title: 82-Mo-DC: Mon// NK

city: Sao Paulo

first: Maria

middle: A.

last: Clavijo-Salomon

state: SP

address: Av. Prof. Lineu Prestes 1730 Room 254

department: Department of Immunology

country: Brazil

institute: University of Sao Paulo

description: RNA from DCs derived from monocytes primed by autologous NK cells through a transwell membrane

hyb_protocol: Samples were hybridized with Human GeneChip HG-U133_Plus_2 array (Affymetrix) and scanned at the Genomics Laboratory from Frederick National Laboratory for Cancer Research from Leidos Biomedical Research, Inc.

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

data_processing: Raw data were processed with BRB-ArrayTools version 4.5.0 developed by Dr. Richard Simon and the BRB-ArrayTools Development Team. We defined a probeset as present when it had a P value <0.005 using a 2-fold filter.

source_name: Healthy Donor # 82 blood, NK//DC

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

growth_protocol: CD14+ monocytes and NK cells were purified by magnetic separation from PBMC's obtained from healthy donor's blood. Monocytes, NK cells and monocyte-derived dendritic cells were cultured in in RPMI medium containing 10% FBS and 1% antibiotics/antimycotic solution.

extract_protocol: RNA was isolated with the RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions.

treatment_protocol: NK cells were pre-activated using IL-2 and IL-15 for 6 h. Then, were co-cultured with untouched purified CD14+ monocytes at a 5:1 ratio (Mo:NK) for 18 hours in V-bottom 96-well plates. NK-Mo groups were co-cultured having direct cell-to-cell contact. NK//Mo groups were co-cultured through a transwell membrane insert with a pore size of 0.4 μm (Corning®). NK cells were depleted from monocytes by magnetic separation. Monocytes were induced to differentiate into DCs in 96-well flat plates using 50 ng/mL of IL-4 and 50 ng/mL of GM-CSF. DCs were obtained after 5 days. CD14+ monocytes and their subsequent Mo-DCs were purified by cell sorting flow cytometry. Briefly, 3 to 5x10^6 cells from monocytes cultured alone (Mo), co-cultured with NK cells (NK-Mo) or co-cultured through a transwell membrane (NK//Mo) were harvested and stained. Life/Cell blue dye (Invitrogen) was used as a viability marker for both types of cells. For monocytes, a cocktail of FITC-labeled antibodies against human CD3, CD15, CD16, CD19, CD34, CD56, CD66b and CD94 were used as lineage-negative. APC-Cy7-labeled anti-human CD14 was used as a positive marker. For Mo-DCs, a cocktail of FITC-labeled antibodies against human CD3, CD15, CD19, CD34, CD56, CD66b and CD94 were used as lineage-negative. PE-labeled anti-human HLA-DR and CD11c were used as positive markers. 300 000 singlets, alive, lineage-negative, CD14 positive monocytes and 300 000 singlets, alive, lineage negative, HLA-DR, CD11c, double-positive Mo-DCs were sorted in sterile conditions in the MoFlo Astrios (Beckman Coulter, Inc) at 9 – 15°C, at a pressure of 10 – 15 psi and recovered in 1.5 mL Eppendorf tubes containing 400 μL of Buffer RLT (Qiagen) supplemented with 1% β-mercaptoethanol, molecular biology grade (Sigma – Aldrich). Right after recovery, cells were vortexed at maximum speed for 1 minute and frozen at -80°C for subsequent RNA extraction.

tag: individual

value: Healthy Donor # 82 blood

tag: Sex

value: male

value: blood


title: 82-Mo-DC: Mon NK

status: Public on Jul 03 2018

type: RNA

description: RNA from DCs derived from monocytes primed by autologous NK cells through direct cell-to-cell contact

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Healthy Donor # 82 blood, NK-DC

tag: tissue

tag: cell type


title: 82-Mon: Mon NK

description: RNA from monocytes primed by autologous NK cells through direct cell-to-cell contact

source_name: Healthy Donor # 82 blood, NK-Mo


title: 3C_WT_VH81Xbait_set8

type: SRA

city: BOSTON

first: Suvi

last: Jain

state: MA

address: 300 LONGWOOD AVE

department: Molecular Medicine

country: USA

institute: Boston Children's Hospital

library_source: genomic

data_processing:
library strategy: 3C-HTGTS
Standard basecalling formats for Miseq reads
Miseq reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (http://code.google.com/p/eautils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
Reads were mapped to the AJ851868/mm9 hybrid reference genome (Lin et al., 2016) in which Chr12 coordinates from 114671120 to 114734564 were replaced with CCCCT to incorporate the DHFL16.1 to JH4 rearrangement, using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) with the top fifty alignments reported that had an alignment score above 50, representing a perfect 25nt local alignment.
We used a best-path searching algorithm to select the optimal sequence of alignments that describe the read’s composition. Aligned reads were filtered on the following conditions: (1) reads must include both a bait alignment and a prey alignment and (2) the bait alignment cannot extend more than 10 nucleotides beyond the targeted site. For vector controls and offset nicking with multiple sites, the longest targeted site was used.
We compared discarded alignments to the selected prey alignment; if any of the discarded alignments surpassed both a coverage and score threshold with respect to the prey alignment, the read was filtered due to low mapping quality.
To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer.
Post-filter stringency was applied to remove background-prone junctions with gaps larger than 30nt and bait sequences shorter than 50nt.
Genome_build: AJ851868/mm9 hybrid genome (Lin et al., 2016). Chr12 coordinates from 114671120 to 114734564 were replaced with CCCCT to incorporate the DHFL16.1 to JH4 rearrangement, if using DHFL16.1JH4 line or its derivatives.
Supplementary_files_format_and_content: Bedgraph file type that allows display of continuous-valued data in track format from bed file. Contains header line with track type, file name, visibility level, and RGB color levels. Also, the following tab delimited information succeeding the header line: chromosome, start coordinate, end coordinate, number of junctions at the start and end coordinates.

molecule: genomic DNA

organism: Mus musculus

extract_protocol:
10 million cells were crosslinked with 2% (v/v) formaldehyde for 10’ at room temperature, followed by quenching with glycine at a final concentration of 125 mM. Cells were lysed in 50 mM Tris-HCl, pH 7.5, containing 150 mM NaCl, 5 mM EDTA, 0.5% NP-40, 1% TritonX-100 and protease inhibitors (Roche, #11836153001). Nuclei were digested with 700 units of NlaIII (NEB, #R0125) or MseI (NEB, #R0525) restriction enzyme at 37℃ overnight, followed by ligation under dilute conditions at 16℃ overnight. Crosslinks were reversed and samples were treated with Proteinase K (Roche, #03115852001) and RNase A (Invitrogen, #8003089) prior to DNA precipitation. The 3C DNA thus obtained was use dto prepare HTGTS libraries.
Libraries were prepared using 3C samples by HTGTS.

value: v-Abl kinase transformed pro-B cell

tag: genotype/variation

tag: bait region

tag: restriction enzyme

value: NlaIII

tag: alignment genome

value: DHFL16.1JH4 AJ851868/mm9 hybrid genome

tag: growth conditions


title: 3C_IGCR1del_VH81X-CBEdel_VH81Xbait_set8

value: Rag2-/- IGCR1del VH81X-CBEdel


title: 77-Mo-DC: Mon// NK

source_name: Healthy Donor # 77 blood, NK//DC

value: Healthy Donor # 77 blood

value: DCs derived from monocytes primed by autologous NK cells through a transwell membrane


title: 82-Mon: Mon//NK

description: RNA from monocytes primed by autologous NK cells through a transwell membrane

source_name: Healthy Donor # 82 blood, NK//Mo


title: 82-Mo-DC: Mon Unt

description: RNA from DCs derived from untouched control monocytes

source_name: Healthy Donor # 82 blood, DC


title: 82-Mon: Mon Unt

description: RNA from untouched control monocytes

source_name: Healthy Donor # 82 blood, Mo

value: untouched control monocytes


title: 3C_IGCR1del_VH81X-CBEdel_VH81Xbait_set7


title: 3C_VH5-1-CBEins_VH5-1bait_set6

value: Rag2-/- VH5-1-CBEins

value: MseI


title: 3C_WT_VH81Xbait_set7


title: 3C_IGCR1del_VH81Xbait_set7

value: Rag2-/- IGCR1del


title: 3C_WT_VH5-1bait_set5


title: 3C_IGCR1del_VH81Xbait_set8


title: 3C_WT_VH5-1bait_set6


title: 3C_VH5-1-CBEins_VH5-1bait_set5


title: 3C_WT_VH2-2bait_set4


title: 3C_VH2-2-CBEscr_VH2-2bait_set3

value: Rag2-/- VH2-2-CBEscr


title: 3C_VH2-2-CBEscr_VH2-2bait_set4


title: 77-Mo-DC: Mon Unt

source_name: Healthy Donor # 77 blood, DC

value: DCs derived from untouched control monocytes


title: 77-Mon: Mon NK

source_name: Healthy Donor # 77 blood, NK-Mo

value: monocytes primed by autologous NK cells through direct cell-to-cell contact


title: 3C_WT_VH2-2bait_set3


title: 77-Mo-DC: Mon NK

source_name: Healthy Donor # 77 blood, NK-DC

value: DCs derived from monocytes primed by autologous NK cells through direct cell-to-cell contact


title: 77-Mon: Mon//NK

source_name: Healthy Donor # 77 blood, NK//Mo

value: monocytes primed by autologous NK cells through a transwell membrane


title: 74-Mon: Mon Unt

description: RNA from untouched control monocytes

source_name: Healthy Donor # 74 blood, Mo

value: Healthy Donor # 74 blood

value: male


title: 77-Mon: Mon Unt

description: RNA from untouched control monocytes

source_name: Healthy Donor # 77 blood, Mo

value: blood


title: 74-Mo-DC: Mon NK

source_name: Healthy Donor # 74 blood, NK-DC


title: 74-Mon: Mon//NK

source_name: Healthy Donor # 74 blood, NK//Mo


title: 74-Mo-DC: Mon// NK

source_name: Healthy Donor # 74 blood, NK//DC


title: 73-Mo-DC: Mon// NK

source_name: Healthy Donor # 73 blood, NK//DC

value: Healthy Donor # 73 blood


title: 3C_VH81X-CBEinv_VH81Xbait_set1

value: v-Abl kinase transformed pro-B cell

value: Rag2-/- VH81X-CBEinv

value: NlaIII

value: DHFL16.1JH4 AJ851868/mm9 hybrid genome


title: 74-Mo-DC: Mon Unt

source_name: Healthy Donor # 74 blood, DC


title: 3C_VH81X-CBEinv_VH81Xbait_set2


title: 3C_VH81X-CBEdel_VH81Xbait_set2

value: Rag2-/- VH81X-CBEdel


title: 3C_VH81X-CBEdel_VH81Xbait_set1


title: 3C_WT_VH81Xbait_set2


title: DJ_IGCR1del_VH81X-CBEdel_rep4

data_processing:
Library strategy: HTGTS
Standard basecalling formats for Miseq reads
Miseq reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (http://code.google.com/p/eautils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
Reads were mapped to the AJ851868/mm9 hybrid reference genome (Lin et al., 2016) using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) with the top fifty alignments reported that had an alignment score above 50, representing a perfect 25nt local alignment.
We used a best-path searching algorithm to select the optimal sequence of alignments that describe the read’s composition. Aligned reads were filtered on the following conditions: (1) reads must include both a bait alignment and a prey alignment and (2) the bait alignment cannot extend more than 10 nucleotides beyond the targeted site. For vector controls and offset nicking with multiple sites, the longest targeted site was used.
We compared discarded alignments to the selected prey alignment; if any of the discarded alignments surpassed both a coverage and score threshold with respect to the prey alignment, the read was filtered due to low mapping quality.
To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer.
Post-filter stringency was applied to remove background-prone junctions with gaps larger than 30nt and bait sequences shorter than 50nt.
Genome_build: AJ851868/mm9 hybrid genome (Lin et al., 2016)
Supplementary_files_format_and_content: tab delimited text files contain all filtered junctions including duplicates and include the following information: sequence ID (Qname); prey chromosome (Rname), prey junction coordinate (Junction), chromosome orientation of prey junction (Strand), beginning (Rstart) and end (Rend) nucleotide position of prey junction aligning to the genome build; bait chromosome (B_Rname); beginning (B_Rstart) and end (B_Rend) nucleotide position of the bait junction; chromosome orientation of the bait junction (B_Strand); position on the read where the bait sequence begins (B_Qstart) and ends (B_Qend); position on the read where the prey junction begins (Qstart) and ends (Qend); the length of the combined and stitched paried end read (Qlen); the entire stitched paired end read sequence (Seq); the sequence in the + orientation at the junction (J_seq); and the experiment associated with the read (Library)

source_name: v-Abl kinase transformed pro-B cell

extract_protocol:
DNA was extracted overnight at 55 degree Celcius in a lysis buffer containing: 200mM NaCl, 0.4% SDS, 100mM Tris-HCl pH7.5, 5mM EDTA pH8.0, 200ug/mL proteinase K, prior to DNA fragmentation
Translocation libraries were prepared using HTGTS.

