title: CDP(common dendritic cell progenitor)_KY034

city: New York City

first: Kang

last: Liu

state: New York

department: Dept of Microbiology & Immunology

institute: Columbia University

description:
processed data file: bulk_counts.txt
processed data file: bulk_counts_norm.txt

data_processing:
RNA-Seq reads were aligned to the Ensembl GRCh 37 genome assembly using STAR with default parameters
featureCounts was used to obtain gene read counts.
DESeq2 was used to normalize the read counts for library size difference correction.
Genome_build: Ensembl GRCh37
Supplementary_files_format_and_content: tab-delimited text files include read counts for each sample

source_name: CDP(common dendritic cell progenitor )

extract_protocol:
For the single cell, Fluidigm C1 system was used. For bulk cell, 2,000-30,000 progenitor cells of each population were purified using flowcytometry sorting. After cell lysis, mRNA was purified using LNA-Oligo-(dT) coated streptavidin-coated C1 DynabeadsRNA was extracted
RNA was amplified with clonetech SMARTer Ultra Low RNA Kit (634935 and 639207, Clontech)

value: healthy donor

value: peripheral blood

value: CDP(common dendritic cell progenitor )


title: CDP(common dendritic cell progenitor)_KY030

status: Public on Jul 16 2019

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: subject status

tag: tissue

tag: cell type


title: preDC(precursor dentritic cell)_KY024

source_name: preDC(precursor dentritic cell)

value: preDC(precursor dentritic cell)


title: CD1c(CD1c+ classic dentritic cell)_KY021

source_name: CD1c(CD1c+ classic dentritic cell)

value: CD1c(CD1c+ classic dentritic cell)


title: 273_14.3_no_stim_veh_24hr

city: Seattle

first: Timothy

middle: George

last: Johnstone

state: WA

address: 400 Dexter Ave N #605

department: Computational Genomics & Data Science

institute: Juno Therapeutics

data_processing:
Strand-specific, poly-A-selected RNA-seq reads were trimmed (minimum quality 2), mapped to hg38 (OmicSoft OSA4 default parameters using OmicSoft GenCodeV24 transcript models as reference), and quantified using ArrayStudio (OmicSoft)
Reads per gene were quantified in a strand-specific manner using ArrayStudio (OmicSoft) to output expression values in the form of TPM-scaled FPKM
Genome_build: hg38
Supplementary_files_format_and_content: tab separated table of TPM-normalized expression values per-gene

molecule: polyA RNA

source_name: Cultured T cell

growth_protocol: Anti-BCMA CAR T cells were cultured in the presence or absence of BCMA beads for either 24 hours or 7 days with or without 1 µM lenalidomide.

extract_protocol:
RNA was extracted using Promega Maxwell HT simplyRNA custom kit
Libraries were prepared with NEB UltraII directional kit using the polyA enrichment module

value: T-cell

tag: treatment

value: veh

tag: stim-status

value: nostim

tag: sample-donor

tag: timepoint


title: CDP(common dendritic cell progenitor)_KY020


title: preDC(precursor dentritic cell)_KY023


title: preDC(precursor dentritic cell)_KY011


title: CD1c(CD1c+ classic dentritic cell)_KY009


title: CD141(CD141+ classic dentritic cell)_KY002

source_name: CD141(CD141+ classic dentritic cell)

value: CD141(CD141+ classic dentritic cell)


title: CD141(CD141+ classic dentritic cell)_KY010


title: mixed of preDC and DCs_MIXED-H10

description:
processed data file: single_cell_counts.txt
processed data file: single_cell_counts_norm.txt

source_name: mixed of preDC and DCs

value: mixed of preDC and DCs


title: mixed of preDC and DCs_MIXED-H12


title: CD141(CD141+ classic dentritic cell)_KY022


title: CD1c(CD1c+ classic dentritic cell)_KY001


title: 276_14.6_stim_veh_24hr

value: stim


title: mixed of preDC and DCs_MIXED-H08


title: mixed of preDC and DCs_MIXED-H05


title: mixed of preDC and DCs_MIXED-H11


title: mixed of preDC and DCs_MIXED-G12


title: mixed of preDC and DCs_MIXED-H01


title: mixed of preDC and DCs_MIXED-G05


title: mixed of preDC and DCs_MIXED-G11


title: mixed of preDC and DCs_MIXED-G08


title: mixed of preDC and DCs_MIXED-G07


title: mixed of preDC and DCs_MIXED-F12


title: mixed of preDC and DCs_MIXED-G03


title: mixed of preDC and DCs_MIXED-G04


title: mixed of preDC and DCs_MIXED-F09


title: mixed of preDC and DCs_MIXED-F10


title: mixed of preDC and DCs_MIXED-F11


title: mixed of preDC and DCs_MIXED-E09


title: mixed of preDC and DCs_MIXED-F03


title: mixed of preDC and DCs_MIXED-E08


title: mixed of preDC and DCs_MIXED-E12


title: mixed of preDC and DCs_MIXED-E07


title: mixed of preDC and DCs_MIXED-E06


title: mixed of preDC and DCs_MIXED-E04


title: mixed of preDC and DCs_MIXED-E05


title: mixed of preDC and DCs_MIXED-E02


title: mixed of preDC and DCs_MIXED-D02


title: mixed of preDC and DCs_MIXED-C05


title: mixed of preDC and DCs_MIXED-C11


title: mixed of preDC and DCs_MIXED-B12


title: mixed of preDC and DCs_MIXED-D03


title: mixed of preDC and DCs_MIXED-C09


title: mixed of preDC and DCs_MIXED-B10


title: mixed of preDC and DCs_MIXED-F06


title: mixed of preDC and DCs_MIXED-C06


title: mixed of preDC and DCs_MIXED-D06


title: mixed of preDC and DCs_MIXED-C03


title: mixed of preDC and DCs_MIXED-B09


title: mixed of preDC and DCs_MIXED-D05


title: mixed of preDC and DCs_MIXED-B01


title: mixed of preDC and DCs_MIXED-A10


title: mixed of preDC and DCs_MIXED-B04


title: mixed of preDC and DCs_MIXED-A07


title: mixed of preDC and DCs_MIXED-A06


title: mixed of preDC and DCs_MIXED-A08


title: mixed of preDC and DCs_MIXED-B07


title: mixed of preDC and DCs_MIXED-A05


title: mixed of preDC and DCs_MIXED-A03


title: precursor dentritic cell_PREDC-H09

source_name: precursor dentritic cell

value: precursor dentritic cell


title: precursor dentritic cell_PREDC-H10


title: precursor dentritic cell_PREDC-H08


title: mixed of preDC and DCs_MIXED-B08


title: precursor dentritic cell_PREDC-H01


title: precursor dentritic cell_PREDC-H07


title: precursor dentritic cell_PREDC-H03


title: precursor dentritic cell_PREDC-G11


title: precursor dentritic cell_PREDC-G09


title: mixed of preDC and DCs_MIXED-B05


title: mixed of preDC and DCs_MIXED-D11


title: precursor dentritic cell_PREDC-G08


title: precursor dentritic cell_PREDC-G07


title: precursor dentritic cell_PREDC-G06


title: mixed of preDC and DCs_MIXED-E03


title: precursor dentritic cell_PREDC-F01


title: precursor dentritic cell_PREDC-G04


title: precursor dentritic cell_PREDC-F04


title: precursor dentritic cell_PREDC-E01


title: precursor dentritic cell_PREDC-F03


title: precursor dentritic cell_PREDC-F05


title: precursor dentritic cell_PREDC-E12


title: precursor dentritic cell_PREDC-E10


title: precursor dentritic cell_PREDC-E06


title: precursor dentritic cell_PREDC-E07


title: precursor dentritic cell_PREDC-F02


title: precursor dentritic cell_PREDC-F06


title: precursor dentritic cell_PREDC-G05


title: precursor dentritic cell_PREDC-G02


title: precursor dentritic cell_PREDC-F07


title: precursor dentritic cell_PREDC-G03


title: precursor dentritic cell_PREDC-E04


title: precursor dentritic cell_PREDC-G01


title: precursor dentritic cell_PREDC-E11


title: precursor dentritic cell_PREDC-D09


title: precursor dentritic cell_PREDC-D12


title: mixed of preDC and DCs_MIXED-A11


title: 282_14.3_stim_len_24hr

value: len


title: precursor dentritic cell_PREDC-D04


title: precursor dentritic cell_PREDC-D07


title: mixed of preDC and DCs_MIXED-A09


title: precursor dentritic cell_PREDC-D03


title: precursor dentritic cell_PREDC-C11


title: precursor dentritic cell_PREDC-C05


title: precursor dentritic cell_PREDC-C10


title: precursor dentritic cell_PREDC-C04


title: precursor dentritic cell_PREDC-C03


title: precursor dentritic cell_PREDC-B08


title: precursor dentritic cell_PREDC-B12


title: precursor dentritic cell_PREDC-C07


title: precursor dentritic cell_PREDC-D01


title: precursor dentritic cell_PREDC-C09


title: precursor dentritic cell_PREDC-B02


title: precursor dentritic cell_PREDC-A11


title: mixed of preDC and DCs_MIXED-F07


title: precursor dentritic cell_PREDC-B01


title: precursor dentritic cell_PREDC-B05


title: precursor dentritic cell_PREDC-B06


title: precursor dentritic cell_PREDC-B04


title: precursor dentritic cell_PREDC-B07


title: mixed of preDC and DCs_MIXED-D12


title: precursor dentritic cell_PREDC-A07


title: precursor dentritic cell_PREDC-A09


title: precursor dentritic cell_PREDC-A08


title: precursor dentritic cell_PREDC-D02


title: precursor dentritic cell_PREDC-A05


title: precursor dentritic cell_PREDC-A04


title: precursor dentritic cell_PREDC-A06


title: precursor dentritic cell_PREDC-A02


title: classic dentritic cell_DC-H9

source_name: classic dentritic cell

value: classic dentritic cell


title: 286_14.1_stim_len_24hr


title: precursor dentritic cell_PREDC-C02


title: classic dentritic cell_DC-H4


title: classic dentritic cell_DC-H3


title: classic dentritic cell_DC-H11


title: classic dentritic cell_DC-H5


title: classic dentritic cell_DC-G6


title: classic dentritic cell_DC-H1


title: classic dentritic cell_DC-G11


title: classic dentritic cell_DC-G10


title: classic dentritic cell_DC-G5


title: classic dentritic cell_DC-G7


title: classic dentritic cell_DC-H12


title: classic dentritic cell_DC-H2


title: classic dentritic cell_DC-G3


title: classic dentritic cell_DC-G9


title: classic dentritic cell_DC-G4


title: classic dentritic cell_DC-F9


title: classic dentritic cell_DC-F11


title: classic dentritic cell_DC-F12


title: classic dentritic cell_DC-F3


title: classic dentritic cell_DC-F2


title: classic dentritic cell_DC-G1


title: classic dentritic cell_DC-F10


title: classic dentritic cell_DC-F4


title: classic dentritic cell_DC-F1


title: classic dentritic cell_DC-F7


title: classic dentritic cell_DC-E7


title: classic dentritic cell_DC-E9


title: classic dentritic cell_DC-F8


title: classic dentritic cell_DC-E6


title: classic dentritic cell_DC-E5


title: classic dentritic cell_DC-D4


title: classic dentritic cell_DC-E2


title: classic dentritic cell_DC-E11


title: classic dentritic cell_DC-D9


title: classic dentritic cell_DC-D10


title: classic dentritic cell_DC-D5


title: classic dentritic cell_DC-E12


title: classic dentritic cell_DC-E4


title: classic dentritic cell_DC-E3


title: classic dentritic cell_DC-D12


title: classic dentritic cell_DC-D11


title: classic dentritic cell_DC-C8


title: classic dentritic cell_DC-E8


title: classic dentritic cell_DC-C5


title: classic dentritic cell_DC-C10


title: classic dentritic cell_DC-B3


title: classic dentritic cell_DC-B9


title: classic dentritic cell_DC-B4


title: classic dentritic cell_DC-B2


title: classic dentritic cell_DC-A9


title: classic dentritic cell_DC-C2


title: classic dentritic cell_DC-B5


title: classic dentritic cell_DC-C3


title: classic dentritic cell_DC-B6


title: classic dentritic cell_DC-A8


title: classic dentritic cell_DC-C1


title: classic dentritic cell_DC-B11


title: classic dentritic cell_DC-B8


title: classic dentritic cell_DC-A3


title: classic dentritic cell_DC-A4


title: classic dentritic cell_DC-A2


title: classic dentritic cell_DC-A12


title: classic dentritic cell_DC-A5


title: classic dentritic cell_DC-A7


title: classic dentritic cell_DC-C4


title: classic dentritic cell_DC-A10


title: Control-Sup-3

city: New York

first: Madison

last: Kelly

state: NY

address: 413 E69th Street

institute: Weill Cornell Medicine

data_processing:
Demultiplexing with CASAVA, v1.8
Reads trimmed with cutadapt, v1.7
Read alignment with HISAT2, v2.1
Differential gene expression analysis with Limma, v3.32.4
Genome_build: mm10
Supplementary_files_format_and_content: RNA seq normalized counts table

organism: Mus musculus

source_name: Control-Sup

extract_protocol:
Samples were lysed with TRIzol reagent (Thermo Fisher Scientific) and total RNA was extracted using a Direct-zol RNA miniprep kit (Zymo Research)
QuantSeq 3’ mRNA-Seq Library Prep Kit (Lexogen)

treatment_protocol: Control or Jak1 sgRNA B16-F10 tumor cells were treated for 7 hours with supernatant derived from a separate WT B16-F10/NK cell overnight 1:1 co-culture. Cells treated with IFN-γ (0.5 ng/mL) were used as a positive control and cells treated with TNF (1 ng/mL) were used as a negative control.

