title: nSyb_48h_ORN (N447Barcode_726-507)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_711-507)

status: Public on Jan 04 2020

type: SRA

city: Houston

first: Hongjie

last: Li

state: TX

address: one Baylor Plaza

country: USA

institute: Baylor College of Medicine

description:
Single cell
df_libs.csv, htseq.tab

library_source: transcriptomic

data_processing:
library strategy: 5’ RACE RNA-seq
alignment (STAR 2.4.2a, ENCODE standard options, except --outFilterScoreMinOverLread 0.4 --outFilterMatchNminOverLread 0.4 --  outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04)
gene count (HTSeq-count 0.7.1, default options, except -m intersection-strict)
Genome_build: Dmel r6.10
Supplementary_files_format_and_content: df_htseq_ORN.csv, df_libs_ORN.csv

molecule: total RNA

organism: Drosophila melanogaster

source_name: in house

extract_protocol:
None
Modified SMART-seq2 (Li et al. 2017)

tag: genotype

tag: number of cells

tag: orn type

value: labels 44 ORN types


title: NT#10_FoxA1

city: Amsterdam

first: Yongsoo

last: Kim

address: De Boelelaan 1118

country: Netherlands

institute: University Medical Center Amsterdam, Location VUmc

library_source: genomic

data_processing:
Sequences were generated by the Illumina Hiseq 2500 genome analyser (using 65bp reads) and were processed by the Illumina pipeline.
Reads were aligned to the Human Reference Genome (hg19) using BWA9. Reads with a BWA alignment quality score less than 20 were removed.
Peaks are called using MACS2 and Dfilter, followed by taking intersect.bedion between them.
Genome_build: Hg19
Supplementary_files_format_and_content: peaks bed

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: MCF-7 cells were cultured in DMEM medium (Gibco), supplemented with 10% FCS, and 1% penicillin/streptomycin.

extract_protocol:
Chromatin immunoprecipitations were performed as described previously with minor changes (Zwart et al., 2013). Samples were crosslinked in solution A with 2mM DSG (CovaChem) for 25 minutes at room temperature. After 25 minutes, 1% formaldehyde was added for 20 minutes and subsequently quenched with glycine. Samples were lysed as described (Schmidt et al., 2009) and sonicated for at least 10 cycles of 30s on, 30s off using a Diagenode Bioruptor Pico. For each ChIP, 5ug of antibody was conjugated with 50ul Protein A magnetic beads. Antibodies used were AR (sc-816, Santa Cruz), H3K27ac (39133, Active Motif), H3K4me3 (Ab8580, Abcam) and H3K27me3 (39155, Active Motif). Immunoprecipitated DNA was processed for library preparation (Part# 0801-0303, KAPA biosystems kit).
Immunoprecipitated DNA was processed for library preparation (Part# 0801-0303, KAPA biosystems kit).

treatment_protocol: MCF-7 cells were infected with the indicated sgRNA.

tag: sgrna

value: Wild type

tag: chip antibody

tag: cell line


title: nSyb_48h_ORN (N447Barcode_710-507)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_728-507)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_707-507)

description:
Single cell
df_libs.csv, htseq.tab


title: Balbc_ThioIL4c_sample_0019

city: Saint Louis

first: Mei San

last: Tang

state: MO

address: 660 S Euclid, Campus Box 8118

department: Pathology & Immunology

institute: Washington University in St Louis

data_processing:
CEL-seq2 reads were first demultiplexed using the bc_demultiplex script from https://github.com/yanailab/CEL-Seq-pipeline
Demultiplexed reads were aligned to the mm10 mouse reference genome using bowtie2 (version 2.2.9).
Aligned reads were counted for each gene using a modified htseq-count script (from https://github.com/yanailab/CEL-Seq-pipeline) adapted for CEL-seq2 reads with unique molecular identified (UMI). We included only reads with MAPQ score > 30.
Finally, singleton genes (genes counted only once) were removed and a count matrix were generated, where each row is a unique gene and each column a unique sample.
Genome_build: mm10
Supplementary_files_format_and_content: Count matrix, where each row is a unique gene and each column is a unique sample.

molecule: polyA RNA

organism: Mus musculus

source_name: Peritoneal macrophages

growth_protocol: C57BL/6 and BALB/c mice used to compare strain effects on accessible chromatin landscape were purchased directly from Jackson laboratory and used immediately for experiments.

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (QIAgen) based on manufacturer’s protocol, with an additional DNase digestion step using the RNase-free DNase set (QIAgen).
RNA from each sample was uniquely barcoded and libraries were constructed using the CELSeq2 protocol as described in Hashimshony et al (Genome Biology 2016).

treatment_protocol:
Mice treated with 2ml Thioglycollate on Day 0 and peritoneal cells harvested on Day 4.
4 days prior to peritoneal cells harvest, all mice were treated with intra-peritoneal injection of IL-4 complexes  (i.e. 5μg of IL-4 and 25μg of anti-IL4) every other day, in addition to the group-specific treatment as detailed in the Samples Section above.

tag: strain

value: BALB/c

tag: macrophage phenotype

value: Monocyte-derived, F4/80int CD206+


title: Balbc_ThioIL4c_sample_0018


title: Balbc_ThioIL4c_sample_0021


title: nSyb_48h_ORN (N447Barcode_706-507)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_705-507)

description:
Single cell
df_libs.csv, htseq.tab


title: Balbc_IL4c_sample_0009

treatment_protocol:
-
4 days prior to peritoneal cells harvest, all mice were treated with intra-peritoneal injection of IL-4 complexes  (i.e. 5μg of IL-4 and 25μg of anti-IL4) every other day, in addition to the group-specific treatment as detailed in the Samples Section above.

value: Tissue resident, F4/80hi CD206-


title: Balbc_ThioIL4c_sample_0020


title: Balbc_ThioIL4c_sample_0017


title: nSyb_48h_ORN (N447Barcode_704-507)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_718-507)

description:
Single cell
df_libs.csv, htseq.tab


title: NT#10_ERa

value: ERa


title: nSyb_48h_ORN (N447Barcode_702-507)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_714-507)

description:
Single cell
df_libs.csv, htseq.tab


title: B6_ThioIL4c_sample_0015


title: nSyb_48h_ORN (N447Barcode_712-507)

description:
Single cell
df_libs.csv, htseq.tab


title: B6_ThioIL4c_sample_0014


title: Balbc_IL4c_sample_0007


title: nSyb_48h_ORN (N447Barcode_715-507)

description:
Single cell
df_libs.csv, htseq.tab


title: B6_ThioIL4c_sample_0013


title: B6_ThioIL4c_sample_0012


title: nSyb_48h_ORN (N447Barcode_726-517)

description:
Single cell
df_libs.csv, htseq.tab


title: B6_ThioIL4c_sample_0011


title: nSyb_48h_ORN (N447Barcode_724-517)

description:
Single cell
df_libs.csv, htseq.tab


title: B6_ThioIL4c_sample_0010


title: nSyb_48h_ORN (N447Barcode_722-517)

description:
Single cell
df_libs.csv, htseq.tab


title: Balbc_IL4c_sample_0008


title: nSyb_48h_ORN (N447Barcode_703-507)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_720-517)

description:
Single cell
df_libs.csv, htseq.tab


title: B6_ThioIL4c_sample_0002


title: Balbc_ThioIL4c_sample_0016


title: nSyb_48h_ORN (N447Barcode_721-517)

description:
Single cell
df_libs.csv, htseq.tab


title: B6_IL4c_sample_0024


title: nSyb_48h_ORN (N447Barcode_723-517)

description:
Single cell
df_libs.csv, htseq.tab


title: Balbc_IL4c_sample_0006


title: B6_IL4c_sample_0023


title: B6_IL4c_sample_0022


title: B6_IL4c_sample_0005


title: B6_IL4c_sample_0025


title: nSyb_48h_ORN (N447Barcode_729-517)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_728-517)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_727-517)

description:
Single cell
df_libs.csv, htseq.tab


title: B6_IL4c_sample_0001


title: nSyb_48h_ORN (N447Barcode_716-517)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_701-507)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_710-517)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_719-517)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_707-517)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_705-517)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_704-517)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_703-517)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_715-517)

description:
Single cell
df_libs.csv, htseq.tab


title: B6_IL4c_sample_0003


title: nSyb_48h_ORN (N447Barcode_714-517)

description:
Single cell
df_libs.csv, htseq.tab


title: B6_IL4c_sample_0004


title: nSyb_48h_ORN (N447Barcode_711-517)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_702-517)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_701-517)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_727-506)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_712-517)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_726-506)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_724-506)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_723-506)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_718-517)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_722-506)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_706-517)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_729-506)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_721-506)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_728-506)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_716-506)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_720-506)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_714-506)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_718-506)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_712-506)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_715-506)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_710-506)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_711-506)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_719-506)

description:
Single cell
df_libs.csv, htseq.tab


title: NSA+TNFa-4

city: Shanghai

first: Dai

last: Jialin

state: Shanghai

address: Room 507-1, Build 6, QiuYue Rd 26, PuDong District

country: China

institute: Interdisciplinary Research Center of Biology and Chemistry

data_processing:
The raw paired-end fastq files were checked for quality control by fastQC and subsequently trimmed using fastp (Ver 0.20.0) with default parameters
Cleaned fastq files were aligned to human genome with STAR (Ver 2.7.2) then Featurecounts (Ver 1.6.4) was used to caculate gene expression and aggregate to expression counts matrix
All the futher data analysis were processed using R (Ver 3.6.1) and  Bioconductor packages (Ver 3.10)
Genome_build: GRCh38
Supplementary_files_format_and_content: raw counts matrix generated by FeatureCounts

growth_protocol: HUVECs were allowed to grow in endothelial cell growth medium 2 containing supplement to confluence.