treatment_protocol: 10 million v-Abl transformed pro-B cells were cultured in R-15 medium containing 3 mM STI-571 for 4 days.

tag: genotype

value: IGCR1del VH81X-CBEdel

tag: treatment protocol

value: 3 mM STI-571 to induce G1 arrest

value: JH4 coding end


title: DJ_IGCR1del_VH81X-CBEdel_rep3


title: DJ_IGCR1del_VH81X-CBEdel_rep2


title: 3C_WT_VH81Xbait_set1


title: DJ_IGCR1del_VH81X-CBEdel_rep1


title: 73-Mo-DC: Mon NK

source_name: Healthy Donor # 73 blood, NK-DC


title: 74-Mon: Mon NK

source_name: Healthy Donor # 74 blood, NK-Mo


title: 73-Mon: Mon NK

source_name: Healthy Donor # 73 blood, NK-Mo


title: DJ_IGCR1del_rep1


title: 73-Mo-DC: Mon Unt

source_name: Healthy Donor # 73 blood, DC


title: DJ_IGCR1del_rep2


title: DJ_IGCR1del_rep3


title: 73-Mon: Mon Unt

description: RNA from untouched control monocytes

source_name: Healthy Donor # 73 blood, Mo

value: untouched control monocytes


title: 70-Mo-DC: Mon// NK

source_name: Healthy Donor # 70 blood, NK//DC

value: Healthy Donor # 70 blood

value: DCs derived from monocytes primed by autologous NK cells through a transwell membrane


title: 73-Mon: Mon//NK

source_name: Healthy Donor # 73 blood, NK//Mo


title: 70-Mo-DC: Mon NK

source_name: Healthy Donor # 70 blood, NK-DC

value: DCs derived from monocytes primed by autologous NK cells through direct cell-to-cell contact


title: DJ_VH5-1-CBEins_rep4


title: 70-Mo-DC: Mon Unt

source_name: Healthy Donor # 70 blood, DC

value: DCs derived from untouched control monocytes


title: DJ_VH5-1-CBEins_rep3


title: DJ_VH5-1-CBEins_rep2


title: 70-Mon: Mon//NK

source_name: Healthy Donor # 70 blood, NK//Mo

value: monocytes primed by autologous NK cells through a transwell membrane


title: null ovaries at 4-6 hours post-eclosion, replicate 4

city: Iowa City

first: Alexey

middle: A

last: Soshnev

state: Iowa

address: 3159C MERF 375 Newton Rd

department: Biochemistry

institute: University of Iowa

hyb_protocol: Biotin-labeled cDNA was mixed with Affymetrix hybridization buffer, placed onto Drosophila 2.0 arrays (Cat #900532), and incubated at 45º C for 18 h with 60 rpm rotation in Affymetrix Model 640 GeneChip Hybridization Oven.  Following hybridization, arrays were washed and stained with streptavidin-phycoerythrin (Molecular Probes). Signal was amplified with anti-streptavidin antibody (Vector Laboratories), followed by staining with streptavidin-phycoerythrin (Molecular Probes) using the Affymetrix Model 450 Fluidics Station (Affymetrix).

scan_protocol: Arrays were scanned with the Affymetrix Model 3000 scanner with 7G upgrade.

data_processing: CEL files were processed using Affymetrix Expression Console version 1.4.1, using default settings and RMA algorithm normalization.

organism: Drosophila melanogaster

source_name: Drosophila virgin female ovaries dissected 4-6 hours post-eclosion

label_protocol: Fifty nanograms of total RNA was converted to cDNA using the Ovation RNA Amplification System v2 (NuGEN). The cDNA product was purified using QIAquick PCR Purification column (Qiagen) and 3.75 µg were fragmented to an average size of 85 bases and biotin labeled using the FL-Ovation cDNA Biotin Module (NuGEN) per the manufacturer’s protocol.

growth_protocol: Flies were raised at 25ºC, 70% humidity on standard cornmeal/agar medium supplemented with yeast.

extract_protocol: Total RNA was isolated from approximately 100 pairs of frozen ovaries per biological replicate using TRIzol reagent (Invitrogen), treated with DNaseI (Qiagen DNaseI) and purified using RNeasy columns (Qiagen) according to the manufacturer instructions.

treatment_protocol: Ovaries were dissected in PBS and stored at -80C until RNA isolation

value: otefinPk, Chk2P6 / otefinG

tag: age

value: 4-6 hours post-eclosion

value: ovary


title: DJ_VH2-2-CBEscr_rep4

value: v-Abl kinase transformed pro-B cell


title: null ovaries at 4-6 hours post-eclosion, replicate 1

value: otefinPk, Chk2P30 / otefinG


title: null ovaries at 4-6 hours post-eclosion, replicate 3


title: DJ_VH5-1-CBEins_rep1


title: 70-Mon: Mon Unt

description: RNA from untouched control monocytes

source_name: Healthy Donor # 70 blood, Mo

value: male

value: blood


title: null ovaries at 4-6 hours post-eclosion, replicate 2


title: het ovaries at 4-6 hours post-eclosion, replicate 3

value: otefinPk, Chk2P6 / CyO


title: het ovaries at 4-6 hours post-eclosion, replicate 4


title: DJ_VH2-2-CBEscr_rep2


title: RNA-seq_seb1-1_rep2

city: San Francisco

first: Hiten

last: Madhani

state: CA

department: Department of Biochemistry and Biophysics

institute: University of California, San Francisco

library_source: transcriptomic

data_processing:
RNA-Seq data were aligned using Topha and indexed, sorted bam files were created.
Analysis of aligned reads was conducted using DEseq2.
Changes in transcript expression levels required >2-fold change in mutants compared to wildtype to be considered significantly changed enough to have a functional consequence.
Genome_build: Schizosaccharomyces_pombe.ASM294v2.20.dna.AB325691.fa from Pombase.org
Supplementary_files_format_and_content: .csv data showing fold expression changes in genes and their p-values of compared samples.

organism: Schizosaccharomyces pombe

source_name: Yeast Cell

extract_protocol:
RNA was isolated by bead beating with 0.5mm zerconia bead in Trizol reagent (Thermo Fisher) and purifying by chloroform extraction.
1g of total RNA was used to isolate mRNA using PolyATtract® Systems III and IV (Promega). Samples were Dnase treated using the Zymo RNA Clean & Concentrator Kit 5® (Zymo Research). Sequencing libraries were constructed using the NEBNext Ultra Directional RNA library Prep Kit for Illumina (New England Biolab).

tag: strain


title: DJ_Intergenic-del_VH81X-CBEdel_rep5

value: Intergenicdel VH81X-CBEdel


title: DJ_VH2-2-CBEscr_rep1

value: 3 mM STI-571 to induce G1 arrest


title: hsl2_rep_2

city: Zürich

first: Andreas

last: Kopf

address: Auguste-Piccard-Hof 1

department: Biology

country: Switzerland

institute: ETH Zürich

data_processing:
The single-end reads that passed Illumina filters were quality filtered and trimmed using Trimmomatic (v0.33).
Read alignment was perfomed using the STAR-aligner (v.2.5.1b) against Araport11 with the genome anntotation downloaded on 2016-09-01
Gene quantification was performed using the featureCount function in the R-package Rsubreads (v1.22.3)
Genome_build: Araport11
Supplementary_files_format_and_content: text files holding gread counts per gene

organism: Arabidopsis thaliana

source_name: 0.5mm outermost tip of primary root 7 days after germination

growth_protocol: 7 days  on vertical agar plartes; Agar plates: 1/s MS without sucrose 1% agar; Long days (16h light, 8 h dark)

extract_protocol:
Trizol/chloroform extraction follow by purification using the RNeasy Plant Mini Kit
RNA libraries were prepared for sequencing using the standard Illumina Truseq v3 stranded protocol.

value: Root tip

tag: ecotype


title: DJ_VH2-2-CBEscr_rep3

value: JH4 coding end


title: hsl2_rep_3


title: Col-0_rep_3

value: wild type


title: hsl2_rep_1


title: DJ_Intergenic-del_VH81X-CBEdel_rep4


title: Col-0_rep_2


title: het ovaries at 4-6 hours post-eclosion, replicate 1

value: otefinPk, Chk2P30 / CyO


title: Col-0_rep_1


title: DJ_Intergenic-del_VH81X-CBEdel_rep3


title: DJ_Intergenic-del_VH81X-CBEdel_rep2


title: RNA-seq_seb1-1_rep1


title: RNA-seq_epe1KO_tfs1DN_rep2

value: epe1delta tfs1DN


title: het ovaries at 4-6 hours post-eclosion, replicate 2


title: RNA-seq_epe1KO_rep1


title: 70-Mon: Mon NK

source_name: Healthy Donor # 70 blood, NK-Mo

value: Healthy Donor # 70 blood

value: monocytes primed by autologous NK cells through direct cell-to-cell contact


title: RNA-seq_epe1KO_tfs1DN_rep1


title: DJ_Intergenic-del_VH81X-CBEdel_rep1


title: NET-seq_clr4KO_seb1-1_rep2

description: RNA Polymerase II Associated RNA

data_processing:
Adapter sequences were removed (using ATCTCGTAT) and reads were flattened to remove sequence duplicates.
Barcoded reads were then mapped to the S. pombe genome using Bowtie1 to remove any misprimed RT sequences.
Unaligned files were collected for further analysis. Barcodes were removed, and the new unique, debarcoded reads were realigned to the genome using bowtie.
Indexed, sorted bam files were created for each dataset using SAMtools and bedgraph files were created using BEDTools. Stranded bedgraphs were created that present only the 5' nt in the read (representing the 3'nt in the RNA we isolated) on each strand.
Genome_build: Schizosaccharomyces_pombe.ASM294v2.20.dna.AB325691.fa from Pombase.org
Supplementary_files_format_and_content: Bedgraphs showing the strandedness of the reads and only presenting the 5'nt of the read which represents the 3'nt of the isolated RNA.

extract_protocol:
RNA was extracted from S. pombe by ball mill (5x 3min 15Hz). RNA was isolated using Anti-FLAG M1 Agarose Affinity Gel (Sigma) and purified using the miRNeasy Mini Kit (Qiagen).
Adaptor ligation was performed using random hexamer-barcoded adaptors and T4 RNA Ligase 2 Truncated K227Q. Samples were subjected to alkaline fragmentation. cDNA was prepared using Superscript III (Thermo Fisher) and circularized by CircLigase (Epicenter). The circularized cDNA was then PCR amplified to obtain our final libraries.
NET-Seq

value: rpb3xFLAG clr4delta seb1-1

tag: temperature


title: RNA-seq_WT_rep1

value: WT


title: DJ_Intergenic-del_rep2

value: Intergenicdel


title: RNA-seq_epe1KO_rep2


title: DJ_VH81X-CBEdel_rep2

value: v-Abl kinase transformed pro-B cell


title: DJ_Intergenic-del_rep1


title: NET-seq_clr4KO_seb1-1_rep1

description: RNA Polymerase II Associated RNA


title: NET-seq_clr4KO_tfs1DN_rep2

description: RNA Polymerase II Associated RNA

value: rpb3xFLAG clr4delta tfs1DN


title: DJ_VH81X-CBEdel_rep3


title: NET-seq_clr4KO_tfs1DN_rep1

description: RNA Polymerase II Associated RNA


title: DJ_VH81X-CBEdel_rep1


title: DJ_WT_rep3


title: DJ_Intergenic-del_rep3


title: DJ_WT_rep1


title: NET-seq_clr4KO_rep2

description: RNA Polymerase II Associated RNA

value: rpb3xFLAG clr4delta


title: DJ_WT_rep2


title: RNA-seq_WT_rep2


title: NET-seq_clr4KO_rep1

description: RNA Polymerase II Associated RNA


title: pro-B_VH81X-CBEscr/scr_rep4

data_processing:
Library strategy: HTGTS
Standard basecalling formats for MiSeq reads.
MiSeq reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (http://code.google.com/p/eautils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep), respectively.
Reads were mapped to the AJ851868/mm9 hybrid reference genome (Lin et al., 2016) using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) with the top fifty alignments reported that had an alignment score above 50, representing a perfect 25nt local alignment.
We used a best-path searching algorithm to select the optimal sequence of alignments that describe the read’s composition. Aligned reads were filtered on the following conditions: (1) reads must include both a bait alignment and a prey alignment and (2) the bait alignment cannot extend more than 10 nucleotides beyond the targeted site. For vector controls and offset nicking with multiple sites, the longest targeted site was used.
We compared discarded alignments to the selected prey alignment; if any of the discarded alignments surpassed both a coverage and score threshold with respect to the prey alignment, the read was filtered due to low mapping quality.
To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer.
Post-filter stringency was applied to remove background-prone junctions with gaps larger than 30nt and bait sequences shorter than 50nt.
Genome_build: AJ851868/mm9 hybrid genome (Lin et al., 2016)
Supplementary_files_format_and_content: Tab-delimited text files contain filtered junctions including duplicates and include the following information: sequence ID (Qname); prey chromosome (Rname), prey junction coordinate (Junction), chromosome orientation of prey junction (Strand), beginning (Rstart) and end (Rend) nucleotide position of prey junction aligning to the genome build; bait chromosome (B_Rname); beginning (B_Rstart) and end (B_Rend) nucleotide position of the bait junction; chromosome orientation of the bait junction (B_Strand); position on the read where the bait sequence begins (B_Qstart) and ends (B_Qend); position on the read where the prey junction begins (Qstart) and ends (Qend); the length of the combined and stitched parried end read (Qlen); the entire stitched paired end read sequence (Seq); the sequence in the + orientation at the junction (J_seq); and the experiment associated with the read (Library).

