mouse model


title: LPS 2_NSCs

source_name: NSCs isolated from LPS depression induced mouse model , replicate2


title: CKD 3

value: CKD 3


title: PBS 1_NSCs

source_name: NSCs isolated from normal mouse

value: PBS mouse


title: CKD 1

value: CKD 1


title: CKD 2

value: CKD 2


title: LPS+L M2_Hippocampus,replicate2

data_processing:
The raw data were normalized using Expression Console Software provided by the Affymetrix following robust multichip average (RMA) algorithm (http://www.affymetrix.com). Subsequent analysis of the gene expression data was carried out in the freely available Transcriptome Analysis Console (TAC) version 4 (Thermofisher inc.). Further analysis was conducted using an online data mining tool DAVID (Database for Annotation, Visualization and Integrated Discovery, ver. 6.8). We used 'Functional Annotation' tool of DAVID to identify the most relevant biological terms, including gene ontology (GO) terms, biological pathways.
Expression console signal intensity. For calculating average value, standard deviation, fold change, and p-value of signal intensity of replicates, we used freely available Transcriptome Analysis Console software V 4.0 (CHP files ).

source_name: Hipocamppus tissue isolated from LPS depression induced mouse modeln°2 treated with luteolin, replicate 2

treatment_protocol: Healthy adult male ICR mice (21 weeks old, weighting between 33 and 46g) were used for animal experiments. All animals were purchased from Charles River Laboratories JAPAN Inc., Kanagawa, Japan and were housed individually at controlled temperature (25°C), with a 12/12 h light/dark cycle, and had access to food and water ad libitum. After acclimatization, the mice were randomly assigned into four experimental groups (n = 6/group): Control group (PBS), the depression model group: lipopolysaccharide group (LPS), control group treated with Luteolin (PBS+L) and lipopolysaccharide group treated with Luteolin (LPS+L). All experimental animals were maintained in accordance with the Guide for the Care and Use of Laboratory Animals, and the protocol was approved by the Animal Ethics Committee of the University of Tsukuba, Japan . At day 1 and prior to depression induction by LPS, the behavioral test: Tail Suspension Test (TST) was performed to all mice to screen their initial stress status. The TST methodology used in our study was as described by Steru (Steru, Chermat et al. 1985). Briefly, the duration of the test was 6 min and the immobility time was measured on the last 4 min of the test. The mouse was considered immobile only when it is hanged passively, showing no resistance to the stress applied by the test. The experiment was recorded using a camera and scored by videos observations. Immediately after performing the TST test, LPS (850µg/kg) was injected via the intraperitoneal route (i.p.) to the LPS and LPS+L groups and PBS was injected by the same route to the PBS and PBS+L groups. Starting from Day 2 and during eight consecutive days, luteolin (10mg/kg) and PBS were orally administrated to mice once per day. Luteolin (10mg/kg) was administrated to the LPS+L and PBS+ L groups and PBS to both PBS and LPS groups. At day 9, mice were sacrified. Two mice brains were used to extract total RNA from mice hippocampus.

value: Hipocamppus

tag: genotype/variation

value: LPS depression induced mouse treated with luteolin


title: nasopharyngeal gene expression of subject M110 at m3 [121146011102]

source_name: nasopharyngeal cells

tag: subject


title: nasopharyngeal gene expression of subject M111 at m3 [121146011112]

tag: time point


title: nasopharyngeal gene expression of subject M106 at m3 [121146011062]

tag: age


title: nasopharyngeal gene expression of subject M107 at m3 [121146011072]

tag: cell type


title: 202292330029_R08C01

type: genomic

first: Quynh

last: Tran

address: 262 Danny Thomas Place, C4029, Mail Stop 250

department: Pathology

institute: St. Jude Children's Research Hospital

hyb_protocol: One hundred and fifty-eight samples from St. Jude Children’s Research Hospital (SJCRH, pediatric) and Stanford Hospital and Clinics (adult) were analyzed using Illumina Methylation BeadChip (EPIC) arrays according to the manufacturer’s instructions. Data were generated from formalin-fixed paraffin-embedded (FFPE) tissue samples. DNA of 158 patients was extracted and hybridized to Illumina Infinium HumanMethylationEPIC BeadChip (850K) arrays.

scan_protocol: Standard Illumina protocol

data_processing: All methylation data were analyzed in R (http://www.r-project.org, version 3.5.3), using a number of packages from Bioconductor and other repositories. Specifically, array data were preprocessed using the minfi package (v.1.28.4) (13). Background correction with dye-bias normalization was performed for all samples using noob (normal-exponential out-of-band) with “single” dye method (14). Filtering was performed to remove probes located on sex chromosomes, probes containing nucleotide polymorphisms (dbSNP132 Common) within five base pairs of and including the targeted CpG-site, or probes mapping to multiple sites on hg19 (allowing for one mismatch), and cross-reactive probes.

