title: E151G_L

city: Zhunan Town

first: Chiou-Hwa

last: Yuh

state: Miaoli County

address: #35 Keyan Road

description:
Gene expression data from embryo TPM3(E151G) zebrafish treated with L-carnitine.
processed data file: All_data.xlsx
embryo_E151G_L_vs_WT_FC2X.xlsx
embryo_E151G_L_vs_E151G_FC2X.xlsx

data_processing:
1. Illumina's bcl2fastq program v2.20 used for basecalling.
2. Both adaptor clipping and sequence quality trimming were performed using Trimmomatic v0.36 with a sliding-window approach.
3. Reads count and Fragments Per Kilobase per Million (FPKM) data of genes and transcripts were calculated with HISAT2 program for transcriptome alignment.
Mapped reads were assigned to annotated genes in the GTF file using featureCounts version 1.6.3.
Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.22.2.
Genome_build: GRCz11
Supplementary_files_format_and_content: Excel files include reads count or FPKM values for each sample.

organism: Danio rerio

source_name: whole embryo

growth_protocol: All zebrafish were maintained at the Zebrafish Core Facility in National Health Research Institute (NHRI, Miaoli, Taiwan). Adult fish were maintained under an automated 14:10 hour light/dark cycle and a constant temperature of 28°C. All experiments were approved by the Institute Animal Care and Use Committee (IACUC) of NHRI.

extract_protocol:
The muscle tissue were grounded using Microtube Pellet Pestle Rods (Violet BioScience, Taipei, Taiwan). TRI Reagent® (Sigma-Aldrich, MI, USA) was mixed with sample and homogenize using a homogenizer. 1/5 of chloroform was added and transfer the supernatant containing RNA to a new Eppendorf. After extracted the total RNA from muscle tissue, total RNA used NucleoSpin® RNA kit (MACHEREY-NAGEL, Nordrhein-Westfalen, Germany) for the cleanup. RNA was isolated using a NucleoSpin® RNA column (MACHEREY-NAGEL, Nordrhein-Westfalen, Germany) per manufacturer‘s protocol. Finally, the concentration were measured using a NanoDrop ND-1000 (Thermo Fisher Scientific, MA, USA), which were then stored in a –80°C freezer. Complementary DNA (cDNA) was synthesized using iScript™ cDNA synthesis kit (BioRad, CA, USA).
All RNA sample preparation procedures were carried out according to the Illumina's official protocol. Agilent's SureSelect Strand-Specific RNA Library Preparation Kit was used for library construction followed by AMPure XP beads (Beckman Coulter, USA) size selection.

treatment_protocol: Embryos were immersed with different chemicals all day from 28 hours-post-fertilization (hpf) to 7 days-post-fertilization (dpf) in a 90 mm dish. The chemical was refreshed every day until 7 dpf.

value: AB

value: whole embryo

value: 2 days

value: L-carnitine


title: APChet tdTOM_negative_WNT_negative_rep4

status: Public on Apr 24 2020

type: SRA

city: New York

first: Irina

last: Matos

address: 1230 York Av

country: USA

institute: The Rockefeller University

description:
processed data column (in AllValuesConf_Irina.xls):
APChet tdTOM_negative_WNT _negative

library_source: transcriptomic

data_processing:
Alignment: Sequence reads were obtained and mapped to the mouse genome (mm9, build 37) using the Bowtie program (Version 0.1.2.7).
Unique reads mapped to a single genomic location (allowing two mismatches) were kept.
Transcript Assembly: Aligned reads were assembled into transcripts using Cufflinks (version 2.2.1)
Genome_build: mm9
Supplementary_files_format_and_content: Cuffdiff gene expression files

molecule: polyA RNA

organism: Mus musculus

extract_protocol:
Keratinocytes were isolated by fluorescence-activated cell sorting (FACS) and total RNA was extracted using the ZYMO Direct-Zol RNA miniprep kit (R2050) according to manufacturer instructions. Purification was done using the sorter markers a6, GFP and either tdTOM (Samples 1-20) or mKO2 (Samples 21-29).
mRNA libarary was prepared using Illumina TruSeq mRNA sample preparation kit and single end sequencing was performed using Illumina HiSeq 2500.

treatment_protocol: For samples 1 to 20: E9.5 Embryos were mosaically transduced with a lentivirus harbouring CRE recombinase and a WNT reporter tagged to GFP.

tag: strain

tag: age

tag: genotype/variation

value: APC fl/+ tdTOM R26 fl/+

tag: tissue

value: developing epidermis

tag: cell type

value: Epidermal keratinocytes


title: SVAM_A3_Vanco_MHB_2

city: La Jolla

first: Henrique

last: Machado

state: CA

address: 9500 Gilman Drive

department: Bioengineering

institute: University of California San Diego

data_processing:
The phred quality scores for the Illumina sequencing reads were generated using FastQC package
Bowtie2 was used to align the raw reads to TCH1516 genome (GCA_000017085.1) and to calculate alignment percentage
The aligned reads were then normalized to transcripts per million (TPM) with DESeq2
Genome_build: GCA_000017085.1
Supplementary_files_format_and_content: csv file with deseq2 TPM values for all samples

molecule: total RNA

organism: Staphylococcus aureus

growth_protocol: The strains were grown in each respective media, with and without vancomycin (at 1/2 MIC). At OD 0.2, cultures without vancomycin were harvested. At the same OD, cultures were treated with 0.5x MIC of vancomycin, and harvested for RNA 30min after. Harvesting of the cells consisted in mixing of 3 mL of culture with two volumes of Qiagen RNA-protect Bacteria Reagent (6 ml), vortexed for 5 s, incubated at room temperature for 5 min and immediately centrifuged for 10 min at 17,500 r.p.m.. The supernatant was decanted, and the cell pellet was stored at −80 °C.

extract_protocol:
Total RNA was isolated using the Quick RNA Fungal/Bacterial Microprep (Zymo Research), following vendor procedures, including an on-column DNase treatment. RNA quality and purity was assessed using Nanodrop and Bioanalyzer RNA nano chip. Ribosomal RNA was removed from total RNA preparations using RNaseH.
RNA was used to build a cDNA library for sequencing using a KAPA Stranded RNA-seq Library Preparation Kit.

tag: gentotype/variation

tag: culture media

value: CA-MHB

tag: treatment

value: vancomycin


title: APChet tdTOM_negative_WNT_negative_rep3


title: E151G

country: Taiwan

institute: National Health Research Institutes

description:
Gene expression data from embryo TPM3(E151G) zebrafish .
processed data file: All_data.xlsx
embryo_E151G_vs_WT_FC2X.xlsx
embryo_E151G_L_vs_E151G_FC2X.xlsx


title: APChet tdTOM_positive_WNT_negative_rep1

description:
processed data column (in AllValuesConf_Irina.xls):
APChet tdTOM_positive_WNT _negative


title: SVAM_A3_Vanco_MHB_1

treatment_protocol: cultures were treated with 0.5x MIC of vancomycin


title: APChel tdTOM_negative_WNT_negative_rep1

description:
processed data column (in AllValuesConf_Irina.xls):
APChel tdTOM_negative_WNT _negative


title: WT

description:
Gene expression data from embryo TPM3(WT) zebrafish .
processed data file: All_data.xlsx
embryo_E151A_vs_WT_FC2X.xlsx
embryo_E151G_vs_WT_FC2X.xlsx
embryo_E151G_L_vs_WT_FC2X.xlsx


title: SVAM_TCH1516_Vanco_MHB_2

value: WT


title: APChet tdTOM_positive_WNT_negative_rep2


title: SVAM_TCH1516_Vanco_MHB_1


title: APChet tdTOM_positive_WNT_positive_rep2

description:
processed data column (in AllValuesConf_Irina.xls):
APChet tdTOM_positive_WNT _positive


title: E151G_F01

description:
Gene expression data from adult TPM3(E151G) zebrafish sample 2.
processed data file: All_data.xlsx
adult_E151G_vs_WT_FC2X.xlsx
adult_E151G_vs_E151A_FC2X.xlsx

source_name: Muscle

value: Muscle

value: 6 months


title: SVAM_A10_Vanco_MHB_2


title: APCnull tdTOM_positive_WNT_negative_rep1

description:
processed data column (in AllValuesConf_Irina.xls):
APCnull tdTOM_positive_WNT _negative

value: APC fl/fl tdTOM R26 fl/+


title: APChet tdTOM_negative_WNT_negative_rep2


title: E151G_E01

description:
Gene expression data from adult TPM3(E151G) zebrafish sample 1.
processed data file: All_data.xlsx
adult_E151G_vs_WT_FC2X.xlsx
adult_E151G_vs_E151A_FC2X.xlsx


title: SVAM_A12_MHB_1

source_name: SVAM_A12_CA-MHB_no vancomycin

value: no vancomycin


title: E151A_D01

description:
Gene expression data from adult TPM3(E151A) zebrafish sample 2.
processed data file: All_data.xlsx
adult_E151A_vs_WT_FC2X.xlsx
adult_E151G_vs_E151A_FC2X.xlsx


title: APCnull tdTOM_positive_WNT_negative_rep2


title: E151A_C01

description:
Gene expression data from adult TPM3(E151A) zebrafish sample 1.
processed data file: All_data.xlsx
adult_E151A_vs_WT_FC2X.xlsx
adult_E151G_vs_E151A_FC2X.xlsx


title: SVAM_A10_MHB_1

source_name: SVAM_A10_CA-MHB_no vancomycin


title: APCnull tdTOM_negative_WNT_negative_rep2

description:
processed data column (in AllValuesConf_Irina.xls):
APCnull tdTOM_negative_WNT _negative


title: APCnull tdTOM_negative_WNT_negative_rep1


title: SVAM_A9_MHB_2

source_name: SVAM_A9_CA-MHB_no vancomycin


title: WT_A01

description:
Gene expression data from adult TPM3(WT) zebrafish sample 1.
processed data file: All_data.xlsx
adult_E151A_vs_WT_FC2X.xlsx
adult_E151G_vs_WT_FC2X.xlsx
adult_E151G_vs_E151A_FC2X.xlsx


title: SVAM_A9_MHB_1


title: E151A

description:
Gene expression data from embryo TPM3(E151A) zebrafish .
processed data file: All_data.xlsx
embryo_E151A_vs_WT_FC2X.xlsx


title: SVAM_STM3_MHB_2

source_name: STM3_CA-MHB_no vancomycin


title: conidia from 10 day old culture grown at 25C

city: Utrecht

first: Maarten

last: Punt

state: Nederland

address: Padualaan 8

country: Netherlands

institute: Utrecht University

description:
Expression_and_annotations.upload.txt
10d_25C

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and then mapped to LCP96 04111 whole genome using Hisat2 v2.1.0 with parameters --min-intronlen 20 --max-intronlen 1000 –no-unal
Reads Per Kilobase of exon per Megabase of library size (RPKM)  were calcuted using CuffDiff
Genome_build: LCP96 04111
Supplementary_files_format_and_content: gene_exp.diff

organism: Penicillium roqueforti

source_name: conidia

growth_protocol: conidia were produced on MEA and harvested after set timepoints

extract_protocol:
Conidia were harvested, suspended in RNA-later ICE and flash frozen in liquid nitrogen. Samples were milled using a tissuelyzer and RNA was extracted with the QIAGEN Power Plant RNA isolation kit.
RNA libraries were prepared for sequencing using standard Illumina protocols (Truseq RNA stranded polyA)

value: 10 day old culture

tag: growth temperature


title: M_108_new

city: Wuerzburg

first: Marie-Therese

last: Eckstein

state: Bavaria

department: Molecular Infection Biology

country: Germany

institute: University Clinic Wuerzburg

data_processing:
Illumina adaptor sequences were removed using the Trimmomatic tool V0:39 (Bolger et al., 2014). Trimmed reads were aligned to the C. albicans reference genome assembly 21 (www.candidagenome.org) using STAR 2.7.0a (Dobin et al., 2013). Read count files were generated using HTSeq 0.11.1.
Genome_build: C. albicans reference genome assembly 21 (www.candidagenome.org)
Supplementary_files_format_and_content: Tab-delimited text files providing raw counts for all annotated C. albicans ORFs

organism: Candida albicans SC5314

source_name: yeast cells

growth_protocol: 800 µL of PBS-washed C. albicans cell suspension (cell density = 5 × 10E8 cells/mL) were inoculated into 20 mL of yeast nitrogen base (YNB) medium (Becton and Dickinson) alone or supplemented either with glucose or mucin from porcine stomach (Sigma). Cultures were incubated at 37°C for 24 h under anaerobic conditions.

extract_protocol:
Cell were collected by centrifugation and RNA was extracted with the RiboPure™ RNA Purification Kit for yeast (Thermo Fisher Scientific) following the manufacturer’s instructions.
Libraries for Illumina sequencing were prepared by Novogene (Cambridge, UK) following standard operating procedures.

treatment_protocol: Yeast nitrogen base medium alone or supplemented with either glucose or mucin.