source_name: Bone marrow pro-B cells

extract_protocol:
DNA was extracted overnight at 55 degree Celsius in a lysis buffer containing: 200mM NaCl, 0.4% SDS, 100mM Tris-HCl pH7.5, 5mM EDTA pH8.0, 200ug/mL proteinase K, prior to DNA fragmentation.
Translocation libraries were prepared using HTGTS.

tag: strain/background

value: 4-6 weeks

value: Bone marrow pro-B cells

tag: markers for facs sorting


title: Primary_2.2

city: West Lafayette

first: Nathaniel

middle: Wesley

last: Mabe

state: Indiana

address: 201 S. University St.

department: Medicinal Chemistry and Molecular Pharmacology

institute: Purdue University

hyb_protocol: Hybridization targets were prepared from total RNA using a MessageAmp Premier RNA Amplification Kit (Applied Biosystems/Ambion, Austin, TX, USA), hybridized to GeneChip™ Mouse 430A Plus 2.0 Array (Affymetrix, Santa Clara, CA, USA) in an Affymetrix GeneChip hybridization Oven 645, washed in Affymetrix GeneChip Fluidics Station 450, and scanned with Affymetrix GeneChip Scanner 7G according to standard Affymetrix GeneChip hybridization, wash, and stain protocols.

scan_protocol: Affymetrix scanning protocol according to manufacturer, Affymetrix GeneChip Command Console Scan Control 3.2.3.1515 and Expression Console version 1.2.0.20

data_processing: CEL files were uploaded into simpleaffy package in R software and GC-RMA normalized. Differential gene expression analysis was determined with limma package in R software, and annotated with annotate package.

label_protocol: Ambion MessageAmp Premier labeling

growth_protocol: Cell lines were grown to ~80% confluence in standard media prior to RNA harvesting.

extract_protocol: Total RNA was extracted according to manufacturer's protocol (Qiagen).

treatment_protocol: Cells were untreated, parental tumor cell lines of low passage.

tag: cell line

value: MTB;TAN-derived tumor cell line 2, parental primary


title: pfs2_input_rep2

data_processing:
ChIP-Seq data were Stripped of adaptor sequences (GATCGGAAGA) and aligned using Bowtie1, allowing up to two mismatches.
Indexed, sorted bam files were created for each dataset using SAMtools and bedgraph files were created using BEDTools.
Bedgraph files were further processed by smoothing over a 1KB window.  Background H3K9me levels were calculated and defined as average coverage in all regions of the genome excluding the 80 kb adjacent to each chromosome end and the centromeric regions. Peaks wer then called as having a singla at least 3 times higher than the background.
Genome_build: Schizosaccharomyces_pombe.ASM294v2.20.dna.AB325691.fa from Pombase.org
Supplementary_files_format_and_content: Bedgraphs represent aligned, not normalized, read densities. .csv list regions in the gneome that had 3 fold higher H3K9me signal than background.

extract_protocol:
ChIP DNA was extracted by bead beater with 0.5mm zirconia beads.  ChIP DNa was isolated by antibodies directed to our protein of interest (H3K9me2 or rpb3x-FLAG).  DNA was then isolated by incubation by SDS/proteinase K followed by column purification (Macherey-Nagel Nucleospin Gel Cleanup Columns).
Libraries were prepared using End-It DNA End Repair Kit (Epicenter) followed by A-tailing using Klenow fragment (NEB), ligation to Illumina adaptors using Rapid T4 DNA Ligase (Enzymatics), PCR amplification for 15 cycles, and size selection between 200-350bp by bead purification and gel extraction.


title: Primary_1.1

value: MTB;TAN-derived tumor cell line 1, parental primary


title: Recurrent_1.1

value: MTB;TAN-derived tumor cell line 1, parental recurrent


title: Recurrent_2.1

value: MTB;TAN-derived tumor cell line 2, parental recurrent


title: Recurrent_1.2


title: Primary_2.1


title: Recurrent_2.2


title: Primary_1.2


title: pfs2-11_rep2

description:
paired with  pfs2_input_rep2
Parent =  pfs2_wt_parent_rep2

tag: antibody

value: Anti-H3K9me2 (abcam ab1220)


title: Healthy individual-8

city: Chengdu

first: Bai

last: Hao

state: Sichuan

address: Wuhou District Guoxue Lane 37

department: Laboratory Medicine

country: China

institute: West China Hospital of Sichuan University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 48°C and 60 rpm on Affymetrix GeneChip miRNA Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Healthy individual_exosomal miRNA

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: The whole blood was collected from participants and centrifuged for plasma isolation within 2 h. And the serums were stored at -80°C.

extract_protocol: Exosomal RNAs were extracted by the miRNeasy Serum/Plasma Advanced Kit according to the manufacturer's instructions.

treatment_protocol: Exosomes were extracted from plasma using the ExoQuick Plus kit (System Biosciences, USA). Transmission electron microscopy (TEM), nanoparticle tracking analysis (NTA), and Western blotting were utilized to confirm the presence of exosomes.

tag: subject status

value: healthy control (HC)

tag: gender

value: Female

tag: tissue

value: Peripheral blood

tag: molecule source

value: exosomes extracted from plasma


title: pro-B_VH81X-CBEscr/scr_rep2

tag: genotype/variation

tag: bait region

value: JH4 coding end


title: pro-B_WT_rep2

value: WT


title: pro-B_WT_rep3


title: pro-B_VH81X-CBEscr/scr_rep1


title: pfs2_wt_parent_rep2

description: paired with  pfs2_input_rep2


title: pro-B_VH81X-CBEscr/scr_rep3


title: pfs2-11

description: paired with  pfs2_input


title: Healthy individual-6


title: Healthy individual-7


title: Healthy individual-2


title: Healthy individual-1

value: Male


title: Healthy individual-3


title: Healthy individual-5


title: TBM patient-4

source_name: TBM patient_exosomal miRNA

value: Tuberculosis (TB) patient

tag: tb subgroup

value: the most lethal (TBM) forms


title: Healthy individual-4


title: pfs2_wt_parent

description: paired with  pfs2_input


title: TBM patient-3


title: TBM patient-2


title: pfs2_input

description: Parent =  pfs2_wt_parent


title: seb1-1_epe1KO_tfs1DN_input


title: pro-B_WT_rep1


title: seb1-1_epe1KO_tfs1DN_9

description:
paired with  seb1-1_epe1KO_tfs1DN_input
Parent =  seb1-1_epe1KO_parent

value: seb1-1 epe1delta tfs1DN


title: seb1-1_epe1KO_tfs1DN_7


title: BMM_LPS_MeAC_sample3

city: San Diego

first: Chi-Yeh

last: Chung

address: 10770 Science Center Drive

institute: Pfizer Inc.

description:
KD_13
BMM_LPS_MeAC_3
processed data file: Table_7.xls

data_processing:
Sequencing reads were quality checked with FastQC and mapped to the mouse genome (mm9) using Hisat2. Transcript assembly and quantification were performed by Stringtie and Ballgown. Gene expression distribution between samples was checked to ensure similar transcriptome quality. Genes that have RPKM variance across samples < 1 were first removed to exclude non-expressed genes. The RPKM values were then log2 transformed and quantile normalized with the R package preprocessCore. Differential expression analysis between tuft and non-tuft epithelial cells was performed with empirical Bayes shrinkage and moderated t-test using the Limma package and p values were converted into false discovery rates (FDR) using the Benjamini-Hochberg procedure.
Genome_build: mm9
Supplementary_files_format_and_content: Quantile normalized log2(RPKM+1) value for each sample

molecule: polyA RNA

growth_protocol: Bone marrow-derived macrophages (BMM) were generated from bone marrow extracted from the femurs of male CD1 mice as previously described (Ali, W. H. et al., 2013).  Briefly, femurs were extracted and cleaned.  Both ends of the bone were removed with scissors and flushed with a 22-gauge needle containing extraction media (DMEM containing FBS) into a petri dish.  Cells were washed twice with extraction media and incubated in BMM high media containing DMEM, FBS, sodium pyruvate, supernatant from L-929 cells (L-sup) and penicillin/streptomycin, which was changed day 3 post-isolation.

extract_protocol:
Pancreatic tuft cells were isolated from 3, 8-9 month old KC PanIN-bearing mice.  The pancreas was quickly dissected, minced in 5 ml of DMEM with FBS and allowed to incubate at room temperature for 2 min.  Supernatant and fat were removed and pancreatic tissue was then incubated in 10 ml DMEM supplemented with 1 mg/ml collagenase I (Sigma), 1 mg/ml soybean trypsin inhibitor (Gibco), 1.5 mg/ml hyaluronidase (Sigma), and 250 μl of DNAse I, shaking gently at 37°C for a maximum of 30 min.  Digestion was monitored and tissue was further digested mechanically by pipetting.  Digested tissue was passed through a 100 μm filter, washed with FACS buffer (PBS, 1 mM EDTA, 0.5% BSA) containing DNase I, and incubated with ACK lysing buffer (Gibco) to remove red blood cells before staining for FACS.
Intestinal tuft cells were isolated as previously described from 3 wild-type littermate mice from our KC colony.  Briefly, the proximal 5 cm of the murine small intestine was dissected, flushed, cut longitudinally, and rinsed to remove luminal contents.  Segments were incubated in a 37°C shaker for 20 min in 5 ml PBS containing 2.5 mM EDTA, 0.75 mM dithiothreitol (DTT), and 10 μg/ml DNaseI.  Tissues were shaken vigorously for 30s, large pieces of intestinal wall were removed, and cells were spun down at 4°C, 1200 rpm, for 5 min.  Supernatant was removed and cells were re-suspended in 5 ml HBSS with 1.0 U/ml Dispase and 10μg/ml DNAse I, shaking for 10 min.  Digested cells were passed through a 100 μm filter and incubated with ACK lysing buffer.
Single cell suspensions were incubated on ice with mouse Fc receptor block (BD Biosciences, 1:200) followed by antigen-specific antibodies in FACS buffer.  DAPI (molecular probes, 1:1000) and Annexin V (Biolegend, Pacific Blue conjugate at 1:200) were used to exclude dead and dying cells.  Cells were labeled with Cd45 (Alexa Fluor 488), EpCAM (Alexa Fluor 647), and Siglec F (PE) (Biolegend, 1:200).  Fluorescence Minus One (FMO) staining controls were included for gating populations of interest. Cells were FACS purified at the Salk Institute’s Flow Cytometry core facility on a BD Biosciences Influx cell sorter (100-µm size nozzle, 1 x PBS sheath buffer with sheath pressure set to 20 PSI). Cells were sorted in 1-drop Single Cell sort mode for counting accuracy; these were deposited directly into lysis buffer composed of DNase/RNase-free water, Triton X-100, and Ribolock (Thermo Fischer) in a 96 well plate.
Low input bulk RNA sequencing (RNA-seq) on intestinal and pancreatic tuft cells was performed using the Smart-Seq2 protocol as previously described. In brief, three biological replicates, each with 100 tuft cells from an individual mouse, were sorted directly into 2 μl of Smart-Seq2 lysis buffer. Full-length cDNA was generated, and size distribution was checked with Agilent TapeStation 4200 to ensure RNA quality. cDNA were then amplified with 18-24 PCR cycles, tagmentated, and amplified again with 10 PCR cycles using a Nextera XT kit (Illumina FC-131-1096). The sequencing library was purified with AMPure XP beads.
For sequencing of macrophages, RNA quality was assessed using the Agilent TapeStation 4200 and RNA-Seq libraries were prepared using the TruSeq stranded mRNA Sample Preparation Kit v2 according to Illumina protocols.
SmartSeq2 (Picelli et al., 2014) or TruSeq stranded mRNA Sample Preparation Kit v2.

treatment_protocol: To induce M1 polarization, macrophages were treated with 100 ng/ml LPS for 4 hours prior to control (MeOAc) or PGD2 treatment (10uM).  Cells were collected 24 hrs later in Trizol for RNA-sequencing.  A minimum of 3 biological replicates was analyzed per experiment.