label: Cy5 and Cy3

source_name: rhabdomyosarcoma

label_protocol: Standard Illumina protocol

tag: molecular group

value: PRMS


title: PBS+L M2_Hippocampus,replicate2

source_name: Hipocamppus tissue isolated from normal mouse treated with luteolin mouse n°2, replicate2


title: LPS+L M2_Hippocampus,replicate1

source_name: Hipocamppus tissue isolated from LPS depression induced mouse model n°2 treated with luteolin, replicate 1


title: Control 3

tag: strain

value: Kidney

value: Control 3


title: nasopharyngeal gene expression of subject M105 at m3 [121146011052]

last: de Steenhuijsen Piters


title: PBS+L M2_Hippocampus,replicate1

source_name: Hipocamppus tissue isolated from normal mouse treated with luteolin mouse n°2, replicate1


title: nasopharyngeal gene expression of subject M102 at m3 [121146011022]


title: Control 1

value: Control 1


title: 202292330029_R07C01

extract_protocol: Data were generated from formalin-fixed paraffin-embedded (FFPE) tissue samples. DNA of 158 patients was extracted and hybridized to Illumina Infinium HumanMethylationEPIC BeadChip (850K) arrays


title: LPS M2_Hippocampus,replicate2

source_name: Hipocamppus tissue isolated from LPS depression induced mouse model n°2, replicate2

value: LPS depression induced mouse


title: LPS M2_Hippocampus,replicate1

source_name: Hipocamppus tissue isolated from LLPS depression induced mouse model n°2, replicate1


title: nasopharyngeal gene expression of subject M100 at m3 [121146011002]

value: nasopharyngeal cells


title: nasopharyngeal gene expression of subject M099 at m3 [121146010992]


title: 202292330029_R04C01


title: 202163550088_R03C01

value: ERMS


title: nasopharyngeal gene expression of subject M098 at m3 [121146010982]


title: SAMP8 Treated Pooled [miRNA-seq]

city: Barcelona

first: Christian

middle: Griñán

last: Ferré

state: Barcelona

address: Joan XIII, s/n

department: Pharmacology, Toxicology and Therapeutic Chemistry

country: Spain

institute: University of Barcelona

data_processing:
To determine the altered microRNAs after treatment with UNC0642 we used the QIAseqmiRNA platform.
TMM normalization and differential expression analysis was carried out using the edgeR program.
The cutoff of differential miRNA was a fold-change threshold of 1.9 and maximum p-value of 0.05.
The miRTarVis tool was used to predict miRNA target8, KEGG, Gene Ontology and GSEA was used to perform the enrichment and pathway analysis.
Genome_build: GRCm38 (39) version of Mus musculus available at https://asia.ensembl.org/Mus_musculus/Info/Index.
Supplementary_files_format_and_content: Adundance measurements; Raw counts

source_name: Hippocampus

extract_protocol:
Hippocampus were removed, flash frozen on dry ice, anr RNA was obtained using Trizol reagent. Library for small RNA-Seq was prepared according to the Qiagen QIAseq miRNA library kit using 100 ng total RNAs as input.
Final library quality and quantity were analyzed by Agilent Bioanalyzer 2100 and Life Technologies Qubit3.0 Fluorometer.

treatment_protocol: Oral Gavage administration of UNC0642 5 mg/Kg

value: Hippocampus


title: PBS M2_Hippocampus,replicate1

source_name: Hipocamppus tissue isolated from normal mouse n°2, replicate1


title: 202292330029_R06C01


title: LPS+L M1_Hippocampus,replicate2

source_name: Hipocamppus tissue isolated from LPS depression induced mouse model n°1 treated with luteolin, replicate 2


title: 202292330029_R05C01


title: MEF_cells_Ribo-seq_DHX29_KO

first: Yuanhui

last: Mao

state: Zhejiang

address: 1369 West Wenyi Road

description: MEF Ribo-seq DHX29 knockout

data_processing:
Library strategy: Ribo-seq
The adaptor and low quality bases of all sequencing data were removed by Cutadapt.
The adaptor  AAAAAAAAAA was trimmed by Cutadapt. The trimmed reads were aligned to mouse transcriptome, using STAR with default parameters.
Genome_build: GRCm38
Supplementary_files_format_and_content: The processed data files are tab separated read count. The first column is gene name, and the second column is footprint count on mRNAs.

source_name: Mouse embryonic fibroblasts

growth_protocol: MEF and HEK293 cells were maintained in Dulbecco’s Modified Eagle’s Medium (DMEM) with 10% fetal bovine serum (FBS).