tag: strain background

tag: cell line background

value: Tumor cell line

tag: genotype/variation

value: wild type; control

value: supernatant derived from a separate WT B16-F10/NK co-culture for 7hrs


title: classic dentritic cell_DC-A1

value: healthy donor


title: Control-Sup-2


title: Control-Sup-1


title: classic dentritic cell_DC-B10

value: peripheral blood


title: Jak1-Untreated-3

value: Jak1 sgRNA

value: none; untreated


title: classic dentritic cell_DC-A6


title: Jak1-Untreated-2


title: Control-Untreated-3

source_name: Control-Untreated


title: Control-Untreated-2


title: Jak1-Untreated-1


title: Jak1-TNF-2

value: TNF (1 ng/mL)


title: Control-TNF-3

source_name: Control-TNF


title: Control-Untreated-1


title: Control-TNF-2


title: Jak1-IFNy-3

value: IFN-γ (0.5 ng/mL)


title: Control-TNF-1


title: Jak1-IFNy-2


title: Jak1-IFNy-1


title: Prep3_condition1

city: Cambridge

first: Faye

last: Zhao

address: 250 Massachusetts Ave

institute: NIBR

description:
name in processed data file:
4-1_1.fastq

data_processing:
Alignment: TopHat v2.0.3, Bowtie v2.0.0
Raw counts: HTSeq0.6
Genome_build: RGSC 5.0/rn5
Supplementary_files_format_and_content: rawcount_GLT.txt

organism: Rattus norvegicus

source_name: 3hr control

extract_protocol: Total RNA was prepared from rat islets (~1000 Islet Equivalents (IEQ)/sample) using the RNeasy kit (Qiagen). RNA quantity and quality were assessed using an Agilent 2100 Bioanalyzer and 1 mg of total RNA was sent to Beijing Genome Institute (BGI) for reverse transcription, library preparation, and sequence analysis (Illumina Hi-Seq2000). Sequencing reads (100 bp) from paired-ends were mapped to the rat genome (rn5) with TopHat2 (version 2.0.3) and Bowtie2 (version 2.0.0) (Kim et al., 2013; Langmead and Salzberg, 2012). Gene expression values were summarized as raw counts by running HT-seq (Anders et al., 2015). The variance-stabilizing transformation from DESeq (Anders and Huber, 2010) was applied to the raw sequencing count data prior to statistical analyses. Islets from different rats were included in the study and a linear mixed effect model was used to account for the random effects of different rat donors.

value: Primary pancreatic islets

tag: strain

value: Sprague Dawley


title: Prep2_condition7

description:
name in processed data file:
3-7_1.fastq

source_name: 3hr GLT + cpd E, 300nM


title: Prep3_condition6

description:
name in processed data file:
4-6_1.fastq

source_name: 24hr GLT + cpd D, 300nM


title: Prep3_condition2

description:
name in processed data file:
4-2_1.fastq

source_name: 24hr control


title: Jak1-TNF-1


title: Prep2_condition5

description:
name in processed data file:
3-5_1.fastq

source_name: 3hr GLT + cpd D, 300nM


title: Jak1-TNF-3


title: Prep3_condition3

description:
name in processed data file:
4-3_1.fastq

source_name: 3hr GLT


title: Prep3_condition5

description:
name in processed data file:
4-5_1.fastq


title: Prep3_condition4

description:
name in processed data file:
4-4_1.fastq

source_name: 24hr GLT


title: Control-IFNy-2

source_name: Control-IFNy


title: Control-IFNy-3


title: Prep2_condition8

description:
name in processed data file:
3-8_1.fastq

source_name: 24hr GLT + cpd E, 300nM


title: Prep2_condition6

description:
name in processed data file:
3-6_1.fastq


title: Prep2_condition2

description:
name in processed data file:
3-2_1.fastq


title: Prep2_condition1

description:
name in processed data file:
3-1_1.fastq


title: Prep1_condition8

description:
name in processed data file:
2-8_1.fastq


title: Prep1_condition6

description:
name in processed data file:
2-6_1.fastq


title: Prep1_condition5

description:
name in processed data file:
2-5_1.fastq


title: Prep2_condition4

description:
name in processed data file:
3-4_1.fastq


title: Jak1-Sup-3


title: Prep2_condition3

description:
name in processed data file:
3-3_1.fastq


title: Control-IFNy-1


title: precursor dentritic cell_PREDC-H05

description:
processed data file: single_cell_counts.txt
processed data file: single_cell_counts_norm.txt


title: Jak1-Sup-2


title: Prep1_condition4

description:
name in processed data file:
2-4_1.fastq


title: Prep1_condition3

description:
name in processed data file:
2-3_1.fastq


title: Prep1_condition2

description:
name in processed data file:
2-2_1.fastq


title: Jak1-Sup-1


title: Prep1_condition1

description:
name in processed data file:
2-1_1.fastq


title: B16F10 CRISPR NK Replicate 1

library_source: genomic

data_processing:
Demultiplexing with CASAVA, v1.8
Reads trimmed with cutadapt, v1.7
20 bp targeting sequences compared to Tend sample using MAGeCK, v0.5.7
Genome_build: mm10
Supplementary_files_format_and_content: CRISPR screen results table
Supplementary_files_format_and_content: CRISPR screen individual replicate results table

molecule: genomic DNA

source_name: B16-F10 Cas9 expressing cells transduced with a genome-wide CRISPR library

extract_protocol:
Genomic DNA was extracted using the DNeasy Blood & Tissue Kit (Qiagen).
Products were amplified by PCR (Broad Institute protocol) and cleaned up using the AMPure XP-Purification system (Beckman Coulter)

treatment_protocol: 3x Overnight co-culture with activated murine NK cells

tag: cell line

value: co-cultured with activated murine NK cells at an equal ratio for 7 hr


title: T0 control

data_processing:
Demultiplexing with CASAVA, v1.8
Reads trimmed with cutadapt, v1.7
20 bp targeting sequences compared to Tend sample using MAGeCK, v0.5.7
Genome_build: mm10
Supplementary_files_format_and_content: CRISPR screen results table

source_name: Tumor cell line

treatment_protocol: 3x overnight IFN-γ treatment and H-2kb low FACS sort (lowest 15%)

tag: strain backtround

value: B16-F10 Cas9 expressing cells transduced with a genome-wide CRISPR library


title: B16F10 CRISPR Tend control

value: none (untreated)


title: B16-F10_untreated-3

data_processing:
Demultiplexing with CASAVA, v1.8
Reads trimmed with cutadapt, v1.7
Read alignment with HISAT2, v2.1
Differential gene expression analysis with Limma, v3.32.4
Genome_build: mm10
Supplementary_files_format_and_content: RNA seq normalzied counts table

treatment_protocol: B16-F10 cells were left untreated or co-cultured with activated murine NK cells at an equal ratio for 7 hours. Viable tumor cells were thoroughly washed with PBS and then lysed


title: Pc_HiChIP_Rep1

city: Omaha

first: M

middle: Jordan

last: Rowley

state: NE

address: 601 S Saddle Creek Rd

department: GCBA

institute: Univ of Nebraska Medical Center

data_processing:
ChIP-seq reads were aligned to the dm6 reference genome using bowtie2 and PCR duplicates were removed. HiChIP reads were processed using the Juicer pipeline.
Genome_build: dm6
Supplementary_files_format_and_content: bigWig containing coverage of ChIP-seq and .hic containing Hi-C contact matrices.

organism: Drosophila melanogaster

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 min at room temperature and quenched with glycine. For ChIP-seq, nuclear lysates were sonicated to generate 200-500 bp fragments . Chromatin was precleared with Protein A or G Dynabeads at 4°C for 2 hours and incubated with antibody overnight at 4°C. Isolated chromatin was washed, eluted, reverse crosslinked and purified by standard methods. For HiChIP nuclei were isolated and chromatin digested by DpnII, filled in with biotin-dCTP, and ligated. After ligation, chromatin was sonicated and precleared with Protein A and G Dynabeads at 4°C for 2 hours, then precipitated using anti-CP190 or anti-Pol2phosphoSerine2 antibody overnight. Isolated chromatin was washed, eluted, reverse crosslinked and purified by standard methods, after which ligation events were enriched by streptavidin precipitation. For ATAC-seq Kc167 cells grown to exponential stage were treated with DMSO or triptolide as previously described. 200,000 ctrl and treated cells were collected and used for Fast-ATAC protocol. Briefly, cell pellets were resuspened in 50 µl transposes Tn5 mixture (0.01% digitonin for permeabilizing cell membrane, 2.5 µl Tn5, 25 µl TD buffer), and incubated at 30°C for 20 min with occasional shaking. After reaction, cells were cooled on ice and continued with DNA extraction by Minelute Kit (Qiagen).
Libraries were constructed using the standard protocol. Genomic fragments were end repaired (NEBNext End Repair Module), A-tailed by adding  adenosine to  the 3’ ends of fragment using Klenow fragment (3’ to 5’ exo minus, New England Biolabs), and adaptors were ligatedat room temperature for 1 hr with T4 DNA ligase (New England Biolabs). Libraries were amplified with Illumina primers using the KAPA SYBR FAST qPCR Master Mix.

value: Drosophila Embryonic Cell Line

tag: chip-antibody

value: Pc

value: under normal conditions


title: PsqTot_20HE_HiChIP_Rep2

value: Psq-M (recognizes PsqTot)

value: after 3 hours 20-HE treatment


title: Pc_HiChIP_Rep2


title: B16-F10_NK-3

value: Tumor cell line


title: MHC I low sorted

value: treated overnight with IFN-γ and FACS sorted for cells that failed to upregulate MHC I expression


title: PsqTot_20HE_HiChIP_Rep3


title: PsqTot_20HE_HiChIP_Rep1


title: B16-F10_untreated-2


title: B16F10 CRISPR NK Replicate 2


title: PsqTot_CTL_HiChIP


title: B16-F10_untreated-1


title: ISWI_ChIP-seq_CTL

description: ChIP-seq under normal conditions

value: ISWI


title: PsqTot_CTL_HiChIP 2

description: HiChIP (Hi-C Chromatin immunoprecipitation) under normal conditions


title: EcR_20HE_ChIP-seq

value: EcR


title: PsqTot_20HE_ChIP-seq_Rep1


title: Pc_ChIP-seq_CTL

description: Pc.bw


title: PsqL_20HE_ChIP-seq

value: Psq-BTB (recognizes PsqL)


title: Respiratory vagal sensory neuron [AM302]

first: Luyi

last: Tian

state: MA

address: 415 main st Cambridge

institute: Broad institute

data_processing:
Sequencing reads were aligned to the ENSEMBL build 88 of the Mus musculus genome by Rsubread (version 1.24.2) using default parameters.  Only uniquely aligned reads were kept for exon mapping using featureCounts and the ENSEMBL build 88 Mus musculus exon annotation.
The computeSumFactors function in the scran (version 1.10.1) Bioconductor package was used to generate the size factors for normalization followed by scran::trendVar and scran::decomposeVar functions used to obtain highly variable genes.
Genome_build: ENSEMBL GREm38 build 88
Supplementary_files_format_and_content: gene_count.csv was the unnormalized read count generated by featurecounts

source_name: Vagal sensory ganglia

extract_protocol: Bronchopulmonary sensory neurons in the vagal ganglia were identified by retrograde neuronal tracing with the retrograde lipophilic tracer 1,1'-Dioctadecyl-3,3,3',3'-Tetramethylindocarbocyanine Perchlorate (DiI 2%).  Retrogradely labeled neurons were collected individually and cellular mRNA was amplified to obtain enough mRNA for sequencing.  Sequencing was performed on NextSeq 500, single stranded and 76bp read length.

value: single neuron

tag: retrograde tracer

value: 2percent DiI


title: Respiratory vagal sensory neuron [AM301]


title: PsqTot_20HE_ChIP-seq_Rep2


title: Respiratory vagal sensory neuron [AM304]


title: EcR_CTL_ChIP-seq_Rep2

description: EcR.bw


title: Pc_ChIP-seq_20HE


title: B16-F10_NK-2


title: PsqTot_CTL_ChIP-seq_Rep2

description: PsqTot.bw


title: B16-F10_NK-1


title: Respiratory vagal sensory neuron [AM300]


title: EcR_CTL_ChIP-seq_Rep1

description: EcR.bw


title: Respiratory vagal sensory neuron [AM299]


title: Respiratory vagal sensory neuron [AM297]


title: PsqL_CTL_ChIP-seq_Rep2

description: PsqL.bw


title: Respiratory vagal sensory neuron [AM298]


title: Respiratory vagal sensory neuron [AM296]


title: Respiratory vagal sensory neuron [AM294]


title: Respiratory vagal sensory neuron [AM292]


title: Respiratory vagal sensory neuron [AM295]


title: PsqTot_CTL_ChIP-seq_Rep1

description: PsqTot.bw


title: Respiratory vagal sensory neuron [AM303]


title: Respiratory vagal sensory neuron [AM293]


title: Respiratory vagal sensory neuron [AM290]


title: Respiratory vagal sensory neuron [AM289]


title: Respiratory vagal sensory neuron [AM288]


title: Respiratory vagal sensory neuron [AM287]


title: WM3623_2h_N1

city: East Lansing

first: Sean

middle: Alexander

last: Misek

state: MI

address: 1355 Bogue Street

institute: Michigan State University

data_processing:
Basecalls performed with Illumina Real Time Analysis, RTA_v2.7.7
Demultiplexing and FastQ conversion with Illumina Bcl2fastq v2.19.0
Quality Control with FastQC v0.11.5
Read Trimming with Trimmomatic v0.33
Read Mapping with HISAT2 v2.1.0
Read Counting/Analysis with HTSeq v0.6.1
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited files include raw HTSeq counts for each sample

source_name: Melanoma Cell Line

growth_protocol: Cells were grown in DMEM + 10% FBS + 1% Anti/Anti and were passaged in 10-cm cell culture plates. To generate experimental samples the cells were seeded into 6-cm plates.