tag: strain background

value: wild type

value: Bone marrow derived macrophage


title: BMM_LPS_PGD2_sample1

description:
KD_2
BMM_LPS_PGD2_1
processed data file: Table_7.xls


title: BMM_LPS_PGD2_sample3

description:
KD_14
BMM_LPS_PGD2_3
processed data file: Table_7.xls


title: seb1-1_epe1KO_tfs1DN_6


title: BMM_LPS_MeAC_sample1

description:
KD_1
BMM_LPS_MeAC_1
processed data file: Table_7.xls


title: ck2ts Rbp1 Rep 2

city: Québec

first: Amine

last: Nourani

state: Québec

address: 9, rue McMahon 3734-1

country: Canada

institute: Centre de recherche du CHU de Québec-Université Laval

data_processing:
Illumina adapters were trimmed from the sequenced reads from each sample using Trimmomatic (Bolger et al., 2014). Trimmed reads were aligned to the S-cerevisiae genome assembly R64-1-1 (GCA_000146045.2) using bowtie v0.12.8 (Langmead et al., 2009). Coverage was calculated using bedtools (http://bedtools.readthedocs.io/) (Quinlan et al., 2010) and was normalized into reads per million (RPM).
Genome_build: sacCer3
Supplementary_files_format_and_content: Bigwigs of coverage.

organism: Saccharomyces cerevisiae

source_name: Frozen yeast cells

growth_protocol: Cells were grown at 30°C in YP-Raffinose to an OD600 of 0.5, arrested in G1 (efficient G1 arrest at least 95% by adding 500 ng/mL alpha-factor for 3h) and then 2% galactose was added to induce Flag-H3 synthesis and shifted to 37ºC for 1h. One hundred mL of yeast cells cultures were cross-linked by adding formaldehyde to a final concentration of 1% and quenched for 5 minutes with 125mM glycine. Cells were centrifuged and the dry yeast pellets were snap frozen in liquid nitrogen and stored at -80ºC.

extract_protocol: Yeast pellets were thawed and resuspended in breaking buffer and lysates were generate by bead beating (1x 1min with glass beads of 0.5 mm diameter). The whole cell extract was mixed with 500ul of FA lysis buffer (50mM HEPES-KOH, pH 7.5 140mM NaCl 1mM EDTA 1% Triton X-100 0.1% Na-deoxycholate 1mM PMSF) and centrifuged at 14000rpm for 1 minute. The pellet were resuspended in 1 ml of FA lysis buffer 140mM NaCl and washed twice. Chromatin solubilization was performed by sonication 10 x 30sec (30 sec on/1 min off) using a Diagenode Bioruptor (average DNA fragment size of 350-500 bp) and subsequently centrifuged at 14000rpm for 30 minutes. The supernatant containing the sonicated chromatin was transferred to a new tube. Immunoprecipitation were performed overnight at 4ºC using 2-3 μg of the 8WG16 anti-CTD antibody per IP (Covance, MMS-126R). To each IP, 10 µl of protein G sepharose beads were added and incubated 6h at 4ºC. Beads were recovered by centrifugation and washed twice with FA lysis buffer 140mM NaCl, twice with with FA lysis buffer 500mM NaCl, twice with ChIP wash buffer (10 mM Tris-HCl [pH 8.0], 250mM LiCL 0.5% NP-40, 0.5% Na-deoxycholate, 1 mM EDTA) and once with TE. DNA-antibody complexes were eluted using 100uL TE 1% SDS, and incubated at 65°C for 20min. The beads were pelleted by centrifugation and the supernatant was collected. Elution was repeated with the addition of 150 µl of TE 1% SDS and incubation at 65oC for 5 min with shaking. After pooling, the two elutions were incubated overnight at 65°C to reverse the crosslinks. To clean up the DNA, the chromatin-containing supernatant was mixed with 100ul of TE containing 3ul of RNAseA (10mg/mL) and 2ul of glycogen (20mg/mL) and incubated for 1 hour at 37°C. To digest the proteins, 7.5ul Proteinase K (20mg/ml) were added and the mixture was incubated for an additional 1 hour at 50°C. The samples were extracted with 360uL phenol/chloroform/isoamyl alcohol (25:24:1). The DNA was precipitated at -20°C with 1 mL of 100% ethanol and 15uL of 5M NaCl. The samples were centrifuged at 14,000rpm for 60 minutes at 4°C. The DNA pellet was washed, dried and resuspended in water.  ChIP-seq experiments were performed fallowing following TruSeq DNA illumina protocol and Illumina next generation sequencing was performed as 50 base pairs single-end reads (McGill University and Génome Québec Innovation Centre, Montréal, Canada).

tag: background

value: Isogenic to S288C (Winston et al., 1995)

tag: genotype

value: mat a leu2D1 lys2-128d bar1D::NAT cka1<delta>0::KanMX6 cka2D225N::NAT ura3-52::HHF1-PGAL1/10-FLAG-HHT1-URA3

value: 8WG16 anti-CTD antibody (Covance, MMS-126R)


title: PTB patient-5

source_name: PTB patient_exosomal miRNA

value: the most frequent (PTB) forms

tag: age


title: PTB patient-6


title: WT Rbp1 Rep 2

tag: strain

value: mat a leu2D1 lys2-128d bar1D::NAT ura3-52::HHF1-PGAL1/10-FLAG-HHT1-URA3


title: BMM_LPS_PGD2_sample2

description:
KD_8
BMM_LPS_PGD2_2
processed data file: Table_7.xls


title: WT Flag-H3 Rep 2

extract_protocol:
Yeast pellets were thawed and resuspended in breaking buffer and lysates were generate by bead beating (1x 1min with glass beads of 0.5 mm diameter). The whole cell extract was mixed with 500ul of FA lysis buffer (50mM HEPES-KOH, pH 7.5 140mM NaCl 1mM EDTA 1% Triton X-100 0.1% Na-deoxycholate 1mM PMSF) and centrifuged at 14000rpm for 1 minute. The pellet were resuspended in 1 ml of FA lysis buffer 140mM NaCl and washed twice. Chromatin solubilization was performed by sonication 10 x 30sec (30 sec on/1 min off) using a Diagenode Bioruptor (average DNA fragment size of 350-500 bp) and subsequently centrifuged at 14000rpm for 30 minutes. The supernatant containing the sonicated chromatin was transferred to a new tube. Immunoprecipitation were performed overnight at 4ºC using 10 μL of anti-Flag agarose beads per IP (Sigma, A2220). Beads were recovered by centrifugation and washed twice with FA lysis buffer 140mM NaCl, twice with with FA lysis buffer 500mM NaCl, twice with ChIP wash buffer (10 mM Tris-HCl [pH 8.0], 250mM LiCL 0.5% NP-40, 0.5% Na-deoxycholate, 1 mM EDTA) and once with TE. DNA-antibody complexes were eluted using 100uL TE 1% SDS, and incubated at 65°C for 20min. The beads were pelleted by centrifugation and the supernatant was collected. Elution was repeated with the addition of 150 µl of TE 1% SDS and incubation at 65oC for 5 min with shaking. After pooling, the two elutions were incubated overnight at 65°C to reverse the crosslinks. To clean up the DNA, the chromatin-containing supernatant was mixed with 100ul of TE containing 3ul of RNAseA (10mg/mL) and 2ul of glycogen (20mg/mL) and incubated for 1 hour at 37°C. To digest the proteins, 7.5ul Proteinase K (20mg/ml) were added and the mixture was incubated for an additional 1 hour at 50°C. The samples were extracted with 360uL phenol/chloroform/isoamyl alcohol (25:24:1). The DNA was precipitated at -20°C with 1 mL of 100% ethanol and 15uL of 5M NaCl. The samples were centrifuged at 14,000rpm for 60 minutes at 4°C. The DNA pellet was washed, dried and resuspended in water.
ChIP-seq experiments were performed fallowing TruSeq DNA illumina protocol and Illumina next generation sequencing was performed as 50 base pairs single-end reads (McGill University and Génome Québec Innovation Centre, Montréal, Canada).

value: anti-Flag agarose beads (Sigma, A2220)


title: ck2ts Flag-H3 Rep 2


title: WT Rbp1 Rep 1


title: ck2ts Rbp1 Rep 1


title: seb1-1_epe1KO_tfs1DN_5

tag: temperature

value: Anti-H3K9me2 (abcam ab1220)


title: ck2ts Flag-H3 Rep 1


title: PTB patient-2

value: Peripheral blood


title: PTB patient-3

value: Female

value: exosomes extracted from plasma


title: BMM_PGD2_sample3

description:
KD_18
BMM_PGD2_3
processed data file: Table_7.xls


title: PTB patient-7


title: PTB patient-1


title: PTB patient-4


title: TBM patient-1


title: seb1-1_epe1KO_tfs1DN_8


title: BMM_PGD2_sample2

description:
KD_12
BMM_PGD2_2
processed data file: Table_7.xls


title: WT Flag-H3 Rep 1


title: seb1-1_epe1KO_tfs1DN_2


title: spt6-7SA Rep 2

data_processing:
Illumina adapters were trimmed from the sequenced reads from each sample using Trimmomatic (Bolger et al., 2014)
Trimmed reads were aligned with bwa (Li et al., 2009) to S.cerevisiae genome assembly R64-1-1 (GCA_000146045.2)
Finally, the numbers of reads for each exon annotated in Ensembl Release 77 was calculated for both the sense and antisense strands using SAMtools.
Genome_build: R64-1-1
Supplementary_files_format_and_content: Tab-separated read counts for exons on both their sense and antisense strands.

growth_protocol: Cells were grown in YPD to an OD600 of 0.5 at 30°C and shifted to 39°C for 2h before RNA extraction.

extract_protocol: Total RNA was extracted using the hot-phenol method. Prior to library preparation, total RNA was depleted for ribosomal RNA using the Ribo-zero Gold yeast kit (Epicentre-Illumina). RNA-seq experiments were performed following following TruSeq stranded total RNA illumina protocol and Illumina next generation sequencing was performed as 50 base pairs single-end reads on an Illumina Hi-Seq2000 (McGill University and Génome Québec Innovation Centre, Montréal, Canada).

treatment_protocol: 2h 39ºC

value: mat a his3D200 ura3<delta>0 leu2D1 lys2-128d bar1D::KanMX6 spt6D::kanMX6/pcc11 (CEN, URA3, FLAG-spt6 7S-A) IWS1-13MYC::HIS3


title: BMM_LPS_MeAC_sample2

description:
KD_7
BMM_LPS_MeAC_2
processed data file: Table_7.xls


title: spt6-7SA Rep 1


title: ck2ts Rep 2


title: seb1-1_epe1KO_tfs1DN_4


title: BMM_PGD2_sample1

description:
KD_6
BMM_PGD2_1
processed data file: Table_7.xls


title: ck2ts Rep 1


title: BMM_MeAC_sample3

description:
KD_17
BMM_MeAC_3
processed data file: Table_7.xls


title: seb1-1_epe1KO_tfs1DN_15


title: seb1-1_epe1KO_tfs1DN_14


title: WT_intestine_non-tuft_sample3

description:
INT3
Intest_non-tuft_3
processed data file: Table_2.xls

value: Mixed

value: Intestine


title: WT_intestine_non-tuft_sample2

description:
INT2
Intest_non-tuft_2
processed data file: Table_2.xls


title: seb1-1_epe1KO_tfs1DN_13


title: BMM_MeAC_sample1

description:
KD_5
BMM_MeAC_1
processed data file: Table_7.xls


title: BMM_MeAC_sample2

description:
KD_11
BMM_MeAC_2
processed data file: Table_7.xls


title: WT_intestine_non-tuft_sample1

description:
INT1
Intest_non-tuft_1
processed data file: Table_2.xls


title: WT Rep 1


title: seb1-1_epe1KO_tfs1DN_11


title: seb1-1_epe1KO_parent

description: paired with  seb1-1_epe1KO_tfs1DN_input

value: seb1-1 epe1delta


title: seb1-1_epe1KO_tfs1DN_10

value: seb1-1 epe1delta tfs1DN


title: seb1-1_epe1KO_tfs1DN_1


title: seb1-1_epe1KO_tfs1DN_12


title: WT_intestine_tuft_sample2

description:
IT2
Intest_tuft_2
processed data file: Table_2.xls

value: wild type


title: epe1KO_VC_parent

description: paired with epe1KO_VC_input


title: Mms21 deleted mutant vs. wild type Replicate 1

city: Montreal

first: Yuan

last: Sun

state: Quebec

address: 7141 Sherbrooke Street West

department: Biology Department

institute: Concordia University

description: YPD medium at 30°C

hyb_protocol: Microarray slides were hybridized with labeled cDNAs overnight at 42°C DIG easy Hyb solution (Roche) containing 0.5 ug/ul of Bakers tRNA and 0.5 ug/ul of salmon sperm DNA. The slides were washed twice with 1X SSC/0.1% SDS and 3 times with 0.1X SSC and spin dry.

scan_protocol: Images were quantified using GenePix Pro 7

data_processing: Normalized Red signal/normalized Green signal. GenePix Pro 7 software was used for image normalization and final normalization and inspection of the data was done using MultiExperiment Viewer.