extract_protocol:
For cell lysates, at least four 10 cm dishes of cells were harvested in 400 µl ice-cold polysome buffer (10 mM HEPES, pH 7.4, 100 mM KCl, 5 mM MgCl2). Cells were then disrupted by vortexing six times for 20s using lysing matrix D (Fisher), followed by a 40 s interval each time on ice, then centrifuged at 12,000g, 4 °C for 10 min. Samples were then subjected to sucrose gradient sedimentation. Sucrose solutions were prepared in polysome buffer (10 mM HEPES, pH 7.4, 100 mM KCl, 5 mM MgCl2 and 2% Triton X-100). A 15%-45% (w/v) sucrose density gradients were freshly prepared in SW41 ultracentrifuge tubes (Backman) using a Gradient Master (BioComp Instruments). 500 µl of supernatant from cell lysates prepared as described above was loaded onto sucrose gradients followed by centrifugation for 2.5 hr at 32,000 rpm, 4 °C in a SW41 rotor. Separated samples were fractionated at 1.5 ml min-1 through an automated fractionation system (Isco) that continually monitors OD254 values. Ribosome fractions separated by sucrose gradient sedimentation were pooled and digested with E. coli RNase I (Ambion, 750 U per 100 A260 units) by incubation at 4 °C for 1 hr. SUPERase•In (50 U per 100 U RNase I) was then added into the reaction mixture to stop the digestion. Total RNA was extracted using TRIzol LS reagent.
Fragmented RNAs were separated on a 15% polyacrylamide TBE-urea gel (Invitrogen) and visualized using SYBR Gold (Invitrogen). Selected regions of the gel corresponding to 20-70 nt (for 40S-seq and eIF3-seq) or 25-35 nt (for Ribo-seq) were excised. The gel slices were disrupted by using centrifugation through the holes at the bottom of the tube. RNA fragments were dissolved by soaking overnight in 400 µl RNA gel elution buffer (300 mM NaOAc pH 5.5, 1 mM EDTA, 0.1 U/µl SUPERase•In). The gel debris was removed using a Spin-X column (Corning), followed by ethanol precipitation.   Purified RNA fragments were re-suspended in Nuclease-free water, then dephosphorylated for 1 hr at 37 °C in a 15 µl reaction (1× T4 polynucleotide kinase buffer, 10 U SUPERase•In and 20 U T4 polynucleotide kinase). Dephosphorylated RNA fragments were precipitated using ethanol and re-suspended in Nuclease-free water. 0.15 μg linker (rApp/NNNNCTGTAGGCACCATCAAT/3ddC) then was added to the RNA fragments, heated at 70 °C for 90 s and then cooled to room temperature, followed by ligation for 3 hr at at 22 °C in a 20 µl reaction (1× T4 Rnl2 reaction buffer, 10 U SUPERase•In, 15% PEG8000 and 20 U T4 RNA ligase 2 truncated). The reaction was heat inactivated at 80 °C for 10 min and the products were separated on a 10% polyacrylamide TBE-urea gel and selected regions in the gel corresponding to 45-95 nt (for 40S-seq and eIF3-seq) or 60-70 nt (for Ribo-seq) were excised. RNA fragments were dissolved by soaking overnight in 400 μl RNA gel elution buffer. RNA fragments were purified from RNA gel elution buffer as described earlier and re-suspended in Nuclease-free water. For reverse transcription, the following oligos containing barcodes were used:   (Phos)CTANNNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGC(SpC18)CACTCA(SpC18)TTCAGACGTGTGCTCTTCCGATCTATTGATGGTGCCTACAG  (Phos)AGCNNNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGC(SpC18)CACTCA(SpC18)TTCAGACGTGTGCTCTTCCGATCTATTGATGGTGCCTACAG  (Phos)ATTNNNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGC(SpC18)CACTCA(SpC18)TTCAGACGTGTGCTCTTCCGATCTATTGATGGTGCCTACAG  (Phos)CCGNNNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGC(SpC18)CACTCA(SpC18)TTCAGACGTGTGCTCTTCCGATCTATTGATGGTGCCTACAG  where Phos represents phosphorylation, NNN represents random sequence, SpC18 represents Hexa-ethyleneglycol spacer.  The linker ligated RNA sample was mixed with 0.5 mM dNTP and 2.5 mM synthesized primer and incubated at 75 ° C for 3 min, followed by incubation on ice for at least 1 min. The reaction master mix was then added with 20 mM Tris (pH 8.4), 50 mM KCl, 5 mM MgCl2, 10 mM DTT, 40 U RNaseOUT and 200 U SuperScript III. Reverse transcription reaction was performed according to the manufacturer’s instruction. Reverse transcription products were separated on a 10% polyacrylamide TBE-urea gel. Corresponding region was excised, which was expected to be approximately 200 nt. The first-strand cDNA products were recovered in DNA gel elution buffer (300 mM NaCl, 1 mM EDTA), then purified and re-suspended in Nuclease-free water as described earlier.  cDNA products were circularized in 20 μl of reaction containing 1×CircLigase buffer, 2.5 mM MnCl2, 1M Betaine and 100 U CircLigase II (Epicentre). Circularization was performed at 60 °C for 1 hr and the reaction was heat inactivated at 80 °C for 10 min.

value: Mouse embryonic fibroblasts

value: DHX29 knockout


title: 202292330029_R01C01


title: Control 4

source_name: Kidney

value: Control 4


title: nasopharyngeal gene expression of subject M097 at m3 [121146010972]


title: Control 2

value: Control 2


title: 201533640050_R05C01


title: MEF_cells_Ribo-seq_Control_for_DHX29_KO

description: MEF Ribo-seq Control for DHX29 knockout

value: control


title: PBS M2_Hippocampus,replicate2

source_name: Hipocamppus tissue isolated from normal mouse n°2, replicate2

value: PBS mouse treated with luteolin


title: nasopharyngeal gene expression of subject M094 at m3 [121146010942]


title: LPS+L M1_Hippocampus,replicate1

source_name: Hipocamppus tissue isolated from LPS depression induced mouse model n°1 treated with luteolin, replicate 1