extract_protocol:
Total cellular RNA was harvested from the cell lines using the Qiagen Rneasy Mini Kit (Cat# 74104)
Libraries were prepared using the Illumina TruSeq Stranded mRNA Library Preparation Kit on a Perkin Elmer Sciclone G3 robot following manufacturer’s recommendations. Completed libraries were QC’d and quantified using a combination of Qubit dsDNA HS and Caliper LabChipGX HS DNA assays. Libraries were pooled and run on two lanes, and sequencing was performed in a 1x50bp single end read format using HiSeq 4000 SBS reagents.

treatment_protocol: Cells were treated with 10 uM CCG-222740 or vehicle control for either 0, 2, 6, or 24 h.

value: melanoma cell line WM3623

tag: treatment time

value: 2 hr


title: WM3623_2h_N2


title: WM3623_24h_N2

value: 24 hr


title: WM3451_24h_N2

value: melanoma cell line WM3451


title: WM3623_6h_N1

value: 6 hr


title: WM3623_0h_N1

value: control

value: 0 hr


title: WM3623_6h_N2


title: PsqL_CTL_ChIP-seq_Rep1

description: PsqL.bw

value: Drosophila Embryonic Cell Line

value: under normal conditions


title: WM3623_24h_N1


title: WM3623_0h_N2


title: Respiratory vagal sensory neuron [AM286]


title: WM3451_24h_N1


title: WM3451_6h_N2


title: Respiratory vagal sensory neuron [AM283]


title: Respiratory vagal sensory neuron [AM284]


title: Respiratory vagal sensory neuron [AM291]


title: Respiratory vagal sensory neuron [AM281]


title: Respiratory vagal sensory neuron [AM278]


title: Respiratory vagal sensory neuron [AM282]


title: WM3451_2h_N1


title: WM3451_0h_N2


title: WM3451_6h_N1


title: Respiratory vagal sensory neuron [AM277]


title: WM3451_2h_N2


title: SKMel147_24h_N2

value: melanoma cell line SKMel147


title: WM3451_0h_N1


title: Respiratory vagal sensory neuron [AM275]


title: SKMel147_24h_N1


title: Respiratory vagal sensory neuron [AM273]


title: Respiratory vagal sensory neuron [AM272]


title: SKMel147_6h_N1


title: SKMel147_2h_N1


title: Respiratory vagal sensory neuron [AM267]


title: SKMel147_6h_N2


title: Respiratory vagal sensory neuron [AM257]


title: Respiratory vagal sensory neuron [AM255]


title: H_2

city: Calgary

first: Justin

last: Deniset

address: University of Calgary 2500 University Dr. NW

country: Canada

institute: University of Calgary

data_processing:
demultiplex to fastq using bcl2fastq version 2.17.1
map to mm10 using Tophat 2.1.1
calculate RPKM using Partek 7.18.0723
calculate ANOVA comparison using Partek 7.18.0723
Genome_build: mm10
Supplementary_files_format_and_content: Excel, RPKM and ANOVA results

source_name: Cardiac macrophages

extract_protocol:
FACS sorted macrophages directly into TRIzol and flash frozen.  RNA extraction completed using Direct-zol RNA isolation kit (Zymo Research) following the included protocol
The harvested RNA was prepared for sequencing using the NEBNext Ultra II RNA Library Prep Kit for Illumina

value: Heart

tag: age

value: 8 weeks


title: SKMel147_0h_N2


title: PL_4

source_name: Pleural cavity macrophages

value: Pleural cavity lavage


title: Respiratory vagal sensory neuron [AM258]


title: PL_3


title: SKMel19_24h_N2

value: melanoma cell line SKMel19


title: SKMel147_0h_N1


title: PL_5


title: PT_4

source_name: Peritoneal cavity macrophages

value: Peritoneal cavity lavage


title: SKMel19_24h_N1


title: Respiratory vagal sensory neuron [AM251]

value: single neuron


title: PL_2


title: H_4


title: PT_3


title: PT_5


title: SKMel19_6h_N2


title: Respiratory vagal sensory neuron [AM252]

value: 2percent DiI


title: PT_2


title: Respiratory vagal sensory neuron [AM271]


title: H_5


title: Respiratory vagal sensory neuron [AM249]


title: SKMel147_2h_N2


title: H_3


title: PF_5

source_name: Pericardial cavity macrophages

value: Pericardial cavity  lavage


title: SKMel19_6h_N1


title: Respiratory vagal sensory neuron [AM253]


title: PF_4


title: Respiratory vagal sensory neuron [AM248]


title: PF_3


title: SKMel19_2h_N1

value: 2 hr


title: Respiratory vagal sensory neuron [AM246]


title: Respiratory vagal sensory neuron [AM244]


title: PF_2


title: SKMel19_2h_N2


title: 5897 GMP: 10 wk GMP, MLL-ENL (x2), No dox

city: St Louis

first: Jeffery

last: Magee

state: Missouri

address: 660 S Euclid Ave.

department: Internal Medicine - Cardiovascular Division

institute: Washington University School of Medicine

description: fetal induction

data_processing:
The resulting sequencing reads were demultiplexed by index with a custom Python demultiplexing script and further demultiplexed by barcode with a custom Perl demultiplexing script.
The RNA-Seq reads were then aligned to the Mus musculus Ensembl release 76 top-level assembly with STAR version 3.0.4.b.
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5.
Sailfish version 0.6.3. was used to produce isoform estimated counts.
Genome_build: Ensemble R76
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: bone marrow

extract_protocol:
Qiagen RNAeasy micro plus
Clontech SMRTr

value: bone marrow

value: 10 weeks

tag: genotype

value: MLL-ENL

value: granulocyte-monocyte progenitor


title: 5900 GMP: 10 wk GMP, MLL-ENL (x2), No dox

description: fetal induction

tag: tissue


title: 5898 GMP: 10 wk GMP, control, No dox

description: fetal induction

value: wild type

tag: cell type


title: 5293 GMP: 10 wk GMP, MLL-ENL (x2), No dox

description: fetal induction


title: Respiratory vagal sensory neuron [AM239]


title: Respiratory vagal sensory neuron [AM237]


title: 4894 GMP: 10 wk GMP, control, No dox

description: fetal induction


title: 4892 GMP: 10 wk GMP, control, No dox

description: fetal induction


title: 5900 PGM: 10 wk pGM, MLL-ENL (x2), No dox

description: fetal induction

value: pre-granulocyte-monocyte progenitor


title: SKMel19_0h_N1

tag: treatment

value: control

value: 0 hr


title: SKMel2_24h_N2

value: melanoma cell line SKMel2

value: 24 hr


title: SKMel19_0h_N2


title: SKMel2_24h_N1


title: Respiratory vagal sensory neuron [AM235]


title: 5293 PGM: 10 wk pGM, MLL-ENL (x2), No dox

description: fetal induction


title: 5897 PGM: 10 wk pGM, MLL-ENL (x2), No dox

description: fetal induction


title: 5899 PGM: 10 wk pGM, control, No dox

description: fetal induction


title: SKMel2_6h_N2

value: 6 hr


title: 5898 PGM: 10 wk pGM, control, No dox

description: fetal induction


title: Respiratory vagal sensory neuron [AM234]


title: Respiratory vagal sensory neuron [AM232]


title: 4894 PGM: 10 wk pGM, control, No dox

description: fetal induction


title: 4892 PGM: 10 wk pGM, control, No dox

description: fetal induction


title: Respiratory vagal sensory neuron [AM230]


title: 5900 HPC: 10 wk HPC, MLL-ENL (x2), No dox

description: fetal induction

value: Committed hematopoietic progenitor cell


title: SKMel2_2h_N2


title: 5899 GMP: 10 wk GMP, control, No dox

description: fetal induction


title: SKMel2_2h_N1


title: 5293 HPC: 10 wk HPC, MLL-ENL (x2), No dox

description: fetal induction


title: Respiratory vagal sensory neuron [AM228]


title: 5898 HPC: 10 wk HPC, control, No dox

description: fetal induction


title: Respiratory vagal sensory neuron [AM226]


title: Respiratory vagal sensory neuron [AM225]


title: HPC 9425: 12 mo HPC, MLL-ENL, 8 wk dox

description: adult induction

value: 12 months


title: SKMel2_0h_N1


title: 5899 HPC: 10 wk HPC, control, No dox

description: fetal induction


title: HPC 9431: 12 mo HPC, MLL-ENL, 8 wk dox

description: adult induction


title: SKMel2_0h_N2


title: LA+PGN

city: Shanghai

first: Ke

last: Cao

address: Pujian Road 160, Shanghai

country: China

institute: Renji Hospital, School of Medicine, Shanghai Jiaotong University

data_processing:
Alignment was processed using HISAT2 and the mapping information was counted.
Gene expression level analysis used  WGCNA and the expression level of the gene was evaluated using StringTie and a known genetic model.
Differential gene expression analysis  was performed using DESeq2 to visualize the results of the expression difference analysis.
Genome_build: GRCh38

source_name: SZ95 sebocytes

extract_protocol:
Total RNA from SZ95 sebocytes was extracted using Trizol (Thermo Fischer) and isopropanol precipitation according to the manufacturer’s protocol and treated with RNase-free DNase I to remove genomic DNA contamination. RNA integrity was evaluated with a 1.0% agarose gel. Thereafter, the quality and quantity of RNA were assessed using a NanoPhotometer® spectrophotometer (IMPLEN, CA, USA) and an Agilent 2100 Bioanalyzer (Agilent Technologies, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: human sebaceous gland cell


title: Respiratory vagal sensory neuron [AM223]

value: single neuron

value: 2percent DiI


title: 4894 HPC: 10 wk HPC, control, No dox

description: fetal induction


title: HPC 9125: 12 mo HPC, MLL-ENL, 8 wk dox

description: adult induction


title: HPC 9814: 12 mo HPC, control, 8 wk dox

description: adult induction


title: SKMel2_6h_N1


title: Respiratory vagal sensory neuron [AM221]


title: LA


title: 5897 HPC: 10 wk HPC, MLL-ENL (x2), No dox

description: fetal induction


title: HPC 9123: 12 mo HPC, MLL-ENL, 8 wk dox

description: adult induction


title: Respiratory vagal sensory neuron [AM219]


title: HPC 9806: 12 mo HPC, control, 8 wk dox

description: adult induction


title: HPC 9756: 12 mo HPC, control, 8 wk dox

description: adult induction


title: HPC 9757: 12 mo HPC, control, 8 wk dox

description: adult induction


title: 33_1622_2-15_96CR-ENZR_SPT_EOS

first: Ilsa

last: Coleman

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

data_processing:
Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18.64.0 software, followed by 'demultiplexing' of indexed reads and generation of FASTQ files, using Illumina's bcl2fastq Conversion Software v1.8.4
Sequencing reads were mapped to the hg38 human and mm10 mouse genomes using TopHat v2.1.0. Sequences aligning to the mouse genome deriving from potential contamination with mouse tissue were removed from the analysis as previously described (PMID: 24278200.) If samples were sequenced more than once, the human filtered bam files were combined prior to further analysis.
Mean and standard deviation of fragment size were calculated with picard-tools v2.18.1.
Transcript abundance was determined from the TopHat alignments in R using the Genomic Alignments Bioconductor package v1.12.0 using the summarizeOverlaps function with mode=IntersectionStrict, counting reads mapping to the exonic regions of genes.
Genome_build: hg38
Supplementary_files_format_and_content: *_processed_data.txt: Processed files are tab-delimited text files. Each file contains 7 columns: Entrez Gene ID, gene symbol, gene name, mRNA size, raw fragment count (by gene), FPM (fragments per million reads mapped) and FPKM (fragments per kilobase per million reads mapped).

source_name: LuCaP 96CR-ENZR: treated with SPT, timepoint EOS, sample: 33_1622_2-15

growth_protocol: Male CB-17 SCID mice (aged 6-8 weeks; Charles River Laboratories, San Diego, CA) were castrated and two weeks later implanted subcutaneously with LuCaP 35CR, LuCaP 96CR, or LuCaP 77CR tumor bits.

extract_protocol:
RNA extraction was performed using RNA STAT 60 (Tel-Test, Friendswood, TX) and RNeasy Mini kit, followed by DNase digestion in solution prior to purification (Qiagen, Germantown, MD) for RNA-seq and quantitative PCR analyses. RNA integrity number was determined using the Agilent Bioanalyzer (Agilent, Santa Clara, CA).
RNA-seq libraries were constructed from 1 ug total RNA using the Illumina TruSeq mRNA LT Sample Prep Kit according to the manufacturer’s protocol.
Barcoded libraries were pooled and sequenced on the Illumina HiSeq 2500 generating 50 bp paired end reads.

treatment_protocol: When the tumor reached 40-100 mm3, mice started ENZ (MedChem Express, TX; 50 mg/kg in PBS containing 1% CMC/0.1% Tween-80/5% DMSO) by oral gavage daily, 5 days on 2 days off a week. When ENZ resistance developed (i.e. after 1 week for LuCaP 35CR and 2 weeks for LuCaP 96CR and LuCaP 77CR), mice were randomized to control or SPT treatment groups; Fig. 2A). Tumor volume and body weight were measured twice weekly, and blood samples were drawn weekly for PSA measurements using Architect Total PSA Assay (Abbott Laboratories, Abbott Park, IL). Five animals in each group were sacrificed 5 days after the initiation of treatment (D5) and the remaining animals were followed and sacrificed when tumors exceeded 1,000 mm3 or after 8 weeks, whichever came earlier (end of study, EOS) or sacrificed if animals became compromised. At sacrifice (D5 or EOS), tumors were harvested for paraffin embedding and frozen for subsequent analyses.