tag: carbon source

value: base medium + mucin

tag: athmosphere

value: anaerobic 37 °C

tag: media

value: yeast nitrogen base (YNB)


title: conidia from 7 day old culture grown at 30C

description:
Expression_and_annotations.upload.txt
7d_30C

value: 7 day old culture


title: conidia from 7 day old culture grown at 15C

description:
Expression_and_annotations.upload.txt
7d_15C


title: SVAM_STM3_MHB_1


title: M_107_new


title: SVAM_A3_MHB_2

source_name: SVAM_A3_CA-MHB_no vancomycin


title: SVAM_A12_MHB_2


title: M_104_new

value: base medium + glucose


title: SVAM_A3_MHB_1


title: SVAM_TCH1516_MHB_2

source_name: WT_CA-MHB_no vancomycin


title: M_102_new

value: base medium


title: conidia from 3 day old culture grown at 25C

description:
Expression_and_annotations.upload.txt
3d_25C

value: 3 day old culture


title: SVAM_A10_MHB_2


title: conidia from 5 day old culture grown at 25C

description:
Expression_and_annotations.upload.txt
5d_25C

value: 5 day old culture


title: SVAM_TCH1516_MHB_1


title: M_101_new


title: Total RNA from miR-574 KO mouse #3

status: Public on Apr 23 2020

city: Rochester

first: Peng

last: Yao

state: NY

address: 601 Elmwood Avenue, Box CVRI

department: Medicine

institute: Univeristy of Rochester Medical Center

data_processing:
DATA FORMATTING (Illumina -> FastQ) & DEMULTIPLEXING - bcltofastq-1.8.4
CLEANING - Trimmomatic-0.32 "TRAILING:13 LEADING:13 ILLUMINACLIP:adapters.fasta:2:30:10 SLIDINGWINDOW:4:20 MINLEN:15"
MAPPING - STAR_2.4.2a "--twopassMode Basic --runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical"
READ COUNTING - subread-1.5.0p3, featurecounts, "-s 2 -t exon -g gene_name"
Genome_build: GRCm38.p4 + Gencode-M6 Annotation
Supplementary_files_format_and_content: tab-delimited text file includes raw count values for each sample

source_name: miR-574 KO heart

growth_protocol: Three pairs of P60 wild type and miR-574 KO mice were prepared.

extract_protocol:
The RNA extraction and purification from fresh heart tissue samples was performed using regular TRIzol reagent (ThermoFisher) and Qiagen RNAeasy fibrous tissue mini kit following instructions in the manual.
RNA libraries were prepared for sequencing using standard Illumina protocols for TruSeq Stranded Total RNA (RIN: 7.0-10.0)

value: heart

tag: background strain

tag: genotype

value: miR-574 KO


title: Total RNA from miR-574 KO mouse #1


title: Total RNA from WT mouse #3

source_name: WT heart


title: Total RNA from miR-574 KO mouse #2


title: Total RNA from WT mouse #2


title: Total RNA from WT mouse #1


title: WT_B01

description:
Gene expression data from adult TPM3(WT) zebrafish sample 2.
processed data file: All_data.xlsx
adult_E151A_vs_WT_FC2X.xlsx
adult_E151G_vs_WT_FC2X.xlsx
adult_E151G_vs_E151A_FC2X.xlsx

value: AB


title: M_105_new


title: TS_5percent_RNA-seq

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

data_processing:
Libraries were sequenced on the Illumina HiSeq 2500 platform or on the BGISeq500 platform for single end ChIP-seq data
Processing by the Babraham Bioinformatics Facility used the clusterflow fastq_hisat2 pipeline, comprising adapter and quality trimming using trim galore v0.6.0 using default single end parameters followed by mapping to the mouse GRCm38 genome guided by gene models from Ensembl release 70 using hisat2 v2.1.0.  Hisat2 mapping parameters were --dta --sp 1000, 1000. Data was imported into SEQMONK (version 1.44.0) as RNA-seq data with a minimum mapping quality of 20.
Genome_build: GRCm38
Supplementary_files_format_and_content: RNA-seq report: tab delimed text files showing log2RPM values for each sample

source_name: Trophoblast Stem Cell

extract_protocol:
Trophoblast stem cells were grown in culture under standard conditions and washed in PBS prior to DNA and RNA extraction
DNA and RNA collected using standard phenol chloroform or trizol extraction protocol respectively
mRNA was isolated using the Dynabeads mRNA Purification Kit (Life Technologies) and processed into indexed, strand-specific libraries using the ScriptSeq v.2 RNA-Seq Library Preparation Kit (Epicentre).

value: Trophoblast Stem Cell

value: WT


title: conidia from 7 day old culture grown at 25C

description:
Expression_and_annotations.upload.txt
7d_25C


title: TS_DIFF_5percent_RNAseq

description:
Total RNA was extracted using TRI Reagent (Sigma), followed by DNase treatment using the TURBO-DNA-free Kit (Life Technologies).
Trophoblast stem cells were grown in culture under standard conditions and washed in PBS prior to DNA and RNA extraction

data_processing:
Libraries were sequenced on the Illumina HiSeq 2500 platform or on the BGISeq500 platform for single end ChIP-seq data
RNA-Seq: Processing by the Babraham Bioinformatics Facility used the clusterflow fastq_hisat2 pipeline, comprising adapter and quality trimming using trim galore v0.6.0 using default single end parameters followed by mapping to the mouse GRCm38 genome guided by gene models from Ensembl release 70 using hisat2 v2.1.0.  Hisat2 mapping parameters were --dta --sp 1000, 1000. Data was imported into SEQMONK (version 1.44.0) as RNA-seq data with a minimum mapping quality of 20.
(h)MeDIP-Seq: Processing was performed by Babraham Bioinformatics Facility using the clusterflow fastq_bowtie2 pipeline, comprising adapter and quality trimming using trim galore v0.6.0 using default single or paired end parameters followed by mapping to the mouse GRCm38 genome assembly using bowtie2 v2.3.2. Mapped reads were imported into SEQMONK (version 1.44.0) for data exploration and analysis. For single end data, reads were extended by 300 base pairs. For comparison of H4K8ac colon to Kcr colon, H4K8ac colon data was mapped as single end.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab delimed text files showing log2RPM values for each sample
Supplementary_files_format_and_content: tab delimited text files showing log2 read counts of 2kb contiguous genomic regions normalised to the the largest data store

source_name: Trophoblast Stem Cell 3 days differentiated

extract_protocol:
DNA and RNA collected using standard phenol chloroform or trizol extraction protocol respectively
(h)MeDIP-Seq: purified genomic DNA was sonicated to yield 150–600 bp fragments, and adaptors for paired‐end sequencing (Illumina) were ligated using NEB Next DNA Sample Prep Reagent Set 1 (New England Biolabs). Immunoprecipitations were carried out using 500ng DNA per sample, 1.25μg anti-5mC antibody (Eurogentec BI-MECY-0100) or anti-5hmC antibody (Active Motif, 39769), and 10μl Dynabeads coupled with M‐280 sheep anti‐mouse IgG or Protein G (Invitrogen). Pulled-down DNA was amplified for 12 (meDIP) or 15 (hmeDIP) cycles with adapter specific indexed primers. Final clean-up and size selection was carried out with Ampure-XP SPRI beads (Beckman Coulter)
RNA-Seq: mRNA was isolated using the Dynabeads mRNA Purification Kit (Life Technologies) and processed into indexed, strand-specific libraries using the ScriptSeq v.2 RNA-Seq Library Preparation Kit (Epicentre).


title: TS_DIFF_20percent_RNAseq

value: Trophoblast Stem Cell 3 days differentiated


title: TS_20percent_RNAseq


title: TS_DIFF_20percent_hmeDIP_rep2

description:
5hydroxymethylcytosine
DNA was extracted using a standard phenol chloroform extraction protocol
Trophoblast stem cells were grown in culture under standard conditions and washed in PBS prior to DNA and RNA extraction

library_source: genomic

molecule: genomic DNA


title: TS_DIFF_5percent_hmeDIP_rep1


title: TS_20percent_hmeDIP_rep2


title: TS_DIFF_20percent_hmeDIP_rep1


title: TS_5percent_hmeDIP_rep2


title: TS_5percent_hmeDIP_rep1


title: Tet1KO_3_TS_hmeDIP


title: TS_20percent_hmeDIP_rep1


title: Tet1KO_1_TS_hmeDIP


title: Tet1KO_2_TS_hmeDIP


title: IgG control

data_processing:
Libraries were sequenced on the Illumina HiSeq 2500 platform or on the BGISeq500 platform for single end ChIP-seq data
(RNA-Seq)Processing by the Babraham Bioinformatics Facility used the clusterflow fastq_hisat2 pipeline, comprising adapter and quality trimming using trim galore v0.6.0 using default single end parameters followed by mapping to the mouse GRCm38 genome guided by gene models from Ensembl release 70 using hisat2 v2.1.0.  Hisat2 mapping parameters were --dta --sp 1000, 1000. Data was imported into SEQMONK (version 1.44.0) as RNA-seq data with a minimum mapping quality of 20.
((h)MeDIP-Seq)Processing was performed by Babraham Bioinformatics Facility using the clusterflow fastq_bowtie2 pipeline, comprising adapter and quality trimming using trim galore v0.6.0 using default single or paired end parameters followed by mapping to the mouse GRCm38 genome assembly using bowtie2 v2.3.2. Mapped reads were imported into SEQMONK (version 1.44.0) for data exploration and analysis. For single end data, reads were extended by 300 base pairs. For comparison of H4K8ac colon to Kcr colon, H4K8ac colon data was mapped as single end.
GRCm38
Supplementary_files_format_and_content: IgG report: tab delimited text files showing log2 read counts of 2kb contiguous genomic regions

extract_protocol:
Sample collection protocol: Trophoblast stem cells were grown in culture under standard conditions and washed in PBS prior to DNA and RNA extraction
DNA and RNA collected using standard phenol chloroform or trizol extraction protocol respectively
((h)MeDIP-Seq) purified genomic DNA was sonicated to yield 150–600 bp fragments, and adaptors for paired‐end sequencing (Illumina) were ligated using NEB Next DNA Sample Prep Reagent Set 1 (New England Biolabs). Immunoprecipitations were carried out using 500ng DNA per sample, 1.25μg anti-5mC antibody (Eurogentec BI-MECY-0100) or anti-5hmC antibody (Active Motif, 39769), and 10μl Dynabeads coupled with M‐280 sheep anti‐mouse IgG or Protein G (Invitrogen). Pulled-down DNA was amplified for 12 (meDIP) or 15 (hmeDIP) cycles with adapter specific indexed primers. Final clean-up and size selection was carried out with Ampure-XP SPRI beads (Beckman Coulter)


title: Tet1KO_1_TS_meDIP

description:
5methylcytosine
DNA was extracted using a standard phenol chloroform extraction protocol
Trophoblast stem cells were grown in culture under standard conditions and washed in PBS prior to DNA and RNA extraction


title: Control_3_TS_meDIP


title: Control_3_TS_hmeDIP


title: Tet1KO_3_TS_meDIP


title: TS_DIFF_5percent_hmeDIP_rep2


title: Control_2_TS_meDIP


title: Control_2_TS_hmeDIP


title: Control_1_TS_meDIP


title: T9_3335_117_CTL_HW_M_G7_21013

city: Duarte

first: Denis

last: OMeally

state: California

address: 1500 E Duarte Rd

department: Arthur Riggs Diabetes & Metabolism Research Institute

institute: City of Hope

data_processing:
Basecalls performed using Illumina RTA version 1.18.64
Raw sequencing reads were processed with the nf-core/RNASeq pipeline version 1.0. Briefly, trimmed reads were mapped using STAR to the GRCm38 reference amended with ERCC sequences and the human MYH11 fusion gene sequence.
Each library was subjected to extensive quality control, including estimation of library complexity, gene body coverage, and duplication rates, among other metrics detailed in the nf-core/rnaseq pipeline repository on GitHub.
Reads were counted across genomic features encoded in the Ensembl GRCm38 annotation using Subread featureCounts and merged into a matrix of counts per gene for each sampled timepoint. CM fusion transcript expression was measured by counting reads that spanned the CM fusion boundary.
Surrogate variable analysis was used to check for confounding experimental effects. None were apparent; however, library preparation batch was used as a covariate in differential expression analyses using the Bioconductor package edgeR as implemented in SARTools.
Genome_build: GRCm38

source_name: PBMC

extract_protocol:
AllPrep DNA/RNA Mini Kit (Qiagen)
Sequencing libraries were constructed using the KapaHyper with RiboErase ( (Kapa Biosystems); Samples were allocated to randomized batches for library preparation, such that samples from each timepoint were distributed evenly over all sequencing runs.

treatment_protocol: To induce expression of CM, Cbfb+/56M/Mx1-Cre C57BL/6 mice (4-8 weeks old, including both females and males) were injected with 14 mg/kg poly (I:C) (InvivoGen, San Diego CA) every other day for 7 doses. Similarly treated, wild-type, Cbfb+/56M or Mx1-Cre littermates were used as controls. As previously described, induction of CM expression results in expansion of preleukemic hematopoietic stem and progenitor cell (HSPC) populations in the bone marrow and subsequent development of overt leukemia characterized by >20% cKit+ leukmia blasts, increased white blood cell counts, and splenomegaly. Peripheral blood samples were taken via retro-orital venous sinus before induction and monthly thereafter for the duration of the experiment. All mice were maintained in an AAALAC-accredited animal facility, and all experimental procedures were performed in accordance with federal and state government guidelines and established institutional guidelines and protocols approved by the Institutional Animal Care and Use Committee at the Beckman Research Institute of City of Hope.

tag: timepoint

tag: mouseid

value: CTL

value: HW

tag: Sex

value: M

value: PBMC


title: T9_3368_52_CM_CHW_M_G1_20884

tag: strain

value: CM

value: CHW


title: T9_3346_95_CTL_CW_M_G7_21010

value: CW


title: Control_1_TS_hmeDIP


title: T9_3370_63_CM_CHW_M_G3_20925


title: T9_3350_139_CTL_WT_F_G3_20936

value: F


title: T9_3349_106_CTL_CW_F_G6_20990


title: Tet1KO_2_TS_meDIP


title: T8_3370_62_CM_CHW_M_G7_21004


title: T9_3339_73_CTL_CW_M_G3_20927


title: T9_3340_128_CTL_HW_M_G5_20974


title: T8_3368_51_CM_CHW_M_G4_20944


title: T8_3335_116_CTL_HW_M_G3_20934


title: T8_3346_94_CTL_CW_M_G3_20930


title: T8_3350_138_CTL_WT_F_G1_20896


title: T8_3340_127_CTL_HW_M_G4_20953


title: T9_3342_84_CTL_CW_M_G2_20908


title: T7_3370_61_CM_CHW_M_G6_20985


title: T8_3339_72_CTL_CW_M_G2_20906


title: Reh EK_H3K9ac

city: Staten Island

first: Joanna

last: Pierro

address: 550 1st Avenue

institute: NYU Langone Health

data_processing:
Align to reference genome (hg19) using Bowtie2
Remove duplicate reads using Sambamba
Peaks calling with MACS2
Genome_build: hg19
Supplementary_files_format_and_content: bigwig contains peak information

organism: Homo sapiens

source_name: B-ALL cell line

growth_protocol: The B-lineage leukemia cell lines RS4;11, Reh (ATCC, Manassas, VA), KOPN8, 697, RCH-ACV (DSMZ, Braunschweig, Germany), and SEM (kindly gifted by Jun Yang, St. Jude Children’s Hospital) were grown in RPMI1640 medium. HEK293T (ATCC) cells were grown in DMEM medium. All media were supplemented with 10% FBS, 1% penicillin/streptomycin under 5% CO2 at 37°C. No cell lines were used beyond passage 20.