title: 202292330029_R02C01


title: 201533640050_R06C01

value: ARMS


title: 201533640050_R08C01


title: MEF_cells_40S-seq_eIF4A1_KD

data_processing:
The adaptor and low quality bases of all sequencing data were removed by Cutadapt.
For Ribo-seq, the adaptor CTGTAGGCACCATCAAT was used. The first SIX nucleotides (3 randome nucleotides + 3-word barcode sequence) and the last FOUR nucleotides were removed (3 random nucleotides). PCR duplicates were removed. PCR duplicates were defined as the reads with exact same random sequences at both sides. More details can be found in PMID: 27450428. For 80S-seq, 40S-seq and eIF3-seq, the adaptor was set as AAAAAAAAAA. The trimmed reads were aligned to mouse (human) transcriptome, using STAR with default parameters.
Genome_build: GRCm38/GRCh38
Supplementary_files_format_and_content: For Ribo-seq, the processed data files are tab separated read count. The first column is gene name, and the second column is footprint count on mRNAs. For 80S-seq, 40S-seq and eIF3-seq,  the processed data files are read count at individual sites of gene, which were seperated by comma. The first column is chromosome name, the second column is strand of the gene, the third column is gene name. The others are read count at individual sites of the gene. The read count section was seperated by colon. The first value is the genomic coordinate, the second value is the length of footprint, the third value is the count of footprint.

source_name: MEF 40S ribo-seq eIF4A1 knockdown

extract_protocol:
For cell lysates, at least four 10 cm dishes of cells were harvested in 400 µl ice-cold polysome buffer (10 mM HEPES, pH 7.4, 100 mM KCl, 5 mM MgCl2). Cells were then disrupted by vortexing six times for 20s using lysing matrix D (Fisher), followed by a 40 s interval each time on ice, then centrifuged at 12,000g, 4 °C for 10 min. Samples were then subjected to sucrose gradient sedimentation. Sucrose solutions were prepared in polysome buffer (10 mM HEPES, pH 7.4, 100 mM KCl, 5 mM MgCl2 and 2% Triton X-100). A 15%-45% (w/v) sucrose density gradients were freshly prepared in SW41 ultracentrifuge tubes (Backman) using a Gradient Master (BioComp Instruments). 500 µl of supernatant from cell lysates prepared as described above was loaded onto sucrose gradients followed by centrifugation for 2.5 hr at 32,000 rpm, 4 °C in a SW41 rotor. Separated samples were fractionated at 1.5 ml min-1 through an automated fractionation system (Isco) that continually monitors OD254 values. Ribosome fractions separated by sucrose gradient sedimentation were pooled and digested with E. coli RNase I (Ambion, 750 U per 100 A260 units) by incubation at 4 °C for 1 hr. SUPERase•In (50 U per 100 U RNase I) was then added into the reaction mixture to stop the digestion. Total RNA was extracted using TRIzol LS reagent.
Fragmented RNAs were separated on a 15% polyacrylamide TBE-urea gel (Invitrogen) and visualized using SYBR Gold (Invitrogen). Selected regions of the gel corresponding to 20-70 nt (for 40S-seq and eIF3-seq) or 25-35 nt (for Ribo-seq) were excised. The gel slices were disrupted by using centrifugation through the holes at the bottom of the tube. RNA fragments were dissolved by soaking overnight in 400 µl RNA gel elution buffer (300 mM NaOAc pH 5.5, 1 mM EDTA, 0.1 U/µl SUPERase•In). The gel debris was removed using a Spin-X column (Corning), followed by ethanol precipitation.
Purified RNA fragments were re-suspended in Nuclease-free water, then dephosphorylated for 1 hr at 37 °C in a 15 µl reaction (1× T4 polynucleotide kinase buffer, 10 U SUPERase•In and 20 U T4 polynucleotide kinase). Dephosphorylated RNA fragments were precipitated using ethanol and re-suspended in Nuclease-free water. 0.15 μg linker (rApp/NNNNCTGTAGGCACCATCAAT/3ddC) then was added to the RNA fragments, heated at 70 °C for 90 s and then cooled to room temperature, followed by ligation for 3 hr at at 22 °C in a 20 µl reaction (1× T4 Rnl2 reaction buffer, 10 U SUPERase•In, 15% PEG8000 and 20 U T4 RNA ligase 2 truncated). The reaction was heat inactivated at 80 °C for 10 min and the products were separated on a 10% polyacrylamide TBE-urea gel and selected regions in the gel corresponding to 45-95 nt (for 40S-seq and eIF3-seq) or 60-70 nt (for Ribo-seq) were excised. RNA fragments were dissolved by soaking overnight in 400 μl RNA gel elution buffer. RNA fragments were purified from RNA gel elution buffer as described earlier and re-suspended in Nuclease-free water. For reverse transcription, the following oligos containing barcodes were used:
(Phos)CTANNNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGC
(SpC18)CACTCA(SpC18)TTCAGACGTGTGCTCTTCCGATCTATTGATGGTGCCTACAG
(Phos)AGCNNNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGC
(SpC18)CACTCA(SpC18)TTCAGACGTGTGCTCTTCCGATCTATTGATGGTGCCTACAG
(Phos)ATTNNNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGC
(SpC18)CACTCA(SpC18)TTCAGACGTGTGCTCTTCCGATCTATTGATGGTGCCTACAG
(Phos)CCGNNNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGC
(SpC18)CACTCA(SpC18)TTCAGACGTGTGCTCTTCCGATCTATTGATGGTGCCTACAG
where Phos represents phosphorylation, NNN represents random sequence, SpC18 represents Hexa-ethyleneglycol spacer.
The linker ligated RNA sample was mixed with 0.5 mM dNTP and 2.5 mM synthesized primer and incubated at 75 ° C for 3 min, followed by incubation on ice for at least 1 min. The reaction master mix was then added with 20 mM Tris (pH 8.4), 50 mM KCl, 5 mM MgCl2, 10 mM DTT, 40 U RNaseOUT and 200 U SuperScript III. Reverse transcription reaction was performed according to the manufacturer’s instruction. Reverse transcription products were separated on a 10% polyacrylamide TBE-urea gel. Corresponding region was excised, which was expected to be approximately 200 nt. The first-strand cDNA products were recovered in DNA gel elution buffer (300 mM NaCl, 1 mM EDTA), then purified and re-suspended in Nuclease-free water as described earlier.
cDNA products were circularized in 20 μl of reaction containing 1×CircLigase buffer, 2.5 mM MnCl2, 1M Betaine and 100 U CircLigase II (Epicentre). Circularization was performed at 60 °C for 1 hr and the reaction was heat inactivated at 80 °C for 10 min.