extract_protocol:
Sangon RNA extraction kit (Order NO. B511321)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HUVECs were starved with basal medium containing 0.5% FBS for 6h, then were treated with vehicle, NSA, TNF-alpha, TNF-alpha+NSA for 6h.

value: HUVEC

tag: treatment

value: NSA+TNFa


title: Bezhta1180

type: genomic

city: Tucson

first: Tatiana

middle: M.

last: Karafet

state: AZ

address: BSW #246, 1041 E Lowell Str.

department: ARL

institute: University of Arizona

description: Genomic DNA extracted from cheek swab was genotyped using Illumina HumanOmniExpress-24 v1.0 BeadChip platform.

hyb_protocol: Standard Illumina procedures.

scan_protocol: Standard Illumina procedures.

data_processing: Illumina GenomeStudio Software has been used to analyze the data. GenomeStudio Genotyping Module Version is  1.9.4.

label: biotin

source_name: cheek swab

label_protocol: Standard Illumina procedures.

extract_protocol: Extraction of genomic DNA from cheek swab was performed using standard extraction protocols.

tag: population

value: Bezhta

tag: village

tag: region

value: Daghestan

tag: gender

value: Female


title: Bezhta1184

value: Male


title: Bezhta1186


title: Bezhta1178


title: Bezhta1191


title: nSyb_48h_ORN (N447Barcode_702-506)

description:
Single cell
df_libs.csv, htseq.tab


title: Karata1075

value: Karata


title: Karata1066


title: NSA+TNFa-3


title: Bezhta1185


title: Bezhta1176


title: Karata1073


title: Bezhta1169


title: Bezhta1182


title: Karata1065


title: nSyb_48h_ORN (N447Barcode_701-506)

description:
Single cell
df_libs.csv, htseq.tab


title: Bezhta1170


title: Bezhta1173


title: Bezhta1183


title: Bezhta1168


title: Karata1070


title: nSyb_48h_ORN (N447Barcode_726-516)

description:
Single cell
df_libs.csv, htseq.tab


title: Bezhta1188


title: Bezhta1177


title: DMSO+TNFa-2

value: DMSO+TNFa


title: nSyb_48h_ORN (N447Barcode_707-506)

description:
Single cell
df_libs.csv, htseq.tab


title: Karata1076


title: Karata1078


title: nSyb_48h_ORN (N447Barcode_719-516)

description:
Single cell
df_libs.csv, htseq.tab


title: Karata1072


title: NSA-4

value: NSA


title: Karata1067


title: nSyb_48h_ORN (N447Barcode_729-516)

description:
Single cell
df_libs.csv, htseq.tab


title: DMSO+TNFa-3


title: nSyb_48h_ORN (N447Barcode_724-516)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_718-516)

description:
Single cell
df_libs.csv, htseq.tab


title: DMSO+TNFa-4


title: nSyb_48h_ORN (N447Barcode_705-506)

description:
Single cell
df_libs.csv, htseq.tab


title: NSA+TNFa-1


title: NSA-2


title: nSyb_48h_ORN (N447Barcode_723-516)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_703-506)

description:
Single cell
df_libs.csv, htseq.tab


title: DMSO-4

value: DMSO


title: NSA-3


title: nSyb_48h_ORN (N447Barcode_712-516)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_722-516)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_716-516)

description:
Single cell
df_libs.csv, htseq.tab


title: Bezhta1187


title: DMSO-3


title: nSyb_48h_ORN (N447Barcode_728-516)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_715-516)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_714-516)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_710-516)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_727-516)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_704-506)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_705-516)

description:
Single cell
df_libs.csv, htseq.tab


title: Godoberi1060

value: Godoberi


title: Godoberi1061


title: Karata1063


title: nSyb_48h_ORN (N447Barcode_721-516)

description:
Single cell
df_libs.csv, htseq.tab

value: labels 44 ORN types


title: nSyb_48h_ORN (N447Barcode_720-516)

description:
Single cell
df_libs.csv, htseq.tab


title: DMSO-2


title: nSyb_48h_ORN (N447Barcode_701-516)

description:
Single cell
df_libs.csv, htseq.tab


title: Balbc_ThioIL4c_4

description:
genomic DNA (transposase-accessible)
Comparison of AAMs from C57BL/6 vs. BALB/c genetics backgrounds
ATACSeqB6BalbcIL4c_union_peaks_max100.txt
Balbc_ThioIL4c_dedup_nochrMY_posSorted_merged.tdf

data_processing:
Raw reads aligned to the reference mouse genomes mm9 (for experiments comparing IL-4 stimulated macrophages to unstimulated macrophages) and mm10 (for experiment comparing AAMs from C57BL/6 and BALB/c mice) using bowtie2 (v2.2.9), with the parameters --maxin 2000 and --local, while keeping all other parameters at default settings.
Reads with mappability score (MAPQ) <30 and duplicate reads, as well as reads mapping to mitochondrial DNA and chromosome Y, were removed.
Filtered reads were merged across all replicates from the same group. Peak calling was done on the merged reads for each group using PeaKDeck v1.1 (McCarthy and O'Callaghan, Bioinformatics 2014), using the parameters: central bin (-bin) 75bp, background bin (-back) 10000bp and step size (-STEP) of 25. Background probability distribution was generated using 100000 randomly selected sites (-npBack). Significance was defined using a p-value of less than 0.0001 (for experiments comparing IL-4 stimulated macrophages to unstimulated macrophages) and 0.00001 (for experiment comparing AAMs from C57BL/6 and BALB/c mice).
Genome_build: mm9, mm10
Supplementary_files_format_and_content: .txt files are count matrix, where each row is a unique accessible region; columns 1-4 correspond to the region genomic locations and subsequent columns correspond to a unique sample.
Supplementary_files_format_and_content: .tdf files are merged reads across biological replicates and converted to a Tiled Data Format (tdf) using IGVtools for visualization on the Integrative Genomics Viewer (IGV)

growth_protocol: C57BL/6 mice used in the experiments to identify the effects of IL-4 stimulation on accessible chromatin landscape were bred at the specific-pathogen free animal facility in NYU. C57BL/6 and BALB/c mice used in the experiment comparing strain effects on accessible chromatin landscape were purchased directly from Jackson laboratory and used immediately for experiments.

extract_protocol:
ATACSeq was performed as described in Buenrostro et al (Nature Methods 2013). FACS-purified cells were spinned down at 1500rpm for 5 min at 4 degree Celsius and washed once with 50ul cold PBS. Cells were then lysed with 50ul lysis buffer (10 mM Tris-HCl, pH7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) and the nuclei were immediately spinned down at 1500rpm for 10 min at 4 degree Celsius. The isolated cell nuclei were then incubated with 50ul of transposase reaction (25ul TD buffer, 2.5ul Tn5 enzyme, 22.5ul nuclease-free water)for 30 mins at 37 degree Celcius. Transposed DNA was purified using the QIAgen MinElute PCR Purification Kit following manufacturer's guide. TD buffer and Tn5 enzyme are from the Nextera DNA Sample Preparation kit (Illumina Cat #FC-121-1030).
Tranposed DNA was amplified using a low-cycle number PCR protocol and custom primers designed for multiplexing based on Buenrostro et al (Nature Methods 2013). Each sample underwent 14-16 cycles of PCR amplification. Amplified libraries of transposed DNA were purified with the QIAgen MinElute Kit and sequenced on the HiSeq 2000.