tag: gender

value: male

tag: tumor type

value: LuCaP 96CR-ENZR tumor

tag: treatment group

value: Supraphysiological testosterone (SPT)

value: End of Study (EOS)


title: Respiratory vagal sensory neuron [AM216]


title: HPC 1714: 6 mo HPC, MLL-ENL, 8 wk dox

description: adult induction

value: bone marrow

value: 6 months

value: MLL-ENL


title: HPC 1485: 6 mo HPC, MLL-ENL, 8 wk dox

description: adult induction


title: 32_1622_2-12_96CR-ENZR_SPT_EOS

source_name: LuCaP 96CR-ENZR: treated with SPT, timepoint EOS, sample: 32_1622_2-12

tag: timepoint


title: LA+P.acnes


title: Respiratory vagal sensory neuron [AM224]


title: 4892 HPC: 10 wk HPC, control, No dox

description: fetal induction

value: 10 weeks

value: wild type


title: Respiratory vagal sensory neuron [AM214]


title: Respiratory vagal sensory neuron [AM212]


title: HPC 1715: 6 mo HPC, control, 8 wk dox

description: adult induction


title: HPC 1717: 6 mo HPC, control, 8 wk dox

description: adult induction


title: HPC 1713: 6 mo HPC, control, 8 wk dox

description: adult induction


title: HPC 1618: 6 mo HPC, control, 8 wk dox

description: adult induction


title: Respiratory vagal sensory neuron [AM210]


title: 81G: 10 wk GMP, MLL-ENL, No dox

description: fetal induction

value: granulocyte-monocyte progenitor


title: 78G: 10 wk GMP, MLL-ENL, No dox

description: fetal induction


title: 29_1622_2-13_96CR-ENZR_SPT_EOS

source_name: LuCaP 96CR-ENZR: treated with SPT, timepoint EOS, sample: 29_1622_2-13


title: 30_1622_2-2_96CR-ENZR_SPT_EOS

source_name: LuCaP 96CR-ENZR: treated with SPT, timepoint EOS, sample: 30_1622_2-2


title: 74G: 10 wk GMP, MLL-ENL, No dox

description: fetal induction


title: 28_1622_2-10_96CR-ENZR_SPT_EOS

source_name: LuCaP 96CR-ENZR: treated with SPT, timepoint EOS, sample: 28_1622_2-10


title: Respiratory vagal sensory neuron [AM086]


title: Respiratory vagal sensory neuron [AM083]


title: HPC 1709: 6 mo HPC, MLL-ENL, 8 wk dox

description: adult induction


title: 87G: 10 wk GMP, control, No dox

description: fetal induction


title: 25_1622_1-3_96CR-ENZR_Control_EOS

source_name: LuCaP 96CR-ENZR: Control, timepoint EOS, sample: 25_1622_1-3

value: Control


title: 26_1622_1-11_96CR-ENZR_Control_EOS

source_name: LuCaP 96CR-ENZR: Control, timepoint EOS, sample: 26_1622_1-11


title: Respiratory vagal sensory neuron [AM078]


title: 80G: 10 wk GMP, control, No dox

description: fetal induction


title: 76G: 10 wk GMP, control, No dox

description: fetal induction


title: Respiratory vagal sensory neuron [AM080]


title: HPC 1704: 6 mo HPC, MLL-ENL, 8 wk dox

description: adult induction


title: 88G: 10 wk GMP, control, No dox

description: fetal induction


title: 31_1622_2-11_96CR-ENZR_SPT_EOS

source_name: LuCaP 96CR-ENZR: treated with SPT, timepoint EOS, sample: 31_1622_2-11


title: Respiratory vagal sensory neuron [AM076]


title: 81P: 10 wk pGM, MLL-ENL, No dox

description: fetal induction

value: pre-granulocyte-monocyte progenitor


title: 78P: 10 wk pGM, MLL-ENL, No dox

description: fetal induction


title: Respiratory vagal sensory neuron [AM075]


title: 23_1622_1-1_96CR-ENZR_Control_EOS

source_name: LuCaP 96CR-ENZR: Control, timepoint EOS, sample: 23_1622_1-1


title: 22_1622_2-20_96CR-ENZR_SPT_D5

source_name: LuCaP 96CR-ENZR: treated with SPT, timepoint D5, sample: 22_1622_2-20

value: Day 5 (D5)


title: 73G: 10 wk GMP, MLL-ENL, No dox

description: fetal induction


title: Respiratory vagal sensory neuron [AM072]

source_name: Vagal sensory ganglia


title: Respiratory vagal sensory neuron [AM070]


title: 21_1622_2-19_96CR-ENZR_SPT_D5

source_name: LuCaP 96CR-ENZR: treated with SPT, timepoint D5, sample: 21_1622_2-19


title: 20_1622_2-18_96CR-ENZR_SPT_D5

source_name: LuCaP 96CR-ENZR: treated with SPT, timepoint D5, sample: 20_1622_2-18


title: 88P: 10 wk pGM, control, No dox

description: fetal induction


title: 76P: 10 wk pGM, control, No dox

description: fetal induction


title: 81H: 10 wk HPC, MLL-ENL, No dox

description: fetal induction

value: Committed hematopoietic progenitor cell


title: 74P: 10 wk pGM, MLL-ENL, No dox

description: fetal induction


title: 87P: 10 wk pGM, control, No dox

description: fetal induction


title: 24_1622_1-2_96CR-ENZR_Control_EOS

source_name: LuCaP 96CR-ENZR: Control, timepoint EOS, sample: 24_1622_1-2


title: 74H: 10 wk HPC, MLL-ENL, No dox

description: fetal induction


title: 73H: 10 wk HPC, MLL-ENL, No dox

description: fetal induction


title: 78H: 10 wk HPC, MLL-ENL, No dox

description: fetal induction


title: Respiratory vagal sensory neuron [AM065]


title: 19_1622_2-5_96CR-ENZR_SPT_D5

source_name: LuCaP 96CR-ENZR: treated with SPT, timepoint D5, sample: 19_1622_2-5


title: 80H: 10 wk HPC, control, No dox

description: fetal induction

source_name: bone marrow


title: 87H: 10 wk HPC, control, No dox

description: fetal induction


title: Respiratory vagal sensory neuron [AM023]


title: 88H: 10 wk HPC, control, No dox

description: fetal induction


title: 76H: 10 wk HPC, control, No dox

description: fetal induction


title: 17_1622_1-6_96CR-ENZR_Control_D5

source_name: LuCaP 96CR-ENZR: Control, timepoint D5, sample: 17_1622_1-6


title: Respiratory vagal sensory neuron [AM069]


title: 73P: 10 wk pGM, MLL-ENL, No dox

description: fetal induction


title: 16_1622_1-5_96CR-ENZR_Control_D5

source_name: LuCaP 96CR-ENZR: Control, timepoint D5, sample: 16_1622_1-5


title: 18_1622_1-18_96CR-ENZR_Control_D5

source_name: LuCaP 96CR-ENZR: Control, timepoint D5, sample: 18_1622_1-18


title: Respiratory vagal sensory neuron [AM059]


title: M5G: P0 GMP, MLL-ENL, No dox

description: fetal induction

source_name: neonatal liver

value: neonatal liver


title: 80P: 10 wk pGM, control, No dox

description: fetal induction


title: 15_1622_1-4_96CR-ENZR_Control_D5

source_name: LuCaP 96CR-ENZR: Control, timepoint D5, sample: 15_1622_1-4


title: M4G: P0 GMP, MLL-ENL, No dox

description: fetal induction


title: Respiratory vagal sensory neuron [AM022]

value: single neuron


title: M3G: P0 GMP, MLL-ENL, No dox

description: fetal induction


title: Respiratory vagal sensory neuron [AM021]

value: 2percent DiI


title: W5G: P0 GMP, control, No dox

description: fetal induction


title: M2G: P0 GMP, MLL-ENL, No dox

description: fetal induction


title: 13_1607_2-12_77CR-ENZR_SPT_D5

source_name: LuCaP 77CR-ENZR: treated with SPT, timepoint D5, sample: 13_1607_2-12

value: male

value: LuCaP 77CR-ENZR tumor


title: W4G: P0 GMP, control, No dox

description: fetal induction


title: 14_1607_2-13_77CR-ENZR_SPT_D5

source_name: LuCaP 77CR-ENZR: treated with SPT, timepoint D5, sample: 14_1607_2-13

value: Supraphysiological testosterone (SPT)


title: W3G: P0 GMP, control, No dox

description: fetal induction


title: W2G: P0 GMP, control, No dox

description: fetal induction


title: Respiratory vagal sensory neuron [AM019]


title: 12_1607_2-11_77CR-ENZR_SPT_D5

source_name: LuCaP 77CR-ENZR: treated with SPT, timepoint D5, sample: 12_1607_2-11


title: M4P: P0 pGM, MLL-ENL, No dox

description: fetal induction


title: Respiratory vagal sensory neuron [AM017]


title: Respiratory vagal sensory neuron [AM018]


title: M2P: P0 pGM, MLL-ENL, No dox

description: fetal induction


title: W5P: P0 pGM, control, No dox

description: fetal induction


title: 11_1607_2-10_77CR-ENZR_SPT_D5

source_name: LuCaP 77CR-ENZR: treated with SPT, timepoint D5, sample: 11_1607_2-10


title: Respiratory vagal sensory neuron [AM020]


title: M3P: P0 pGM, MLL-ENL, No dox

description: fetal induction


title: 10_1607_1-13_77CR-ENZR_Control_D5

source_name: LuCaP 77CR-ENZR: Control, timepoint D5, sample: 10_1607_1-13


title: Respiratory vagal sensory neuron [AM013]


title: W2P: P0 pGM, control, No dox

description: fetal induction


title: M5H: P0 HPC, MLL-ENL, No dox

description: fetal induction


title: W3P: P0 pGM, control, No dox

description: fetal induction


title: 8_1607_1-11_77CR-ENZR_Control_D5

source_name: LuCaP 77CR-ENZR: Control, timepoint D5, sample: 8_1607_1-11


title: Respiratory vagal sensory neuron [AM010]

source_name: Vagal sensory ganglia


title: M4H: P0 HPC, MLL-ENL, No dox

description: fetal induction


title: 9_1607_1-12_77CR-ENZR_Control_D5

source_name: LuCaP 77CR-ENZR: Control, timepoint D5, sample: 9_1607_1-12


title: Respiratory vagal sensory neuron [AM011]


title: M3H: P0 HPC, MLL-ENL, No dox

description: fetal induction


title: 7_1607_1-10_77CR-ENZR_Control_D5

source_name: LuCaP 77CR-ENZR: Control, timepoint D5, sample: 7_1607_1-10


title: Respiratory vagal sensory neuron [AM007]


title: M2H: P0 HPC, MLL-ENL, No dox

description: fetal induction


title: 6_1546_5-6_35CR-ENZR_SPT_EOS

source_name: LuCaP 35CR-ENZR: treated with SPT, timepoint EOS, sample: 6_1546_5-6

value: LuCaP 35CR-ENZR tumor

value: End of Study (EOS)


title: W5H: P0 HPC, control, No dox

description: fetal induction


title: M5P: P0 pGM, MLL-ENL, No dox

description: fetal induction


title: W4H: P0 HPC, control, No dox

description: fetal induction


title: 5_1546_5-4_35CR-ENZR_SPT_EOS

source_name: LuCaP 35CR-ENZR: treated with SPT, timepoint EOS, sample: 5_1546_5-4


title: Respiratory vagal sensory neuron [AM006]


title: W3H: P0 HPC, control, No dox

description: fetal induction


title: Respiratory vagal sensory neuron [AM005]


title: 16_1550_3-6_35CR-ENZR_SPT_D5

source_name: LuCaP 35CR-ENZR: treated with SPT, timepoint D5, sample: 16_1550_3-6


title: Old LLPC #3

city: Los Angeles

first: Kenneth

last: Dorshkind

state: California

address: 10833 Le Conte Avenue

department: Pathology and Laboratory Medicine

institute: David Geffen School of Medicine at UCLA

description: RNA-Seq

data_processing:
Data quality check was done on an Illumina SAV. Demultiplexing was performed with the Illumina Bcl2fastq2 v 2.17 program.
The STAR ultrafast universal RNA-seq aligner (v2.5.2b) was used to generate the genome index and perform paired-end alignments. Reads were aligned to a genome index that includes both the genome sequence (GRCm38 primary assembly) and the exon/intron structure of known gene models (Gencode M12 genome annotation). Alignment files were used to generate strand-specific, gene-level count summaries with STAR's built-in gene counter. Differential expression analysis was performed with DESeq2.
Counts were normalized per-sample in units of FPKMs after correcting for gene mappable length and sample total counts.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Tab delimited, per-sample, gene expression estimates in units of FPKMs

source_name: Bone Marrow Long-lived Plasma Cell

growth_protocol: Young (2-3 months old) C57BL/6J were obtained from the Jackson Laboratory or the UCLA Division of Laboratory Animal Medicine. Old C57BL/6J mice were obtained from the National Institute on Aging colony and were used at 17-19 months of age. Bone marrow LLPCs were identified as CD45R(B220)- IgD- CD138high TCRb- TCRgd- CD11b- Gr-1- and purified using Aria Cell sorters (BD Biosciences) located in the Jonsson Comprehensive Cancer Center flow cytometry core.