tag: cell line/type

tag: genotype/treatment

value: eIF4A1 knockdown

tag: molecule subtype

value: Ribosome associated RNA


title: 202292330029_R03C01


title: nasopharyngeal gene expression of subject M078 at m3 [121146010782]


title: MEF_cells_40S-seq_Control

source_name: MEF 40S ribo-seq Control

value: Control


title: PBS+L M1_Hippocampus,replicate2

source_name: Hipocamppus tissue isolated from normal mouse treated with luteolin mouse n°1, replicate2

tag: tissue

value: Hipocamppus


title: 201533640050_R07C01


title: 201533640050_R03C01

value: SC/SRMS


title: nasopharyngeal gene expression of subject M138 at m2 [121145011382]

source_name: nasopharyngeal cells


title: LPS M1_Hippocampus,replicate2

source_name: Hipocamppus tissue isolated from LPS depression induced mouse model, replicate2


title: MEF_cells_eIF3-seq_Control

source_name: MEF eIF3 associated ribo-seq Control


title: PBS+L M1_Hippocampus,replicate1

source_name: Hipocamppus tissue isolated from normal mouse treated with luteolin mouse n°1, replicate1


title: MEF_cells_eIF3-seq_eIF4A1_KD


title: MEF_cells_80S-seq_eIF4A1_KD

source_name: MEF 80S ribosome-seq eIF4A1 knockdown


title: 201533640050_R02C01

source_name: rhabdomyosarcoma


title: nasopharyngeal gene expression of subject M133 at m2 [121145011332]


title: 201533640046_R05C01


title: 201533640050_R04C01


title: SAMP8 Control Pooled [miRNA-seq]


title: 201533640046_R07C01


title: nasopharyngeal gene expression of subject M134 at m2 [121145011342]


title: PBS M1_Hippocampus,replicate1

source_name: Hipocamppus tissue isolated from normal mouse n°1, replicate1

value: PBS mouse


title: PBS M 1_Hippocampus,replicate2

source_name: Hipocamppus tissue isolated from normal mouse n°1, replicate2


title: MEF_cells_80S-seq_Control

source_name: MEF 80S ribosome-seq Control


title: 201533640046_R06C01


title: 201533640046_R08C01


title: 201533640046_R04C01


title: nasopharyngeal gene expression of subject M130 at m2 [121145011302]


title: nasopharyngeal gene expression of subject M071 at m3 [121146010712]


title: RNA-dES-1.56e4cellsmL

city: Austin

first: Jonghwan

last: Kim

state: TX

address: 2506 Speedway

department: Molecular Biosciences

institute: University of Texas at Austin

description: Grown in -LIF for 96 hr

data_processing:
For ChIP-seq, reads from .fastq files were aligned to the mm10 genome using Bowtie 2 version 2.4.2 using multithreading and default settings.
Peaks were then called using MACS2 version 2.2.7.1 using input as control and an effective genome size of 2652783500. Input represents chromatin-associated DNA from mouse embryonic stem cells that were grown, differentiated, fixed, sheared, washed, etc. the same as samples but without dox treatment (meaning no expression of biotinylated transcription factor).
For RNA-seq, reads were pseudoaligned to the mm10 genome using kallisto version 0.46.1 with sequence bias correction enabled as well as bootstrapping (n = 100) in either single or paired-end mode depending on the samples.
Genome_build: mm10
Supplementary_files_format_and_content: peak text files for ChIP-seq, TPM output for RNA-seq

molecule: polyA RNA

source_name: Mouse embryonic stem cells, differentiated

growth_protocol: J1 mouse embryonic stem cells were routinely cultured in serum and LIF-containing media (+LIF) for self-renewal or without LIF for differentiation (-LIF). Differentiation was carried out for 72 hr or 96 hr as indicated in sample description. Cells were either seeded at high density (1.9e5 cells/cm^2) in a 6-well plate or low density (2.3e4 cells/cm^2) in a 12-well plate or at the densities indicated in sample name in a 24-well plate.