treatment_protocol:
Intra-peritoneal 2ml thioglycollate on Day 0 and IL-4 complexes (i.e. 5μg of IL-4 and 25μg of anti-IL4 in 100ul sterile PBS) on Day 0 and Day 2.
All mice were treated with group-specific treatment as detailed in the Samples Section above and peritoneal cells were harvested on Day 4.


title: nSyb_48h_ORN (N447Barcode_703-516)

description:
Single cell
df_libs.csv, htseq.tab


title: Balbc_ThioIL4c_2


title: nSyb_48h_ORN (N447Barcode_729-505)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_711-516)

description:
Single cell
df_libs.csv, htseq.tab


title: Karata1069


title: nSyb_48h_ORN (N447Barcode_704-516)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_702-516)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_727-505)

description:
Single cell
df_libs.csv, htseq.tab


title: Balbc_ThioIL4c_3


title: nSyb_48h_ORN (N447Barcode_707-516)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_706-516)

description:
Single cell
df_libs.csv, htseq.tab


title: Balbc_ThioIL4c_1


title: nSyb_48h_ORN (N447Barcode_726-505)

description:
Single cell
df_libs.csv, htseq.tab


title: Balbc_IL4c_2

description:
genomic DNA (transposase-accessible)
Comparison of AAMs from C57BL/6 vs. BALB/c genetics backgrounds
ATACSeqB6BalbcIL4c_union_peaks_max100.txt
Balbc_IL4c_dedup_nochrMY_posSorted_merged.tdf

treatment_protocol:
Intra-peritoneal IL-4 complexes  (i.e. 5μg of IL-4 and 25μg of anti-IL4 in 100ul sterile PBS) on Day 0 and Day 2.
All mice were treated with group-specific treatment as detailed in the Samples Section above and peritoneal cells were harvested on Day 4.


title: nSyb_48h_ORN (N447Barcode_721-505)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_720-505)

description:
Single cell
df_libs.csv, htseq.tab


title: Balbc_IL4c_1


title: nSyb_48h_ORN (N447Barcode_716-505)

description:
Single cell
df_libs.csv, htseq.tab


title: Godoberi1062


title: Balbc_IL4c_3


title: nSyb_48h_ORN (N447Barcode_719-505)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_715-505)

description:
Single cell
df_libs.csv, htseq.tab


title: B6_ThioIL4c_4

description:
genomic DNA (transposase-accessible)
Comparison of AAMs from C57BL/6 vs. BALB/c genetics backgrounds
ATACSeqB6BalbcIL4c_union_peaks_max100.txt
B6_ThioIL4c_dedup_nochrMY_posSorted_merged.tdf


title: nSyb_48h_ORN (N447Barcode_714-505)

description:
Single cell
df_libs.csv, htseq.tab


title: B6_ThioIL4c_3


title: nSyb_48h_ORN (N447Barcode_724-505)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_723-505)

description:
Single cell
df_libs.csv, htseq.tab


title: B6_ThioIL4c_2


title: nSyb_48h_ORN (N447Barcode_712-505)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_728-505)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_706-505)

description:
Single cell
df_libs.csv, htseq.tab


title: B6_ThioIL4c_1


title: nSyb_48h_ORN (N447Barcode_705-505)

description:
Single cell
df_libs.csv, htseq.tab


title: Godoberi1057


title: nSyb_48h_ORN (N447Barcode_704-505)

description:
Single cell
df_libs.csv, htseq.tab


title: B6_IL4c_4

description:
genomic DNA (transposase-accessible)
Comparison of AAMs from C57BL/6 vs. BALB/c genetics backgrounds
ATACSeqB6BalbcIL4c_union_peaks_max100.txt
B6_IL4c_dedup_nochrMY_posSorted_merged.tdf


title: nSyb_48h_ORN (N447Barcode_703-505)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_702-505)

description:
Single cell
df_libs.csv, htseq.tab


title: B6_IL4c_3


title: Botlikh1052

value: Botlikh


title: Godoberi1053


title: nSyb_48h_ORN (N447Barcode_729-515)

description:
Single cell
df_libs.csv, htseq.tab


title: Botlikh1051


title: B6_IL4c_2


title: Botlikh1050


title: B6_IL4c_1


title: nSyb_48h_ORN (N447Barcode_711-505)

description:
Single cell
df_libs.csv, htseq.tab


title: Botlikh1044


title: nSyb_48h_ORN (N447Barcode_722-505)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_707-505)

description:
Single cell
df_libs.csv, htseq.tab


title: ThioIL4c-3_R2

description:
genomic DNA (transposase-accessible)
Effect of IL-4 stimulation, Run2
ATACSeqIL4cMacs_union_peaks_max100.txt
M3_merged_runs_nochrMY_dedup.tdf


title: nSyb_48h_ORN (N447Barcode_728-515)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_724-515)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_723-515)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_701-505)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_722-515)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_710-505)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_720-515)

description:
Single cell
df_libs.csv, htseq.tab


title: ThioIL4c-2_R1

description:
genomic DNA (transposase-accessible)
Effect of IL-4 stimulation, Run1
ATACSeqIL4cMacs_union_peaks_max100.txt
M3_merged_runs_nochrMY_dedup.tdf


title: Botlikh1046


title: nSyb_48h_ORN (N447Barcode_721-515)

description:
Single cell
df_libs.csv, htseq.tab


title: ThioIL4c-3_R1


title: ThioIL4c-2_R2


title: Botlikh1045


title: Godoberi1058


title: Botlikh1035


title: nSyb_48h_ORN (N447Barcode_718-515)

description:
Single cell
df_libs.csv, htseq.tab


title: Godoberi1032


title: nSyb_48h_ORN (N447Barcode_716-515)

description:
Single cell
df_libs.csv, htseq.tab


title: Godoberi1041


title: nSyb_48h_ORN (N447Barcode_719-515)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_727-515)

description:
Single cell
df_libs.csv, htseq.tab


title: Thio-3_R2

description:
genomic DNA (transposase-accessible)
Effect of IL-4 stimulation, Run2
ATACSeqIL4cMacs_union_peaks_max100.txt
M2_merged_runs_nochrMY_dedup.tdf

treatment_protocol:
Intra-peritoneal 2ml thioglycollate on Day 0.
All mice were treated with group-specific treatment as detailed in the Samples Section above and peritoneal cells were harvested on Day 4.


title: Godoberi1038


title: Godoberi1029


title: Botlikh1033


title: Botlikh1042


title: nSyb_48h_ORN (N447Barcode_706-515)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_715-515)

description:
Single cell
df_libs.csv, htseq.tab


title: ΔES27Lb_polysome associated mRNA_rep2

city: Bern

first: Norbert

last: Polacek

address: Freiestrasse 3

department: Chemistry and Biochemistry

country: Switzerland

institute: University of Bern

description:
ΔES27Lb_polysome associated mRNA_rep2
L2P

data_processing:
Quality control using fastqc tool
Mapping performed using HISAT2; more than 95% mapping rate, -p 8
counting was performed using featureCounts
Genome_build: strain BY4742
Supplementary_files_format_and_content: counts

organism: Saccharomyces cerevisiae

source_name: Yeast strain yJD1055

extract_protocol:
Yeast cells were grown in YPD media to OD = 0.8. Cells were harvested by centrifugation and pellets were opened using a FastPrep. Lysates  were cleared by centrifugation and loaded on a density gradient for Ultracentrifugation. Fractions containg polysomes were pooled and RNA was extracted via hot acid phenole extraction.
polyA enriched mRNAs were transformed into a cDNA library using the Illumina TrueSeq stranded mRNA Kit. Library size was determined using Qbit.

tag: rrna expression

value: plasmid born ΔES27Lb rRNA sequence

tag: mrna enrichment

value: poly-A-Enrichment via oligo-dT-beads


title: nSyb_48h_ORN (N447Barcode_726-515)

description:
Single cell
df_libs.csv, htseq.tab


title: ThioIL4c-1_R1

value: Monocyte-derived, F4/80int CD206+


title: nSyb_48h_ORN (N447Barcode_705-515)

description:
Single cell
df_libs.csv, htseq.tab


title: ΔES27Lb_polysome associated mRNA_rep3

description:
ΔES27Lb_polysome associated mRNA_rep3
L3P

source_name: Yeast strain yJD1056


title: Thio-2_R2


title: nSyb_48h_ORN (N447Barcode_704-515)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_710-515)

description:
Single cell
df_libs.csv, htseq.tab


title: Godoberi1020


title: Godoberi1019


title: nSyb_48h_ORN (N447Barcode_707-515)

description:
Single cell
df_libs.csv, htseq.tab


title: Thio-1_R2


title: ΔES27Lb_total mRNA_rep3

description:
ΔES27Lb_total mRNA_rep3
L3T

source_name: Yeast strain yJD1053

extract_protocol:
Yeast cells were grown in YPD media to OD = 0.8. Cells were harvested by centrifugation and pellets were opened using a FastPrep. Lysates  were cleared by centrifugation and total RNA was extracted by hot acid phenole extraction.
polyA enriched mRNAs were transformed into a cDNA library using the Illumina TrueSeq stranded mRNA Kit. Library size was determined using Qbit.