organism: Candida albicans

source_name: Total RNA extracted from mms21Δ/Δ

label_protocol: Direct cDNA labelling with Cy3-5 dCTP

growth_protocol: Cultures were grown in YPD at 30 degrees celsius

extract_protocol: Total RNA extracted using QIAGEN RNeasy minikit protocol

treatment_protocol: The mms21Δ/Δ and SN148 cultures were grown in YPD overnight at 30 °C, diluted to OD600 = 0.1 in YPD at 30 °C, grown to an OD600 = 0.8 - 1.2, then harvested and stored at -80 °C until RNA extraction. Total RNA isolation and cDNA preparation were performed as previously described (TEBBJI et al. 2014).

tag: cell type

value: Yeast cells

source_name: Total RNA extracted from wild type


title: Mms21 deleted mutant vs. wild type Replicate 2

description: YPD medium at 30°C


title: WT_intestine_tuft_sample1

description:
IT1
Intest_tuft_1
processed data file: Table_2.xls


title: seb1-1_epe1KO_tfs1DN_3

description:
paired with  seb1-1_epe1KO_tfs1DN_input
Parent =  seb1-1_epe1KO_parent


title: 48-hr-Treatment

city: Boston

first: Harm-Jan

last: Westra

address: 77 Avenue Louis Pasteur

department: Center for Data Sciences

institute: Brigham and Women's Hospital

description:
Sample 1 - Timepoint 8
20141202-48-hrs-Treatment-ED1530_S8

data_processing:
Sequenced reads were mapped to the hg19 reference genome using BWA-mem.
Reads mapping to the mitochondrial genome or to multiple genomic locations, and duplicate reads (labeled by Picard MarkDuplicates) were removed, and reads were shifted +4 and -5 bp for the reverse and forward strands respectively.
Enrichment for open chromatin was determined by calling peaks using MACS v2 (default settings).
Genome_build: UCSC hg19
Supplementary_files_format_and_content: MACS peak caller output (BED file compatible)

source_name: Leukocytes

growth_protocol: We used a leukopak (30 mL whole blood) from a healthy anonymous donor to isolate PBMCs using Ficoll tubes, which were stored in 500 µL aliquots of 100x10E6 cells in liquid nitrogen. Cells were subsequently thawed and stained with anti-biotin microbeads to magnetically select CD4+ Tmem cells.

extract_protocol:
Nucleosome isolation was performed as described earlier (Buenrostro et al, Nature Methods 2013).
ATAC-seq open chromatin sequencing was performed as described earlier (Buenrostro et al, Nature Methods 2013).

treatment_protocol: Cells were resuspended and transferred to 24-wells plate in 3 mL aliquots of 6x10E6 cells and stimulated using Dynabeads (Human T-Activator CD3/CD28 for T Cell Expansion and Activation; Life Technologies) in a ratio of 2 cells/bead. Samples of 100,000 cells were taken at 0, 1, 2, 4, 8, 12, 24, and 48 hours after stimulation.

value: healthy anonymous donor

value: whole blood

value: CD4+ Tmem cells

tag: stimulated with

value: anti-CD3/CD28 beads for 48hr


title: 24-hr-Treatment

description:
Sample 1 - Timepoint 7
20141202-24-hrs-Treatment-ED1530_S7

value: anti-CD3/CD28 beads for 24hr


title: epe1KO_VC_9

description:
paired with  epe1KO_VC_input
Parent = epe1KO_VC_parent

value: epe1delta pDUAL-nmt1-vector_only


title: epe1KO_VC_input


title: KC_pan_non-tuft_sample3

description:
4070_NT
Pan_non-tuft_3
processed data file: Table_1.xls

value: KrasG12D;Ptf1aCre/+ (KC)

value: Pancreas


title: epe1KO_VC_8

value: Anti-H3K9me2 (abcam ab1220)


title: 12-hr-Treatment

description:
Sample 1 - Timepoint 6
20141202-12-hrs-Treatment-ED1530_S6

value: anti-CD3/CD28 beads for 12hr


title: KC_pan_non-tuft_sample2

description:
4071_NT
Pan_non-tuft_2
processed data file: Table_1.xls


title: WT Rep 2

value: Isogenic to S288C (Winston et al., 1995)

value: mat a leu2D1 lys2-128d bar1D::NAT ura3-52::HHF1-PGAL1/10-FLAG-HHT1-URA3


title: WT_intestine_tuft_sample3

description:
IT3
Intest_tuft_3
processed data file: Table_2.xls

value: Mixed

value: Intestine


title: epe1KO_VC_7


title: 2-hr-Treatment

description:
Sample 1 - Timepoint 3
20141202-2-hrs-Treatment-ED1530_S3

value: anti-CD3/CD28 beads for 2hr


title: 4-hr-Treatment

description:
Sample 1 - Timepoint 4
20141202-4-hrs-Treatment-ED1530_S4

value: anti-CD3/CD28 beads for 4hr


title: KC_pan_non-tuft_sample1

description:
4003_NT
Pan_non-tuft_1
processed data file: Table_1.xls


title: 1-hr-Treatment

description:
Sample 1 - Timepoint 2
20141202-1-hrs-Treatment-ED1530_S2

value: anti-CD3/CD28 beads for 1hr


title: 0-hr-Treatment

description:
Sample 1 - Timepoint 1
20141202-0-hr-Treatment-ED1530_S1

value: healthy anonymous donor


title: 8-hr-Treatment

description:
Sample 1 - Timepoint 5
20141202-8-hrs-Treatment-ED1530_S5

value: whole blood

value: anti-CD3/CD28 beads for 8hr


title: epe1KO_VC_6


title: Input DNA

data_processing:
Sequencing reads were checked by FastQC and aligned to mm9 with Bowtie (-k 1 -m 20 --best -S -n 2 -l 40). MACS2 (--nomodel --shift 100 --bw 150 --SPMR) was used to remove duplicated reads, call peaks, and generate Bedgraph files that show fold change enrichment over input. To ensure the quality of Pou2f3 binding sites, only peaks (peak calling FDR<0.05) common between the two biological replicates were called, and any peaks that overlap with the control IgG peaks (FDR<0.05) and/or the Encode blacklist regions were removed. Bedgraph files were then converted into BigWig files.
Sequence reads were then aligned to the NCBI Build 37 mouse genome (mm9) with Bowtie (version 0.12.8) using the following parameters: -m 1 --best -S -n 2 -l 40. Sam files were converted/sorted to Bam files with samtools (version 1.3.1).
Tuft_POU2F3_ChIP1+2.bigwig represents signal file combining sample 1 and sample 2 over the input DNA. Tuft_POU2F3_binding_sites.bed represents MACS2 called POU2F3 peaks of common regions between sample 1 and sample 2 excluding IgG peaks and Encode blacklist regions.
Genome_build: mm9
Supplementary_files_format_and_content: Tuft_POU2F3_ChIP1+2.bigwig represents signal file (reads per million per genomic region) combining sample 1 and sample 2 over the input DNA. Tuft_POU2F3_binding_sites.bed represents MACS2 called POU2F3 peaks (FDR<0.05) of common regions between sample 1 and sample 2 excluding IgG peaks (FDR<0.05) and Encode blacklist regions.

source_name: Input DNA

extract_protocol:
Intestinal tuft cells were isolated from male C57BL/6J mice.  Briefly, the proximal 5 cm of the murine small intestine was dissected, flushed, cut longitudinally, and rinsed to remove luminal contents.  Segments were incubated in a 37°C shaker for 20 min in 5 ml PBS containing 2.5 mM EDTA, 0.75 mM dithiothreitol (DTT), and 10 μg/ml DNaseI.  Tissues were shaken vigorously for 30s, large pieces of intestinal wall were removed, and cells were spun down at 4°C, 1200 rpm, for 5 min.  Supernatant was removed and cells were re-suspended in 5 ml HBSS with 1.0 U/ml Dispase and 10μg/ml DNAse I, shaking for 10 min.  Digested cells were passed through a 100 μm filter and incubated with ACK lysing buffer.
Single cell suspensions were incubated on ice with mouse Fc receptor block (BD Biosciences, 1:200) followed by antigen-specific antibodies in FACS buffer.  DAPI (molecular probes, 1:1000) and Annexin V (Biolegend, Pacific Blue conjugate at 1:200) were used to exclude dead and dying cells.  Cells were labeled with Cd45 (Alexa Fluor 488), EpCAM (Alexa Fluor 647), and Siglec F (PE) (Biolegend, 1:200).  Fluorescence Minus One (FMO) staining controls were included for gating populations of interest. Cells were FACS purified at the Salk Institute’s Flow Cytometry core facility on a BD Biosciences Influx cell sorter (100-µm size nozzle, 1 x PBS sheath buffer with sheath pressure set to 20 PSI). Cells were sorted in 1-drop Single Cell sort mode for counting accuracy.
Two pools of intestinal tuft cells from three individual mice were used as biological replicates. Around 10000 sorted tuft cells were crosslinked with 1% PFA in PBS at room temperature for 10 minutes, sonicated with Covaris M220 into 200-700 bp fragments, and incubated with 0.6 μg of anti-Pou2f3 antibody (Santa Cruz #SC330) or control antibody (anti-IgG Cell Signaling #2729) overnight at 4C. Protein A bead pull down (Invitrogen 10001D), washing, on-bead tagmentation (Illumina Nextera FC-121-1030), reverse crosslinking, library amplification (16-18 PCR cycles), and DNA purification were performed as previously described (Schmidl et al., 2015). The input library was prepared by direct tagmentation of genomic DNA prepared from fixed, sonicated, and reverse-cross linked mouse chromatin and then amplified and processed as the ChIP DNA.
ChIPmentation method (Schmidl et al., 2015)

value: intestinal tuft cells


title: KC_pan_tuft_sample1

description:
4003_T
Pan_tuft_1
processed data file: Table_1.xls


title: KC_pan_tuft_sample2

description:
4071_T
Pan_tuft_2
processed data file: Table_1.xls


title: epe1KO_VC_4


title: epe1KO_VC_3


title: epe1KO_VC_5


title: Intestinal tuft IgG control

source_name: Intestinal tuft IgG control

tag: chip antibody

value: control antibody (anti-IgG Cell Signaling #2729)


title: F1 B96 T. urticae (Replicate 4)

city: Salt Lake City

first: Richard

middle: M

last: Clark

state: Utah

department: Department of Biology

institute: University of Utah

description:
F1-B73-B96-T4
14999X5

data_processing:
Following transfer of the flowcell to an Illumina HiSeq 2500 instrument (HCS v2.2.38 and RTA v1.18.61), a 125 cycle paired-end sequence run was performed using HiSeq SBS Kit v4 sequencing reagents (FC-401-4003), and the resulting reads were aligned to the Z. mays AGPv4 reference genome with STAR 2.5.3a in two-pass alignment mode (alignments were independent of the existing reference annotation).
Read counts for genes in the AGPv4 (Ensembl Release 39) annotation were obtained using HTSeq 0.9.1 with --stranded reverse.
Genome_build: The AGPv4 genome sequence and annotation (Ensembl Release 39) were downloaded from the maize genome site at ensembl.org.
Supplementary_files_format_and_content: Tab-delimited text file with counts of reads per gene from alignments as assessed with HTSeq (expression across all samples is included in the single processed data file; column names correspond to the prefixes of raw data files).

organism: Zea mays

source_name: F1 B96 T. urticae, leaf tissue

growth_protocol: The maize inbred and F1 plants used for the experiments were germinated and grown in a greenhouse with 16h-light/8h-dark photoperiod at a temperature of average 25 degrees C. They were cultivated using SunGrow® Metro-Mix® 900 Grower Mix, watered as needed, and fertilized weekly with 200ppm NutriCulture 16N-3P-16K.

extract_protocol:
Leaf tissue was ground to fine powder in liquid nitrogen. Total RNA was prepared using the DirectZol RNA extraction kit (Zymo Research). Quality of the RNA extractions was assessed using a Bioanalyzer (Agilent).
The libraries were prepared at the University of Utah High Throughput Genomics facility using the Illumina TruSeq Stranded mRNA Library Preparation Kit with poly(A) selection.

treatment_protocol: The 4th leaves of 22-day-old maize plants were used for the experiment. Mite movement was restrained by barriers made of a non-toxic wax (TangleFoot). Mites were allowed to feed on both sides of a leaf section defined by TangleFoot barriers. The maize leaf sections were infested with 200 healthy adult female mites for 24 hours. The control leaves received the TangleFoot barriers but not the mites. Samples in given experiments (those involving B75 or B96) were arranged in a randomized block design and collected at the same time to limit the effects of the circadian cycle and any minor environmental differences on gene expression.