extract_protocol:
RNA was extracted using the Qiagen RNeasy Micro Kit (Cat#: 74004) as per the manufacturer’s instructions.
RNA sequencing and library preparation (5 ng input RNA per sample) was performed by the UCLA Technology Center for Genomics and Bioinformatics using theClontech SMARTer Stranded Total RNA-seq  (Pico) Kit (Cat#: 634411) according to the manufacturer’s instructions. The library preparation workflow consisted of first-strand cDNA synthesis, template switching, adaptor ligation and cleavage of ribosomal cDNA and PCR amplification. Unique adaptors were utilized for each library to facilitate multiplexing of samples. One hundred fifty base pair paired-end sequencing was performed using 3 lanes on an Illumina Hiseq3000. Data quality was verified with Illumina SAV and de-multiplexing was performed with Illumina bcl2fastq2 v2.17.

tag: Sex

value: Male

value: 17-19 months


title: Old LLPC #1

description: RNA-Seq


title: 15_1550_3-5_35CR-ENZR_SPT_D5

source_name: LuCaP 35CR-ENZR: treated with SPT, timepoint D5, sample: 15_1550_3-5


title: Respiratory vagal sensory neuron [AM003]


title: Old LLPC #2

description: RNA-Seq


title: Respiratory vagal sensory neuron [AM004]


title: Young LLPC #3

description: RNA-Seq

value: Female

value: 2-3 months


title: Young LLPC #1

description: RNA-Seq


title: shYAP1 Veh GROseq

city: San Antonio

first: Zhijie

middle: Jason

state: TEXAS

address: 7703 Floyd Curl Drive

department: Department of Molecular Medicine

institute: Universality of Texas Health Science Center at San Antonio

description:
shYAP1_Veh_GROseq
GRO-seq, shYAP1, 1hr treatment with vehicle control.
Nascent RNA

data_processing:
Library strategy: GRO-seq
Basecalls performed using Illumina CASAVA software.
GRO-seq reads were aligned to human genome (hg19) using bowtie with “--best --strata –m 1 –v 2” parameters. Duplicated reads were eliminated for subsequent analysis.
To balance the clonal amplification bias and total useful reads, only at most three reads was allowed for each unique genomic position.
edgeR 3.16.5 was used to call the differential eRNAs.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: bigwig

growth_protocol: MCF7 obtained from ATCC were cultured in DMEM media supplemented with 10% FBS in a 5% CO2 humidified incubator at 37°C.

extract_protocol:
MCF7 cells were subjected to nuclear run-on for 5 minutes at 30°C with BrU labeling. The run-on RNAs were pulled down by BrU beads and subjected to library preparation for deep sequencing.
We followed a previous published protocol (Ingolia et al., 2009 Science; Wang et al., 2011 Nature). Briefly, the run-on RNA were first added with a polyA tracts by RNA polyA polymerase. This polyA tail enables the run-on RNA to be reverse transcribed into single strand cDNA by Reverse Transcriptase. The cDNA was circularized by CircLigase (Epicentre) and re-linearized by APE I, subsequently subjected to PCR amplification and deep sequencing.

treatment_protocol: For knockdown of TEAD4 and YAP1, MCF7 cells were infected with shRNA lentiviruses and selected by puromycin (1 ug/ml) for 3 days to establish TEAD4 or YAP knockdown MCF7 stable cell lines. Before experiment, the MCF7 cells were hormone-stripped in phenol red-free DMEM medium plus 5% charcoal-treated FBS for 3 days, followed by treatment of either 100 nM 17β-estradiol (E2) or ethanol as vehicle control for 1 hour.

value: Breast cancer cell line

tag: shRNA

value: Veh, 1 hr


title: shTEAD4 E2 GROseq

description:
shTEAD4_E2_GROseq
GRO-seq, shTEAD4, 1hr treatment with 100nM E2.
Nascent RNA


title: 12_1550_2-4_35CR-ENZR_Control_D5

source_name: LuCaP 35CR-ENZR: Control, timepoint D5, sample: 12_1550_2-4

value: Control


title: shYAP1 E2 GROseq

description:
shYAP1_E2_GROseq
GRO-seq, shYAP1, 1hr treatment with 100nM E2.
Nascent RNA


title: Young LLPC #2

description: RNA-Seq

tag: strain


title: Ash2l_WT_Rep2_AM_ChIPSeq

city: Beijing

first: Xiaozhong

last: Peng

address: No.5, Dongdan Santiao, Dongcheng District

department: Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences

institute: Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College

data_processing:
The 75-nt sequence reads generated by Illumina sequencing were mapped to the genome using the Burrows-Wheeler Aligner algorithm with default settings.Only reads that passed Illumina’s purity filter, aligned with no more than 2 mismatches, and mapped uniquely to the mouse genome (mm10) were used in the subsequent analysis
For identifying intervals over input control, the MACS cutoff for the false discovery rate after controlling for significance was P=1×10^ –7.
The two main peak callers used at this study are MACS (Zhang et al., Genome Biology 2008, 9:R137) and SICER (Zang et al., Bioinformatics 25, 1952-1958, 2009)
Genome_build: mm10
Supplementary_files_format_and_content: bigWig. Files with extension *.bw. Binary files that can be opened in or uploaded to genome browsers and show the fragment density for 32-nt bins along the genome (“signal map”)

source_name: dorsal cortex

extract_protocol:
Lysates were clarified from sonicated nuclei of E14.5 dorsal cortex and Ash2l/histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions

value: dorsal cortex

value: WT

tag: chip antibody

value: Ash2l (Active Motif, 39099)


title: 11_1550_2-3_35CR-ENZR_Control_D5

source_name: LuCaP 35CR-ENZR: Control, timepoint D5, sample: 11_1550_2-3

value: Day 5 (D5)


title: Ash2l_WT_Rep1_AM_ChIPSeq


title: W2H: P0 HPC, control, No dox

description: fetal induction

source_name: neonatal liver

value: neonatal liver

value: wild type

value: Committed hematopoietic progenitor cell


title: shTEAD4 Veh GROseq

description:
shTEAD4_Veh_GROseq
GRO-seq, shTEAD4, 1hr treatment with vehicle control.
Nascent RNA

tag: cell line


title: shCtrl E2 GROseq

description:
shCtrl_E2_GROseq
GRO-seq, shCTL, 1hr treatment with 100nM E2.
Nascent RNA

value: shCtrl


title: shCtrl Veh GROseq

description:
shCtrl_Veh_GROseq
GRO-seq, shCTL, 1hr treatment with vehicle control.
Nascent RNA


title: 10_1550_2-2_35CR-ENZR_Control_D5

source_name: LuCaP 35CR-ENZR: Control, timepoint D5, sample: 10_1550_2-2

value: male

value: LuCaP 35CR-ENZR tumor


title: vqsM-1

city: Hong Kong

first: Xin

last: DENG

address: 1/F, Block 1, To Yuen Building, City University of Hong Kong, 31 To Yuen Street, Kowloon Tong

department: Department of Biomedical Sciences

country: Hong Kong

institute: City University of Hong Kong

description:
processed data file: VqsM_RNA-seq_analyzed.xlsx
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1 vqsM mutant

data_processing:
RNA-seq reads were mapped to the P. aeruginosa genomes (NC_002516) using STAR, only the uniquely mapped reads were kept for the subsequent analyses.
The gene differential expression analysis was performed using DESeq2 R package.
Genome_build: Pseudomonas aeruginosa PAO1
Supplementary_files_format_and_content: comparisons between differnt mutant and wild-type

organism: Pseudomonas aeruginosa PAO1

source_name: vqsM

growth_protocol: liquid culture in LB (Luria-Bertani)  medium

extract_protocol:
To examine the effect of TFs (taking an example of QscR) on the transcriptome, 2 ml of mid-log-phase (OD600 = 0.6) bacterial cultures (PAO1 and rpoN::Tc mutant strains) were collected by centrifugation (12,000 rpm, 4℃). An RNeasy minikit (Qiagen) was used for subsequent RNA purification with DNaseI (NEB) treatment. After removing rRNA by using the MICROBExpress kit (Ambion), mRNA was used to generate the cDNA library according to the NEBNext® UltraTM II RNA Library Prep Kit protocol (Illumina), which was then sequenced using the Illumina HiSeq 2000. Each sample in RNA-seq assay was repeated twice.
TruSeq RNA sample prep kit protocol (Illumina)
To examine the effect of RpoN on the transcriptome, 2 ml of mid-log-phase (OD600= 0.6) bacterial cultures (PAO1 and ∆rpoN strains) were collected by centrifugation (12,000 rpm, 4℃). An RNeasy minikit (Qiagen) was used for subsequent RNA purification with DNaseI (NEB) treatment. After removing rRNA by using the MICROBExpress kit (Ambion), mRNA was used to generate the cDNA library according to the TruSeq RNA sample prep kit protocol (Illumina), which was then sequenced using the Illumina HiSeq 2000. Bacterial RNA-seq reads were mapped to the P. auruginosa genome (ASM676v1, NC 002516.2) by using TopHat (version 2.0.0), with two mismatches allowed. Only the uniquely mapped reads were kept for the subsequent analyses. The gene differential expression analysis was performed using Cuffdiff software (version 2.0.0). GO enrich-ment analyses were conducted on all differentially transcribed genes using DAVID before data sets were imported into Cytoscape with an Enrichment Map plugin. The each sample in RNA-seq assay was repeated twice.
TruSeq RNA sample prep kit protocol (Illumina)

treatment_protocol:
grow until mid-log phase in LB
grow until mid-log phase

tag: genotype/variation

value: vqsM mutant


title: WT-vqsM-2

description:
processed data file: VqsM_RNA-seq_analyzed.xlsx
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1 Wild Type

source_name: WT-vqsM


title: vqsM-2


title: 4_1546_5-1_35CR-ENZR_SPT_EOS

source_name: LuCaP 35CR-ENZR: treated with SPT, timepoint EOS, sample: 4_1546_5-1

value: Supraphysiological testosterone (SPT)

value: End of Study (EOS)


title: Respiratory vagal sensory neuron [AM002]

value: single neuron

tag: retrograde tracer

value: 2percent DiI


title: 8_1546_5-10_35CR-ENZR_SPT_EOS

source_name: LuCaP 35CR-ENZR: treated with SPT, timepoint EOS, sample: 8_1546_5-10


title: WT-vqsM-1


title: 9_1550_2-1_35CR-ENZR_Control_D5

source_name: LuCaP 35CR-ENZR: Control, timepoint D5, sample: 9_1550_2-1


title: LCM_in_vivo_3

city: South San Francisco

first: Shannon

last: Turley

address: 1 DNA Way, Building 15, MS 231b

department: Cancer Immunology

institute: Genentech

data_processing: Reads were aligned to the GRCm38 genome using GSNAP and genes were counted using the HTSeqGenie Bioconductor package. Gene models were from our internal database and available in the manuscript supplementary material. "nRPKM" normalization was performed. This is similar to "RPKM" normalization but includes an extra step for sizeFactor adjustment and is described in the Methods of the manuscript. Supplementary files use Entrez Gene IDs, counts and nRPKM statistics.

source_name: samid: mbb340_pt_lavage

extract_protocol: RNA was isolated at expression analysis from RLT Buffer at Expression Analysis using QIAGEN reagents.

tag: group

value: mac

tag: mbatch

tag: rin

tag: condition


title: shYAP1 E2 replicate1

description:
shYAP1_E2_rep1
RNA-seq, shYAP1, 6hrs treatment with 100nM E2.
Cells were infected with YAP1 shRNAs.
processed data file: readCounts.txt

data_processing:
Basecalls were performed using Illumina Casava software.
Reads were aligned to hg19 genome assembly using STAR 2.5.2b. RefSeq transcripts were supplied in GTF format file.
featureCounts package was used to count the uniquely mapped reads in union mode.
Differentially expressed genes were detected by DESeq2 with FDR threshold 0.05.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: readCounts.txt: Tab-delimited text file includes reads counts for each Sample.

extract_protocol:
Total RNA was extracted by RNase Plus Mini Kit from Qiagen RNeasy Mini Kit (Cat no 74106).
RNA library was prepared by the KAPA RNA HyperPrep Kits with RiboErase (KK8560), according to the manufacturer’s instructions.

treatment_protocol: For knockdown of TEAD4 and YAP1, MCF7 cells were infected with shRNA lentiviruses and selected by puromycin (1 ug/ml) for 3 days to establish TEAD4 or YAP knockdown MCF7 stable cell lines. Before experiment, the MCF7 cells were hormone-stripped in phenol red-free DMEM medium plus 5% charcoal-treated FBS for 3 days, followed by treatment of either 100 nM 17β-estradiol (E2) or ethanol as vehicle control for 6 hours.