title: nSyb_48h_ORN (N447Barcode_712-515)

description:
Single cell
df_libs.csv, htseq.tab


title: Godoberi1024


title: nSyb_48h_ORN (N447Barcode_714-515)

description:
Single cell
df_libs.csv, htseq.tab


title: ΔES27Lb_polysome associated mRNA_rep1

description:
ΔES27Lb_polysome associated mRNA_rep1
L1P

source_name: Yeast strain yJD1054


title: Thio-2_R1

description:
genomic DNA (transposase-accessible)
Effect of IL-4 stimulation, Run1
ATACSeqIL4cMacs_union_peaks_max100.txt
M2_merged_runs_nochrMY_dedup.tdf


title: nSyb_48h_ORN (N447Barcode_703-515)

description:
Single cell
df_libs.csv, htseq.tab


title: Thio-1_R1


title: IL4c-3_R2

description:
genomic DNA (transposase-accessible)
Effect of IL-4 stimulation, Run2
ATACSeqIL4cMacs_union_peaks_max100.txt
M1_merged_runs_nochrMY_dedup.tdf

value: Tissue resident, F4/80hi CD206-


title: ΔES27Lb_total mRNA_rep1

description:
ΔES27Lb_total mRNA_rep1
L1T

source_name: Yeast strain yJD1051


title: nSyb_48h_ORN (N447Barcode_729-503)

description:
Single cell
df_libs.csv, htseq.tab


title: ΔES27Lb_total mRNA_rep2

description:
ΔES27Lb_total mRNA_rep2
L2T

source_name: Yeast strain yJD1052


title: nSyb_48h_ORN (N447Barcode_728-503)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_702-515)

description:
Single cell
df_libs.csv, htseq.tab


title: WT_polysome associated mRNA_rep3

description:
WT_polysome associated mRNA_rep3
W3P

source_name: Yeast strain yJD1050

value: plasmid born WT rRNA sequence


title: nSyb_48h_ORN (N447Barcode_727-503)

description:
Single cell
df_libs.csv, htseq.tab


title: IL4c-2_R2


title: nSyb_48h_ORN (N447Barcode_726-503)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_706-506)

description:
Single cell
df_libs.csv, htseq.tab


title: Botlikh1027


title: WT_polysome associated mRNA_rep2

description:
WT_polysome associated mRNA_rep2
W2P

source_name: Yeast strain yJD1049


title: nSyb_48h_ORN (N447Barcode_724-503)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_723-503)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_701-515)

description:
Single cell
df_libs.csv, htseq.tab


title: Botlikh1016


title: nSyb_48h_ORN (N447Barcode_722-503)

description:
Single cell
df_libs.csv, htseq.tab


title: IL4c-3_R1

description:
genomic DNA (transposase-accessible)
Effect of IL-4 stimulation, Run1
ATACSeqIL4cMacs_union_peaks_max100.txt
M1_merged_runs_nochrMY_dedup.tdf


title: WT_polysome associated mRNA_rep1

description:
WT_polysome associated mRNA_rep1
W1P

source_name: Yeast strain yJD1048


title: nSyb_48h_ORN (N447Barcode_716-503)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_718-503)

description:
Single cell
df_libs.csv, htseq.tab


title: WT_total mRNA_rep3

description:
WT_total mRNA_rep3
W3T

source_name: Yeast strain yJD1047


title: IL4c-1_R2


title: WT_total mRNA_rep2

description:
WT_total mRNA_rep2
W2T

source_name: Yeast strain yJD1046


title: Botlikh1011


title: nSyb_48h_ORN (N447Barcode_715-503)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_714-503)

description:
Single cell
df_libs.csv, htseq.tab


title: Res-2_R2

description:
genomic DNA (transposase-accessible)
Effect of IL-4 stimulation, Run2
ATACSeqIL4cMacs_union_peaks_max100.txt
M0_merged_runs_nochrMY_dedup.tdf

treatment_protocol:
100ul of intra-peritoneal sterile PBS on Day 0 and Day 2.
All mice were treated with group-specific treatment as detailed in the Samples Section above and peritoneal cells were harvested on Day 4.


title: nSyb_48h_ORN (N447Barcode_721-503)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_720-503)

description:
Single cell
df_libs.csv, htseq.tab


title: Res-2_R1

description:
genomic DNA (transposase-accessible)
Effect of IL-4 stimulation, Run1
ATACSeqIL4cMacs_union_peaks_max100.txt
M0_merged_runs_nochrMY_dedup.tdf


title: Godoberi1010


title: Res-1_R2


title: Replicate2_T16

city: Barcelona

first: Alberto

last: Perez-Posada

address: Passeig Marítim de la Barceloneta, 37-49

country: Spain

institute: Institut de Biologia Evolutiva

description:
R2_T16_25000_ACTGAT
processed data file: R2_table_tpms.txt

data_processing:
Transcriptome mapping for every independent time point using kallisto v0.43.1 with standard parameters (-q read1 read2) onto a set of the largest isoforms of the Capsaspora transcriptome.
Genome_build: Capsaspora genome v3 (Iñaki Ruiz-Trillo lab)
https://figshare.com/articles/Genome_-_Capsaspora_owczarzaki_v3_/4123158/2
Supplementary_files_format_and_content: Resulting transcript-per-million lists from kallisto of every sample bound together in columns of a single matrix using bash and awk

organism: Capsaspora owczarzaki

source_name: Capsaspora adherent cells_13h15 after release

growth_protocol: Cells were incubated at 23 degrees Celsius in ATCC medium 1034 (modified PYNFH medium).

extract_protocol:
Time point samples were washed in 1xPBS, poured in Trizol, and frozen at -80oC. Total RNA was purified using Zymo RNA miniprep kit (Zymo Research, Irvine, CA, USA, #R2050).
mRNA libraries were prepared using the TruSeq Stranded mRNA Sample Prep kit

treatment_protocol: Cultures at 30-50% confluency were treated with Hydroxyurea to a final concentration of 10mM, and left incubating for 14 hours overnight. Cells were released from Hydroxyurea by washing prior to elution in fresh medium; samples were collected by scraping and washing two hours after release, and from there on every 45 minutes until thirteen hours.

tag: cell type

value: Filopodial

value: Released from cell cycle overnight arrest using Hydroxyurea 10mM

tag: time point

value: 13h15 after release


title: nSyb_48h_ORN (N447Barcode_719-503)

description:
Single cell
df_libs.csv, htseq.tab

tag: genotype


title: WT_total mRNA_rep1

description:
WT_total mRNA_rep1
W1T

source_name: Yeast strain yJD1045


title: Thio-3_R1


title: Botlikh1013

description: Genomic DNA extracted from cheek swab was genotyped using Illumina HumanOmniExpress-24 v1.0 BeadChip platform.

value: Daghestan

value: Female


title: Res-1_R1


title: Replicate2_T15

description:
R2_T15_24999_GAGTGG
processed data file: R2_table_tpms.txt

source_name: Capsaspora adherent cells_12h30 after release

value: 12h30 after release


title: Godoberi1021

value: Male


title: nSyb_48h_ORN (N447Barcode_706-503)

description:
Single cell
df_libs.csv, htseq.tab

source_name: in house

tag: number of cells


title: nSyb_48h_ORN (N447Barcode_705-503)

description:
Single cell
df_libs.csv, htseq.tab

tag: orn type


title: pnoc_TRAP_RNA

city: St Louis

first: Joseph

middle: D

last: Dougherty

state: Missouri

address: 4566 Scott Ave, box 8232

department: Genetics and Psychiatry

institute: Washington University

description: ribosome bound RNA

data_processing:
Library strategy: TRAP Ribosome profiling
Trimmomatic v0.33
rRNA depletion, STAR alignment
Alignment to genome (mouse ensembl 77), STAR alignment
Read counts, HTSeq, UCSS Genome Browser assembly ID: mm10
Genome_build: mm10
Supplementary_files_format_and_content: gene counts table (tab-delimited)

source_name: Brain

extract_protocol:
GFP immunoprecipitation for TRAP RNA, Trizol LS RNA extraction
Nugen Ovation RNA-Seq System V2 followed by NEBNext Library Prep for Illumina