tag: line

tag: Stage

value: V4-22 days old

value: leaf

tag: leaf number

value: leaf number 4

tag: mite strain

value: Tetranychus urticae


title: F1 B96 T. urticae (Replicate 2)

description:
F1-B73-B96-T2
14999X15

tag: tissue


title: F1 B96 T. urticae (Replicate 3)

description:
F1-B73-B96-T3
14999X26


title: F1 B96 T. urticae (Replicate 1)

description:
F1-B73-B96-T1
14999X41


title: epe1KO_VC_15

value: epe1delta pDUAL-nmt1-vector_only

tag: antibody

value: Anti-H3K9me2 (abcam ab1220)


title: Intestinal tuft POU2F3 ChIP sample2

source_name: Intestinal tuft POU2F3 ChIP

value: anti-Pou2f3 antibody (Santa Cruz #SC330)


title: epe1KO_VC_2


title: F1 B96 Control (Replicate 4)

description:
F1-B73-B96-C4
14999X6

source_name: F1 B96 Control, leaf tissue


title: KC_pan_tuft_sample3

description:
4070_T
Pan_tuft_3
processed data file: Table_1.xls

value: Mixed

tag: genotype/variation

value: KrasG12D;Ptf1aCre/+ (KC)

value: Pancreas


title: epe1KO_VC_14


title: epe1KO_VC_13


title: KO rep3

city: Dallas

first: Joshua

last: Mendell

state: TX

address: 5323 Harry Hines Boulevard

department: Molecular Biology

institute: UT Southwestern Medical Center Dallas

data_processing:
Reads were aligned to the mm10 reference genome with GENCODE M16 annotation using HISAT2 version 2.1.0 using default parameters
Read count per gene was generated by featureCounts
Differential expression analysis was performed on uniquely mapped reads with edgeR version 3.20.1
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files including gene id, gene name, logFC, logCPM, LR, p-value, FDR, and cpm within each sample

source_name: KO, primary nephron progenitor cells

growth_protocol: Primary nephron progenitor cells isolated accoding to protocol "A synthetic niche for nephron progenitor cells" (Brown et al 2015)

extract_protocol:
RNA collection was performed in well using miRNeasy Mini Kit with On-Column DNase Digestion (Qiagen) according to protocol
RNA-seq libraries were prepared using the TruSeq Stranded Total RNA LT Sample Prep Kit (Illumina) and sequenced using 50 base pair single-end reads on an Illumia HiSeq2500

treatment_protocol: Cells derived from either Dis3l2+/+ or Dis3l2-/- embryos passaged once in culture before collection

value: primary nephron progenitor cells

tag: passages


title: F1 B96 Control (Replicate 3)

description:
F1-B73-B96-C3
14999X29


title: KO rep2


title: F1 B96 Control (Replicate 2)

description:
F1-B73-B96-C2
14999X18


title: WT rep2

source_name: WT, primary nephron progenitor cells


title: F1 B96 Control (Replicate 1)

description:
F1-B73-B96-C1
14999X40


title: epe1KO_VC_12

source_name: Yeast Cell


title: KO rep1


title: F1 B75 T. urticae (Replicate 4)

description:
F1-B73-B75-T4
14999X31

source_name: F1 B75 T. urticae, leaf tissue


title: epe1KO_VC_11


title: WT rep1


title: F1 B75 T. urticae (Replicate 3)

description:
F1-B73-B75-T3
14999X45


title: Intestinal tuft POU2F3 ChIP sample1


title: epe1KO_VC_1


title: F1 B75 T. urticae (Replicate 2)

description:
F1-B73-B75-T2
14999X8


title: PolII_ChIP-seq_input


title: PolII_ChIP-seq_clr4KO_seb1-1_rep1

description: paired with  PolII_ChIP-seq_input

value: rpb3-3xFLAG clr4delta seb1-1

value: Anti-FLAG


title: epe1KO_VC_10


title: RKO DMSO YM155 10 nM R2

city: Heidelberg

first: Tianzuo

last: Zhan

address: Im Neuenheimer Feld 580

country: Germany

institute: German Cancer Research Center

description: Colorectal cancer cell line treated with YM155

hyb_protocol: Standard Illumina Hybridisation Protocol  Part # 11322355  (Whole-Genome Gene Expression  Direct Hybridization Assay Guide)  750 ng of cRNA were hybridized for 17 hr at 58°C on Illumina Human HT-12-Microarray.

scan_protocol: Gene Expression Microarrays were scanned using the Illumina iScan-Scanner according to Standard Illumina Scanning Protocol  Part # 11322355  (Whole-Genome Gene Expression  Direct Hybridization Assay Guide)

data_processing:
Non-normalized data were generated by the Illumina GenomeStudio software version V2011.1 Raw expression values were processed using the R/Bioconductor package 'lumi' (version 2.30.0). Normalization steps include background correction using the 'rma' method, variance stabilization and quantile normalization.
Signal values and detection P-values are as provided by the Illumina Genome Studio software. Normalized signal values are as provded by the 'lumi' R/Bioconductor package.

label: Biotin, Cy3-Streptavidin

source_name: RKO cancer cell line

label_protocol: The Illumina TotalPrep RNA Amplification Kit (Life Technologies) is used to generate single-stranded cRNA from input amounts of 200ng total RNA  The Illumina TotalPrep RNA Amplification Kit (life technologies) is used to generate single-stranded cRNA from input amounts of 200ng total RNA, Label: Biotin, Cy3-Streptavidin

growth_protocol: HCT116 was cultured in McCoy’s 5A medium + 10% FCS. RKO, CaCo2 and HT55 were cultured in DMEM with 4 mM glutamine + 10% FCS.

extract_protocol: Qiagen RNeasy Extraction Kit

treatment_protocol: treatment with YM155 for 24 h

value: colorectal cancer


title: RKO DMSO YM155 10 nM R3


title: RKO DMSO R1

description: Colorectal cancer cell line treated with DMSO


title: KC-GEMM-ESC-shRen.713 #3

city: New York

first: Yu-Jui

last: Ho

state: New York

address: 417 E 68th St

department: Cancer Biology & Genetics Program

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Illumina  read quality was checked for each sample using FastQC v0.11.5.
Raw fastq files were aligned to GRCm37-mm9 using STAR (STAR_2.5.0a), Algined reads were quantified using HTSeq (HTSeq-0.5.3). Raw read counts were normalized to FPKM value.
Differential expression analysis was performed with DESeq package in R (R-3.2.0)
Genome_build: GRCm37 - mm9
Supplementary_files_format_and_content: text file includes raw count value for each sample

growth_protocol: KC-GEMM-ESC mice (males, chimerism >90%) were put on Doxycycline diet for 5 days

extract_protocol:
Trizol RNA extraction protocol
Ribosomal RNA was depleted using RiboZero (Illumina) and stranded KAPA RNA libraries were prepared from 1ug RNA. Paired-end 50.

treatment_protocol: Pancretata were harvested at day 5 post-doxycycline diet and processed for FACS sorting as described in Methods section. mKate+ cells were sorted using Aria3 sorter, and collected directly into Trizol-LS.

value: GEMM derived from p48-9C ESCs (Saborowski et al., PNAS, 2013) targeted with the TRE-GFP-shRNA against Renilla (sh713)

value: 5 weeks old

tag: treatment

value: Doxycycline (5 days)

value: pancreas

value: sorted pancreaatic epithelial cells


title: KC-GEMM-ESC-shArid1a.1803 #3

value: GEMM derived from p48-9C ESCs (Saborowski et al., PNAS, 2013) targeted with the TRE-GFP-shRNA against Arid1a (sh1803)


title: F1 B75 Control (Replicate 3)

description:
F1-B73-B75-C3
14999X48

source_name: F1 B75 Control, leaf tissue

value: V4-22 days old

value: leaf

value: leaf number 4


title: F1 B75 Control (Replicate 4)

description:
F1-B73-B75-C4
14999X36


title: RKO DMSO YM155 10 nM R1


title: HCT116 DMSO YM155 10 nM R2

source_name: HCT116 cancer cell line


title: KC-GEMM-ESC-shArid1a.6421 #3

value: GEMM derived from p48-9C ESCs (Saborowski et al., PNAS, 2013) targeted with the TRE-GFP-shRNA against Arid1a (sh6421)


title: PolII_ChIP-seq_clr4KO_seb1-1_rep2

description: paired with  PolII_ChIP-seq_input

value: rpb3-3xFLAG clr4delta seb1-2


title: RKO DMSO R2


title: F1 B75 T. urticae (Replicate 1)

description:
F1-B73-B75-T1
14999X22

value: Tetranychus urticae


title: HCT116 DMSO YM155 10 nM R1


title: RKO DMSO R3


title: HCT116 DMSO R3


title: HT55 DMSO YM155 10 nM R3

source_name: HT55 cancer cell line


title: HCT116 DMSO R2


title: HCT116 DMSO YM155 10 nM R3


title: KC-GEMM-ESC-shArid1a.6421 #2


title: epe1KO_ago1KO_set3_tfs1DN_isolate5

description:
paired with  epe1KO_ago1KO_set3_input
Parent = epe1KO_ago1KO_set3_parent

value: epe1delta ago1delta tfs1DN

value: Anti-H3K9me2 (abcam ab1220)


title: KC-GEMM-ESC-shArid1a.1803 #2


title: PolII_ChIP-seq_clr4KO_rep2

description: paired with  PolII_ChIP-seq_input

value: rpb3-3xFLAG clr4delta


title: KC-GEMM-ESC-shRen.713 #2


title: PolII_ChIP-seq_clr4KO_rep1

description: paired with  PolII_ChIP-seq_input

value: Anti-FLAG


title: HCT116 DMSO R1

value: colorectal cancer


title: F1 B75 Control (Replicate 2)

description:
F1-B73-B75-C2
14999X7


title: KC-GEMM-ESC-shArid1a.6421 #1


title: HT55 DMSO R3


title: KC-GEMM-ESC-shRen.713 #1

value: GEMM derived from p48-9C ESCs (Saborowski et al., PNAS, 2013) targeted with the TRE-GFP-shRNA against Renilla (sh713)


title: B96 T. urticae (Replicate 2)

description:
B96-T2
14999X17

source_name: B96 T. urticae, leaf tissue


title: KC-GEMM-ESC-shRen.713 #4

last: Koche

data_processing:
ATAC-seq reads were filtered for quality and 3' trimmed for adapter sequences.
Reads were aligned to mouse assembly mm9 using bowtie2 (v2.2.2) with default parameters.
Read count tables were created using featureCounts v1.6.0.
To create density files, read overlap density was calculated with an extension of 0 bp, the signal was then normalized to ten million mapped reads and converted to BigWig using BEDTools.
Genome_build: mm9
Supplementary_files_format_and_content: BigWig files containing read densities normalized to 10 million reads

source_name: sorted pancreaatic epithelial cells

extract_protocol:
Lysis Buffer 10mM Tris·Cl, pH 7.4; 10mM NaCl; 3mM MgCl2; 0.1% (v/v) Igepal CA-630 (Buenrostro et al., 2015 protocol)
ATAC-seq was performed as previously described (Buenrostro et al. 2013 Nature Methods). For each sample, cell nuclei were prepared from 50,000 cells, and incubated with 2.5 uL transposase (Illumina) in a 50 uL reaction for 30 min at 37°C. Following purification of transposase fragmented DNA, the library was amplified by PCR and subjected to high-throughput sequencing using Illumina HiSeq 2500 platform.

treatment_protocol: Pancretata were harvested at day 5 post-doxycycline diet and processed for FACS sorting as described in Methods section. mKate+ cells were sorted using Aria3 sorter, and collected directly into FACS Buffer.

value: 5 weeks old


title: HT55 DMSO YM155 10 nM R2


title: KC-GEMM-ESC-shArid1a.1803 #1

value: Doxycycline (5 days)


title: B96 T. urticae (Replicate 3)

description:
B96-T3
14999X27


title: B96 T. urticae (Replicate 4)

description:
B96-T4
14999X1


title: F1 B75 Control (Replicate 1)

description:
F1-B73-B75-C1
14999X20


title: epe1KO_ago1KO_set3_parent

description: paired with  epe1KO_ago1KO_set3_input

value: epe1delta ago1delta


title: epe1KO_ago1KO_set3_tfs1DN_isolate11


title: B96 T. urticae (Replicate 1)

description:
B96-T1
14999X37


title: B96 Control (Replicate 4)

description:
B96-C4
14999X2

source_name: B96 Control, leaf tissue


title: epe1KO_ago1KO_set3_input


title: B96 Control (Replicate 3)

description:
B96-C3
14999X28


title: KC-GEMM-ESC-shRen.713 #2

value: pancreas


title: KC-GEMM-ESC-shArid1a.6421 #3

value: GEMM derived from p48-9C ESCs (Saborowski et al., PNAS, 2013) targeted with Arid1a shRNA -6421


title: KC-GEMM-ESC-shRen.713 #3


title: CaCo2 DMSO YM155 10 nM R3

source_name: CaCo2 cancer cell line


title: epe1KO_ago1KO_set3_tfs1DN_isolate3


title: B96 Control (Replicate 2)

description:
B96-C2
14999X14

value: V4-22 days old


title: epe1KO_ago1KO_set3_tfs1DN_isolate12


title: epe1KO_ago1KO_set2_tfs1DN_isolate8

description:
paired with  epe1KO_ago1KO_set2_input
Parent = epe1KO_ago1KO_set2_parent


title: HT55 DMSO YM155 10 nM R1


title: KC-GEMM-ESC-shArid1a.6421 #2


title: CaCo2 DMSO R3


title: HT55 DMSO R1


title: epe1KO_ago1KO_set2_tfs1DN_isolate4


title: KC-GEMM-ESC-shArid1a.6421 #1


title: B75 T. urticae (Replicate 3)