tag: cell type

value: Breast cancer cell line

value: 100 nM E2, 6hrs


title: qscR-2

description:
processed data file: QscR_RNA-seq_analyzed.xlsx
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1 qscR mutant

source_name: qscR

value: qscR mutant


title: shYAP1 E2 replicate2

description:
shYAP1_E2_rep2
RNA-seq, shYAP1, 6hrs treatment with 100nM E2.
Cells were infected with YAP1 shRNAs.
processed data file: readCounts.txt

tag: treatment


title: 13_1550_3-3_35CR-ENZR_SPT_D5

source_name: LuCaP 35CR-ENZR: treated with SPT, timepoint D5, sample: 13_1550_3-3

tag: gender


title: Input_AM_DNA

tag: tissue

value: dorsal cortex

tag: age

tag: genotype

value: WT


title: 7_1546_5-7_35CR-ENZR_SPT_EOS

source_name: LuCaP 35CR-ENZR: treated with SPT, timepoint EOS, sample: 7_1546_5-7

tag: tumor type

tag: treatment group

tag: timepoint


title: LCM_PDPN_tw_3

source_name: samid: mbb340_mac_tw

value: tw


title: shYAP1 Veh replicate1

description:
shYAP1_Veh_rep1
RNA-seq, shYAP1, 6hrs treatment with vehicle control.
Cells were infected with YAP1 shRNAs.
processed data file: readCounts.txt

tag: shRNA

value: Veh, 6 hrs


title: LCM_bms_3

source_name: samid: mbb340_mac_bms


title: qscR-1


title: PDPN_LCM_tw_3

source_name: samid: mbb340_frc_tw


title: shYAP1 Veh replicate2

description:
shYAP1_Veh_rep2
RNA-seq, shYAP1, 6hrs treatment with vehicle control.
Cells were infected with YAP1 shRNAs.
processed data file: readCounts.txt

tag: cell line


title: 6_1546_5-5_35CR-ENZR_SPT_EOS

source_name: LuCaP 35CR-ENZR: treated with SPT, timepoint EOS, sample: 6_1546_5-5


title: 5_1546_5-2_35CR-ENZR_SPT_EOS

source_name: LuCaP 35CR-ENZR: treated with SPT, timepoint EOS, sample: 5_1546_5-2


title: WT-qscR-2

description:
processed data file: QscR_RNA-seq_analyzed.xlsx
paired-end RNA-seq data of Pseudomonas aeruginosa PAO1 Wild Type

source_name: WT-qscR

tag: genotype/variation


title: shTEAD4 E2 replicate2

description:
shTEAD4_E2_rep2
RNA-seq, shTEAD4, 6hrs treatment with 100nM E2.
Cells were infected with TEAD4 shRNAs.
processed data file: readCounts.txt


title: WT-qscR-1


title: 4_1546_4-7_35CR-ENZR_Control_EOS

source_name: LuCaP 35CR-ENZR: Control, timepoint EOS, sample: 4_1546_4-7

value: Control


title: shTEAD4 E2 replicate1

description:
shTEAD4_E2_rep1
RNA-seq, shTEAD4, 6hrs treatment with 100nM E2.
Cells were infected with TEAD4 shRNAs.
processed data file: readCounts.txt


title: LCM_in_vitro_3

source_name: samid: mbb340_pt_alone


title: shTEAD4 Veh replicate2

description:
shTEAD4_Veh_rep2
RNA-seq, shTEAD4, 6hrs treatment with vehicle control.
Cells were infected with TEAD4 shRNAs.
processed data file: readCounts.txt


title: LCM_PDPN_cc_3

source_name: samid: mbb340_co_mac

value: co


title: PDPN_3

source_name: samid: mbb340_frc_alone


title: shTEAD4 Veh replicate1

description:
shTEAD4_Veh_rep1
RNA-seq, shTEAD4, 6hrs treatment with vehicle control.
Cells were infected with TEAD4 shRNAs.
processed data file: readCounts.txt


title: PDPN_LCM_cc_3

source_name: samid: mbb340_co_frc


title: 2_1546_4-4_35CR-ENZR_Control_EOS

source_name: LuCaP 35CR-ENZR: Control, timepoint EOS, sample: 2_1546_4-4

value: male


title: PAO1-7

description:
processed data file: ExsA_RNA-seq_analyzed.xlsx
PAO1-7_combined

data_processing:
ChIP-seq reads were mapped to the P. aeruginosa genomes (NC_002516) using Bowtie (Version 1.2.1.1). Only the uniquely mapped reads were kept for the subsequent analyses. Binding peaks (q < 0.05) were identified using MACS software (version 2.1.0).
RNA-seq reads were mapped to the P. aeruginosa genomes (NC_002516) using STAR, only the uniquely mapped reads were kept for the subsequent analyses.
The gene differential expression analysis was performed using DESeq2 R package.
Genome_build: P. aeruginosa genomes (NC_002516)
Supplementary_files_format_and_content: xls file containing comparisons between differnt mutant and wild-type, and different narrow peak files (as indicated in the column headers)

source_name: paired-end RNA-seq_P. aeruginosa PAO1 wild type

growth_protocol: grow until mid-log phase in LB

extract_protocol:
To examine the effect of TFs (taking an example of RpoN) on the transcriptome, 2 ml of mid-log-phase (OD600 = 0.6) bacterial cultures (PAO1 and rpoN::Tc mutant strains) were collected by centrifugation (12,000 rpm, 4℃). An RNeasy minikit (Qiagen) was usedr subsequent RNA purification with DNaseI (NEB) treatment. After removing rRNA by using the MICROBExpress kit (Ambion), mRNA was used to generate the cDNA library according to the NEBNext® UltraTM II RNA Library Prep Kit protocol (Illumina), which was then sequenced using the Illumina HiSeq 2000. Each sample in RNA-seq assay was repeated twice.
TruSeq RNA sample prep kit protocol (Illumina)

tag: sample type

value: mid-log phase liquid culture in LB (Luria-Bertani)  medium


title: PAO1-8

description:
processed data file: ExsA_RNA-seq_analyzed.xlsx
PAO1-8_combined


title: PAO1-6

description:
processed data file: AlgR_RNA-seq_analyzed.xlsx
PAO1-6_combined


title: 1_1546_4-1_35CR-ENZR_Control_EOS

source_name: LuCaP 35CR-ENZR: Control, timepoint EOS, sample: 1_1546_4-1

value: LuCaP 35CR-ENZR tumor


title: PAO1-5

description:
processed data file: AlgR_RNA-seq_analyzed.xlsx
PAO1-5_combined


title: LCM_atra_3

source_name: samid: mbb340_atra

tag: group


title: PDPN_bms_3

source_name: samid: mbb340_frc_bms

tag: mbatch


title: shCtrl E2 replicate1

description:
shCtrl_E2_rep1
RNA-seq, shCTL, 6hrs treatment with 100nM E2.
Cells were infected with control shRNAs.
processed data file: readCounts.txt


title: shCtrl Veh replicate2

description:
shCtrl_Veh_rep2
RNA-seq, shCTL, 6hrs treatment with vehicle control.
Cells were infected with control shRNAs.
processed data file: readCounts.txt


title: PAO1-4

description:
processed data file: LasR_RNA-seq_analyzed.xlsx
PAO1-4_combined


title: 3_1546_4-5_35CR-ENZR_Control_EOS

source_name: LuCaP 35CR-ENZR: Control, timepoint EOS, sample: 3_1546_4-5


title: LCM_PDPN_tw_2

source_name: samid: mbb339_mac_tw

tag: rin


title: shCtrl Veh replicate1

description:
shCtrl_Veh_rep1
RNA-seq, shCTL, 6hrs treatment with vehicle control.
Cells were infected with control shRNAs.
processed data file: readCounts.txt


title: PAO1-2

description:
processed data file: GacA_RNA-seq_analyzed.xlsx
PAO1-2_combined


title: LCM_in_vitro_2

source_name: samid: mbb339_pt_alone

tag: condition


title: PAO1-3

description:
processed data file: LasR_RNA-seq_analyzed.xlsx
PAO1-3_combined


title: MCF7_BLRP_TEAD4_MT_Dox_E2_ChipSeq

data_processing:
Basecalls performed using Illumina CASAVA software.
ChIP-seq reads were aligned to the hg19 genome assembly using bowtie v1.1.2 with only uniquely mapped reads retained.
Peaks were called using MACS2 with q-value less than 1e-5. The peaks overlapped with the blacklist regions downloaded from UCSC were removed.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: bigWig files

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody or by streptavidin magnet beads pull-down.
The extracted ChIP DNA was ligated to specific adaptors of KAPA Hyper Prep system (KK8504), according to the manufacturer’s instructions.

treatment_protocol: For knockdown of TEAD4 and YAP1, MCF7 cells were infected with shRNA lentiviruses and selected by puromycin (1 ug/ml) for 3 days to establish TEAD4 or YAP knockdown MCF7 stable cell lines. Before experiment, the MCF7 cells were hormone-stripped in phenol red-free DMEM medium plus 5% charcoal-treated FBS for 3 days, followed by treatment of either 100 nM 17β-estradiol (E2) or ethanol as vehicle control for 1hr. For knockdown of ERalpha in MCF7, at the second day of stripping, cells were treated with either 100 nM ICI182780 or DMSO for 24 hours before hormone treatment. To perform Biotin-ChIP experiments through Biotin-streptavidin pull-down, we used some BLRP-tagged MCF7 Tet-On inducible stable lines that can in vivo biotinylate BLRP-tagged proteins. To induce BLRP-tagged protein expression, 2 μg/ml doxycycline was added into culture media for about 24 hours before hormone treatment and collection.

tag: cell type

tag: doxycycline

value: Dox

tag: chip antibody

value: Biotin-ChIP using Streptavidin Magnetic beads (Solulink)


title: shCtrl E2 replicate2

description:
shCtrl_E2_rep2
RNA-seq, shCTL, 6hrs treatment with 100nM E2.
Cells were infected with control shRNAs.
processed data file: readCounts.txt

tag: treatment


title: GW182 dsRNA rep 2

city: Chongqiing

first: Chuan

last: Huang

state: C

address: No.174 Shazhengjie

institute: Chongqing University, China

description: Treated with GW182 dsRNA

data_processing:
Filter low quality reads and remove the adaptors from both end of each read with fastp.
To measure the linear RNA expresson, the remaining reads were mapped to the Drosophila genome (BDGP6.22, downloaded from Ensembl) using TopHat2 (version 2.0.14) with default parameters. For each library, gene expression levels were estimated by using Cufflinks version 2.2.1 3 based on Ensembl annotation (BDGP6.22, version 96).
To identify circRNAs with CIRI2 (version 2.0.6), RNA-seq reads were first mapped to Drosophila genome (BDGP6.22, downloaded from Ensembl) with bwa 6 and then the alignments were inputted to CIRI2 with default parameters.
Genome_build: BDGP6.22, downloaded from Ensembl
Supplementary_files_format_and_content: Txt files contain the raw output of the RPKM value from cufflinks

source_name: S2 cells Treated with GW182 dsRNA

growth_protocol: Drosophila S2 cells were cultured at 25°C with Schneider’s Drosophila medium (Sigma, S9895) plus 10% fetal bovine serum (HyClone, SH30910.03) and 1% (v/v) penicillin-streptomycin (Thermo Fisher Scientific, 15140122).

extract_protocol:
RNA was isolated using Trizol (Thermo Fisher Scientific, 15596018) according to the manufacturer’s instructions.
RNA-Seq libraries were prepared by using TruSeq Stranded Total RNA Library Prep Gold kit (Illumina 20020598) following the manufacturer's instructions and were subsequently sequenced for 150 nt from both ends on Illumina HiSeq 2500 platform.

treatment_protocol: Drosophila S2 cells were treated with either β-gal dsRNA (controls) or GW182 dsRNA for 3 days.

tag: tissue

value: S2 cells


title: β-gal dsRNA rep 3

description: Treated with β-gal dsRNA

source_name: S2 cells Treated with β-gal dsRNA


title: GW182 dsRNA rep 1

description: Treated with GW182 dsRNA


title: PAO1-1

description:
processed data file: GacA_RNA-seq_analyzed.xlsx
PAO1-1_combined


title: VqsR-2

source_name: paired-end RNA-seq_P. aeruginosa PAO1 vqsR mutant

value: vqsR mutant


title: PDPN_LCM_tw_2

source_name: samid: mbb339_frc_tw


title: LCM_bms_2

source_name: samid: mbb339_mac_bms

value: mac


title: β-gal dsRNA rep 2

description: Treated with β-gal dsRNA


title: MCF7_BLRP_TEAD4_MT_Dox_Veh_ChipSeq

value: Breast cancer cell line

value: Veh


title: GW182 dsRNA rep 3

description: Treated with GW182 dsRNA


title: MCF7_BLRP_TEAD4_MT_noDox_ChipSeq

value: No Dox

value: Full medium


title: PDPN_BMS_2

source_name: samid: mbb339_frc_bms


title: β-gal dsRNA rep 1

description: Treated with β-gal dsRNA


title: LCM_in_vivo_2

source_name: samid: mbb339_pt_lavage


title: L136

city: Lexington

first: Udeni

middle: B. R.

last: Balasuriya

state: KY

address: 108 Maxwell H. Gluck Equine Research Center

department: Veterinary Science

institute: University of Kentucky

data_processing:
The sequencing results were initially trimmed for adapters and quality using TrimGalore Version 0.4.4 (Babraham Bioinformatics; www.bioinformatics.babraham.ac.uk).
The sequences were mapped to EquCab2.0 using Burrows-Wheeler Aligner (V bwa-0.7.12).
Final quantification at the gene level was performed by analyzing the BAM files in Cufflinks (2.2.1) using the Equus_caballus_ENSEMBL_88 gtf file as Guide.
normalized abundance measurements- Cufflink Gene.FPKM.Tracking
Genome_build: EquCab2.0 (GCA_000002305.1)
Supplementary_files_format_and_content: normalized abundance measurements- Cufflink Gene.FPKM.Tracking

organism: Equus caballus

source_name: Ampulla

extract_protocol:
Total RNA was extracted from 5 to 6 10um cryosections of tissue using the RNeasy Micro kit kit (Qiagen, Valencia, CA)
cDNA libraries were prepared using the TruSeq® stranded total RNA sample preparation kit with rRNA depletion (Illumina Inc., San Diego, CA) and performed by a commercial company (Exiqon Services, Vedbæk, Denmark, and Qiagen Genomic Services, Hilden Germany).
Libraries for each batch were pooled in equimolar ratios and sequenced on two High Output NextSeq500 runs with 2x50bp paired-end read length (2x30 million reads/sample) plus 2x8bp for demultiplexing. After sequencing, raw data were demultiplexed using the bcl2fastq v. 2.17 software (Illumina Inc.). FastQ for each of the two were combined and QC was performed using the FastQC software package v. 0.10.1 (Babraham Bioinformatics, Babraham Institute, Cambridge, UK).