treatment_protocol: AAV injection

tag: tissue

value: brain

tag: brain region

value: IPN

tag: developmental stage

value: adult

tag: rna fraction

value: ribosome-bound RNA


title: Replicate2_T14

description:
R2_T14_24998_GTCCGC
processed data file: R2_table_tpms.txt

source_name: Capsaspora adherent cells_11h45 after release

tag: strain

value: 11h45 after release


title: nSyb_48h_ORN (N447Barcode_712-503)

description:
Single cell
df_libs.csv, htseq.tab

value: labels 44 ORN types


title: IPN_input_RNA

description: total RNA

value: total RNA


title: nSyb_48h_ORN (N447Barcode_711-515)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_701-503)

description:
Single cell
df_libs.csv, htseq.tab


title: Godoberi1023

source_name: cheek swab

value: Godoberi


title: Replicate2_T12

description:
R2_T12_24996_ATGTCA
processed data file: R2_table_tpms.txt

source_name: Capsaspora adherent cells_10h15 after release

tag: treatment

value: 10h15 after release


title: nSyb_48h_ORN (N447Barcode_703-503)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_704-503)

description:
Single cell
df_libs.csv, htseq.tab


title: KI1_24h

city: Bayreuth

first: Claus

last: Kuhn

address: Universitätsstr. 30

department: BIOmac Research Center, NW I

country: Germany

institute: University of Bayreuth

description: rRNA depleted total RNA from HCT116 E33Q MED12 knock-in cell line treated for 24 hours with IFN-gamma

data_processing:
RTA2 was used for base-calling on NextSeq 500
Following adapter trimming with Trimmomatic (Bolger et al., 2014)) and ribosomal RNA filtering with SortMeRNA (Kopylova et al., 2012), sequenced reads were assigned to full human transcriptome from Ensembl (GRCh38) in strand-specific mode using kallisto (Bray et al., 2016).
Genome_build: human transcriptome Ensembl GRCh38
Supplementary_files_format_and_content: abundance in estimated counts file was generated by assigning the sequenced reads to human transcriptome GRCh38 with kallisto (Bray et al., 2016).

source_name: HCT116 E33Q MED12 knock-in

growth_protocol: HCT116 and HCT116 E33Q MED12 knock-in cell lines were maintained in McCoy’s 5A  media supplemented with 10% fetal bovine serum (FBS). Cells were cultivated at 37°C in 5% CO2 humidity.

extract_protocol:
Total RNA was extracted from 500,000 HCT116 cells  using TriFast reagent  (peqlab) according to manufacturer’s extraction. Small RNAs (< 200 nt) were discarded from total extracted RNA with Zymo-spin IC columns (RNA Clean and Concentrator-5, Zymo Research). Total RNA (1 µg) was subjected to rRNA depletion as described  (Kim et.al, 2019, doi: https://doi.org/10.1101/670604 ).
RNA libraries from 1 µg of total RNA were constructed as described (Zhang et al., 2012).

treatment_protocol: For IFN-γ treatment, cells were seeded in 10 cm plates at a confluency of 70%. IFN-γ was added to a final concentration of 5 ng/ml. After 24 hours of IFN-γ treatment cells were washed twice with ice-cold PBS and collected into Trifast (peqLAB).

tag: cell line

value: HCT116 E33Q MED12 knock-in

value: colon

tag: crispr-cas9 knock-in

value: E33Q MED12

value: 24 hours treatment with  Interferon-gamma (IFN-gamma)


title: IL4c-2_R1

source_name: Peritoneal macrophages

tag: macrophage phenotype

value: Tissue resident, F4/80hi CD206-


title: nSyb_48h_ORN (N447Barcode_702-503)

description:
Single cell
df_libs.csv, htseq.tab


title: Replicate2_T13

description:
R2_T13_24997_CCGTCC
processed data file: R2_table_tpms.txt

source_name: Capsaspora adherent cells_11h after release

value: Filopodial

value: Released from cell cycle overnight arrest using Hydroxyurea 10mM

value: 11h after release


title: Botlikh1005

tag: population

value: Botlikh

tag: village

tag: region

value: Daghestan

tag: gender

value: Male


title: nSyb_48h_ORN (N447Barcode_711-503)

description:
Single cell
df_libs.csv, htseq.tab


title: Botlikh0706


title: KI2_24h


title: KI2_0h

description: rRNA depleted total RNA from HCT116 E33Q MED12 knock-in cell line, untreated

value: untreated


title: nSyb_48h_ORN (N447Barcode_710-503)

description:
Single cell
df_libs.csv, htseq.tab


title: Botlikh1012

value: Female


title: nSyb_48h_ORN (N447Barcode_729-513)

description:
Single cell
df_libs.csv, htseq.tab

value: labels 44 ORN types


title: nSyb_48h_ORN (N447Barcode_724-513)

description:
Single cell
df_libs.csv, htseq.tab


title: Replicate2_T11

description:
R2_T11_24995_AGTCAA
processed data file: R2_table_tpms.txt

source_name: Capsaspora adherent cells_9h30 after release

tag: cell type

tag: time point

value: 9h30 after release


title: Replicate2_T9

description:
R2_T9_24993_GGCTAC
processed data file: R2_table_tpms.txt

source_name: Capsaspora adherent cells_8h after release

value: 8h after release


title: nSyb_48h_ORN (N447Barcode_722-513)

description:
Single cell
df_libs.csv, htseq.tab

tag: genotype

tag: number of cells


title: nSyb_48h_ORN (N447Barcode_723-513)

description:
Single cell
df_libs.csv, htseq.tab

tag: orn type


title: KI1_0h

tag: tissue


title: Replicate2_T10

description:
R2_T10_24994_CTTGTA
processed data file: R2_table_tpms.txt

source_name: Capsaspora adherent cells_8h45 after release

value: 8h45 after release


title: Botlikh1006


title: Replicate2_T8

description:
R2_T8_24992_TAGCTT
processed data file: R2_table_tpms.txt

source_name: Capsaspora adherent cells_7h15 after release

value: 7h15 after release


title: nSyb_48h_ORN (N447Barcode_707-503)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_721-513)

description:
Single cell
df_libs.csv, htseq.tab


title: WT2_24h

description: rRNA depleted total RNA from HCT116 wild-type cell line treated with IFN-gamma for 24 hours

value: colon

value: Wild-type


title: WT1_24h

value: 24 hours treatment with  Interferon-gamma (IFN-gamma)


title: Replicate2_T7

description:
R2_T7_24991_GATCAG
processed data file: R2_table_tpms.txt

source_name: Capsaspora adherent cells_6h30 after release

value: 6h30 after release


title: nSyb_48h_ORN (N447Barcode_727-513)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_726-513)

description:
Single cell
df_libs.csv, htseq.tab


title: Godoberi0924

value: Godoberi


title: WT2_0h

description: rRNA depleted total RNA from HCT116 wild-type cell line, untreated


title: WT1_0h


title: nSyb_48h_ORN (N447Barcode_715-513)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_716-513)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_714-513)

description:
Single cell
df_libs.csv, htseq.tab


title: Replicate2_T5

description:
R2_T5_24989_ACAGTG
processed data file: R2_table_tpms.txt

source_name: Capsaspora adherent cells_5h after release

value: Filopodial

value: Released from cell cycle overnight arrest using Hydroxyurea 10mM

value: 5h after release


title: nSyb_48h_ORN (N447Barcode_712-513)

description:
Single cell
df_libs.csv, htseq.tab


title: Godoberi1008

value: Daghestan


title: nSyb_48h_ORN (N447Barcode_711-513)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_718-513)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_719-513)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_710-513)

description:
Single cell
df_libs.csv, htseq.tab


title: 12_SL08_72EF

city: Bandung

first: Fenny

last: Dwivany

address: Jl. Ganesha No. 10

country: Indonesia

institute: Institut Teknologi Bandung

data_processing:
Raw paired-end reads were examined for a possible low base score, Illumina adapter and PCR contaminations using FastQC
Clean reads were mapped against genome reference using TopHat-Cufflink pipeline (Trapnell et al. 2013)
Reads that aligned to annotated loci were quantified and normalized with FPKM value using Cufflinks V2.2.1 (Trapnell et al. 2010)
Genome_build: Musa acuminata DH Pahang V2 (available at https://banana-genome-hub.southgreen.fr)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Musa acuminata AAA Group

source_name: root

growth_protocol: All banana plantlets are 57-weeks-old in vitro grown using solid plant tissue culture media from local nursery.Banana plantlet were transferred into split root assay with compartment size of 5 x 5 x 6 cm3. 25 grams of vermiculite supplemented with 50 mL 1/2MS supplemented with 1 ppm IBA was used as medium in split root assay. Plantlet were grown for another even weeks before experiment. All culture were kept in a culture room with temperature of 25-30°C and 16h light and 8h dark.