extract_protocol:
For ChIP-seq, chromatin was sheared from formaldehyde-fixed mouse embryonic stem cells. Protein-DNA complexes of interest were pulled down with magnetic streptaviding beads that were extensively washed in buffer before elution. For RNA-seq, total RNA was isolated using the RNeasy Mini Plus Kit from Qiagen and quantified on a Nanodrop.
For ChIP-seq, libraries were prepared according to the manufacturer's instructions in the NEBNext Ultra™ II DNA Library Prep Kit for Illumina (NEB) and sequenced on a NovaSeq 6000. For RNA-seq, paired-end libraries were prepared according to the manufacturer's instructions in the NEBNext Ultra™ II RNA Library Prep Kit for Illumina (NEB) and sequenced on a NovaSeq 6000. Unpaired libraries were prepared using the NEBNext Ultra™ II RNA Library Prep Kit for Illumina (NEB) and sequenced on a NextSeq500.

treatment_protocol: Dox was used at the indicated concentrations for last 48 hr (included in the 72 hr of differentiation). Inducible expression was achieved through transfection with pSB vector containing FLAG-BIO-tagged Esrrb, Tcfl7l1, or beta-catenin in BirA-expressing cells, followed by double selection with puromycin and neomycin. shRNA was transduced using lentivirus (constitutive KD, puromycin selection) with non-targeting shRNA as control.

value: J1 mouse embryonic stem cells

tag: treatment


title: wild-type neonate scATAC-seq

city: Pullman

first: Sean

last: Thompson

state: WA

address: BLS 240

department: School of Molecular Biosciences

institute: Washington State University

description:
WT1 to WT4
Isolated cells were pooled from each sample prior to library construction; both scRNA-seq and scATAC-seq were run in parallel from the same pool of cells.
Accessible DNA fragments

data_processing:
CellRanger 5.0.0's cellranger function to align Fastq files to mm10 for scRNA-seq.
cellranger-atac 1.2.0 function to align Fastq files to mm10 for scATAC-seq.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Cell Ranger 1.2.0 processing of FASTQ to standard scATAC-seq and scRNA-seq outputs.
Supplementary_files_format_and_content: peaks.bed: peak coordinates for scATAC from the P0 WT mice; default cell ranger output in filtered_peak_bc_matrix folder.
Supplementary_files_format_and_content: barcodes.tsv: single-cell barcodes for P0 WT scATAC; default cell ranger output in filtered_peak_bc_matrix folder.
Supplementary_files_format_and_content: matrix.mtx: filtered peak reads for P0 WT scATAC; default cell ranger output in filtered_peak_bc_matrix folder.
Supplementary_files_format_and_content: unpublished_peaks.bed: peak coordinates for scATAC from a currently unpublished dataset and experiment. This unpublished_peaks.bed is used to create a common set of peak coordinates in order to allow two scATAC-seq dataset Seurat objects to be merged into one Seurat object. The peak coordinates between the two Seurat objects must be the same, so we use these unpublished peak coordinates to create a common set of peak coordinates in order to allow direct merging of these unpublished samples with the P0 WT dataset that is analyzed in this study as part of a manuscript that is currently in progress. The peaks.bed file is genomic coordinates and does not affect the P0 WT sequencing data in any way.
Supplementary_files_format_and_content: singlecell.csv: metadata for P0 WT scATAC.
Supplementary_files_format_and_content: fragments.tsv.gz: peak reads for P0 WT scATAC.
Supplementary_files_format_and_content: fragments.tsv.gz.tbi: indices to quickly call P0 WT scATAC fragments.tsv data into R w/o reading the entire fragments.tsv.gz file into memory.
Supplementary_files_format_and_content: WT_filtered_feature_bc_matrix.h5: P0 WT scRNA reads, barcodes, metadata.

source_name: trunk skin

growth_protocol: Cells were freshly isolated.

extract_protocol:
Cells were isolated from mouse skin samples as in Jensen & Driskell et al. Nature Protocols (2010). Nuclei for scATAC-seq were isolated using an optimized version of 10x Genomics protocol CG000169 Rev D.
10x Genomics Chromium Single Cell 3' Kit V3.

treatment_protocol: No treatment or cell sorting were utilized.