treatment_protocol: Samples from the ampullae were collected at post-mortem and snap-frozen in OCT compound and stored at -80C.

tag: infection status

value: Long-term carrier

tag: collection timepoint

value: 726 days post-infection


title: MCF7_BLRP_TEAD4_WT_Dox_E2_ChipSeq

last: Liu


title: MCF7_BLRP_TEAD4_WT_Dox_Veh_ChipSeq


title: SphR-2

source_name: paired-end RNA-seq_P. aeruginosa PAO1 sphR mutant

value: sphR mutant


title: PDPN_2

source_name: samid: mbb339_frc_alone


title: LCM_PDPN_cc_2

source_name: samid: mbb339_co_mac


title: L139

value: Short-term carrier


title: SphR-1

extract_protocol:
To examine the effect of TFs (taking an example of RpoN) on the transcriptome, 2 ml of mid-log-phase (OD600 = 0.6) bacterial cultures (PAO1 and rpoN::Tc mutant strains) were collected by centrifugation (12,000 rpm, 4℃). An RNeasy minikit (Qiagen) was used
TruSeq RNA sample prep kit protocol (Illumina)


title: N121

value: Naïve


title: MCF7_BLRP_TEAD4_WT_noDox_ChipSeq


title: L137


title: PDPN_LCM_cc_2

source_name: samid: mbb339_co_frc

value: co


title: VqsR-1

value: mid-log phase liquid culture in LB (Luria-Bertani)  medium


title: MCF7_TEAD4_ICI_ChipSeq

value: ICI

value: TEAD4 (Santa Cruz, sc-101184)


title: LCM_atra_2

source_name: samid: mbb339_atra


title: PDPN_LCM_tw_1

source_name: samid: mbb336_tw_frc

value: tw


title: PhoB-2

source_name: paired-end RNA-seq_P. aeruginosa PAO1 phoB mutant

value: phoB mutant


title: O103


title: RsaL-1

source_name: paired-end RNA-seq_P. aeruginosa PAO1 rsaL mutant

value: rsaL mutant


title: MCF7_YAP1_DMSO_ChipSeq

value: DMSO

value: YAP (Cell Signaling Technology,14074S)


title: PDPN_LCM_cc_1

source_name: samid: mbb336_ptl-om_frc_mac


title: MCF7_YAP1_ICI_ChipSeq

value: Breast cancer cell line


title: PchR-2

source_name: paired-end RNA-seq_P. aeruginosa PAO1 pchR mutant

value: pchR mutant


title: PhoB-1


title: MCF7_ER_ICI_ChipSeq

value: ERalpha (Santa Cruz, sc-7207)


title: L142


title: E

value: Long-term carrier


title: O113


title: MCF7_TEAD4_DMSO_ChipSeq


title: PchR-1


title: LasR-2

source_name: paired-end RNA-seq_P. aeruginosa PAO1 lasR mutant

value: lasR mutant


title: LCM_in_vivo_1

source_name: samid: mbb336_pt_lavage

value: mac


title: MCF7_ER_DMSO_ChipSeq


title: MCF7_MED1_shYAP1_E2_ChipSeq

description:
MCF7_MED1_shYAP1_E2
Cells were infected with YAP1 shRNAs.

value: MED1 (Santa Cruz, sc-74475 and Bethyl laboratories, A300-793A)


title: L141

value: Short-term carrier

value: 726 days post-infection


title: LasR-1

value: mid-log phase liquid culture in LB (Luria-Bertani)  medium


title: RsaL-2


title: MCF7_MED1_shCtrl_E2_ChipSeq

description:
MCF7_MED1_shCtrl_E2
Cells were infected with control shRNAs.

value: Control


title: MCF7_MED1_shYAP1_Veh_ChipSeq

description:
MCF7_MED1_shYAP1_Veh
Cells were infected with YAP1 shRNAs.

value: Veh


title: LCM_in_vitro_1

source_name: samid: mbb336_ptl_alone


title: ZEN_high_j rep4

city: Tulln

first: Bertrand

last: Grenier

address: Technopark 1

department: Research Center

country: Austria

institute: BIOMIN

description:
38j; 5307-036
processed data file: data_ref_5307_Pool2_Jejunum.xlsx

data_processing:
Raw data were de-multiplexed and FASTQ files for each sample were generated using the bcl2fastq software (Illumina)
Total reads were adapter trimmed using Cutadapt and quality filtered (Q-Score > 30) using the FastQC tool v0.10.1
Trimmed and quality filtered reads were aligned to reference microRNA sequences in miRBase release 21 (www.mirbase.org) using bowtie2 v2.2.6. Subsequently, reads were mapped against the Sus scrofa genome assembly Sscrofa10.2 as well as Ensembl small non-coding RNA reference databases
Reads were normalized to the total read count per library to generate tags per million (TPM) values
EdgeR was used for differential expression analysis based on TPM values. The p-values obtained were adjusted for multiple testing using Benjamini-Hochberg false discovery rate (FDR).
Genome_build: Sscrofa10.2
Supplementary_files_format_and_content: abundance measurements & expression analysis

organism: Sus scrofa

extract_protocol:
Approximately 30 mg of tissue were disrupted via a bead-beating step, and the total RNA, including RNA from approximately 18 nucleotides upwards, was extracted and purified with the miRNeasy Mini Kit (Qiagen).
1 µg of total RNA was used for construction of small RNA sequencing libraries with the NEBNext Multiplex Small RNA Library preparation set for Illumina (New England Biolabs Inc.). Adapter ligated total RNA was reverse transcribed into cDNA, which served as template for PCR amplification (15 cycles) using Illumina´s SR Primer and Index Primers 1-18. Barcoded DNA libraries were purified using the QIAQuick PCR purification protocol (Qiagen) and quantified by DNA 1000 high sensitivity chip (Agilent Technologies). Purified samples were pooled at equimolar (50 nM) concentration. Size selection was performed using gel purification to select for insert sizes between 18 and 50 nucleotides.

treatment_protocol: Small pieces of the uterus and the mid-jejunum were dissected, placed into 1 mL of RNAlater (Ambion Inc.), stored overnight at 4 °C, and transferred to -80 °C until transcriptomics analysis

tag: age

value: post weaned day 28

value: 4.58 mg/kg ZEN (ZEN medium) for 28 days

value: jejunum

tag: molecule subtype

value: small RNA


title: GbdR-2

source_name: paired-end RNA-seq_P. aeruginosa PAO1 gbdR mutant

value: gbdR mutant


title: PDPN_BMS_1

source_name: samid: mbb336_bms_frc


title: MCF7_MED1_shCtrl_Veh_ChipSeq

description:
MCF7_MED1_shCtrl_Veh
Cells were infected with control shRNAs.

value: Breast cancer cell line

tag: shRNA


title: GbdR-1


title: GacA-1

source_name: paired-end RNA-seq_P. aeruginosa PAO1 gacA mutant

value: gacA mutant


title: L140

source_name: Ampulla


title: LCM_PDPN_cc_1

source_name: samid: mbb336_ptl-om_frc_frc

value: co


title: L143


title: GacA-2


title: ZEN_high_j rep3

description:
43j; 5307-034
processed data file: data_ref_5307_Pool2_Jejunum.xlsx


title: Spleen_fibroblasts_2

data_processing: Reads were aligned to the GRCm38 genome using Salmon. The Salmon index was created using the parameter, k = 25. Gene models were from our internal database. "nRPKM" normalization was performed. This is similar to "RPKM" normalization but includes an extra step for sizeFactor adjustment and is described in the Methods of the manuscript. Supplementary files use Entrez Gene IDs, counts and nRPKM statistics.

extract_protocol: RNA was isolated from TRIZOL as described (Painter et al., 2011).

value: Spl

tag: region

value: spleen

tag: pdgfra

value: PDGFRApos

tag: gfp

value: GFPneg


title: MCF7_ER_shYAP1_ChipSeq

description:
MCF7_ER_shYAP1
Cells were infected with YAP1 shRNAs.

tag: cell line

value: ERalpha (Santa Cruz, sc-7207)


title: LCM_atra_1

source_name: samid: mbb336_ptl_atra

tag: group

value: mac

tag: mbatch


title: MCF7_ER_shTEAD4_ChipSeq

description:
MCF7_ER_shTEAD4
Cells were infected with TEAD4 shRNAs.


title: L138

value: Short-term carrier

value: 726 days post-infection


title: MCF7_ER_shCtrl_ChipSeq

description:
MCF7_ER_shCtrl
Cells were infected with control shRNAs.

value: Control


title: PDPN_1

source_name: samid: mbb336_frc_alone

tag: rin

tag: condition


title: Spleen_fibroblasts_1


title: FleQ-1

source_name: paired-end RNA-seq_P. aeruginosa PAO1 fleQ mutant

tag: genotype/variation

value: fleQ mutant

tag: sample type

value: mid-log phase liquid culture in LB (Luria-Bertani)  medium


title: ZEN_low_j rep4

description:
50j; 5307-032
processed data file: data_ref_5307_Pool2_Jejunum.xlsx

value: post weaned day 28

tag: treatment

value: 0.17 mg/kg ZEN (ZEN medium) for 28 days

value: jejunum


title: ZEN_medium_j rep4

description:
115j; 5307-033
processed data file: data_ref_5307_Pool2_Jejunum.xlsx

value: 1.46 mg/kg ZEN (ZEN medium) for 28 days

tag: tissue

value: small RNA


title: Control_j rep6

description:
18j; 5307-035
processed data file: data_ref_5307_Pool2_Jejunum.xlsx

value: uncontaminated feed (Control) for 28 days


title: LCM_BMS_1

source_name: samid: mbb336_bms_mac


title: T47D_YAP1_E2_ChIPSeq

tag: cell type

value: Breast cancer cell line

tag: chip antibody

value: YAP (Cell Signaling Technology,14074S)


title: LCM_PDPN_tw_1

source_name: samid: mbb336_tw_mac

value: tw


title: ExsA-2

source_name: paired-end RNA-seq_P. aeruginosa PAO1 exsA mutant

extract_protocol:
To examine the effect of TFs (taking an example of RpoN) on the transcriptome, 2 ml of mid-log-phase (OD600 = 0.6) bacterial cultures (PAO1 and rpoN::Tc mutant strains) were collected by centrifugation (12,000 rpm, 4℃). An RNeasy minikit (Qiagen) was used for subsequent RNA purification with DNaseI (NEB) treatment. After removing rRNA by using the MICROBExpress kit (Ambion), mRNA was used to generate the cDNA library according to the NEBNext® UltraTM II RNA Library Prep Kit protocol (Illumina), which was then sequenced using the Illumina HiSeq 2000. Each sample in RNA-seq assay was repeated twice.
TruSeq RNA sample prep kit protocol (Illumina)

value: exsA mutant


title: ZEN_medium_j rep3

description:
2j; 5307-031
processed data file: data_ref_5307_Pool2_Jejunum.xlsx

tag: age


title: sLN_fibroblasts_2

value: sLN

value: PDGFRApos

value: GFPneg


title: ExsA-1


title: ZEN_medium_j rep2

description:
42j; 5307-030
processed data file: data_ref_5307_Pool2_Jejunum.xlsx

tag: molecule subtype


title: T47D_YAP1_Veh_ChIPSeq

value: Veh


title: T47D_TEAD4_Veh_ChIPSeq

value: TEAD4 (Santa Cruz, sc-101184)


title: sLN_fibroblasts_1


title: Pancreas_fibroblasts_2

value: Panc

value: pancreas


title: Panc_fibroblasts_1


title: T47D_ER_E2_ChIPSeq

value: ERalpha (Santa Cruz, sc-7207)


title: T47D_TEAD4_E2_ChIPSeq


title: ZEN_low_j rep3

description:
136j; 5307-029
processed data file: data_ref_5307_Pool2_Jejunum.xlsx

value: post weaned day 28

value: 0.17 mg/kg ZEN (ZEN medium) for 28 days


title: CdpR-1

source_name: paired-end RNA-seq_P. aeruginosa PAO1 cdpR mutant

value: cdpR mutant

value: mid-log phase liquid culture in LB (Luria-Bertani)  medium


title: ZEN_low_j rep2

description:
45j; 5307-027
processed data file: data_ref_5307_Pool2_Jejunum.xlsx

value: jejunum

value: small RNA


title: AlgR-2

source_name: paired-end RNA-seq_P. aeruginosa PAO1 algR mutant

value: algR mutant


title: Omentum_fibroblasts_3

value: OmAdipose


title: T47D_ER_Veh_ChIPSeq

value: Breast cancer cell line


title: Input2

source_name: Input ChIP-seq_P. aeruginosa PAO1

extract_protocol:
Wild-type P. aeruginosa containing empty pAK1900 or pAK1900-TFs-VSVG/FLAG was cultured in LB medium supplemented with ampicillin until mid-log phase (OD600 = 0.6), then treated with 1% formaldehyde for 10 min at 37℃. Cross-linking was stopped by the addition of 125 mM glycine. Bacterial pellets were washed twice with a Tris buffer (20 mM Tris– HCl [pH 7.5] and 150 mM NaCl), re-suspended in 500 μl IP buffer (50 mM HEPES–KOH [pH 7.5], 150mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS, and mini-protease inhibitor cocktail (Roche), and then subjected to sonication to produce 100–300 bp DNA fragments. Insoluble cellular debris was removed by centrifugation at 4℃ and the supernatant was used as the input sample in IP experiments. Both control and IP samples were washed with protein A beads (General Electric) and then incubated with 50 μl agarose-conjugated anti-VSV antibodies (Sigma) in IP buffer. Washing, crosslink reversal, and purification of the ChIP DNA were conducted as previously described. DNA fragments (150–250 bp) were selected for library construction and sequencing libraries were prepared using the NEXTflex™ ChIP-Seq Kit (Bioo Scientific). The libraries were sequenced using the Illumina HiSeq 2000. All the experiment has two repeats.
TruSeq RNA sample prep kit protocol (Illumina)