extract_protocol:
Cells were cross-linked in 1% formaldehyde, lysed and then sheared chromatin was immunoprecipitated with antibodies targeting histone marks [H3K36me2 (Abcam, ab9049), H3K27me3 (Abcam, ab6002), H3K27ac (Abcam, ab4729) and H3K9ac (Millipore, 06-942)]. A small aliquot was set aside prior to immunoprecipitation as input DNA. Quality control was performed using an Agilent Technologies 2100 Bioanalyzer prior to library preparation.
KAPA HyperPrep Kit was used for library construction

value: bone marrow


title: Reh EK_input


title: Reh EK_H3K27ac


title: T8_3349_105_CTL_CW_F_G2_20912


title: Reh EK_H3K36me2


title: Reh WT_H3K36me2


title: Reh WT_input


title: Reh EK_H3K27me3


title: T7_3350_137_CTL_WT_F_G4_20956


title: T7_3335_115_CTL_HW_M_G6_20993


title: Reh WT_H3K27ac


title: Reh WT_H3K27me3


title: Reh WT_H3K9ac


title: T7_3336_17_CM_CHW_F_G3_20919


title: Reh EV_input


title: T8_3342_83_CTL_CW_M_G6_20988


title: T6p5_3334_8_CM_CHW_M_G6_20977


title: T7_3346_93_CTL_CW_M_G2_20910


title: Reh EV_H3K27me3


title: T7_3368_50_CM_CHW_M_G7_21001


title: T7_3340_126_CTL_HW_M_G2_20915


title: T6_3341_31_CM_CHW_F_G3_20922


title: Reh EV_H3K27ac


title: Reh EV_H3K9ac


title: T7_3342_82_CTL_CW_M_G7_21008


title: RS411 sh2-B_K9ac


title: T5_3370_59_CM_CHW_M_G1_20885


title: T7_3349_104_CTL_CW_F_G5_20971


title: T6_3339_70_CTL_CW_M_G7_21006


title: T7_3339_71_CTL_CW_M_G6_20986


title: RS411 sh2-B_K27ac


title: RS411 sh2-B_K36me2


title: T6p5_3336_16_CM_CHW_F_G4_20939


title: T6_3334_7_CM_CHW_M_G5_20972


title: RS411 sh2-A_K9ac


title: RS411 sh2-B_input


title: RS411 sh2-B_K27me3


title: T5_3350_135_CTL_WT_F_G6_20996


title: Reh EV_H3K36me2


title: T6_3336_15_CM_CHW_F_G6_20978


title: RS411 sh2-A_K36me2


title: T5_3368_48_CM_CHW_M_G7_21002


title: RS411 sh2-A_K27me3


title: T6_3349_103_CTL_CW_F_G4_20950


title: RS411 sh2-A_K27ac


title: T6_3368_49_CM_CHW_M_G6_20982


title: T6_3346_92_CTL_CW_M_G5_20970


title: RS411 sh2-A_input


title: T6_3335_114_CTL_HW_M_G2_20898


title: RS411 NT-B_K9ac


title: RS411 NT-B_K27me3


title: RS411 NT-B_K27ac


title: T6_3342_81_CTL_CW_M_G2_20907


title: RS411 NT-B_K36me2


title: RS411 NT-B_input


title: T6_3370_60_CM_CHW_M_G5_20965


title: RS411 NT-A_K9ac


title: T5_3346_91_CTL_CW_M_G7_21009


title: RS411 NT-A_K27ac


title: RS411 NT-A_K36me2


title: T5_3339_69_CTL_CW_M_G1_20887


title: T6_3340_125_CTL_HW_M_G1_20894


title: T5_3342_80_CTL_CW_M_G4_20947


title: RS411 NT-A_K27me3


title: RS411 NT-A_input


title: T4_3370_58_CM_CHW_M_G6_20984


title: T5_3340_124_CTL_HW_M_G7_21014


title: T5_3336_14_CM_CHW_F_G2_20899


title: T4_3350_134_CTL_WT_F_G5_20976


title: T6_3350_136_CTL_WT_F_G2_20916


title: siSGK3_3_LETR

first: Charles

middle: David

last: Warden

address: 1500 East Duarte Rd

department: Department of Molecular and Cellular Biology

description:
RNA-Seq data, siSGK3 Treatment, Replicate 3
RPKM_table.txt

data_processing:
We believe Real Time Analysis (RTA) was used for base calling and bcl2fastq v1 was used to generate FASTQ files.
Reads were aligned using TopHat v2.0.8b
Partek "RNA-Seq" Workflow (in version 6.6, release 6.13.0731) was used mRNA quantification (as well as differential expression, enrichment, and visualization)
Genome_build: hg19
Supplementary_files_format_and_content: A tab-delimited text file was exported from Partek for Read Per Kilobase per Million (RPKM) normalized expression values

source_name: letrozole resistant breast cancer cells

growth_protocol: LET-R cells were cultured in MEM medium with 10% CD FBS in the presence of 1nM testesterone and 200nM letrozole.

extract_protocol:
RNA was extracted using TRIZOL reagent (Invitrogen)
TruSeq RNA Sample Preparation Kit V2 (Illumina, San Diego, CA)
unstranded 40 bp, 6 bp single-barcode, single-end polyA libraries were sequenced on a HiSeq 2500 (which was a HiSeq 2000, upgraded to have a new camera to be a HiSeq 2500)

treatment_protocol: LET-R cells were reversely transfected with 30nM siRNA negative control, AREG siRNA or SGK3 siRNA using siPORT NeoFX transfection agent (Ambion) for 48 h, and then harvested for RNA sequencing.

value: MCF7aro cells were long-term exposed to letrozole (>6 months)

tag: transfection

value: reverse transfection using siPORT NeoFX transfection agent (Ambion)

tag: sirna

value: the pool of three individual SGK3 siRNA (30nM) (sc-44852, Santa Cruz)


title: siAREG_3_LETR

description:
RNA-Seq data, siAREG Treatment, Replicate 3
RPKM_table.txt

value: the pool of three individual AREG siRNA (30nM) (sc-39412, Santa Cruz)


title: siAREG_2_LETR

description:
RNA-Seq data, siAREG Treatment, Replicate 2
RPKM_table.txt


title: siAREG_1_LETR

description:
RNA-Seq data, siAREG Treatment, Replicate 1
RPKM_table.txt


title: siSGK3_1_LETR

description:
RNA-Seq data, siSGK3 Treatment, Replicate 1
RPKM_table.txt


title: T4_3357_36_CM_CHW_F_G1_20881

tag: tissue


title: siSGK3_2_LETR

description:
RNA-Seq data, siSGK3 Treatment, Replicate 2
RPKM_table.txt

tag: cell type


title: T5_3341_29_CM_CHW_F_G3_20921


title: siNC_2_LETR

description:
RNA-Seq data, siNC Treatment, Replicate 2
RPKM_table.txt

value: siRNA negative control (30nM) (Ambion)


title: T5_3349_102_CTL_CW_F_G3_20932


title: T4_3349_101_CTL_CW_F_G7_21011


title: T5_3334_113_CM_CHW_M_G4_20952


title: siNC_1_LETR

description:
RNA-Seq data, siNC Treatment, Replicate 1
RPKM_table.txt


title: T4_3338_23_CM_CHW_F_G1_20879


title: T4_3336_13_CM_CHW_F_G1_20878


title: T3_3368_46_CM_CHW_M_G5_20963


title: T4_3368_47_CM_CHW_M_G2_20904


title: T4_3346_90_CTL_CW_M_G4_20948


title: T4_3340_123_CTL_HW_M_G3_20935


title: Stau2 Rep1

first: Gene

last: Yeo

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

data_processing:
Takes output from raw files.  Run to trim off both 5’ and 3’ adapters on both reads. Command: quality-cutoff 6  -m 18  -a NNNNNAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC  -g CTTCCGATCTACAAGTT -g CTTCCGATCTTGGTCCT  -A AACTTGTAGATCGGA -A AGGACCAAGATCGGA -A ACTTGTAGATCGGAA -A GGACCAAGATCGGAA -A CTTGT  AGATCGGAAG -A GACCAAGATCGGAAG -A TTGTAGATCGGAAGA -A ACCAAGATCGGAAGA -A TGTAGATCGGAAGAG -A CCAAGATCGGAAGAG -A GTAGATCGGAAGAGC -A CAAGATCGGAAGAGC -A TAGATCGGAAGAGCG -A AAGATCGGAAGAGCG -A AGATCGGAAGAGCGT -A GATCGGAAGAGCGTC -A ATCGGAAGAGCGTCG -A TCGGAAGAGCGTCGT -A CGGAAGAGCGTCGTG -A GGAAGAGCGTCGTGT  -o /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.fastq.gz  -p /full/path/to/files/file_R2.C01.fastq.gz.adapterTrim.fastq.gz  /full/path/to/files/file_R1.C01.fastq.gz /full/path/to/files/file_R2.C01.fastq.gz > /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.metrics
Takes output from cutadapt round 1. Run to trim off the 3’ adapters on read 2, to control for double ligation events. Command: cutadapt -f fastq --match-read-wildcards  --times 1  -e 0.1  -O 5  --quality-cutoff 6  -m 18  -A AACTTGTAGATCGGA -A AGGACCAAGATCGGA -A ACTTGTAGATCGGAA -A GGACCAAGATCGGAA -A CTTGTAGATCGGAAG -A GACCAAGATCGGAAG -A TTGTAGATCGGAAGA -A ACCAAGATCGGAAGA -A TGTAGATCGGAAGAG -A CCAAGATCGGAAGAG -A GTAGATCGGAAGAGC -A CAAGATCGGAAGAGC -A TAGATCGGAAGAGCG -A AAGATCGGAAGAGCG -A AGATCGGAAGAGCGT -A GATCGGAAGAGCGTC -A ATCGGAAGAGCGTCG -A TCGGAAGAGCGTCGT -A CGGAAGAGCGTCGTG -A GGAAGAGCGTCGTGT  -o /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.fastq.gz  -p /full/path/to/files/file_R2.C01.fastq.gz.adapterTrim.round2.fastq.gz  /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.fastq.gz  /full/path/to/files/file_R2.C01.fastq.gz.adapterTrim.fastq.gz > /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.metrics
Takes output from cutadapt round 2.  Maps to human specific version of RepBase used to remove repetitive elements, helps control for spurious artifacts from rRNA (& other) repetitive reads.  Command: STAR  --runMode alignReads  --runThreadN 16  --genomeDir /path/to/RepBase_human_database_file --genomeLoad LoadAndRemove  --readFilesIn /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.fastq.gz /full/path/to/files/file_R2.C01.fastq.gz.adapterTrim.round2.fastq.gz --outSAMunmapped Within  --outFilterMultimapNmax 30  --outFilterMultimapScoreRange 1  --outFileNamePrefix /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rep.bam --outSAMattributes All  --readFilesCommand zcat  --outStd BAM_Unsorted  --outSAMtype BAM Unsorted  --outFilterType BySJout  --outReadsUnmapped Fastx  --outFilterScoreMin 10  --outSAMattrRGline ID:foo  --alignEndsType EndToEnd > /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rep.bam
Takes output from STAR rmRep.  Maps unique reads to the human genome.  Command: STAR  --runMode alignReads  --runThreadN 16  --genomeDir  /path/to/STAR_database_file --genomeLoad LoadAndRemove  --readFilesIn  /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rep.bamUnmapped.out.mate1  /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rep.bamUnmapped.out.mate2  --outSAMunmapped Within  --outFilterMultimapNmax 1  --outFilterMultimapScoreRange 1  --outFileNamePrefix /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.bam  --outSAMattributes All  --outStd BAM_Unsorted  --outSAMtype BAM Unsorted  --outFilterType BySJout  --outReadsUnmapped Fastx  --outFilterScoreMin 10  --outSAMattrRGline ID:foo  --alignEndsType EndToEnd > /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.bam
takes output from STAR genome mapping.  Custom random-mer-aware script for PCR duplicate removal. Command: barcode_collapse_pe.py  --bam /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.bam  --out_file /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.bam  --metrics_file /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.metrics
Takes output from barcode collapse PE.  Sorts resulting bam file for use downstream.  Command: java  -Xmx2048m  -XX:+UseParallelOldGC  -XX:ParallelGCThreads=4  -XX:GCTimeLimit=50  -XX:GCHeapFreeLimit=10  -Djava.io.tmpdir=/full/path/to/files/.queue/tmp  -cp /path/to/gatk/dist/Queue.jar  net.sf.picard.sam.SortSam  INPUT=/full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.bam  TMP_DIR=/full/path/to/files/.queue/tmp  OUTPUT=/full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.sorted.bam  VALIDATION_STRINGENCY=SILENT  SO=coordinate  CREATE_INDEX=true
Takes output from sortSam, makes bam index for use downstream.  Command: samtools index  /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.sorted.bam  /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.sorted.bam.bai
Takes inputs from multiple final bam files.  Merges the two technical replicates for further downstream analysis.  Command: samtools  merge  /full/path/to/files/CombinedID.merged.bam  /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.sorted.bam /full/path/to/files/file_R1.D08.fastq.gz.adapterTrim.round2.rmRep.rmDup.sorted.bam
Takes output from sortSam, makes bam index for use downstream.  Command: samtools  index  /full/path/to/files/CombinedID.merged.bam  /full/path/to/files/CombinedID.merged.bam.bai
Takes output from sortSam.  Only outputs the second read in each pair for use with single stranded peak caller.  This is the final bam file to perform analysis on.  Command: samtools view -hb -f 128  /full/path/to/files/CombinedID.merged.bam  >  /full/path/to/files/CombinedID.merged.r2.bam
Takes results from samtools view.  Calls peaks on those files.  Command: clipper  -b /full/path/to/files/CombinedID.merged.r2.bam  -s hg19  -o /full/path/to/files/CombinedID.merged.r2.peaks.bed  --bonferroni  --superlocal  --threshold-method binomial  --save-pickle
Genome_build: hg19
Supplementary_files_format_and_content: bed format, contains clusters of predicted RBP binding
Supplementary_files_format_and_content: 764.01v02.IDR.out.0102merged.bed.narrowPeak.bed: a combined sample between 764_01 and 764_02, normalized against an input background (764_INPUT).