value: trunk skin

tag: genotype

value: wild-type

value: postnatal day 0 (P0)


title: LPS M1_Hippocampus,replicate1

source_name: Hipocamppus tissue isolated from LPS depression induced mouse model n°1, replicate1

value: LPS depression induced mouse


title: RNA-dES-7.8e3cellsmL

description: Grown in -LIF for 96 hr


title: RNA-dES-3.1e4cellsmL

description: Grown in -LIF for 96 hr


title: RNA-dES-6.3e4cellsmL

description: Grown in -LIF for 96 hr


title: Ly6G(high) T1-binding myeloid cells 2

city: Houston

first: Thomas

last: Welte

address: 6670 Bertner Ave

department: Nanomedicine

institute: Houston Methodist Research Institute

description: intratumoral PMN cell subset that binds T1 aptamer

data_processing:
Combination of programs including STAR, Htseqq, Cufflink
Alignments were parsed using Tophat program
Reads mapping to the reference genome: paired-end clean reads were aligned to reference genome using STAR v2.5
HTSeq v0.6.1 was used to count read numbers mapped of each gene
FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene
Genome_build: mm10
Supplementary_files_format_and_content: Excel-files: Column 1: gene ID, column 2: gene name, column 3: gene expression quantification readcount, column 4: gene expression quantification fpkm

source_name: Tumor of CT26 tumor-bearing mouse 2

growth_protocol: BALB/C mice were implanted s.c. with CT26 colon cancer model, tumors reaching 1,800 mm^3 were digested, stained for FACS and indicated myeloid subsets were isolated by FACS sorting.

extract_protocol:
RNA isolation with Qiagen's Rneasy Micro Kit following supplier's protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

value: BALB/C

value: tumor

value: PMN myeloid cell subset


title: Ly6G(high) T1-binding myeloid cells 1

source_name: Tumor of CT26 tumor-bearing mouse 1


title: nasopharyngeal gene expression of subject M128 at m2 [121145011282]

value: nasopharyngeal cells


title: RNA-dES-1.25e5cellsmL

description: Grown in -LIF for 96 hr


title: SPLiT-seq Mouse Brain

city: Irvine

first: Mathew

last: Blurton-Jones

state: CA

address: 3400 Bio Sci 3

department: Neurobiology and Behavior

institute: University of California, Irvine

data_processing:
Raw sequencing data was processed to quantify gene expression in single nuclei using the split-pipe software from Parse Biosciences.
Downstream processing including normalization, clustering, differential gene expression analysis, and visualization were done using Seurat. Network analysis was done using WGCNA. Cell communication analysis was done using CellChat.
Genome_build: mm10
Supplementary_files_format_and_content: Seurat objects (.rds) containing gene expression matrices and relevant meta-data for all single-nucleus RNA-seq profiles, before and after quality-control filtering.

source_name: brain

extract_protocol:
Single nucleus suspensions were generated from n=48 (6 groups, 4 female 4 male) of tissue as previously described (Morabito et al., 2020) except after the 40μm filtration, nuclei were immediately processed using the Nuclei Fixation kit (Parse Biosciences, formerly Split Biosciences) and then cryopreserved with DMSO until library preparation. Nuclei isolation was performed in randomized groups of eight samples.
library preparation was performed in a single batch of all 48 samples. Single-nucleus RNAseq libraries were generated with the Single Cell Whole Transcriptome library preparation kit (Parse Biosciences), which utilizes split-pool ligation-based transcriptome-sequencing (SNucseq)as described in in (cite Rosenberg 2018 Science). Briefly, each sample, normalized by nuclei number, was added to one well of a 96-well plate to perform reverse transcription, adding a well-specific barcode (first barcode). All the wells were then pooled together and randomly distributed across a new 96-well plate with new well-specific barcodes (second barcode) for ligation. After ligating the second barcode, the wells are again pooled and randomly distributed across another 96-well plate for a third round of barcoding. Throughout this process, the nuclei are still intact but permeabilized to allow the reactions to append three different barcodes to each transcript.
The nuclei were then pooled into 8 sublibraries of 12,500 nuclei and lysed to allow the construction of the final cDNA libraries, in which a fourth, sublibrary-specific barcode is added. This thus results in single-nucleus transcriptomes that can be identified based up on the combination of the four different barcodes. cDNA library quality was assessed using the Agilent 4200 Tapestation, and concentrations were determined using Qubit. Libraries were sequenced using the Illumina NovaSeq 6000 S4 at UCI’s Genomics High-Throughput Facility for a sequencing depth of 50,000 read pairs/cell.
library preparation was performed in a single batch of all 48 samples. Single-nucleus RNAseq libraries were generated with the Single Cell Whole Transcriptome library preparation kit (Parse Biosciences), which utilizes split-pool ligation-based transcriptome-sequencing (SNucseq)as described in in (cite Rosenberg 2018 Science). Briefly, each sample, normalized by nuclei number, was added to one well of a 96-well plate to perform reverse transcription, adding a well-specific barcode (first barcode). All the wells were then pooled together and randomly distributed across a new 96-well plate with new well-specific barcodes (second barcode) for ligation. After ligating the second barcode, the wells are again pooled and randomly distributed across another 96-well plate for a third round of barcoding. Throughout this process, the nuclei are still intact but permeabilized to allow the reactions to append three different barcodes to each transcript.
The nuclei were then pooled into 8 sublibraries of 12,500 nuclei and lysed to allow the construction of the final cDNA libraries, in which a fourth, sublibrary-specific barcode is added. This thus results in single-nucleus transcriptomes that can be identified based up on the combination of the four different barcodes. cDNA library quality was assessed using the Agilent 4200 Tapestation, and concentrations were determined using Qubit. Libraries were sequenced using the Illumina NovaSeq 6000 S4 at UCI’s Genomics High-Throughput Facility for a sequencing depth of 50,000 read pairs/cell.