description:
B75-T3
14999X47

source_name: B75 T. urticae, leaf tissue

value: leaf


title: KC-GEMM-ESC-shRen.713 #1


title: CaCo2 DMSO R2


title: epe1KO_ago1KO_set2_tfs1DN_isolate1


title: CaCo2 DMSO YM155 10 nM R2


title: B75 T. urticae (Replicate 4)

description:
B75-T4
14999X35

value: leaf number 4


title: epe1KO_ago1KO_set2_tfs1DN_isolate10


title: B75 T. urticae (Replicate 2)

description:
B75-T2
14999X10


title: epe1KO_ago1KO_set2_parent

description: paired with  epe1KO_ago1KO_set2_input


title: CaCo2 DMSO R1


title: epe1KO_ago1KO_set2_tfs1DN_isolate9


title: B75 T. urticae (Replicate 1)

description:
B75-T1
14999X19


title: CaCo2 DMSO YM155 10 nM R1


title: epe1KO_ago1KO_set2_input


title: B75 Control (Replicate 4)

description:
B75-C4
14999X33

source_name: B75 Control, leaf tissue


title: epe1KO_ago1KO_set1_tfs1DN_isolate7

description:
paired with  epe1KO_ago1KO_set1_input
Parent = epe1KO_ago1KO_set1_parent


title: B75 Control (Replicate 3)

description:
B75-C3
14999X46


title: epe1KO_ago1KO_set1_tfs1DN_isolate6


title: B75 Control (Replicate 2)

description:
B75-C2
14999X9


title: B96 Control (Replicate 1)

description:
B96-C1
14999X39


title: epe1KO_ago1KO_set1_parent

description: paired with  epe1KO_ago1KO_set1_input


title: B73 T. urticae (Replicate 8)

description:
B73-T8
14999X34

source_name: B73 T. urticae, leaf tissue


title: epe1KO_ago1KO_set1_input


title: epe1KO_tfs1DN_input_DN2-DN11


title: NK04

city: Austin

first: Ningling

last: Kang

state: MN

address: 801 16th AVE NE

department: Hormel Institute

institute: University of Minnesota

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

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

growth_protocol: Cells were incubated in DMEM media in regular cell culture plates, supplemented with penicillin and streptomycin

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Cells were treated with or without TGFbeta for 24 hours

value: hepatic stellate cells


title: B75 Control (Replicate 1)

description:
B75-C1
14999X23


title: epe1KO_ago1KO_set1_tfs1DN_isolate2


title: B73 T. urticae (Replicate 6)

description:
B73-T6
14999X12


title: NK06

source_name: cell+conshRNA+TGFβ


title: epe1KO_tfs1DN9

description:
paired with epe1KO_tfs1DN_input_DN2-DN11
Parent =  epe1KO_parent_of_DN2-DN12

value: epe1delta tfs1DN


title: NK08


title: NK03


title: B73 T. urticae (Replicate 5)

description:
B73-T5
14999X24

value: Tetranychus urticae


title: B73 T. urticae (Replicate 7)

description:
B73-T7
14999X44


title: epe1KO_tfs1DN8


title: NK05

source_name: cell+conshRNA


title: B73 T. urticae (Replicate 4)

description:
B73-T4
14999X4


title: epe1KO_tfs1DN7


title: B73 T. urticae (Replicate 3)

description:
B73-T3
14999X30


title: epe1KO_tfs1DN6


title: B73 T. urticae (Replicate 2)

description:
B73-T2
14999X13


title: epe1KO_tfs1DN5


title: B73 T. urticae (Replicate 1)

description:
B73-T1
14999X38


title: NK02

source_name: cell+DMSO+TGFβ


title: HT55 DMSO R2


title: epe1KO_tfs1DN3


title: BMSC(ML)

city: Macao

first: Renhe

last: Xu

address: Avenida de Universidade  Taipa

department: Faculty of Health Sciences

institute: University of Macao

data_processing: The microarray dataset was normalized and filtered to remove probes with detection P value > 0.01 in at least 50% of the samples . Two normalization methods were utilized to analyze the dataset on the basis of their biological relevance. First, average probe intensity of all biological and technical replicates was used to make comparison in gene expression profile between test and control groups. Second, the probe intensity of analyzed genes in hESC was used as a baseline to identify the gene expression differences between EMSCML and EMSCSp-ML.

source_name: bone marrow

growth_protocol: hESC line CT3  was used in this study had been registered with the National Institutes of Health, USA. hESC were cultured on Matrigel in E8 medium (StemCell Technologies). For EMSCSp-ML generation, we first made hESC spheroids of homogenous sizes as described. Briefly, typical hESC colonies were digested for 5-10 min. with 1 mg/ml dispase (StemCell Technologies). Once hESC colonies began to roll up, dispase was removed and cells were rinsed with Ca2- and Mg2-free PBS twice. The colonies were gently washed off the plate with mTeSR1, and collected with 5-ml pipette. We then cut the colonies by passing them through a strainer with pore size at 50 μm in diameter (CellTrics) under pipette pressure to generate cell clusters of about 50-μm. The clusters were collected, re-suspended in 3 ml/well pre-warmed mTeSR1 medium (StemCell Technologies) supplemented with 10-μM Y-27632 (Sigma) to inhibit apoptosis, and cultured in suspension on 35 cm ultra-low attachment plate (Corning).  On day 2, hESC spheroids were treated with 10-ng/ml BMP4 and 1-μM A83-01 in mTeSR1 Minus Select Factors (StemCell Technologies) to induce differentiation into trophoblast-like cells, similar as we derived MSC from hESC cultured in monolayer via trophoblast differentiation in 2D [9]. On day 5, the spent medium was removed and replaced with the MSC medium, i.e., MEM basal medium supplemented with 20% FBS, 1% NEAA, and 1% L-Glutamine. The culture medium was refreshed with the MSC medium every 3 days. Initial analyses were conducted on cell spheroids collected at various days during the differentiation. For continuous analyses, some spheroids were dissociated at day 20 with 0.25% trypsin for 5 min. and then plated into a T75 flask for expansion and passaging in 2D in the MSC medium.  BMSC were derived from bone marrow aspirates donated by two healthy male adults under approval of the University of Macau Panel of Research Ethics #APP004-FHS. The aspirates were washed with PBS twice followed by isolation of the mononucleocyte (MNC) fraction via centrifugation over Picoll (Sigma) at 800 RCF. BMSCs were plated in T75 flasks in the MSC medium and fed every 3 days. When cells reached 80% confluence, they were detached with 0.05% trypsin and re-plated at 30 cells/cm2 (as passage 1 or p1) for further expansion. Resultant BMSC were passaged every 5-7 days.

extract_protocol: we used the Qiagen RNA easy kit(Cat.No.74136) to extract the RNA follow its manunal book.

treatment_protocol: RNA was isolated from EMSCML and EMSCSp-ML treated with or without IFNγ for 24 h, using RNAeasy mini kit (Qiagen), and cDNA libraries were synthesized and processed by using HumanHT-12 v4 Expression BeadChip. Further analysis was performed using the BeadStudio Data Analysis software (Illumina) and Excel.

tag: cells

value: mesenchymal stems cells using monolayer


title: NK01

source_name: cell+DMSO


title: Non-diabetic Control, 4

first: Towia

last: Libermann

address: 99 Brookline Ave.

department: Medicine

institute: Beth Israel Deaconess Medical Center

description: Gene expression data from kidney of non-diabetic controls

hyb_protocol: Following fragmentation, 5.5 ug of ss-cDNA were hybridized for 16 hr at 45C on Human Transcriptome 2.0 GeneChip. GeneChips were washed and stained in the Affymetrix GeneChips Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner 3000.

data_processing: The data were analyzed with Partek Genomics Suite using Partek default analysis settings and RMA as normalization method.

source_name: Non-diabetic Control

label_protocol: Biotinylated ss-cDNA was prepared according to the standard Affymetrix protocol from 500 ng total RNA (GeneChipTM WT PLUS Reagent Kit Manual Target Preparation for GeneChipTM Whole Transcript (WT) Expression Arrays, 2017, Thermo Fisher).

growth_protocol: Postmortem kidney from non-diabetic controls and EDN

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Total RNA from flash-frozen kidney tissue was extracted exclusively from postmortem kidney cortical tissue. Pathologic staging of diabetic tissues was performed using the 2010 Renal Pathology Society classification system for diabetic kidney disease.9  From each postmortem nephrectomy sample more than 100 glomeruli were reviewed in tissue sections.  Pathologic stages I-III diabetic kidney disease were considered as EDN and used in the study.  Stage III kidneys were included since the renal function in these donors are preserved.

value: Kidney Cortical Tissue

tag: disease

value: Control


title: Non-diabetic Control, 3


title: B73 Control (Replicate 8)

description:
B73-C8
14999X32

source_name: B73 Control, leaf tissue


title: NK07


title: Non-diabetic Control, 2


title: EMSC(Sp-ML/p8)

source_name: embryonic stem cells derived

value: mesenchymal stems cells using spheroid method(Sp)

tag: passage

tag: gender

value: female


title: EMSC(Sp-ML/p3)


title: EMSC(Sp-ML/p3+iFN-r)

value: stimulated with IFN-gama


title: B73 Control (Replicate 7)

description:
B73-C7
14999X43


title: Non-diabetic Control, 1


title: Rao-2017-CHIP034-input-treated

city: Houston

first: Suhas

last: Rao

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

data_processing:
Reads were aligned using BWA against the b37 human build
Reads were deduplicated using PicardTools
Reads were analyzed with MACS 2.0 (Liu, 2014). All data was normalized against the corresponding input control using the ‘-c’ option of MACS 2.0.
Genome_build: b37 (human)

source_name: Colorectal carcinoma

growth_protocol: Cell lines were cultured according to manufacturer's instructions

extract_protocol:
ChIP-Seq for H3K27Ac, H3K4me1, H3K4me3, H3K36me3, H3K27me3, H3K9me3, H4K16Ac, H4K20me3, H3K79me2, and H2.AZ was performed using a native ChIP-Seq protocol. Chromatin from untreated HCT-116 RAD21-mAC cells or cells treated for 6 hours with 500uM IAA was digested with Mnase (Sigma) in digestion buffer (50 mM Tris-HCl, pH7.6, 1 mM CaCl2, 0.2% Triton X-100, butyrate 5 mM) for 5’ at 37°C and dialyzed against RIPA buffer for 2hrs at 4°C. Five microgram of respective antibody was incubated with 40 μl of Dynabeads Protein A (or G) for 40 min at room temperature. Antibody-bound beads were added to 500 μl of sonicated or Mnase-digested chromatin, incubated at 4°C overnight, and washed twice with RIPA buffer, twice with RIPA buffer containing 0.3M NaCl, twice with LiCl buffer (0.25 M LiCl, 0.5% Igepal-630, 0.5% sodium deoxycholate), once with TE (pH 8.0) plus 0.2% Triton X-100, and once with TE (pH 8.0). ChIP DNA was purified by phenol-chloroform extraction followed by ethanol precipitation. Libraries were prepped for Illumina sequencing and 50bp single-end reads were sequenced on a HiSeq2000 or 2500 (Illumina). We also performed ChIP-Seq for RAD21 and CTCF following the same protocol as above, except that cells were fixed with 1% formaldehyde for 10 minutes at 37°C and fixation was quenched by the addition of glycine to a final concentration of 125mM for 10 minutes. The fixed cells were sonicated using a Branson sonifier at amplitude 35%, 12 cycles of 20 seconds of sonication and 30 seconds of pause. Antibody was added to the sonicated chromatin as above and the samples were further processed as above.    We also performed ChIP-Seq for SMC1 and an additional replicate for CTCF following the protocol outlined by the ENCODE consortium (2012).
standard Illumina library construction protocol, Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 8-12 cycles and library fragments of 400-600 bp (insert plus adaptor and PCR primer sequences) were purified using SPRI beads. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the HiSeqX Ten, NextSeq 500, or HiSeq 2500 following the manufacturer's protocols

treatment_protocol: Cells were treated with 500uM auxin as described in the characteristics above

tag: cell line

tag: protocol

value: ChIP-Seq

value: 500uM auxin (360 min)


title: EMSC(ML/p8)


title: EDN, 4

description: Gene expression data from kidney of patients with EDN

source_name: early diabetic nephropathy

value: early diabetic nephropathy


title: Cocaine 10

first: Efrain

last: Ribeiro

address: 1425 Madison Ave, Icahn bldg. Rm 10-24

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

description:
C38
c10_CTTGTA
SST-TLG517

data_processing:
STAR
featureCounts from Subread package
Normalized vy weight trimmed mean of M-values
Voom differential expression analysis
Genome_build: Ensembl GRCm38.74
Supplementary_files_format_and_content: logCPM

source_name: cocaine_FACs isolated nucleus accumbens somatostatin interneuron nuclei

extract_protocol:
FACS
SMARTER Stranded Total RNA-seq kit V2 pico input mammalian (Clontech 063017)
Libraries were made from RNA isolated from ~2000-4000 FACS isolated somatostatin interneuron nuclei. Libraries were pooled across two lanes and both groups were equally balanced.