growth_protocol: K562 cells were grown in suspension in standard media (RPMI + 10% FBS + Pen/Strep (100U / mL)).

extract_protocol:
Cells were lysed in iCLIP lysis buffer, followed by limited digestion with RNase I (Ambion), immunoprecipitation of RBP-RNA complexes with a specific antibody of interest (Protein G sheep anti-rabbit Dynabeads), and stringent washes.
After dephosphorylation with FastAP (Thermo Fisher) and T4 PNK (NEB), a barcoded RNA adapter is ligated to the 3’ end (T4 RNA Ligase, NEB) (at this step, multiple replicates of the same RBP, or potentially RBPs of similar size and bound RNA amount, can be uniquely barcoded and pooled after ligation to simplify downstream steps - see Supplementary Fig. 2A). Ligations are performed on-bead (to allow washing away unincorporated adapter) in high concentration of PEG8000, which improves ligation efficiency to > 90%. Samples are then run on standard protein gels and transferred to nitrocellulose membranes, and a region 75 kDa (~150 nt of RNA) above the protein size is isolated and proteinase K (NEB) treated to isolate RNA. RNA is reverse transcribed with AffinityScript (Agilent), and treated with ExoSAP-IT (Affymetrix) to remove excess oligonucleotides. A second DNA adapter (containing a random-mer of 5 (N5) or 10 (N10) random bases at the 5’ end) is then ligated to the cDNA fragment 3’ end (T4 RNA Ligase, NEB), performed with high concentration of PEG8000 (to improve ligation efficiency) and DMSO (to decrease inhibition of ligation due to secondary structure). After cleanup (Dynabeads MyOne Silane, ThermoFisher), an aliquot of each sample is first subjected to qPCR (to identify the proper number of PCR cycles), and then the remainder is PCR amplified (Q5, NEB) and size selected via agarose gel electrophoresis.

treatment_protocol: K562 suspension cells were pelleted at 200g and resuspended in 1X PBS to 20 million cells per mL. 60 million cells in 3 mL were UV crosslinked (254 nm, 400 mJ/cm2) per 10 cm dish, pelleted, and snap frozen.

tag: antibody

tag: antibody manufacturer

value: MBL

tag: antibody catalog #

tag: antibody lot#

tag: cell line

tag: rnase i fragmentation condition


title: T5_3335_6_CTL_HW_M_G7_20997

tag: treatment


title: Stau2 Rep2


title: Fibroblasts

city: Cheonan-si, Chungcheongnam-do

first: Man Ryul

last: Lee

address: 25 Bongjeong-ro

country: South Korea

institute: Soonchunhyang Institute of medi-bio science (SIMS)

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 hg19 whole genome using Tophat
Read count extraction and nomalization were performed using edgeR.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include normalized read count values for each Sample

source_name: BJ1 cell line

growth_protocol:
hESCs: Dulbecco's modified Eagle's medium/F12 containing 20% serum replacement, 1mM glutamine, 0.1% nonessential amino acids, 0.1% penicillin/streptomycin, 0.1mM beta-mercaptoethanol, and 10ng/ml recombinant human FGF-2 (Invitrogen, Carlsbad, CA).
hiPSCs: Dulbecco's modified Eagle's medium/F12 containing 20% serum replacement, 1mM glutamine, 0.1% nonessential amino acids, 0.1% penicillin/streptomycin, 0.1mM beta-mercaptoethanol, and 10ng/ml recombinant human FGF-2 (Invitrogen, Carlsbad, CA).
Fibroblasts: Dulbecco's modified Eagle's medium supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using SMARTER mRNA-Seq Library Prep Kit standard protocols.

value: Human fibroblasts

tag: cell status

value: Differentiated

tag: markers

value: TRA-1-60 negative


title: Undifferentiated hESCs

source_name: H9 cell line

value: Human embryonic stem cell(hESCs)

value: Undifferentiated

value: TRA-1-60 positive


title: Undifferentiated hiPSCs

source_name: CMC-iPSCs

value: CMC-iPSCs

value: Human induced pluripotent stem cell(hiPSCs)


title: T3_3357_35_CM_CHW_F_G5_20961

tag: timepoint

value: CM

tag: genotype

value: CHW

value: PBMC


title: T4_3335_5_CTL_HW_M_G4_20937

tag: mouseid

value: CTL

value: HW

tag: Sex

value: M


title: siNC_3_LETR

description:
RNA-Seq data, siNC Treatment, Replicate 3
RPKM_table.txt

value: MCF7aro cells were long-term exposed to letrozole (>6 months)

tag: transfection

value: reverse transfection using siPORT NeoFX transfection agent (Ambion)


title: Lovastatin + SGA315 replicate3

city: University Park

first: Gary

last: Perdew

state: PA

address: 309 LSB

department: Veterinary and Biomedical Sciences

institute: Pennsylvania State University

description:
Lov-315-3_S9
LOV-SGA315_rep3_tagcount

data_processing:
RNAseq reads were aligned to the human genome (hg19) using TopHat version 2.0.13 with default parameters
Reads mapping to hg19 RefSeq genes were counted using HTseq-count version 0.5.4p3 with parameters ‘-s no -a 10 -nonunique all’
Genome_build: hg19 human genome
Supplementary_files_format_and_content: tag counts (the output of HTseq-count tool) are given for each gene

source_name: Caco-2_Lovastatin + SGA315

growth_protocol: Caco-2 cells were treated in aMEM media supplemented with 10% lipid-depleted FBS and antibotics

extract_protocol:
Total RNA from cultured Caco-2 cells were extracted with trizol. RNAseq libraries were made from polyA enriched toRNA.
Libraries were preapred as described in the Illumina RNAseq cloning kit

treatment_protocol: Cells were co-treated with 10 uM lovastatin and SGA360 or SGA315 for 48 h. Cells were harvested at the end of treatment.

value: human colon adenocarcinoma cell line

tag: expression

value: endogenous

value: 10 µM lovastatin, 10 µM SGA315, 48 h


title: Lovastatin + SGA315 replicate1

description:
Lov-315-1_S7
LOV-SGA315_rep1_tagcount


title: Lovastatin + SGA315 replicate2

description:
Lov-315-2_S8
LOV-SGA315_rep2_tagcount


title: T4_3342_79_CTL_CW_M_G3_20928

tag: strain

value: CW

tag: tissue


title: T3_3370_57_CM_CHW_M_G4_20945


title: Lovastatin + SGA360 replicate3

description:
Lov-360-3_S6
LOV-SGA360_rep3_tagcount

source_name: Caco-2_Lovastatin + SGA360

tag: cell type

value: 10 µM lovastatin, 10 µM SGA360, 48 h


title: Lovastatin + SGA360 replicate2

description:
Lov-360-2_S5
LOV-SGA360_rep2_tagcount


title: Lovastatin + SGA360 replicate1

description:
Lov-360-1_S4
LOV-SGA360_rep1_tagcount


title: T3_3350_133_CTL_WT_F_G1_20895

value: WT

value: F


title: Stau2 Input

tag: antibody

tag: antibody manufacturer

value: MBL


title: T3_3349_100_CTL_CW_F_G1_20891


title: T3_3346_89_CTL_CW_M_G2_20909


title: Lovastatin replicate2

description:
LoV-2_S2
LOV_rep2_tagcount

value: 10 µM lovastatin, 48 h


title: T4_3341_28_CM_CHW_F_G2_20901

value: CM


title: Lovastatin replicate1

description:
LoV-1_S1
LOV_rep1_tagcount


title: T3_3342_78_CTL_CW_M_G1_20889


title: T4_3334_112_CM_CHW_M_G2_20913

value: CHW


title: T4_3339_68_CTL_CW_M_G4_20946

value: PBMC


title: T3_3340_122_CTL_HW_M_G2_20914

value: CTL


title: T3_3336_12_CM_CHW_F_G5_20958


title: Cor_42_POS

city: Philadelphia

first: Brian

last: Estevez

state: Pennsylvania

address: 3615 Civic Center Blvd

department: Pediatrics

institute: Children's Hospital of Philadelphia

data_processing:
Demultiplexed FASTQ files were processed using the CellRanger count pipeline (10x Genomics, v.3.1.014) for alignment of sequencing reads to the GRCh38 transcriptome and creation of feature-barcode matrices.
The Seurat package (v.3.0.215) within the R computing environment was used to aggregate and analyze the dataset.
To account for possible batch effects, a canonical correlation analysis was used to integrate and aggregate the individual libraries.
Gene expression matrices were log normalized and scaled, and a Wilcoxon rank sum test was used to determine differentially expressed genes between experimental groups.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include log2FC values for each Sample

source_name: hematopoietic progenitor cells

extract_protocol:
10X genomics Single Cell 3’ Reagent Kits v2
Sorted cells were counted, and adjusted to a target of 5,000 cells in a 38 µL volume of 1X PBS (Gibco) and 0.04% BSA (Sigma-Aldrich). Cells, reverse transcription (RT) master mix (10X Genomics), primer-coated 10X gel beads, and partitioning oil were loaded onto a Single Cell A chip (10X Genomics) and into a 10X Genomics Chromium Controller instrument for microfluidic droplet-based encapsulation of cells, RT reagents, and gel beads. RT reaction was performed within droplets in a thermocycler (Bio-Rad) and following the 10X Genomics incubation protocol. Droplets were then broken down, and the released barcoded cDNAs were purified using magnetic beads, and amplified by PCR. cDNA concentrations were determine using a Qubit 3.0 fluorometer and Qubit HS dsDNA assay kit (both, ThermoFisher). Enzymatic digestion and size selection were performed to generate the optimal cDNA size for library construction. Sequencing primers P5, P7, R2 and sample-specific index primers were added during library construction. Quality and size of generated libraries was verified using the Bioanalyzer high-sensitivity DNA analysis kit (Agilent). Library concentrations were determined using kapa DNA library quantification kit (KAPA Biosystems). Libraries were sequenced on an Illumina HiSeq 4000

value: iPSC-derived iHPCs

tag: surface markers


title: FPD_42_NEG_1


title: FPD_42_NEG_2


title: Cor_42_NEG

description: COR2_42 _NEG_DMSO_83561_S1_L004


title: FPD_42_POS_1


title: Lovastatin replicate3

description:
LoV-3_S3
LOV_rep3_tagcount

tag: cell line


title: T3_3339_67_CTL_CW_M_G3_20926

value: M


title: T2_3357_34_CM_CHW_F_G2_20902


title: T2_3350_132_CTL_WT_F_G6_20995


title: T2_3346_88_CTL_CW_M_G5_20969


title: T3_3334_111_CM_CHW_M_G3_20933


title: T2_3368_45_CM_CHW_M_G1_20883


title: T2_3342_77_CTL_CW_M_G7_21007


title: T1_3370_55_CM_CHW_M_G5_20964


title: GC059869_P22

city: Bruxelles

first: Cedric

last: Blanpain

address: 808, route de Lennik, CP 637

country: Belgium

institute: Université Libre de Bruxelles (ULB)

description:
single-cell smartSeq2 RNAseq
single-cell RNA

data_processing:
Adapter trimming using cutadapt (v 1.13)
Reads aligned to GRCm38 + ERCC sequences using STAR (v 2.5.2b)
Counts were generated using HTSeq (v 0.6.0) on GENCODE M12 transcript annotation
Genome_build: GRCm38
Supplementary_files_format_and_content: Raw comma-separated file containing raw expression matrix and Seurat R data object file

source_name: Mammary Gland Epithelium

growth_protocol: Mouse colonies were maintained in a certified animal facility in accordance with the European guidelines.