value: WT

value: mid-log phase liquid culture in LB (Luria-Bertani) medium

value: ANTI-FLAG M2 Affinity Gel

tag: chip antibody vendor

value: Sigma-Aldrich

tag: chip antibody cat.#

tag: chip antibody lot #


title: Omentum_fibroblasts_2

tag: region

tag: pdgfra

value: PDGFRApos

tag: gfp

value: GFPneg


title: Control_j rep4

description:
8j; 5307-026
processed data file: data_ref_5307_Pool2_Jejunum.xlsx

value: uncontaminated feed (Control) for 28 days


title: MCF7_YAP1_E2_ChIPSeq

tag: cell line

value: YAP (Cell Signaling Technology,14074S)


title: sLN_fibroblasts_3

tag: group

value: sLN


title: ZEN_high_j rep2

description:
85j; 5307-025
processed data file: data_ref_5307_Pool2_Jejunum.xlsx

value: post weaned day 28

value: 4.58 mg/kg ZEN (ZEN medium) for 28 days


title: Omentum_fibroblasts_1


title: CdpR-2

value: cdpR mutant

value: mid-log phase liquid culture in LB (Luria-Bertani)  medium


title: AlgR-1


title: FleQ-2

value: fleQ mutant


title: Input1


title: MCF7_YAP1_Veh_ChIPSeq

value: Veh


title: Control_j rep3

description:
117j; 5307-024
processed data file: data_ref_5307_Pool2_Jejunum.xlsx

value: jejunum

value: small RNA


title: Control_j rep5

description:
3j; 5307-028
processed data file: data_ref_5307_Pool2_Jejunum.xlsx


title: MCF7_TEAD4_E2_ChIPSeq

value: Breast cancer cell line

value: TEAD4 (Santa Cruz, sc-101184)


title: Omentum_mesothelial_cells_3

value: OmAdipose

value: PDGFRAneg


title: MCF7_TEAD4_Veh_ChIPSeq


title: Control_j rep2

description:
116j; 5307-023
processed data file: data_ref_5307_Pool2_Jejunum.xlsx


title: Omentum_mesothelial_cells_2


title: ZEN_low_j rep1

description:
4j; 5307-022
processed data file: data_ref_5307_Pool2_Jejunum.xlsx

value: 0.17 mg/kg ZEN (ZEN medium) for 28 days


title: Input S2 cells

city: Moscow

first: Nadezhda

middle: E

last: Vorobyeva

address: Vavilova 34/5

country: Russia

institute: Institute of Gene Biology RAS

data_processing:
bcl2fastq v2.17.1.14 Conversion Software (Illumina)
ChIP-seq reads were aligned to the dm6 genome by bowtie2 v2.3.4.2 (using UseGalaxy.eu online tools)
Genome_build: dm6 (Drosophila melanogaster Release 6 plus ISO1 MT)
Supplementary_files_format_and_content: BigWig files were generated using  bamCoverage 3.0.2. Scores represent number of reads normalized by the size of the library.

source_name: S2 Schneider cells

growth_protocol: Drosophila Schneider line 2 (S2) cells were maintained at 25°C in the Schneider’s insect medium (Sigma) containing 10% FBS (HyClone).

extract_protocol:
Crosslinking was performed with 1% formaldehyde for 10 min at RT and stopped by adding glycine. After washings, chromatin was lysed in SDS-containing buffer (50 mM HEPESKOH, pH 7.9; 140 mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na deoxycholate, 0.1% SDS) with protease inhibitors cocktail (Roche) and sheared to 500-bp fragments by sonication. Sonicated chromatin was centrifuged twice at 16 000 g for 20 min, and used in immunoprecipitation experiments. For one experiment, about 5 ug of antibodies and 8 uL of MabSelect sepharose (GE healthcare) were taken; BSA were added to a final concentration of 1%. The precipitated chromatin was sequentially washed twice with SDS-containing buffer and with TE buffer (20mM Tris-HCl, pH 8.0; 1mM EDTA). Precipitated chromatin complexes were eluted by sequential incubation in two portions of elution buffer (50mM Tris-HCl, pH 8.0; 1mM EDTA, 1% SDS), 30 min each, at room temperature. The eluted chromatin solution was supplemented with 5 M NaCl (16 uL per 500 uL sample) and incubated at 65°C for 16 h on a thermoshaker for de-crosslinking. De-crosslinked chromatin was subjected to proteinase treatment (3 uL of proteinase K and 5 uL of 0.5M EDTA per 500 uL sample) and incubated at 55°C for 4 h on thermoshaker. DNA was extracted with a phenol/chloroform mixture and precipitated with isopropanol. The precipitate was dissolved in TE buffer and subjected to library preparation.
DNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were co-transfected by expression contructs and pCoBlast plasmid giving blasticidin resistance in 1 to 20 molar ratio using Effectene transfection reagent (Qiagen). Stable cell lines were selected and cultivated in blasticidin-containing S2 medium (20 ug/ml final concentration).

tag: expression of nuclear receptor

value: no stable expression

tag: isoform of nuclear receptor

value: input chromatin (before precipitation)


title: SphR1

data_processing:
ChIP-seq reads were mapped to the P. aeruginosa genomes (NC_002516) using Bowtie (Version 1.2.1.1). Only the uniquely mapped reads were kept for the subsequent analyses. Binding peaks (q < 0.05) were identified using MACS software (version 2.1.0). The P<1e-5 cutoff value was used in peak calling step.
RNA-seq reads were mapped to the P. aeruginosa genomes (NC_002516) using STAR, only the uniquely mapped reads were kept for the subsequent analyses.
The gene differential expression analysis was performed using DESeq2 R package.
Genome_build: P. aeruginosa genomes (NC_002516)
Supplementary_files_format_and_content: xls file containing comparisons between differnt mutant and wild-type, and different narrow peak files (as indicated in the column headers)

source_name: SphR ChIP-seq_P. aeruginosa PAO1

tag: genotype/variation

value: WT

tag: sample type

value: mid-log phase liquid culture in LB (Luria-Bertani) medium

value: ANTI-FLAG M2 Affinity Gel

value: Sigma-Aldrich


title: PhoB2

source_name: PhoB ChIP-seq_P. aeruginosa PAO1


title: ZEN_high_u rep4

description:
38_B; 5307-018
processed data file: data_ref_5307_Pool1_Uterus.xlsx

value: post weaned day 28

tag: treatment

value: 4.58 mg/kg ZEN (ZEN medium) for 28 days

tag: tissue

value: uterus


title: 3xFLAG_EcR

value: 3xFLAG-EcR expression under Act5C promoter

value: Drosophila melanogaster EcR-A isoform full length (1-849 aa)

tag: chip antibody

value: Monoclonal ANTI-FLAG® M2 antibody produced in mouse F3165 (Sigma-Aldrich)


title: ZEN_high_j rep1

description:
99j; 5307-020
processed data file: data_ref_5307_Pool2_Jejunum.xlsx

tag: age

value: jejunum

value: small RNA


title: Mesentery_fibroblasts_2

value: MesAdipose

value: PDGFRApos

value: GFPneg


title: Mesentery_fibroblasts_3


title: Control_j rep1

description:
71j; 5307-019
processed data file: data_ref_5307_Pool2_Jejunum.xlsx

value: uncontaminated feed (Control) for 28 days

tag: molecule subtype


title: ZEN_medium_j rep1

description:
98j; 5307-021
processed data file: data_ref_5307_Pool2_Jejunum.xlsx

value: 1.46 mg/kg ZEN (ZEN medium) for 28 days


title: Mesentery_mesothelial_cells_3

value: PDGFRAneg


title: ZEN_low_u rep4

description:
4; 5307-017
processed data file: data_ref_5307_Pool1_Uterus.xlsx

value: 0.17 mg/kg ZEN (ZEN medium) for 28 days


title: GbdR1

source_name: GbdR ChIP-seq_P. aeruginosa PAO1

value: WT

value: mid-log phase liquid culture in LB (Luria-Bertani) medium

value: ANTI-FLAG M2 Affinity Gel

tag: chip antibody vendor


title: PchR1

source_name: PchR ChIP-seq_P. aeruginosa PAO1

value: Sigma-Aldrich

tag: chip antibody cat.#


title: GbdR2

tag: chip antibody lot #


title: Mesentery_mesothelial_cells_2

tag: region


title: Control_u rep6

description:
18; 5307-015
processed data file: data_ref_5307_Pool1_Uterus.xlsx

value: post weaned day 28

value: uterus


title: SphR2


title: Mesentery_fibroblasts_1

tag: pdgfra


title: FleQ2

source_name: FleQ ChIP-seq_P. aeruginosa PAO1


title: 3xFLAG_ERR

value: 3xFLAG-ERR expression under Act5C promoter

value: Drosophila melanogaster ERR-A isoform full length (1-484 aa)


title: PchR2


title: PhoB1


title: WT_7

data_processing:
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential gene expression analysis was performed through DESeq2 (v1.16.1)
Genome_build: mm10
Supplementary_files_format_and_content: featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.

source_name: primary neurosphere derived from dorsal cortex

growth_protocol: NPCs were isolated from E14.5 mice by dissection of the lateral walls of the lateral ventricles and digested into single cell suspension with Accutase (Sigma). Cells were cultured in DMEM/F12 proliferation medium supplemented with 2% B27 supplement, 20 ng/ml EGF, 20 ng/ml bFGF and 0.2% BSA for proliferation.

extract_protocol:
Neurosphere RNA isolated from the 6th day culturing NPCs dissected from E14.5 mice.
A total amount of 3 µg RNAper sample was used as input material for the RNAsample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

tag: strain

tag: genotype


title: KO_1

value: primary neurosphere derived from dorsal cortex

value: Ash2l cKO


title: ZEN_medium_u rep4

description:
98_B; 5307-016
processed data file: data_ref_5307_Pool1_Uterus.xlsx

value: small RNA


title: KO_2


title: Omentum_mesothelial_cells_1

tag: group

value: OmAdipose

tag: gfp


title: KO_3


title: 3xFLAG_S2 cells

tag: cell line

tag: expression of nuclear receptor

value: no stable expression

tag: isoform of nuclear receptor

value: Monoclonal ANTI-FLAG® M2 antibody produced in mouse F3165 (Sigma-Aldrich)


title: FleQ1

tag: genotype/variation

tag: sample type


title: ZEN_medium_u rep3

description:
42; 5307-014
processed data file: data_ref_5307_Pool1_Uterus.xlsx

tag: treatment

value: 1.46 mg/kg ZEN (ZEN medium) for 28 days

tag: tissue


title: WT_6

tag: age


title: Inguinal_adipose_fibroblasts_2

value: IngAdipose

value: PDGFRApos

value: GFPneg


title: Inguinal_adipose_fibroblasts_1


title: Mesentery_mesothelial_cells_1

value: MesAdipose

value: PDGFRAneg


title: CK-1_HLR11

description:
qscR_RNA_seq_analyzed.XLSX
HLR11

data_processing:
Bacterial RNA-seq reads were mapped to the P. auruginosa genome by using STAR (2.6), with two mismatches allowed
Only the uniquely mapped reads were kept for the subsequent analyses.
The gene differential expression analysis was performed using DESeq2 R package
Genome_build: Pseudomonas aeruginosa PAO1
Supplementary_files_format_and_content: xls file containing comparisons between MvfR, RhlR and QscR mutant and wild-type, respectively

source_name: liquid culture in LB (Luria-Bertani)  medium

extract_protocol:
2 ml of mid-log-phase (OD600= 0.6) bacterial cultures (PAO1 and ∆rpoN strains) were collected by centrifugation (12,000 rpm, 4℃). An RNeasy minikit (Qiagen) was used for subsequent RNA purification with DNaseI (NEB) treatment. After removing rRNA by using the MICROBExpress kit (Ambion), mRNA was used to generate the cDNA library according to the TruSeq RNA sample prep kit protocol (Illumina).
TruSeq RNA sample prep kit protocol (Illumina)

treatment_protocol: grow until mid-log phase in LB

value: WT


title: Control_u rep5

description:
3; 5307-013
processed data file: data_ref_5307_Pool1_Uterus.xlsx

value: post weaned day 28

value: uncontaminated feed (Control) for 28 days

tag: molecule subtype


title: H3K4me3_KO_ChIPSeq

data_processing:
The 150-nt sequence reads generated by Illumina sequencing were mapped to the genome using the Burrows-Wheeler Aligner algorithm with default settings.Only reads that passed Illumina’s purity filter, aligned with no more than 2 mismatches, and mapped uniquely to the mouse genome (mm10) were used in the subsequent analysis
For identifying intervals over input control, the MACS cutoff for the false discovery rate after controlling for significance was P=1×10 –7.
The two main peak callers used at this study are MACS (Zhang et al., Genome Biology 2008, 9:R137) and SICER (Zang et al., Bioinformatics 25, 1952-1958, 2009)
Genome_build: mm10
Supplementary_files_format_and_content: bigWig. Files with extension *.bw. Binary files that can be opened in or uploaded to genome browsers and show the fragment density for 32-nt bins along the genome (“signal map”)

source_name: dorsal cortex

extract_protocol:
Lysates were clarified from sonicated nuclei of E14.5 dorsal cortex and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions

value: dorsal cortex

value: KO

tag: chip antibody