extract_protocol:
Total RNA were extracted from the root using the RNA isolation method according to Cordeiro et al. (2008)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: We have one treatment (endophyte inoculation and Foc TR4 infection) and three different control groups (positive control: endophyte inoculation, no Foc TR4 infection; negative control: no endophyte inoculation, Foc TR4 infection; and neutral control: no endophyte inoculation and no Foc TR4 infection) for each endophyte bacteria species (BR-49 and SL-08). We also have 4 time points: 72 hours after endophyte inoculation (72E) and 6 (6EF), 24 (24EF), and 72 hours (72EF) after Foc TR4 infection of endophyte bacteria preinoculated banana plantlet. 5 ml of bacterial endophyte suspension at mid-log phase was used as inoculum (6.50 × 107 CFU/mL of BR-49 isolate and 7.57 × 107 CFU/mL of SL-08 isolate) and inoculated to endophyte compartment in split root assay. 5 mL of Foc TR4 (5 x 106 spores/mL) was used for infection and inoculated to Fusarium compartment in split root assay. NaCl 0.85% was used as control.

tag: cultivar

value: Pisang ambon kuning (AAA group)

value: root

tag: experiment group

value: Treatment

tag: endophyte bacteria inoculation

value: K. rhizophila

tag: fusarium infection

value: Yes

value: 72 hours after Foc TR4 infection

tag: age

value: 57 weeks after initiation


title: 10_CTRL_72EF

value: Negative control

value: No endophyte bacteria


title: 11_BR49_72EF

value: S. nitritireducens


title: nSyb_48h_ORN (N447Barcode_728-513)

description:
Single cell
df_libs.csv, htseq.tab

value: labels 44 ORN types


title: nSyb_48h_ORN (N447Barcode_704-513)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_703-513)

description:
Single cell
df_libs.csv, htseq.tab


title: Replicate2_T3

description:
R2_T3_24987_TTAGGC
processed data file: R2_table_tpms.txt

source_name: Capsaspora adherent cells_3h30 after release

tag: strain

tag: treatment

value: 3h30 after release


title: nSyb_48h_ORN (N447Barcode_720-513)

description:
Single cell
df_libs.csv, htseq.tab


title: 8_BR49_24EF

value: 24 hours after Foc TR4 infection


title: nSyb_48h_ORN (N447Barcode_707-513)

description:
Single cell
df_libs.csv, htseq.tab


title: 9_SL08_24EF


title: nSyb_48h_ORN (N447Barcode_702-513)

description:
Single cell
df_libs.csv, htseq.tab


title: Replicate2_T1

description:
R2_T1_24985_ATCACG
processed data file: R2_table_tpms.txt

source_name: Capsaspora adherent cells_2h after release

value: Filopodial

value: 2h after release


title: Replicate2_T2

description:
R2_T2_24986_CGATGT
processed data file: R2_table_tpms.txt

source_name: Capsaspora adherent cells_2h45 after release

value: Released from cell cycle overnight arrest using Hydroxyurea 10mM

value: 2h45 after release


title: 7_CTRL_24EF

value: Pisang ambon kuning (AAA group)


title: Replicate2_T6

description:
R2_T6_24990_GCCAAT
processed data file: R2_table_tpms.txt

source_name: Capsaspora adherent cells_5h45 after release

value: 5h45 after release


title: nSyb_48h_ORN (N447Barcode_705-513)

description:
Single cell
df_libs.csv, htseq.tab

source_name: in house


title: Replicate1_T15

description:
t15_23786_CCGTCC_L007
processed data file: R1_table_tpms.txt

source_name: Capsaspora adherent cells_12h30 after release

value: 12h30 after release


title: nSyb_48h_ORN (N447Barcode_701-513)

description:
Single cell
df_libs.csv, htseq.tab


title: 6_SL08_6EF

value: root

value: Treatment

value: K. rhizophila

value: 6 hours after Foc TR4 infection


title: nSyb_48h_ORN (N447Barcode_727-502)

description:
Single cell
df_libs.csv, htseq.tab


title: Replicate1_T14

description:
t14_23785_ATGTCA_L007
processed data file: R1_table_tpms.txt

source_name: Capsaspora adherent cells_11h45 after release

value: 11h45 after release


title: Replicate2_T4

description:
R2_T4_24988_TGACCA
processed data file: R2_table_tpms.txt

source_name: Capsaspora adherent cells_4h15 after release

value: 4h15 after release


title: nSyb_48h_ORN (N447Barcode_722-502)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_728-502)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_724-502)

description:
Single cell
df_libs.csv, htseq.tab


title: 2_BR49_72E

value: Positive control

value: S. nitritireducens

value: No

value: 72 hours after endophyte inoculation

value: 57 weeks after initiation


title: nSyb_48h_ORN (N447Barcode_715-502)

description:
Single cell
df_libs.csv, htseq.tab

value: labels 44 ORN types


title: nSyb_48h_ORN (N447Barcode_729-502)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_716-502)

description:
Single cell
df_libs.csv, htseq.tab


title: Replicate1_T13

description:
t13_23784_AGTTCC_L007
processed data file: R1_table_tpms.txt

value: Filopodial

value: Released from cell cycle overnight arrest using Hydroxyurea 10mM

value: 11h after release


title: 3_SL08_72E

value: Pisang ambon kuning (AAA group)


title: Replicate1_T9

description:
t9_23780_TAGCTT_L007
processed data file: R1_table_tpms.txt

value: 8h after release


title: 5_BR49_6EF

value: root

value: Yes


title: 4_CTRL_6EF

value: Negative control

value: No endophyte bacteria


title: nSyb_48h_ORN (N447Barcode_726-502)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_723-502)

description:
Single cell
df_libs.csv, htseq.tab


title: Replicate1_T10

description:
t10_23781_GGCTAC_L007
processed data file: R1_table_tpms.txt

value: 8h45 after release


title: nSyb_48h_ORN (N447Barcode_721-502)

description:
Single cell
df_libs.csv, htseq.tab


title: Replicate1_T8

description:
t8_23779_GATCAG_L007
processed data file: R1_table_tpms.txt

value: 7h15 after release


title: Replicate1_T12

description:
t12_23783_AGTCAA_L007
processed data file: R1_table_tpms.txt

source_name: Capsaspora adherent cells_10h15 after release

value: 10h15 after release


title: nSyb_48h_ORN (N447Barcode_718-502)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_714-502)

description:
Single cell
df_libs.csv, htseq.tab


title: Replicate1_T16

description:
t16_23787_GTCCGC_L007
processed data file: R1_table_tpms.txt

source_name: Capsaspora adherent cells_13h15 after release

value: 13h15 after release


title: nSyb_48h_ORN (N447Barcode_720-502)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_706-513)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_719-502)

description:
Single cell
df_libs.csv, htseq.tab


title: Replicate1_T11

description:
t11_23782_CTTGTA_L007
processed data file: R1_table_tpms.txt

source_name: Capsaspora adherent cells_9h30 after release

value: 9h30 after release


title: Replicate1_T7

description:
t7_23778_ACTTGA_L007
processed data file: R1_table_tpms.txt

value: 6h30 after release


title: 1_CTRL_72E

value: Neutral control

value: No

value: 72 hours after endophyte inoculation

value: 57 weeks after initiation


title: nSyb_48h_ORN (N447Barcode_710-502)

description:
Single cell
df_libs.csv, htseq.tab

value: labels 44 ORN types


title: 5/6 nephrectomy CKD mice, rep 3

type: RNA

city: Chongqing

first: Yinghui

last: Huang

address: Shapingba

institute: Army medical university

description: Expression data from the heart of CKD mice

hyb_protocol: Following labeling, cDNA was hybridized on a Affymetrix Clariom S mouse.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Command Console installed in the GeneChip® Scanner 3000 7G.

data_processing: The data was analyzed with the Robust Multichip Analysis (RMA) algorithm, using the Affymetrix default analysis settings.

source_name: heart of CKD mice

label_protocol: Biotinylated cDNA was prepared from 250 ng total RNA according to the manufacturer’s standard protocol (Affymetrix).

growth_protocol: Mice were housed in a specific pathogen-free animal facility in plastic cages with a 12 hours light/dark cycle.

extract_protocol: Total RNA was extracted using Trizol according to the manufacturer's instructions.