extract_protocol:
Samples were incubated in 250µl of 2% FBS/PBS with fluorochrome-conjugated primary antibodies for 30 minutes, with shaking every 10 minutes. Primary antibodies were washed with 2% FBS/PBS, and cells were resuspended in 2.5mg/ml DAPI (Invitrogen D1306) before analysis. The following primary antibodies were used: APC-conjugated anti-CD45 (1:100, clone 30-F11, eBiosciences), APC-conjugated anti-CD31 (1:100, clone 390, eBiosciences), APC-conjugated anti-CD140a (1:100, cloneAPA5, eBiosciences), PE-Cy7-conjugated anti-CD24 (1:100, clone M1/69, BD), FITC-conjugated anti-CD29 (1:100, clone Ha2/5, BD Biosciences),APC-Cy7-conjugated anti Epcam (1:100, clone G8.8, Biolegend). Data analysis andcell sorting were performed on a FACSAria sorter using the FACS DiVa software (BDBiosciences). Dead cells were excluded with DAPI; CD45+, CD31+ and CD140a+ cells excluded (Lin+) before analysis of the Tomato+ cells
scRNA-seq was performed using a modified Smartseq-2 protocol. 1µL lysis buffer in384 well PCR plates for cell sorting was prepared with 0.4% v/v Triton-X lysis buffer,2.5mM dNTPs and 2.5µM oligo-dT30-VN. Reverse transcription and PCR was performed according to the Smartseq-2 protocol with reduced volumes: 1µl of reverse241 transcription mix instead of 5.7µl and 3µl PCR Master mix instead of 15µl. cDNA was amplified for 23 cycles and cleaned using HighPrep PCR beads (MagBio Genomics) at a 0.8x ratio on a Hamilton STAR (Hamilton Germany GmbH) liquid handler, eluted in 30µl buffer EB (Qiagen) and transferred to 384_PP acoustic plates (LabCyte). DNA quantification was performed with Picogreen assay (Thermofisher) and a subset of samples were selected for quality control using a Agilent 2100 BioAnalyser (Agilent Technologies) using a High Sensitivity DNA kit. Next-generation sequencing library preparation was performed using a Nextera XT DNA library preparation kit with volumes reduced by one-tenth (Illumina) using an acoustic dispenser. In brief, 100pg of cDNA in a volume of 500nL was tagmented by adding 1.5µl Tn5-buffer mix and incubating for 10 min at 55°C. Tagmented samples were barcoded with Nextera index sets A - D and amplified with 12 cycles of PCR. After PCR, all samples were pooled and cleaned using HighPrep PCR beads at a 0.6x ratio. Library pools were eluted in buffer EB and quality control performed using an Agilent 2100 BioAnalyser and High Sensitiviy DNA chip before adjusting to a concentration of 4nM. The diluted pools were quantified using a KAPA qPCR library quantification kit on a LightCycler 480 (Roche) before a final dilution to 2nM. The pool of 384 samples was sequenced on 2 lanes of a HiSeq4000 with 1x51bp read length

treatment_protocol: For the ablation condition, mice were anesthetized (5% xylazine, 10% ketamine in PBS), abdominal skin removed with depilatory cream and the nipple region disinfected with ETOH 70%. The intraductal injection of 0.2 mg doxycycline was performed using a stereoscope. One week after injection the mice have been sacrificed and the epithelial cells of the mammary gland FACS sorted into a 384 wells PCR plate.

value: K8rtta/TetO-DTA/K5CreER/Rosa-Tomato mice, mixed background

value: Doxycycline treatment single-cell

tag: cell-type

value: Hybrid cell


title: GC059869_P20

tag: treatment


title: GC059869_P23


title: GC059869_P24


title: GC059869_P17


title: GC059869_P19


title: GC059869_P18


title: T3_3341_27_CM_CHW_F_G4_20941


title: T3_3335_4_CTL_HW_M_G2_20897

value: HW


title: FPD_42_POS_2


title: T3_3338_22_CM_CHW_F_G4_20940


title: T2_3339_66_CTL_CW_M_G7_21005


title: GC059869_P15


title: T2_3370_56_CM_CHW_M_G2_20905


title: GC059869_P21


title: T1_3350_131_CTL_WT_F_G5_20975


title: GC059869_P13


title: T2_3341_26_CM_CHW_F_G1_20880


title: GC059869_P11


title: T1_3341_25_CM_CHW_F_G5_20960


title: GC059869_P12


title: GC059869_P09


title: GC059869_P10


title: GC059869_P16


title: T2_3340_121_CTL_HW_M_G6_20994


title: GC059869_P08


title: GC059869_P07


title: T2_3335_3_CTL_HW_M_G3_20917


title: T1_3368_44_CM_CHW_M_G3_20924


title: GC059869_P06


title: GC059869_P05


title: T1_3357_33_CM_CHW_F_G4_20942


title: T1_3349_98_CTL_CW_F_G3_20931


title: GC059869_P04


title: GC059869_P03


title: T1_3342_76_CTL_CW_M_G6_20987


title: GC059869_P02


title: T2_3349_99_CTL_CW_F_G4_20949


title: T1_3346_87_CTL_CW_M_G6_20989


title: GC059869_O24


title: GC059869_P14


title: GC059869_P01


title: T2_3334_110_CM_CHW_M_G7_21012


title: T1_3339_65_CTL_CW_M_G5_20966


title: T0_3368_43_CM_CHW_M_G5_20962


title: GC059869_O23


title: T1_3335_2_CTL_HW_M_G5_20957


title: GC059869_O20


title: GC059869_O22


title: T2_3338_21_CM_CHW_F_G3_20920


title: GC059869_O19


title: GC059869_O21


title: T1_3338_20_CM_CHW_F_G7_20999


title: T1_3340_120_CTL_HW_M_G1_20893


title: T0_3370_54_CM_CHW_M_G7_21003


title: GC059869_O18


title: GC059869_O16


title: T0_3335_1_CTL_HW_M_G1_20877


title: GC059869_O17


title: GC059869_O15


title: T1_3334_109_CM_CHW_M_G6_20992


title: T0_3350_130_CTL_WT_F_G4_20955


title: GC059869_O14


title: T0_3334_108_CM_CHW_M_G4_20951


title: GC059869_O13


title: T0_3357_32_CM_CHW_F_G6_20980


title: T0_3336_9_CM_CHW_F_G3_20918


title: T0_3340_119_CTL_HW_M_G5_20973


title: GC059869_O12


title: GC059869_O11


title: T0_3349_97_CTL_CW_F_G2_20911


title: GC059869_O09


title: GC059869_O10


title: T0_3342_75_CTL_CW_M_G5_20968


title: T0_3339_64_CTL_CW_M_G1_20886


title: T0_3346_86_CTL_CW_M_G3_20929


title: GC059869_O07


title: T1_3336_10_CM_CHW_F_G4_20938


title: GC059869_O06


title: T10_3346_96_CTL_CW_M_G1_20888


title: T0_3341_24_CM_CHW_F_G2_20900


title: GC059869_O04


title: T10_3335_118_CTL_HW_M_G1_20892


title: T10_3349_107_CTL_CW_F_G6_20991


title: T0_3338_19_CM_CHW_F_G6_20979


title: GC059869_O02


title: GC059869_O01


title: T10_3350_140_CTL_WT_F_G7_21015


title: T10_3339_74_CTL_CW_M_G5_20967


title: GC059869_N24


title: GC059869_N23


title: T10_3340_129_CTL_HW_M_G4_20954


title: GC059869_N22


title: GC059869_N21


title: T10_3342_85_CTL_CW_M_G1_20890


title: GC059869_O08


title: GC059869_N20


title: T10_3368_53_CM_CHW_M_G6_20983


title: Sample 5 (TdTomato -ve)

city: St Louis

first: Vijay

last: Samineni

state: MO

address: 4940 Parkview Place, Room 5539 Department of Anesthesiology

institute: Washington university St. louis

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with custom demultipler written in python
Technical replicate fastq files were combined and aligned with STAR 2.0.4b
Gene counts dervied with Subread:featureCount 1.45 and annotated with Ensembl Biomart
Genome_build: Ensembl GRCm38.76
Supplementary_files_format_and_content: Gene counts in tab-delimitted text MS Excel format

source_name: Central Amygdala

extract_protocol: Clontech SMARTer v1

value: Central Amygdala

value: CeA TdTomato-ve Neurons

tag: cell population

value: Facs amygdala cells after FosTRAP

value: cFos Cre Mice X TdTomato (Ai9) Mice


title: GC059869_N19


title: GC059869_N18


title: Sample 4 (TdTomato +ve)

value: CeA TdTomato+ve Neurons


title: GC059869_N17


title: Sample 2 (TdTomato +ve)


title: GC059869_O05


title: GC059869_N16


title: GC059869_O03


title: Sample 1 (TdTomato +ve)


title: GC059869_N15


title: Sample 3 (TdTomato +ve)


title: GC059869_N13


title: 1307-slide

city: Groton

first: Thomas

middle: A

last: Lanz

state: CT

address: Eastern Point Rd

department: Multi-Omics & Biomarkers

institute: Pfizer

data_processing:
Base calling was performed on the NextSeq 500 instrument (RTA 2.0)
Sequenced reads were aligned to the human genome using SALMON and TPM values were generated at a transcript level and mapped to genes
Differential expression was measured using DESEQ2
Genome_build: hg38
Supplementary_files_format_and_content: tsv files files containing Ensembl ID, count and TPM

source_name: Cortex Brodmann Area 9

extract_protocol:
Samples were collected into RLT buffer, and RNA was extracted using Qiagen RNeasy Micro kit
Libraries were prepared using Takara SMARTER Stranded Total RNA-Seq kit v2 - Pico input mammalian for Illumina sequencing

value: Cortex Brodmann Area 9

value: whole brain tissue

tag: age (years)

tag: pmi

tag: rin


title: 1307-aggLCM

value: interneuron


title: 1086-pyr

value: pyramidal neuron


title: GC059869_N11


title: GC059869_N10


title: 1086-slide


title: 1086-aggLCM


title: GC059869_N09


title: GC059869_N08


title: GC059869_N07


title: 970-slide


title: GC059869_N06


title: 970-aggLCM


title: GC059869_N05


title: GC059869_N04


title: 592-aggLCM


title: 592-slide


title: GC059869_N02


title: 1307-pyr


title: GC059869_N12


title: 592-pyr


title: GC059869_N03


title: GC059869_N01


title: GC059869_N14


title: 2LQ

city: Rome

first: Linda

last: Quatrini

address: Via San Paolo 15

department: Immunology

country: Italy

institute: IRCCS Bambino Gesù Pediatric Hospital

data_processing:
RNA sequencing was performed with a NextSeq 500 (Illumina; paired-end reads 2 × 75 with 30 M reads per sample)
The fastq files were assessed with the fastqc program (http://www.bioinformatics.babraham.ac.uk/projects/fastqc)
Cutadapt (https://journal.embnet.org/index.php/embnetjournal/article/view/200) was used to remove the adapter sequence (if present) and the very short reads (reads length < 20)
Genome_build: The samples were mapped on reference Homo Sapiens genome (HG38)
Supplementary_files_format_and_content: the number of reads mapped to each gene was determined with featureCounts

source_name: peripheral blood mononuclear cells

extract_protocol:
RNA was extracted with an RNeasy Plus Micro Kit (Qiagen)
The DNA libraries were generated with the TruSeq stranded mRNA prep kit (Illumina)

tag: cell subset

value: CD56 bright NK cells

tag: in vitro culture conditions

value: 6 days with IL-15+IL-12+IL-18+ Dexamethasone


title: 6LQ


title: GC059869_M23


title: 3LQ

value: 6 days with IL-15+IL-12+IL-18+ vehicle (DMSO)


title: GC059869_M24


title: 1LQ


title: 970-pyr


title: GC059869_M21


title: 5LQ


title: GC059869_M22


title: GC059869_M20


title: 4LQ


title: GC059869_M18


title: GC059869_M17


title: GC059869_M16


title: COVID_BasalStim_BEAS_A09_S105

first: Alex

last: Shalek

state: MA

address: 45 Carleton Street

department: Chemistry

institute: MIT

description:
Human basal cells from BEAS-2B cell line with three replicates of each stimulation with IFNA, IFNG, IL17A, or IL4, each at increasing doses (0, 0.1 ,0.5, 1, 2, 5, 10 ng/mL) and 12 replicates of unstimulated samples
BEAS_Basal_Pops_TPM.txt

data_processing:
Aligned using cumulus platform https://cumulus-doc.readthedocs.io/en/0.12.0/smart_seq_2.html and output as TPM using RSEM v1.3.3
hg19
Supplementary_files_format_and_content: Processed data is a tab or comma delimited text file containing TPM

source_name: BEAS-2B cell line

growth_protocol: placed into culture at a number of 10,000 cells seeded at passage 5 (e.g. 5 weeks ex vivo) and cultured at confluence in 96 well flat-bottom collagen-coated tissue culture plates (Corning 3596) for 48 hours in Pneumacult-Ex serum-free media (Stemcell Technologies)

extract_protocol: Bulk RNA-seq (Ordovas-Montanes et al., 2018)