value: brain


title: nasopharyngeal gene expression of subject M126 at m2 [121145011262]


title: nasopharyngeal gene expression of subject M129 at m2 [121145011292]


title: RNA-dES-2.5e5cellsmL

description: Grown in -LIF for 96 hr


title: nasopharyngeal gene expression of subject M122 at m2 [121145011222]


title: 201533640042_R05C01

value: ERMS


title: 201533640046_R02C01

value: ARMS


title: nasopharyngeal gene expression of subject M119 at m2 [121145011192]


title: 201533640042_R06C01

value: PRMS


title: 201533640046_R03C01


title: Ly6G(high) T1-non-binding myeloid cells 2

description: intratumoral PMN cell subset that does not bind T1 aptamer


title: Ly6G(low) T1-binding myeloid cells 2

description: intratumoral myeloid cell subset that binds T1 aptamer

value: myeloid cell subset


title: Ly6G(high) T1-non-binding myeloid cells 1


title: nasopharyngeal gene expression of subject M120 at m2 [121145011202]


title: RNA-dES-5e5cellsmL

description: Grown in -LIF for 96 hr


title: Ly6G(low) T1-binding myeloid cells 1


title: nasopharyngeal gene expression of subject M118 at m2 [121145011182]


title: RNA-ES-1.56e4cellsmL

description: Grown in +LIF for 96 hr

source_name: Mouse embryonic stem cells


title: RNA-ES-7.8e3cellsmL

description: Grown in +LIF for 96 hr


title: RNA-EsrrbOE+dox_lowdensity_r2

description: Differentiation in -LIF for 72 hr

value: 500 ng/mL dox 48 hr


title: RNA-EsrrbOE+dox_lowdensity_r1

description: Differentiation in -LIF for 72 hr


title: nasopharyngeal gene expression of subject M116 at m2 [121145011162]


title: nasopharyngeal gene expression of subject M110 at m2 [121145011102]


title: nasopharyngeal gene expression of subject M117 at m2 [121145011172]


title: RNA-ES-3.1e4cellsmL

description: Grown in +LIF for 96 hr


title: RNA-ES-6.3e4cellsmL

description: Grown in +LIF for 96 hr


title: RNA-ES-1.25e5cellsmL

description: Grown in +LIF for 96 hr


title: RNA-EsrrbOE-dox_highdensity_r1

description: Differentiation in -LIF for 72 hr


title: RNA-EsrrbOE-dox_lowdensity_r2

description: Differentiation in -LIF for 72 hr


title: nasopharyngeal gene expression of subject M107 at m2 [121145011072]


title: 201533640042_R04C01


title: nasopharyngeal gene expression of subject M109 at m2 [121145011092]


title: RNA-ES-5e5cellsmL

description: Grown in +LIF for 96 hr


title: nasopharyngeal gene expression of subject M106 at m2 [121145011062]


title: RNA-ES-2.5e5cellsmL

description: Grown in +LIF for 96 hr


title: RNA-Yap1OE+dox_highdensity_r2

description: Differentiation in -LIF for 72 hr


title: 201533640042_R03C01


title: nasopharyngeal gene expression of subject M105 at m2 [121145011052]


title: 201533640042_R02C01


title: RNA-Yap1OE-dox_highdensity_r1

description: Differentiation in -LIF for 72 hr


title: 201533640031_R06C01


title: nasopharyngeal gene expression of subject M102 at m2 [121145011022]


title: nasopharyngeal gene expression of subject M101 at m2 [121145011012]


title: RNA-Esrrb_KD1_lowdensity_r1

description: Differentiation in -LIF for 72 hr

value: shRNA against Esrrb


title: 201533640031_R07C01


title: 201533640042_R01C01


title: RNA-Yap1OE+dox_highdensity_r1

description: Differentiation in -LIF for 72 hr


title: nasopharyngeal gene expression of subject M098 at m2 [121145010982]


title: RNA-Yap1OE-dox_lowdensity_r2

description: Differentiation in -LIF for 72 hr


title: RNA-Esrrb_KD1_highdensity_r2

description: Differentiation in -LIF for 72 hr


title: nasopharyngeal gene expression of subject M104 at m2 [121145011042]


title: 201533640031_R03C01


title: nasopharyngeal gene expression of subject M097 at m2 [121145010972]


title: 201533640031_R05C01

value: SC/SRMS


title: RNA-Esrrb_KD1_highdensity_r1

description: Differentiation in -LIF for 72 hr

value: J1 mouse embryonic stem cells


title: nasopharyngeal gene expression of subject M094 at m2 [121145010942]


title: RNA-shCon_lowdensity_r2

description: Differentiation in -LIF for 72 hr


title: 201533640031_R02C01


title: RNA-shCon_highdensity_r2

description: Differentiation in -LIF for 72 hr


title: 201533640024_R08C01


title: RNA-swapld2_lowdensity_r2

description: Differentiation in -LIF for 72 hr

value: swap media w high density cells 4 hr


title: 201533640024_R07C01


title: 201533640024_R06C01


title: nasopharyngeal gene expression of subject M071 at m2 [121145010712]


title: nasopharyngeal gene expression of subject M078 at m2 [121145010782]