treatment_protocol: Mice were inflicted with 2/3 electrocoagulation of the right renal cortex and received left total nephrectomy 2 weeks later to construct CKD model. Mice underwent laparotomy without kidney operation served as sham group.

value: heart

value: Balb/c


title: 5/6 nephrectomy CKD mice, rep 2


title: Replicate1_T6

description:
t6_23777_CAGATC_L007
processed data file: R1_table_tpms.txt

value: Filopodial

value: Released from cell cycle overnight arrest using Hydroxyurea 10mM

value: 5h45 after release


title: nSyb_48h_ORN (N447Barcode_704-502)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_706-502)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_705-502)

description:
Single cell
df_libs.csv, htseq.tab


title: Replicate1_T5

description:
t5_23776_GCCAAT_L007
processed data file: R1_table_tpms.txt

value: 5h after release


title: nSyb_48h_ORN (N447Barcode_712-502)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_702-502)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_711-502)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N510Barcode_715-502)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_707-502)

description:
Single cell
df_libs.csv, htseq.tab


title: Replicate1_T3

description:
t3_23774_TGACCA_L007
processed data file: R1_table_tpms.txt

value: 3h30 after release


title: Replicate1_T4

description:
t4_23775_ACAGTG_L007
processed data file: R1_table_tpms.txt

value: 4h15 after release


title: nSyb_48h_ORN (N510Barcode_720-517)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N510Barcode_707-507)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N447Barcode_703-502)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N509Barcode_722-505)

description:
Single cell
df_libs.csv, htseq.tab


title: N-0240-M

city: Toronto

first: Muhammad

middle: Atif

last: Zahoor

state: Ontario

address: 101 College St.

country: Canada

institute: University Health Network

description: total RNA

hyb_protocol: Un-ligated miRtags was removed by enzymatic puriﬁcation, and the miRtagged mature miRNAs were then hybridized with the nCounter Human (V3) miRNA Expression Assay Code Set overnight at 65 °C.

scan_protocol: Samples were then injected into the nCounter SPRINTTM cartridge and read using the nCounter® SPRINT Proﬁler (NanoString Technologies®, Inc., Seattle, WA, USA). The instrument performed the necessary magnetic bead separation, liquid transfers and immobilization of molecular labels on the sample surface before beingﬁnally analyzed by the system.

data_processing:
The counts of the reporter probes were documented for each samplebythenCounterDigitalAnalyzer,whichwas subsequently analyzed using the nSolver Software (V 4.0).
Exosomal miRNA ratio analysis between groups was selected based on an arbitrary |fold change|≥1 and False Discovery Rate (FDR) ≤0.05 with all expression data represented in Log2 scale.

label: Biotin

source_name: Human Breast Milk

label_protocol: OnehundrednanogramsofexosomalRNAfromeachsample was analyzed using the NanoString nCounter SPRINT Proﬁler (NanoString Technologies®, Inc., Seattle, WA, USA). Brieﬂy, miRNAs were ligated to a species-speciﬁc tag sequence (nCounter miRtag) through a thermally controlled splinted ligation.

extract_protocol: Exosomes were isolated from the skim milk supernatants using the Total Exosomes Isolation reagent (from other body fluids) as per manufacturer’s recommendations (Cat # 4484453; Thermo Fisher, Canada). Briefly, 500µl volume of each HM sample was centrifuged at 2000 x g for 10 minutes (1st spin). Without disrupting the pellet, supernatant was transferred to a new tube and centrifuged again at 10,000 x g for 30 minutes (2nd spin). The supernatant was transferred to a new tube and centrifuged at 10,000 x g for 10 minutes (3rd spin). To the clear supernatant, 500µl of 1xPBS and 500µl of exosome isolation reagent was added, vortex-mixed and incubated for 30 minutes at room temperature. After, incubation, the samples were centrifuged at 10,000 x g for 10 minutes and the supernatant was removed carefully and discarded. The exosomes in the pellets were dissolved in 50µl of exosome resuspension buffer (Cat # 4478562; Thermo Fisher, Canada), vortex-mixed and again centrifuged at 10,000 x g for 5 minutes at room temperature. Without disturbing the non-organic particulate matter in the pellet, the supernatants containing the purified HM exosomes were transferred to a new tube and stored at -20oC until further use.

tag: biomaterial

value: Liquid Milk

tag: sample type

value: exosomes

tag: infection


title: nSyb_48h_ORN (N447Barcode_701-502)

description:
Single cell
df_libs.csv, htseq.tab


title: N-0239-M

description: total RNA


title: nSyb_48h_ORN (N509Barcode_716-518)

description:
Single cell
df_libs.csv, htseq.tab


title: sham mice, rep 3

description: Expression data from the heart of sham mice

source_name: heart of sham mice


title: N-0238-M

description: total RNA


title: Am29_48h_ORN (N543Barcode_729-517)

description:
Single cell
df_libs.csv, htseq.tab

value: labels 2 ORN types


title: 85A10_48h_ORN (N543Barcode_723-510)

description:
Single cell
df_libs.csv, htseq.tab

value: labels 5 ORN types


title: Unsynchronous

description:
control_23771_ATCACG_L007
processed data file: R1_table_tpms.txt

source_name: Capsaspora adherent cells_non-synchronized culture

value: non-synchronized culture


title: Replicate1_T2

description:
t2_23773_TTAGGC_L007
processed data file: R1_table_tpms.txt

value: 2h45 after release


title: 85A10_48h_ORN (N543Barcode_715-502)

description:
Single cell
df_libs.csv, htseq.tab


title: Worker_ATAC_Rep4

city: shenzhen

first: CNSA

last: CNGB

address: BGI

institute: BGI

data_processing:
RNA-seq total reads were aligned to the Monomorium pharaonis ASM326058v2 genome using hisat2.ATAC-seq total reads were aligned to the Monomorium pharaonis ASM326058v2 genome using Bowtie2.
The read counts per gene of each sample were calculated with featureCounts; ATAC-seq readcount per peak of each sample were calculated with bedtools.
The differentially expressed genes (DEGs) between castes were identified by DESeq2;The differentially accessible regions (DARs) between castes were identified by DESeq2.
Genome_build: ASM326058v2
Supplementary_files_format_and_content: tab-delimited Excel files include read counts for each sample

organism: Monomorium pharaonis

source_name: Brain

growth_protocol: Ants were kept under a constant temperature of 25 °C and 50% humidity and fed with mealworm.

extract_protocol:
Whole-brain RNA was extracted immediately after dissection with RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol and eluted in 10 μl nuclease-free water (Ambion). Total amounts of RNA were quantified using an Invitrogen Qubit RNA High Sensitivity assay.In brief, brains were dissected and then washed twice with 500 μl ice-cold PBS. After centrifugation at 500 x g for 5 min, the brain samples were lysed with 50 μl lysis buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630).
We used an optimized Smart-seq2 method for RNA-seq library construction.The supernatant was discarded and replaced with a 50 μl transposition reaction mix containing 10 mM TAPS-NaOH (pH 8.5), 5 mM MgCl2, 10% DMF, 2.5 μl of in-house Tn5 transposase (0.8 U/μl) and NF-water for ATAC-seq.

treatment_protocol: Ants were put on ice to reduce activity and then brains were dissected23 and transferred into 1.5 ml centrifuge tubes with phosphate-buffered saline (PBS, Gibco). Washed the brains twice with 500 μl ice-cold PBS.