tag: agent

value: Untreated

tag: dose

value: BEAS-2B cell line


title: COVID_BasalStim_BEAS_A06_S102


title: COVID_BasalStim_BEAS_A07_S103


title: COVID_BasalStim_BEAS_A12_S108


title: COVID_BasalStim_BEAS_A11_S107


title: COVID_BasalStim_BEAS_A10_S106


title: COVID_BasalStim_BEAS_A08_S104


title: GC059869_M14

tag: strain

value: K8rtta/TetO-DTA/K5CreER/Rosa-Tomato mice, mixed background

value: Doxycycline treatment single-cell


title: GC059869_M15

value: Hybrid cell


title: COVID_BasalStim_BEAS_A02_S98


title: COVID_BasalStim_BEAS_A03_S99


title: COVID_BasalStim_BEAS_A05_S101


title: GC059869_M11


title: GC059869_M12


title: GC059869_M13


title: COVID_BasalStim_BEAS_A01_S97


title: COVID_BasalStim_BEAS_F12_S168


title: GC059869_M10


title: GC059869_M09


title: COVID_BasalStim_BEAS_F10_S166


title: GC059869_M19


title: GC059869_M08


title: COVID_BasalStim_BEAS_F11_S167


title: GC059869_M06


title: GC059869_M05


title: COVID_BasalStim_BEAS_A04_S100


title: COVID_BasalStim_BEAS_F08_S164


title: GC059869_M01

value: Luminal cell


title: GC059869_M02


title: GC059869_M04


title: COVID_BasalStim_BEAS_F06_S162


title: COVID_BasalStim_BEAS_F07_S163


title: GC059869_L24


title: GC059869_M03


title: COVID_BasalStim_BEAS_F09_S165


title: COVID_BasalStim_BEAS_F05_S161


title: GC059869_M07


title: COVID_BasalStim_BEAS_F01_S157


title: T2_3336_11_CM_CHW_F_G7_20998

tag: timepoint

tag: mouseid

value: CM

tag: genotype

value: CHW

tag: Sex

value: F

tag: tissue

value: PBMC


title: COVID_BasalStim_BEAS_E12_S156

tag: cell line


title: GC059869_L21

tag: cell-type


title: GC059869_L20

tag: treatment


title: COVID_BasalStim_BEAS_E11_S155


title: COVID_BasalStim_BEAS_F04_S160


title: COVID_BasalStim_BEAS_F03_S159


title: GC059869_L22


title: GC059869_L19


title: GC059869_L15


title: GC059869_L18


title: COVID_BasalStim_BEAS_E10_S154


title: COVID_BasalStim_BEAS_F02_S158


title: COVID_BasalStim_BEAS_E07_S151


title: GC059869_L16


title: GC059869_L14


title: COVID_BasalStim_BEAS_E03_S147


title: COVID_BasalStim_BEAS_E05_S149


title: GC059869_L13


title: COVID_BasalStim_BEAS_E08_S152


title: COVID_BasalStim_BEAS_D12_S144

value: IFNG


title: COVID_BasalStim_BEAS_E01_S145


title: COVID_BasalStim_BEAS_E04_S148


title: COVID_BasalStim_BEAS_D11_S143


title: GC059869_L09


title: GC059869_L12


title: GC059869_L23


title: GC059869_L17


title: GC059869_L07


title: GC059869_L10


title: GC059869_L11


title: COVID_BasalStim_BEAS_D10_S142


title: COVID_BasalStim_BEAS_E02_S146


title: GC059869_L08


title: COVID_BasalStim_BEAS_D08_S140


title: COVID_BasalStim_BEAS_E09_S153


title: COVID_BasalStim_BEAS_E06_S150


title: GC059869_L04


title: COVID_BasalStim_BEAS_D06_S138


title: GC059869_L06


title: GC059869_L05


title: GC059869_L03


title: COVID_BasalStim_BEAS_D07_S139


title: COVID_BasalStim_BEAS_D05_S137


title: COVID_BasalStim_BEAS_D09_S141


title: COVID_BasalStim_BEAS_D04_S136


title: GC059869_L01


title: GC059869_L02


title: GC059869_K24


title: COVID_BasalStim_BEAS_D02_S134


title: GC059869_K23


title: COVID_BasalStim_BEAS_D03_S135


title: COVID_BasalStim_BEAS_C12_S132


title: COVID_BasalStim_BEAS_D01_S133


title: GC059869_K22


title: COVID_BasalStim_BEAS_C10_S130


title: GC059869_K21


title: COVID_BasalStim_BEAS_C11_S131


title: GC059869_K20


title: GC059869_K19


title: GC059869_K18


title: GC059869_K17


title: COVID_BasalStim_BEAS_C09_S129


title: COVID_BasalStim_BEAS_C07_S127


title: COVID_BasalStim_BEAS_C06_S126

value: IFNA


title: COVID_BasalStim_BEAS_C08_S128


title: GC059869_K16


title: GC059869_K14


title: GC059869_K13


title: COVID_BasalStim_BEAS_C04_S124


title: GC059869_K15


title: COVID_BasalStim_BEAS_C03_S123


title: GC059869_K12


title: GC059869_K11


title: COVID_BasalStim_BEAS_B12_S120


title: GC059869_K09


title: COVID_BasalStim_BEAS_C02_S122


title: COVID_BasalStim_BEAS_C01_S121


title: COVID_BasalStim_BEAS_B11_S119


title: GC059869_K07


title: GC059869_K08


title: COVID_BasalStim_BEAS_B10_S118


title: COVID_BasalStim_BEAS_B09_S117


title: COVID_BasalStim_BEAS_B08_S116


title: GC059869_K06


title: COVID_BasalStim_BEAS_B07_S115


title: GC059869_K05


title: GC059869_K04


title: COVID_BasalStim_BEAS_C05_S125


title: COVID_BasalStim_BEAS_B06_S114


title: GC059869_K02


title: COVID_BasalStim_BEAS_B05_S113


title: COVID_BasalStim_BEAS_B04_S112


title: GC059869_J24


title: GC059869_J23


title: GC059869_K01


title: GC059869_J22


title: GC059869_K10


title: COVID_BasalStim_BEAS_B03_S111


title: GC059869_J21


title: COVID_BasalStim_BEAS_B01_S109


title: GC059869_J20


title: COVID_BasalStim_Human2344_A11_S107

description:
Human basal cells from non-polyp surgical resections from ethmoid sinus with three replicates of each stimulation with IFNA, IFNG, IL17A, or IL4, each at increasing doses (0, 0.1 ,0.5, 1, 2, 5, 10 ng/mL) and 12 replicates of unstimulated samples
Human2_Basal_Pops_TPM.txt

source_name: ethmoid sinus

tag: cell type

value: ethmoid sinus


title: COVID_BasalStim_BEAS_B02_S110


title: GC059869_J19


title: COVID_BasalStim_Human2344_A09_S105


title: GC059869_J18


title: GC059869_K03


title: COVID_BasalStim_Human2344_A07_S103


title: COVID_BasalStim_Human2344_A08_S104


title: GC059869_J16


title: GC059869_J14


title: GC059869_J15


title: GC059869_J12


title: GC059869_J13


title: COVID_BasalStim_Human2344_A04_S100


title: GC059869_J11


title: COVID_BasalStim_Human2344_A05_S101


title: COVID_BasalStim_Human2344_A02_S98


title: COVID_BasalStim_Human2344_F12_S168


title: COVID_BasalStim_Human2344_A03_S99


title: GC059869_J08


title: GC059869_J09


title: COVID_BasalStim_Human2344_A01_S97


title: COVID_BasalStim_Human2344_A12_S108


title: GC059869_J17


title: GC059869_J07


title: COVID_BasalStim_Human2344_F08_S164


title: GC059869_J06


title: COVID_BasalStim_Human2344_F06_S162


title: COVID_BasalStim_Human2344_A10_S106


title: GC059869_J04


title: COVID_BasalStim_Human2344_F11_S167


title: GC059869_J03


title: COVID_BasalStim_Human2344_F10_S166


title: GC059869_J01


title: COVID_BasalStim_Human2344_F07_S163


title: COVID_BasalStim_Human2344_F05_S161


title: COVID_BasalStim_Human2344_F04_S160


title: GC059869_J02


title: COVID_BasalStim_Human2344_A06_S102


title: GC059869_I24


title: GC059869_J10


title: COVID_BasalStim_Human2344_F03_S159


title: COVID_BasalStim_Human2344_F02_S158


title: GC059869_I23


title: COVID_BasalStim_Human2344_F01_S157


title: COVID_BasalStim_Human2344_E12_S156


title: GC059869_I20


title: GC059869_I21


title: GC059869_J05


title: COVID_BasalStim_Human2344_E11_S155


title: COVID_BasalStim_Human2344_E10_S154


title: COVID_BasalStim_Human2344_E08_S152


title: COVID_BasalStim_Human2344_E09_S153


title: COVID_BasalStim_Human2344_E06_S150


title: GC059869_I13


title: COVID_BasalStim_Human2344_E07_S151


title: COVID_BasalStim_Human2344_E05_S149


title: COVID_BasalStim_Human2344_E04_S148


title: GC059869_I17


title: COVID_BasalStim_Human2344_E03_S147


title: GC059869_I16


title: GC059869_I12


title: GC059869_I11


title: GC059869_I10


title: GC059869_I19


title: GC059869_I09

value: Basal cell


title: GC059869_I22


title: COVID_BasalStim_Human2344_D12_S144


title: COVID_BasalStim_Human2344_E01_S145


title: COVID_BasalStim_Human2344_D11_S143


title: GC059869_I08


title: GC059869_I14


title: COVID_BasalStim_Human2344_D10_S142


title: COVID_BasalStim_Human2344_E02_S146


title: GC059869_I07


title: GC059869_I18


title: GC059869_I06


title: GC059869_I15


title: COVID_BasalStim_Human2344_D09_S141


title: GC059869_I05


title: COVID_BasalStim_Human2344_D08_S140


title: COVID_BasalStim_Human2344_D07_S139


title: COVID_BasalStim_Human2344_D06_S138


title: GC059869_I04


title: GC059869_I03


title: GC059869_I02


title: COVID_BasalStim_Human2344_D05_S137


title: COVID_BasalStim_Human2344_D04_S136


title: COVID_BasalStim_Human2344_D03_S135


title: COVID_BasalStim_Human2344_D02_S134


title: COVID_BasalStim_Human2344_D01_S133


title: GC059869_H22


title: GC059869_H23


title: GC059869_H21


title: COVID_BasalStim_Human2344_C12_S132


title: GC059869_H24


title: COVID_BasalStim_Human2344_C10_S130


title: GC059869_H19


title: GC059869_H18


title: COVID_BasalStim_Human2344_C09_S129


title: GC059869_H20


title: COVID_BasalStim_Human2344_C11_S131


title: GC059869_H17


title: COVID_BasalStim_Human2344_F09_S165


title: COVID_BasalStim_Human2344_C08_S128


title: GC059869_H16


title: COVID_BasalStim_Human2344_C07_S127


title: GC059869_H15


title: COVID_BasalStim_Human2344_C06_S126


title: COVID_BasalStim_Human2344_C05_S125


title: GC059869_H14


title: GC059869_I01


title: GC059869_H13


title: COVID_BasalStim_Human2344_C03_S123


title: GC059869_H12


title: COVID_BasalStim_Human2344_C02_S122


title: GC059869_H10


title: COVID_BasalStim_Human2344_C01_S121


title: COVID_BasalStim_Human2344_B12_S120


title: GC059869_H08


title: GC059869_H09


title: COVID_BasalStim_Human2344_B11_S119


title: GC059869_H06


title: COVID_BasalStim_Human2344_B08_S116


title: COVID_BasalStim_Human2344_B10_S118


title: COVID_BasalStim_Human2344_B09_S117


title: COVID_BasalStim_Human2344_B07_S115


title: GC059869_H05


title: COVID_BasalStim_Human2344_B06_S114


title: COVID_BasalStim_Human2344_B05_S113


title: GC059869_H02


title: GC059869_H03


title: COVID_BasalStim_Human2344_B04_S112


title: GC059869_H01


title: GC059869_G24


title: COVID_BasalStim_Human2344_B03_S111


title: GC059869_H11


title: COVID_BasalStim_Human2344_B02_S110


title: COVID_BasalStim_Human2344_C04_S124


title: GC059869_G22


title: GC059869_G21


title: COVID_BasalStim_Human1334_A09_S9

description:
Human basal cells from non-polyp surgical resections from ethmoid sinus with three replicates of each stimulation with IFNA, IFNG, IL17A, or IL4, each at increasing doses (0, 0.1 ,0.5, 1, 2, 5, 10 ng/mL) and 12 replicates of unstimulated samples
Human1_Basal_Pops_TPM.txt

data_processing:
Aligned using cumulus platform https://cumulus-doc.readthedocs.io/en/0.12.0/smart_seq_2.html and output as TPM using RSEM v1.3.2
hg19
Supplementary_files_format_and_content: Processed data is a tab or comma delimited text file containing TPM