treatment_protocol: Saline or 7.5mg/kg cocaine

tag: strain background

value: 7.5mg/kg cocaine

tag: number of nuclei

value: 1 Hour

tag: region

value: Nucleus Accumbens


title: B73 Control (Replicate 6)

description:
B73-C6
14999X11

tag: line

tag: Stage

value: V4-22 days old

value: leaf


title: EDN, 3


title: EMSC(ML/p3+iFN-r)


title: epe1KO_tfs1DN4

first: Hiten

last: Madhani

institute: University of California, San Francisco

data_processing:
ChIP-Seq data were Stripped of adaptor sequences (GATCGGAAGA) and aligned using Bowtie1, allowing up to two mismatches.
Indexed, sorted bam files were created for each dataset using SAMtools and bedgraph files were created using BEDTools.
Bedgraph files were further processed by smoothing over a 1KB window.  Background H3K9me levels were calculated and defined as average coverage in all regions of the genome excluding the 80 kb adjacent to each chromosome end and the centromeric regions. Peaks wer then called as having a singla at least 3 times higher than the background.
Genome_build: Schizosaccharomyces_pombe.ASM294v2.20.dna.AB325691.fa from Pombase.org
Supplementary_files_format_and_content: Bedgraphs represent aligned, not normalized, read densities. .csv list regions in the gneome that had 3 fold higher H3K9me signal than background.

source_name: Yeast Cell

extract_protocol:
ChIP DNA was extracted by bead beater with 0.5mm zirconia beads.  ChIP DNa was isolated by antibodies directed to our protein of interest (H3K9me2 or rpb3x-FLAG).  DNA was then isolated by incubation by SDS/proteinase K followed by column purification (Macherey-Nagel Nucleospin Gel Cleanup Columns).
Libraries were prepared using End-It DNA End Repair Kit (Epicenter) followed by A-tailing using Klenow fragment (NEB), ligation to Illumina adaptors using Rapid T4 DNA Ligase (Enzymatics), PCR amplification for 15 cycles, and size selection between 200-350bp by bead purification and gel extraction.

tag: strain

tag: temperature

value: Anti-H3K9me2 (abcam ab1220)


title: Cocaine 9

description:
C36
c9_TAGCTT
SST-TLG516


title: Rao-2017-CHIP033-input-untreated


title: epe1KO_tfs1DN12

value: epe1delta tfs1DN

tag: antibody


title: epe1KO_tfs1DN2


title: B73 Control (Replicate 5)

description:
B73-C5
14999X21

tag: tissue

tag: leaf number

value: leaf number 4

tag: mite strain


title: Cocaine 8

description:
C17
C8_CGATGT
SST-TLG515

tag: treatment


title: EMSC(ML/p3)

tag: cells

value: mesenchymal stems cells using monolayer


title: pRH5

city: Tehran

first: Ali

last: Sharifi-Zarchi

address: Royan Institute, Bani Hashem Sq.

country: Iran

institute: Royan Institute for Stem Cell Biology and Technology

description: Primed hESCs from Royan H5 cell line

data_processing:
The resulting raw reads were assessed for quality, adapter content and duplication rates with FastQC (Andrews 2010). Reaper version 13-100 was employed to trim reads after a quality drop below a mean of Q20 in a window of 10 nucleotides (Davis et al. 2013). Only reads between 30 and 150 nucleotides were cleared for further analyses.
Trimmed and filtered reads were aligned versus the Ensembl human genome version hg19 (GRCh37.p5) using STAR 2.4.0a with the parameter “--outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10% (Dobin et al. 2013).
The number of reads aligning to genes was counted with feature Counts 1.4.5-p1 tool from the Subread package (Liao et al. 2014). Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded.
RAW number of reads aligned to each gene were normalized using Bioconductor package DESeq2 (Wickham 2010). Expression values were calculated using log2 transform of (normalized gene counts + 1). Principal Componets Analysis (PCA) was done using mean-centered gene expression values. We also visualized pairwise Pearson correlation heatmaps for each pair of samples based on the genes having the highest expression variances among the samples, using pheatmap package.
Differentially expressed genes were identified using DESeq2. Only genes with a minimum absolute log2-fold change of +1 a maximum Benjamini-Hochberg corrected p-value of 0.05 were deemed to be significantly differentially expressed. Volcano plots were created by R package ggplot2 (Wickham 2010) using the log2 fold-changes as the x-axis and –log10 of Benjamini-Hochberg adjusted p-values as the y-axis.
Genome_build: hg19 (GRCh37.p5)
Supplementary_files_format_and_content: Unnormalized count of reads aligned to each gene

source_name: Human embryo

growth_protocol: 2a2iL-induced naïve cells were routinely passaged every 3-4 days using trypsin and cultured on inactivated-MEF in 2iL medium. Primed hESCs were cultured on inactivated-MEF in medium containing bFGF.

extract_protocol:
RNA was isolated from samples using the Purelink miRNA isolation Kit (Ambion) in combination with PureLink. RNA Mini Kit for isolation of RNA >150nt. Large sized RNA fraction were treatened with on-column DNase digestion (DNase-Free DNase Set, Qiagen) to avoid contamination by genomic DNA.
RNA and library preparation integrity were verified with a BioAnalyzer 2100 (Agilent) or LabChip Gx Touch 24 (Perkin Elmer). 1µg of total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian (Clontech). Sequencing was performed on the NextSeq500 instrument (Illumina) using v2 chemistry, resulting in minimum of 30M reads per library with 2x75bp paired end setup.

value: Royan H5

tag: passage no.

tag: prime status

value: primed


title: pRH6

description: Primed hESCs from Royan H6 cell line

tag: cell line

value: Royan H6


title: B73 Control (Replicate 4)

description:
B73-C4
14999X3


title: B73 Control (Replicate 3)

description:
B73-C3
14999X25


title: hESC

value: embryonic stem cells

tag: gender

value: female


title: EDN, 1

value: Kidney Cortical Tissue

tag: disease


title: epe1KO_parent_of_DN2-DN11

description: paired with epe1KO_tfs1DN_input_DN2-DN11


title: Cocaine 5

description:
C14
C5_CAGATC
SST-TLG512

tag: strain background

tag: number of nuclei


title: B73 Control (Replicate 2)

description:
B73-C2
14999X16

tag: line


title: nRH5_2

description: Naïve hESCs from Royan H5 cell line

value: naive


title: nRH5_1

description: Naïve hESCs from Royan H5 cell line


title: epe1KO_tfs1DN1

description:
paired with  epe1KO_input_DN1_DN13
Parent =  epe1KO_parent_of_DN1_DN13


title: EDN, 2

value: early diabetic nephropathy


title: B73 Control (Replicate 1)

description:
B73-C1
14999X42

tag: Stage


title: nRH6_2

description: Naïve hESCs from Royan H6 cell line


title: Cocaine 4

description:
C11
C4_ATCACG
SST-TLG511

value: 7.5mg/kg cocaine

tag: region


title: epe1KO_tfs1DN13

tag: strain

tag: temperature


title: epe1KO_parent_of_DN1_DN13

description: paired with  epe1KO_input_DN1_DN13

tag: antibody


title: epe1KO_tfs1DN10


title: nRH6_1

description: Naïve hESCs from Royan H6 cell line


title: Cocaine 2

description:
C2
c2_TTAGGC
SST-TLG509

value: 1 Hour


title: Cocaine 3

description:
C4
c3_CAGATC
SST-TLG510

value: Nucleus Accumbens


title: epe1KO_input_DN1_DN13


title: Cocaine 7

description:
C16
C7_GGCTAC
SST-TLG514


title: epe1KO_tfs1DN11


title: Cocaine 1

description:
C1
c1_ATCACG
SST-TLG508


title: Run2_rRELMa_3

city: Riverside

first: Meera

middle: Goh

last: Nair

address: 301 School of Medicine Research Building, 900 University Avenue,

department: Division of Biomedical Sciences

institute: University of California Riverside

description: cell lystes collected after treatment for mRNA quantification

hyb_protocol: Followed NanoString nCounter XT gene expression assay protocol. Briefly, hybridization buffer was mixed with the nCounter Myeloid Innate Immunity Panel reporter codeset to prepare a master mix. Master mix, sample and Rnase-fee water was combined with nCounter Myeloid Innate Immunity Panel Capture codeset. Samples were then incubated for 18 h at 65 deg C.

scan_protocol: Raw counts of mRNA hybridized to oligos were counted using the NanoString nCounter instrument.

data_processing: Data generated through applying raw files to NanoString nSolver 4.0 software.

source_name: CD11c+ cells

growth_protocol: CD11c+ cells isolated from Nb infected mouse lungs were plated overnight at 37 deg C and serum starved for 1 hour.

extract_protocol: Cells were rinsed in 1X PBS and lysed using cell lysis buffer (Qiagen).

treatment_protocol: Samples received either PBS or 500ng/ml recombinant RELMa treatement for 4 h at 37 deg C.

tag: tissue

value: CD11c+ cells

tag: cell type

value: Nippostrongylus brasiliensis infected lungs


title: Run2_rRELMa_2

label_protocol: Followed NanoString nCounter XT gene expression assay protocol. Briefly, hybridization buffer was mixed with the nCounter Myeloid Innate Immunity Panel reporter codeset to prepare a master mix. Master mix, sample and Rnase-fee water was combined with nCounter Myeloid Innate Immunity Panel Capture codeset. Samples were then incubated for 18 h at 65 deg C.


title: Cocaine 6

description:
C15
C6_GATCAG
SST-TLG513

tag: treatment


title: Saline 10

description:
S46
s10_ATCACG
SST-TLG507

source_name: saline_FACs isolated nucleus accumbens somatostatin interneuron nuclei

value: Saline


title: Run2_PBS_3


title: CD45-3

first: Lora

last: Bankova

address: 60 Fenwood Road

data_processing:
Illumina NextSeq500
Each sample’s sequences were aligned utilizing STAR v2.4.2a (Dobin, Davis et al. Bioinformatics 2013) and the following parameters: --twopassMode Basic, -- alignIntronMax 1000000, --alignMatesGapMax 1000000, --sjdbScore 2, --quantMode TranscriptomeSAM, --sjdbOverhang 24. Alignments were processed using Picard v1.1073 tools to add read groups and other sequencing information, reorder the BAM file to the reference, and mark duplicate sequences.
The data was assessed for quality using RNA-SeQC (DeLuca, Levin et al.Bioinformatics 2012). TPM were quantified using RSEM v1.2.21 (Li and Dewey BMC Bionformatics 2011) with the paired-end option. Raw counts for differential expression analysis were generated using the FeatureCounts function of Rsubread (Liao, Smyth et al.Nucleic Acids Res 2013)
Differential expression analysis was conducted using the DEseq2 package (Love, Huber et al. Genome Biol 2014). Genes were considered to be significantly differentially regulated based on a fold change in expression of > 4-fold and a false discovery rate of <0.05 based on a Benjamini-Hochberg adjusted p-value to correct for multiple comparisons.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM and FPKM values for each sample
Supplementary_files_format_and_content: tab-delimited text file with normalized counts from Deseq2 analysis

source_name: trachea

extract_protocol:
RTracheal epithelial cell suspensions were derived through a 2 step protocol: incubation with high dose dispase followed by papain digestion. Brush cells were identified flow cytometrically as CD45-EpCAM+eGFP+ cells, EpCAM+ cells were identified as CD45−EpCAM+ cells and CD45+ cells were separately sorted using monoclonal antibodies against CD45 and EpCAM, after dead cell exclusion with propidium iodide. Cells were sorted into TCL buffer supplemented with RNAprotect Cell Reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: tracheal CD45+ hematopoetic cells


title: Run2_rRELMa_1


title: Saline 9

description:
S43
s9_ACTTGA
SST-TLG506


title: CD45-2


title: CD45-1


title: CD45-4


title: Run2_PBS_1


title: Saline 8

description:
S40
s8_CGATGT
SST-TLG505


title: EpCAM-7

value: tracheal EpCAM+ epithelial cells


title: Saline 6

description:
S14
S6_ACTTGA
SST-TLG503


title: EpCAM-5


title: EpCAM-6


title: Run1_PBS_3


title: Run1_PBS_2


title: EpCAM-4


title: Saline 3

description:
S6
s3_CTTGTA
SST-TLG500


title: Saline 5

description:
S13
S5_GCCAAT
SST-TLG502


title: EpCAM-3


title: Run1_PBS_1


title: Saline 2

description:
S3
s2_GCCAAT
SST-TLG499


title: Run1_rRELMa_2


title: Saline 7

description:
S15
S7_TAGCTT
SST-TLG504


title: Saline 1

description:
S1
s1_CGATGT
SST-TLG498


title: Run1_rRELMa_1


title: ChAT-eGFP-7

value: tracheal ChAT-eGFP+ brush cells


title: Run1_rRELMa_3


title: EpCAM-1


title: Run2_PBS_2


title: ChAT-eGFP-6