title: GC059869_H07


title: COVID_BasalStim_Human1334_A08_S8


title: COVID_BasalStim_Human1334_A07_S7


title: GC059869_G19


title: COVID_BasalStim_Human1334_A05_S5


title: GC059869_G18


title: GC059869_H04


title: COVID_BasalStim_Human1334_A06_S6


title: GC059869_G16


title: GC059869_G14


title: COVID_BasalStim_Human1334_A02_S2


title: COVID_BasalStim_Human1334_A04_S4


title: GC059869_G15


title: COVID_BasalStim_Human1334_A01_S1


title: GC059869_G12


title: GC059869_G13


title: COVID_BasalStim_Human1334_F10_S70


title: GC059869_G11


title: GC059869_G09


title: GC059869_G10


title: COVID_BasalStim_Human1334_F11_S71


title: COVID_BasalStim_Human2344_B01_S109


title: GC059869_G20


title: GC059869_G23


title: GC059869_G08


title: COVID_BasalStim_Human1334_F08_S68


title: COVID_BasalStim_Human1334_F07_S67


title: COVID_BasalStim_Human1334_A03_S3


title: COVID_BasalStim_Human1334_F12_S72


title: GC059869_G06


title: GC059869_G17


title: COVID_BasalStim_Human1334_F06_S66


title: COVID_BasalStim_Human1334_F05_S65


title: GC059869_G05


title: GC059869_G04


title: COVID_BasalStim_Human1334_F04_S64


title: COVID_BasalStim_Human1334_F03_S63


title: GC059869_G03


title: GC059869_G02


title: COVID_BasalStim_Human1334_F01_S61


title: COVID_BasalStim_Human1334_E12_S60


title: COVID_BasalStim_Human1334_F09_S69


title: COVID_BasalStim_Human1334_F02_S62


title: GC059869_F23


title: COVID_BasalStim_Human1334_E11_S59


title: COVID_BasalStim_Human1334_E08_S56


title: GC059869_F22


title: COVID_BasalStim_Human1334_E09_S57


title: COVID_BasalStim_Human1334_E10_S58


title: COVID_BasalStim_Human1334_E06_S54


title: COVID_BasalStim_Human1334_E05_S53


title: GC059869_F21


title: GC059869_F18


title: GC059869_F19


title: GC059869_F17


title: GC059869_F16


title: COVID_BasalStim_Human1334_E04_S52


title: GC059869_F20


title: GC059869_F15


title: GC059869_G01


title: COVID_BasalStim_Human1334_E03_S51


title: COVID_BasalStim_Human1334_E02_S50


title: COVID_BasalStim_Human1334_E01_S49


title: GC059869_F14


title: GC059869_F13


title: GC059869_F24


title: COVID_BasalStim_Human1334_D12_S48


title: COVID_BasalStim_Human1334_D11_S47


title: GC059869_F12


title: GC059869_F11


title: GC059869_F09


title: GC059869_F10


title: COVID_BasalStim_Human1334_D09_S45


title: COVID_BasalStim_Human1334_D10_S46


title: COVID_BasalStim_Human1334_D08_S44


title: COVID_BasalStim_Human1334_E07_S55


title: COVID_BasalStim_Human1334_D05_S41


title: COVID_BasalStim_Human1334_D03_S39


title: GC059869_F07


title: GC059869_F08


title: COVID_BasalStim_Human1334_D07_S43


title: COVID_BasalStim_Human1334_D02_S38


title: GC059869_F06


title: GC059869_F03


title: GC059869_F04


title: COVID_BasalStim_Human1334_D01_S37


title: GC059869_F05


title: COVID_BasalStim_Human1334_C12_S36


title: GC059869_E24


title: GC059869_F01


title: COVID_BasalStim_Human1334_D04_S40


title: GC059869_E23


title: COVID_BasalStim_Human1334_C11_S35


title: COVID_BasalStim_Human1334_C10_S34


title: GC059869_E21


title: COVID_BasalStim_Human1334_D06_S42


title: GC059869_E20


title: GC059869_E19


title: COVID_BasalStim_Human1334_C07_S31


title: COVID_BasalStim_Human1334_C09_S33


title: COVID_BasalStim_Human1334_C08_S32


title: COVID_BasalStim_Human1334_C05_S29


title: GC059869_E17


title: COVID_BasalStim_Human1334_C06_S30


title: GC059869_E18


title: COVID_BasalStim_Human1334_C04_S28


title: COVID_BasalStim_Human1334_C03_S27


title: GC059869_E13

value: Wild-type single-cell


title: COVID_BasalStim_Human1334_C02_S26


title: GC059869_E16


title: GC059869_E14


title: COVID_BasalStim_Human1334_C01_S25


title: GC059869_E22


title: GC059869_E10


title: GC059869_E11


title: COVID_BasalStim_Human1334_B10_S22


title: COVID_BasalStim_Human1334_B12_S24


title: GC059869_E12


title: COVID_BasalStim_Human1334_B11_S23


title: GC059869_E09


title: COVID_BasalStim_Human1334_B09_S21


title: GC059869_E07


title: GC059869_E08


title: COVID_BasalStim_Human1334_B08_S20


title: COVID_BasalStim_Human1334_B07_S19


title: COVID_BasalStim_Human1334_B06_S18


title: GC059869_E06


title: COVID_BasalStim_Human1334_B04_S16


title: COVID_BasalStim_Human1334_B05_S17


title: GC059869_E15


title: GC059869_E04


title: GC059869_E02


title: GC059869_E01


title: GC059869_E03


title: COVID_BasalStim_Human1334_B01_S13


title: COVID_BasalStim_Human1334_B02_S14


title: COVID_BasalStim_Human1334_B03_S15


title: GC059869_D23


title: Human Lung Epithelial Cells

description:
Human surgically resected lung tissue from donors with HIV and active Tuberculosis, active tuberculosis, previous tuberculosis, or no tuberculosis
Human_lung_epithelial_cell_raw_counts.txt.gz

data_processing:
Reads aligned and pre-processed according to the DropSeq Computational Protocol v2.0 (https://github.com/broadinstitute/Drop-seq)
Data was normalized, scaled, and clustered using the Seurat R package v3.1.0 (https://github.com/satija.lab/seurat). Clusters were annotated based on the identification of highly expressed genes and cells identified as epithelial were included in these matrices.
hg19
Supplementary_files_format_and_content: Processed data is a tab or comma delimited text file containing a digital gene expression matrix with the number of UMIs for each gene (rows) and cell barcode (columns)

source_name: Lung epithelial cells

growth_protocol: Surgical samples from diseased lung tissue were processed as described in (Ardain et al., Nature 2019)

extract_protocol: Single-cell RNA capture, barcoding, and multiplexing according to the Seq-Well S^3 method (Hughes et al., BioRxiv 2019)

value: Lung epithelial cells


title: GC059869_E05


title: GC059869_D24


title: Human Scrapings SeqWell, Polyp13CEPISSS

description:
Cells scraped from inferior trubinate of donor, Polyp13CEPISSS
NasalSSS_cleaned_raw_expression_counts.csv.gz

data_processing:
Reads aligned and pre-processed according to the DropSeq Computational Protocol v2.0 (https://github.com/broadinstitute/Drop-seq)
hg19
Supplementary_files_format_and_content: Processed data is a tab or comma delimited text file containing a digital gene expression matrix with the number of UMIs for each gene (rows) and cell barcode (columns)

source_name: Human Adult Inferior Turbinate, Polyp13CEPISSS

value: inferior trubinate


title: GC059869_D22


title: Hypoxia-Acidosis-Polysome (HAP)

city: Miami

first: Stephen

state: Florida

department: Biochemistry & Molecular Biology

institute: University of Miami

data_processing:
Illumina Nextseq 500 uses Reat-Time Analysis (RTA) version 2 for base calling and quality scoring. Bcl2fastq converts output bcl files to fastq files.
RNA-seq data were aligned to GRCh38 with STAR 2.5.0 default parameters
Alignment files (BAM files) were annotated and processed through the Cufflinks 2.2.1 pipeline
Gene FPKM values were obtained with Cuffnorm within Cufflinks 2.2.1
FPKM values were adjusted by RNA concentrations (see columns AS to BO in RNA_seq_TEanalysis)
Genome_build: GRCh38 (gencode v27)
Supplementary_files_format_and_content: Excel spreadsheet: gene list with FPKM values

source_name: Hypoxia (1% oxygen), Acidosis, pH = 6.0

growth_protocol: U87MG cells were maintained with DMEM with 10% FBS and 1% Pen/Strep until they reached 80% confluency, cells were then subjected to respective conditions (hypoxia: 1% O2, acidosis: pH = 6.

extract_protocol:
Total RNA was extracted by phenol/chloroform and ethanol precipitation following riboosome density fractionation.
Library construction for mRNA sequencing was performed by the SCCC Onco-Genomics Share Resource using the KAPA Stranded mRNA-Seq Kit (KAPA Biosystems).

treatment_protocol: Cells were treated for 24 hours before lysis.

value: brain

value: Glioblastoma


title: Human Scrapings SeqWell, Polyp14DEPISSS

description:
Cells scraped from inferior trubinate of donor, Polyp14DEPISSS
NasalSSS_cleaned_raw_expression_counts.csv.gz

source_name: Human Adult Inferior Turbinate, Polyp14DEPISSS


title: GC059869_D21

value: K8rtta/TetO-DTA/K5CreER/Rosa-Tomato mice, mixed background


title: Hypoxia-Acidosis-Oligosome (HAO)


title: GC059869_D19


title: Hypoxia-Acidosis-Monosome (HAM)


title: GC059869_D18


title: GC059869_D17


title: Hypoxia-Polysome (HNP)

source_name: Hypoxia (1% oxygen), pH = 7.4


title: Hypoxia-Oligosome (HNO)


title: GC059869_D16


title: Hypoxia-Monosome (HNM)


title: GC059869_D15


title: Normoxia-Acidosis-Polysome (NAP)

source_name: Normoxia Acidosis, pH = 6.0


title: Normoxia-Acidosis-Oligosome (NAO)


title: Normoxia-Acidosis-Monosome (NAM)


title: GC059869_D11


title: GC059869_D20


title: GC059869_D12


title: GC059869_D13


title: GC059869_D10


title: GC059869_D09


title: Normoxia-Oligosome (NNO)

source_name: Normoxia, pH = 7.4


title: Normoxia-Polysome (NNP)


title: ATAC_Cord_d8_Rep1

city: Ottawa

first: Marjorie

last: Brand

state: Ontario

address: 501 Smyth Road

country: Canada

institute: Ottawa Hospital Research Institute

description: CD34+ cells were subjected to ex vivo erythropoiesis according to the protocol described in Palii et al. (doi: 10.3791/2813. J Vis Exp. 53, 2011)

data_processing:
Reads were mapped to the hg38 genome using bowtie version 1.0.0 using the following parameters --chunkmb 256 --phred33-quals -m 2 --best --strata --maxins 400.
Peak calling was performed with MACS2 version 2.1.1.20160309 using the following parameters --nomodel --shift -100 --extsize 200 -p 0.001 -g hs
Genome_build: hg38
Supplementary_files_format_and_content: Bed files contains the genomic coordinates of peaks called by MACS2.

source_name: Umbilical cord blood

extract_protocol:
performed as previously described in Hay et al. (doi: 10.1038/ng.3605. Nat Gen 2016) and Buenrostro et al. (doi: 10.1038/nmeth.2688 Nat Meth 2013). Briefly, 75000 cells per technical replicate (x2) per sample per timepoint were lysed in cold lysis buffer, nuclear pellets were obtained after 10 min centrifugation at 4°C at 500G and resuspended in 50ul of tagmentation mix (FC-121-1030, Illumina), then incubated for 30 min at 37°C. DNA was purified using the Qiagen MinElute columns (28004, Qiagen).
Tagmented DNA was indexed with custom primers using NEB Next High-Fidelity 2x PCR Master Mix (M0541S, NEB). And purified with Qiagen PCR Cleanup Kit (28104, Qiagen).
Samples were multiplexed sequenced on a next generation sequencing platform using the NextSeq® 500/550 High Output Kit v2 (75 cycles; FC-404-2005, Illumina) using paired-end reads

value: CD34+ cells

value: Umbilical cord blood

tag: differentiation day


title: ATAC_Cord_d16_Rep1

growth_protocol: described in Palii et al. (doi: 10.3791/2813. J Vis Exp. 53, 2011)


title: GC059869_D08


title: ATAC_Cord_d16_Rep2


title: GC059869_D06


title: GC059869_D07


title: ATAC_Cord_d12_Rep2


title: ATAC_Cord_d10_Rep2


title: GC059869_D04


title: GC059869_D14


title: ATAC_Cord_d12_Rep1


title: GC059869_D03


title: ATAC_Cord_d10_Rep1


title: 2-P

description: Final_FPKM-HIF1alpha_vs_HIF2alpha_knockdown.xlsx

data_processing:
Illumina Nextseq 500 uses Reat-Time Analysis (RTA) version 2 for base calling and quality scoring. Bcl2fastq converts output bcl files to fastq files.
RNA-seq data were aligned to GRCh38 with STAR 2.5.0 default parameters
Alignment files (BAM files) were annotated and processed through the Cufflinks 2.2.1 pipeline
Gene FPKM values were obtained with Cuffnorm within Cufflinks 2.2.1
Genome_build: GRCh38 (gencode v27)
Supplementary_files_format_and_content: Excel spreadsheet: gene list with FPKM values

growth_protocol: U87MG cells were maintained with DMEM with 10% FBS and 1% Pen/Strep.

treatment_protocol: Cells were treated with non-silencing control or HIF-2α-specific or HIF-1α-specific siRNA pools for 48 hr, and then subjected to 1% oxygen (hypoxia) for 24 hr.

tag: isolate

tag: disease

tag: transfection

value: HIF-2α siRNA

tag: fraction

value: polysome


title: GC059869_D02


title: GC059869_G07

value: Doxycycline treatment single-cell


title: 2-O

value: oligosome


title: Normoxia-Monosome (NNM)


title: GC059869_D01


title: GC059869_C23


title: GC059869_C24


title: 1-P

value: HIF-1α siRNA


title: 2-M

value: free/monosome


title: GC059869_C19


title: 1-O


title: 1-M


title: GC059869_D05


title: M-CTL

value: Hypoxia control siRNA


title: GC059869_C17


title: P-CTL


title: GC059869_C20


title: GC059869_C16


title: U87MG-Hyp24-Oligo

description: Final_FPKM-Normoxia_vs_Hypoxia-Exiqon.xlsx

data_processing:
Data processing was performed by Exiqon
Final report was generated by Exiqon
Supplementary_files_format_and_content: Excel spreadsheet: gene list with FPKM values

extract_protocol:
Total RNA was extracted by phenol/chloroform and ethanol precipitation following riboosome density fractionation.
Library construction for mRNA sequencing was performed by Exiqon.

treatment_protocol: Cells transfected with control siRNA were subjected to 21% (normoxia) or 1% (hypoxia) oxygen for 24 hours

tag: disease state

value: oligosome fraction


title: U87MG-Hyp24-Poly

value: polysome fraction


title: GC059869_C15

value: Wild-type single-cell

value: Basal cell


title: GC059869_C13


title: U87MG-Norm24-Poly

value: Normoxia control siRNA


title: GC059869_C14


title: U87MG-Norm24-Oligo

value: brain


title: GC059869_C12

value: Luminal cell


title: GC059869_C22

value: K8rtta/TetO-DTA/K5CreER/Rosa-Tomato mice, mixed background


title: GC059869_C11


title: U87MG-Norm24-Mono

value: Glioblastoma

value: free/monosome fraction


title: ELAV-P

treatment_protocol: Cells were treated with non-silencing control or HuR-specific siRNA pools for 48 hr, and then subjected to 1% oxygen for 24 hr.

tag: source

value: HuR siRNA


title: GC059869_C21

tag: strain


title: GC059869_C10


title: GC059869_C18


title: ELAV-M


title: GC059869_C09


title: GC059869_C07


title: GC059869_C08


title: CTL-O


title: ELAV-O


title: GC059869_C06


title: O-CTL


title: CTL-M


title: GC059869_C05


title: U87MG-Hyp24-Mono


title: GC059869_C04


title: GC059869_C03


title: Mouse_basal_stim_Untreated_0_REP10

description: Mouse basal cells from the trachea three replicates of each stimulation with IFNA, IFNB, or IFNG, each at increasing doses (0, 0.1 ,0.5, 1, 2, 5, 10 ng/mL) and 12 replicates of unstimulated samples

data_processing:
Aligned using cumulus platform https://cumulus-doc.readthedocs.io/en/0.12.0/smart_seq_2.html and output as TPM using RSEM v1.3.67
mm10
Supplementary_files_format_and_content: Processed data is a tab or comma delimited text file containing TPM

source_name: tracheal basal cells

tag: agent

value: Untreated

tag: dose

value: tracheal basal cells


title: Mouse_basal_stim_Untreated_0_REP11

data_processing:
Aligned using cumulus platform https://cumulus-doc.readthedocs.io/en/0.12.0/smart_seq_2.html and output as TPM using RSEM v1.3.68
mm10
Supplementary_files_format_and_content: Processed data is a tab or comma delimited text file containing TPM


title: GC059869_C02


title: Mouse_basal_stim_Untreated_0_REP12

data_processing:
Aligned using cumulus platform https://cumulus-doc.readthedocs.io/en/0.12.0/smart_seq_2.html and output as TPM using RSEM v1.3.69
mm10
Supplementary_files_format_and_content: Processed data is a tab or comma delimited text file containing TPM


title: Mouse_basal_stim_Untreated_0_REP9

data_processing:
Aligned using cumulus platform https://cumulus-doc.readthedocs.io/en/0.12.0/smart_seq_2.html and output as TPM using RSEM v1.3.66
mm10
Supplementary_files_format_and_content: Processed data is a tab or comma delimited text file containing TPM


title: Mouse_basal_stim_Untreated_0_REP8

data_processing:
Aligned using cumulus platform https://cumulus-doc.readthedocs.io/en/0.12.0/smart_seq_2.html and output as TPM using RSEM v1.3.65
mm10
Supplementary_files_format_and_content: Processed data is a tab or comma delimited text file containing TPM


title: Mouse_basal_stim_Untreated_0_REP7

data_processing:
Aligned using cumulus platform https://cumulus-doc.readthedocs.io/en/0.12.0/smart_seq_2.html and output as TPM using RSEM v1.3.64
mm10
Supplementary_files_format_and_content: Processed data is a tab or comma delimited text file containing TPM


title: GC059869_B24

data_processing:
Adapter trimming using cutadapt (v 1.13)
Reads aligned to GRCm38 + ERCC sequences using STAR (v 2.5.2b)
Counts were generated using HTSeq (v 0.6.0) on GENCODE M12 transcript annotation
Genome_build: GRCm38
Supplementary_files_format_and_content: Raw comma-separated file containing raw expression matrix and Seurat R data object file


title: Mouse_basal_stim_Untreated_0_REP5

data_processing:
Aligned using cumulus platform https://cumulus-doc.readthedocs.io/en/0.12.0/smart_seq_2.html and output as TPM using RSEM v1.3.62
mm10
Supplementary_files_format_and_content: Processed data is a tab or comma delimited text file containing TPM


title: Mouse_basal_stim_Untreated_0_REP6

data_processing:
Aligned using cumulus platform https://cumulus-doc.readthedocs.io/en/0.12.0/smart_seq_2.html and output as TPM using RSEM v1.3.63
mm10
Supplementary_files_format_and_content: Processed data is a tab or comma delimited text file containing TPM


title: GC059869_B23


title: GC059869_B21


title: Mouse_basal_stim_Untreated_0_REP4

data_processing:
Aligned using cumulus platform https://cumulus-doc.readthedocs.io/en/0.12.0/smart_seq_2.html and output as TPM using RSEM v1.3.61
mm10
Supplementary_files_format_and_content: Processed data is a tab or comma delimited text file containing TPM


title: GC059869_B22


title: CTL-P

value: polysome


title: GC059869_B20


title: Mouse_basal_stim_Untreated_0_REP3

data_processing:
Aligned using cumulus platform https://cumulus-doc.readthedocs.io/en/0.12.0/smart_seq_2.html and output as TPM using RSEM v1.3.60
mm10
Supplementary_files_format_and_content: Processed data is a tab or comma delimited text file containing TPM


title: GC059869_B19


title: Mouse_basal_stim_Untreated_0_REP2

data_processing:
Aligned using cumulus platform https://cumulus-doc.readthedocs.io/en/0.12.0/smart_seq_2.html and output as TPM using RSEM v1.3.59
mm10
Supplementary_files_format_and_content: Processed data is a tab or comma delimited text file containing TPM


title: GC059869_B18


title: GC059869_B17


title: Mouse_basal_stim_IFNG_10_REP3

data_processing:
Aligned using cumulus platform https://cumulus-doc.readthedocs.io/en/0.12.0/smart_seq_2.html and output as TPM using RSEM v1.3.57
mm10
Supplementary_files_format_and_content: Processed data is a tab or comma delimited text file containing TPM

value: IFNG


title: Mouse_basal_stim_Untreated_0_REP1

data_processing:
Aligned using cumulus platform https://cumulus-doc.readthedocs.io/en/0.12.0/smart_seq_2.html and output as TPM using RSEM v1.3.58
mm10
Supplementary_files_format_and_content: Processed data is a tab or comma delimited text file containing TPM


title: GC059869_B16


title: GC059869_B15


title: GC059869_B14


title: GC059869_B13


title: Mouse_basal_stim_IFNG_10_REP1

data_processing:
Aligned using cumulus platform https://cumulus-doc.readthedocs.io/en/0.12.0/smart_seq_2.html and output as TPM using RSEM v1.3.55
mm10
Supplementary_files_format_and_content: Processed data is a tab or comma delimited text file containing TPM


title: Mouse_basal_stim_IFNG_5_REP3

data_processing:
Aligned using cumulus platform https://cumulus-doc.readthedocs.io/en/0.12.0/smart_seq_2.html and output as TPM using RSEM v1.3.54
mm10
Supplementary_files_format_and_content: Processed data is a tab or comma delimited text file containing TPM


title: GC059869_C01


title: GC059869_B11


title: Mouse_basal_stim_IFNG_5_REP2

data_processing:
Aligned using cumulus platform https://cumulus-doc.readthedocs.io/en/0.12.0/smart_seq_2.html and output as TPM using RSEM v1.3.53
mm10
Supplementary_files_format_and_content: Processed data is a tab or comma delimited text file containing TPM


title: Mouse_basal_stim_IFNG_2_REP3

data_processing:
Aligned using cumulus platform https://cumulus-doc.readthedocs.io/en/0.12.0/smart_seq_2.html and output as TPM using RSEM v1.3.51
mm10
Supplementary_files_format_and_content: Processed data is a tab or comma delimited text file containing TPM


title: GC059869_B10


title: GC059869_B09


title: Mouse_basal_stim_IFNG_2_REP2

data_processing:
Aligned using cumulus platform https://cumulus-doc.readthedocs.io/en/0.12.0/smart_seq_2.html and output as TPM using RSEM v1.3.50
mm10
Supplementary_files_format_and_content: Processed data is a tab or comma delimited text file containing TPM


title: Mouse_basal_stim_IFNG_2_REP1

data_processing:
Aligned using cumulus platform https://cumulus-doc.readthedocs.io/en/0.12.0/smart_seq_2.html and output as TPM using RSEM v1.3.49
mm10
Supplementary_files_format_and_content: Processed data is a tab or comma delimited text file containing TPM


title: GC059869_B08


title: Mouse_basal_stim_IFNG_1_REP3

data_processing:
Aligned using cumulus platform https://cumulus-doc.readthedocs.io/en/0.12.0/smart_seq_2.html and output as TPM using RSEM v1.3.48
mm10
Supplementary_files_format_and_content: Processed data is a tab or comma delimited text file containing TPM


title: GC059869_B07


title: GC059869_B06


title: Mouse_basal_stim_IFNG_1_REP1

data_processing:
Aligned using cumulus platform https://cumulus-doc.readthedocs.io/en/0.12.0/smart_seq_2.html and output as TPM using RSEM v1.3.46
mm10
Supplementary_files_format_and_content: Processed data is a tab or comma delimited text file containing TPM


title: GC059869_B05


title: Mouse_basal_stim_IFNG_10_REP2

data_processing:
Aligned using cumulus platform https://cumulus-doc.readthedocs.io/en/0.12.0/smart_seq_2.html and output as TPM using RSEM v1.3.56
mm10
Supplementary_files_format_and_content: Processed data is a tab or comma delimited text file containing TPM


title: GC059869_B03

data_processing:
Adapter trimming using cutadapt (v 1.13)
Reads aligned to GRCm38 + ERCC sequences using STAR (v 2.5.2b)
Counts were generated using HTSeq (v 0.6.0) on GENCODE M12 transcript annotation
Genome_build: GRCm38
Supplementary_files_format_and_content: Raw comma-separated file containing raw expression matrix and Seurat R data object file


title: Mouse_basal_stim_IFNG_0.5_REP3

data_processing:
Aligned using cumulus platform https://cumulus-doc.readthedocs.io/en/0.12.0/smart_seq_2.html and output as TPM using RSEM v1.3.45
mm10
Supplementary_files_format_and_content: Processed data is a tab or comma delimited text file containing TPM


title: Mouse_basal_stim_IFNG_1_REP2

data_processing:
Aligned using cumulus platform https://cumulus-doc.readthedocs.io/en/0.12.0/smart_seq_2.html and output as TPM using RSEM v1.3.47
mm10
Supplementary_files_format_and_content: Processed data is a tab or comma delimited text file containing TPM


title: GC059869_B04


title: Mouse_basal_stim_IFNG_0.5_REP2

data_processing:
Aligned using cumulus platform https://cumulus-doc.readthedocs.io/en/0.12.0/smart_seq_2.html and output as TPM using RSEM v1.3.44
mm10
Supplementary_files_format_and_content: Processed data is a tab or comma delimited text file containing TPM


title: GC059869_B02


title: Mouse_basal_stim_IFNG_0.5_REP1

data_processing:
Aligned using cumulus platform https://cumulus-doc.readthedocs.io/en/0.12.0/smart_seq_2.html and output as TPM using RSEM v1.3.43
mm10
Supplementary_files_format_and_content: Processed data is a tab or comma delimited text file containing TPM


title: Mouse_basal_stim_IFNG_0.1_REP3

data_processing:
Aligned using cumulus platform https://cumulus-doc.readthedocs.io/en/0.12.0/smart_seq_2.html and output as TPM using RSEM v1.3.42
mm10
Supplementary_files_format_and_content: Processed data is a tab or comma delimited text file containing TPM


title: GC059869_B01


title: Mouse_basal_stim_IFNG_0.1_REP1

data_processing:
Aligned using cumulus platform https://cumulus-doc.readthedocs.io/en/0.12.0/smart_seq_2.html and output as TPM using RSEM v1.3.40
mm10
Supplementary_files_format_and_content: Processed data is a tab or comma delimited text file containing TPM


title: Mouse_basal_stim_IFNG_5_REP1

data_processing:
Aligned using cumulus platform https://cumulus-doc.readthedocs.io/en/0.12.0/smart_seq_2.html and output as TPM using RSEM v1.3.52
mm10
Supplementary_files_format_and_content: Processed data is a tab or comma delimited text file containing TPM


title: GC059869_A24


title: GC059869_A23


title: Mouse_basal_stim_IFNG_0.1_REP2

data_processing:
Aligned using cumulus platform https://cumulus-doc.readthedocs.io/en/0.12.0/smart_seq_2.html and output as TPM using RSEM v1.3.41
mm10
Supplementary_files_format_and_content: Processed data is a tab or comma delimited text file containing TPM


title: GC059869_B12


title: Mouse_basal_stim_IFNB_10_REP3

data_processing:
Aligned using cumulus platform https://cumulus-doc.readthedocs.io/en/0.12.0/smart_seq_2.html and output as TPM using RSEM v1.3.39
mm10
Supplementary_files_format_and_content: Processed data is a tab or comma delimited text file containing TPM

value: IFNB


title: GC059869_A22


title: Mouse_basal_stim_IFNB_10_REP2

data_processing:
Aligned using cumulus platform https://cumulus-doc.readthedocs.io/en/0.12.0/smart_seq_2.html and output as TPM using RSEM v1.3.38
mm10
Supplementary_files_format_and_content: Processed data is a tab or comma delimited text file containing TPM


title: GC059869_A21


title: Mouse_basal_stim_IFNB_10_REP1

data_processing:
Aligned using cumulus platform https://cumulus-doc.readthedocs.io/en/0.12.0/smart_seq_2.html and output as TPM using RSEM v1.3.37
mm10
Supplementary_files_format_and_content: Processed data is a tab or comma delimited text file containing TPM


title: GC059869_A20


title: Mouse_basal_stim_IFNB_5_REP3

data_processing:
Aligned using cumulus platform https://cumulus-doc.readthedocs.io/en/0.12.0/smart_seq_2.html and output as TPM using RSEM v1.3.36
mm10
Supplementary_files_format_and_content: Processed data is a tab or comma delimited text file containing TPM


title: GC059869_A19


title: GC059869_A18


title: Mouse_basal_stim_IFNB_5_REP2

data_processing:
Aligned using cumulus platform https://cumulus-doc.readthedocs.io/en/0.12.0/smart_seq_2.html and output as TPM using RSEM v1.3.35
mm10
Supplementary_files_format_and_content: Processed data is a tab or comma delimited text file containing TPM


title: GC059869_A16


title: Mouse_basal_stim_IFNA_10_REP3

data_processing:
Aligned using cumulus platform https://cumulus-doc.readthedocs.io/en/0.12.0/smart_seq_2.html and output as TPM using RSEM v1.3.33
mm10
Supplementary_files_format_and_content: Processed data is a tab or comma delimited text file containing TPM

value: IFNA


title: Mouse_basal_stim_IFNA_10_REP2

data_processing:
Aligned using cumulus platform https://cumulus-doc.readthedocs.io/en/0.12.0/smart_seq_2.html and output as TPM using RSEM v1.3.32
mm10
Supplementary_files_format_and_content: Processed data is a tab or comma delimited text file containing TPM


title: Mouse_basal_stim_IFNA_10_REP1

data_processing:
Aligned using cumulus platform https://cumulus-doc.readthedocs.io/en/0.12.0/smart_seq_2.html and output as TPM using RSEM v1.3.31
mm10
Supplementary_files_format_and_content: Processed data is a tab or comma delimited text file containing TPM


title: GC059869_A14

data_processing:
Adapter trimming using cutadapt (v 1.13)
Reads aligned to GRCm38 + ERCC sequences using STAR (v 2.5.2b)
Counts were generated using HTSeq (v 0.6.0) on GENCODE M12 transcript annotation
Genome_build: GRCm38
Supplementary_files_format_and_content: Raw comma-separated file containing raw expression matrix and Seurat R data object file


title: Mouse_basal_stim_IFNA_5_REP3

data_processing:
Aligned using cumulus platform https://cumulus-doc.readthedocs.io/en/0.12.0/smart_seq_2.html and output as TPM using RSEM v1.3.30
mm10
Supplementary_files_format_and_content: Processed data is a tab or comma delimited text file containing TPM


title: GC059869_A13