value: Brain cells

tag: caste

value: worker


title: 5/6 nephrectomy CKD mice, rep 1


title: sham mice, rep 2


title: Worker_ATAC_Rep3

tag: cell type


title: N-0234-M

description: total RNA


title: Replicate1_T1

description:
t1_23772_CGATGT_L007
processed data file: R1_table_tpms.txt

tag: time point

value: 2h after release


title: nSyb_48h_ORN (N510Barcode_726-506)

description:
Single cell
df_libs.csv, htseq.tab

tag: genotype

value: labels 44 ORN types


title: Worker_ATAC_Rep2


title: nSyb_48h_ORN (N509Barcode_705-510)

description:
Single cell
df_libs.csv, htseq.tab

tag: number of cells


title: nSyb_48h_ORN (N510Barcode_707-506)

description:
Single cell
df_libs.csv, htseq.tab

tag: orn type


title: nSyb_48h_ORN (N510Barcode_720-516)

description:
Single cell
df_libs.csv, htseq.tab


title: Worker_ATAC_Rep1


title: N-0233-M

description: total RNA


title: sham mice, rep 1

tag: tissue

value: heart

value: Balb/c


title: N-0226-M

description: total RNA


title: nSyb_48h_ORN (N509Barcode_722-503)

description:
Single cell
df_libs.csv, htseq.tab


title: Queen_ATAC_Rep4

value: queen


title: Am29_48h_ORN (N543Barcode_729-506)

description:
Single cell
df_libs.csv, htseq.tab


title: N-0222-M

description: total RNA


title: N-0211-M

description: total RNA


title: 85A10_48h_ORN (N543Barcode_714-522)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N543Barcode_707-518)

description:
Single cell
df_libs.csv, htseq.tab


title: 85A10_48h_ORN (N543Barcode_723-520)

description:
Single cell
df_libs.csv, htseq.tab


title: Queen_ATAC_Rep3


title: nSyb_48h_ORN (N543Barcode_707-507)

description:
Single cell
df_libs.csv, htseq.tab


title: N-0207-M

description: total RNA


title: Queen_ATAC_Rep2


title: nSyb_48h_ORN (N510Barcode_726-505)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N509Barcode_705-508)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N510Barcode_720-515)

description:
Single cell
df_libs.csv, htseq.tab


title: Queen_ATAC_Rep1


title: N-0196-M

description: total RNA


title: Male_ATAC_Rep4

value: male


title: nSyb_48h_ORN (N510Barcode_707-505)

description:
Single cell
df_libs.csv, htseq.tab


title: N-0192M

description: total RNA


title: N-0181-M

description: total RNA


title: nSyb_48h_ORN (N510Barcode_702-517)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N509Barcode_727-515)

description:
Single cell
df_libs.csv, htseq.tab


title: Male_ATAC_Rep3


title: N-0178-M

description: total RNA


title: nSyb_48h_ORN (N509Barcode_711-518)

description:
Single cell
df_libs.csv, htseq.tab


title: Male_ATAC_Rep2


title: Am29_48h_ORN (N543Barcode_729-516)

description:
Single cell
df_libs.csv, htseq.tab


title: N-0164-M

description: total RNA


title: 85A10_48h_ORN (N543Barcode_723-508)

description:
Single cell
df_libs.csv, htseq.tab


title: 85A10_48h_ORN (N543Barcode_720-513)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N543Barcode_702-518)

description:
Single cell
df_libs.csv, htseq.tab


title: 85A10_48h_ORN (N543Barcode_714-511)

description:
Single cell
df_libs.csv, htseq.tab


title: N-0160-M

description: total RNA


title: Gyne_ATAC_Rep4

value: gyne


title: nSyb_48h_ORN (N543Barcode_702-507)

description:
Single cell
df_libs.csv, htseq.tab


title: Gyne_ATAC_Rep2


title: Gyne_ATAC_Rep3


title: N-0140-M

description: total RNA


title: nSyb_48h_ORN (N510Barcode_726-503)

description:
Single cell
df_libs.csv, htseq.tab


title: N-0138-M

description: total RNA


title: nSyb_48h_ORN (N509Barcode_705-507)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N510Barcode_714-522)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N509Barcode_722-502)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N509Barcode_711-516)

description:
Single cell
df_libs.csv, htseq.tab


title: N-0130-M

description: total RNA


title: nSyb_48h_ORN (N509Barcode_711-517)

description:
Single cell
df_libs.csv, htseq.tab


title: Worker_RNA_Rep4


title: 85A10_48h_ORN (N543Barcode_720-502)

description:
Single cell
df_libs.csv, htseq.tab


title: Am29_48h_ORN (N543Barcode_729-505)

description:
Single cell
df_libs.csv, htseq.tab


title: N-0251-M

description: total RNA


title: Male_ATAC_Rep1


title: N-0249-M

description: total RNA


title: Worker_RNA_Rep3


title: 85A10_48h_ORN (N543Barcode_714-521)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N543Barcode_707-517)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N510Barcode_720-513)

description:
Single cell
df_libs.csv, htseq.tab


title: Worker_RNA_Rep2


title: Worker_RNA_Rep1


title: nSyb_48h_ORN (N510Barcode_720-511)

description:
Single cell
df_libs.csv, htseq.tab


title: Queen_RNA_Rep4


title: nSyb_48h_ORN (N510Barcode_714-521)

description:
Single cell
df_libs.csv, htseq.tab


title: N-0248-M

description: total RNA


title: nSyb_48h_ORN (N509Barcode_705-506)

description:
Single cell
df_libs.csv, htseq.tab


title: Gyne_ATAC_Rep1


title: nSyb_48h_ORN (N510Barcode_707-503)

description:
Single cell
df_libs.csv, htseq.tab


title: N-0236-M

description: total RNA


title: N-0247-M

description: total RNA


title: Queen_RNA_Rep3


title: nSyb_48h_ORN (N509Barcode_727-513)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N510Barcode_707-502)

description:
Single cell
df_libs.csv, htseq.tab


title: Queen_RNA_Rep2


title: nSyb_48h_ORN (N509Barcode_711-515)

description:
Single cell
df_libs.csv, htseq.tab


title: Am29_48h_ORN (N543Barcode_729-515)

description:
Single cell
df_libs.csv, htseq.tab


title: N-0232-M

description: total RNA


title: N-0230-M

description: total RNA


title: Queen_RNA_Rep1


title: 85A10_48h_ORN (N543Barcode_719-522)

description:
Single cell
df_libs.csv, htseq.tab


title: N-0231-M

description: total RNA


title: 85A10_48h_ORN (N543Barcode_723-518)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N543Barcode_702-517)

description:
Single cell
df_libs.csv, htseq.tab


title: 85A10_48h_ORN (N543Barcode_714-510)

description:
Single cell
df_libs.csv, htseq.tab


title: N-0374-M

description: total RNA

value: Control


title: Male_RNA_Rep4


title: nSyb_48h_ORN (N543Barcode_707-506)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N510Barcode_724-522)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N510Barcode_720-510)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N510Barcode_726-502)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N543Barcode_702-506)

description:
Single cell
df_libs.csv, htseq.tab


title: Male_RNA_Rep1


title: Male_RNA_Rep2


title: N-0371-M

description: total RNA


title: Male_RNA_Rep3


title: N-0369-M

description: total RNA


title: nSyb_48h_ORN (N510Barcode_706-522)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N509Barcode_705-505)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N510Barcode_714-520)

description:
Single cell
df_libs.csv, htseq.tab


title: nSyb_48h_ORN (N509Barcode_721-522)

description:
Single cell
df_libs.csv, htseq.tab


title: N-0364-M

description: total RNA


title: nSyb_48h_ORN (N509Barcode_716-517)

description:
Single cell
df_libs.csv, htseq.tab


title: Am29_48h_ORN (N543Barcode_729-503)

description:
Single cell
df_libs.csv, htseq.tab


title: N-0356-M

description: total RNA


title: Gyne_RNA_Rep3


title: nSyb_48h_ORN (N509Barcode_711-513)

description:
Single cell
df_libs.csv, htseq.tab


title: N-0353-M

description: total RNA


title: Gyne_RNA_Rep2


title: 85A10_48h_ORN (N543Barcode_723-507)

description:
Single cell
df_libs.csv, htseq.tab


title: N-0380-M

description: total RNA


title: N-0382-M

description: total RNA


title: 85A10_48h_ORN (N543Barcode_719-511)

description:
Single cell
df_libs.csv, htseq.tab


title: Gyne_Brain_Rep1


title: 85A10_48h_ORN (N543Barcode_714-520)

description:
Single cell
df_libs.csv, htseq.tab


title: Gyne_RNA_Rep4


title: nSyb_48h_ORN (N510Barcode_702-516)

description:
Single cell
df_libs.csv, htseq.tab


title: N-0379-M

description: total RNA


title: N-0254-M

description: total RNA


title: SMY2605_HMX1_t90

status: Public on Jan 03 2020

city: South San Francisco

first: Scott

last: McIsaac

state: CA

address: 1170 Veterans Blvd.

institute: Calico Life Sciences LLC

hyb_protocol: 8x15k Microarray hybridization: Set up 60°C heat block; Prepare 10x Blocking Agent: Add 1250 µL of nuclease-free water to vial containing 10x lyophilized Gene Expression Blocking Agent (part #5188-5281); Vortex and spin down; Prepare hybridization samples; For 8x15k (8-pack) microarrays, mix the following components: 450 ng Cy3-amplified cRNA, 450 ng Cy5-amplified cRNA, 7.5 µL 10X Gene Expression Blocking Agent, bring volume to 36 µL with water, and then add 1.5 µL 25x fragmentation buffer; Incubate at 60°C for 30 minutes to fragment the RNA; Add 37.5 µL of 2x Hi-RPM Hybridization Buffer to strip tube and leave on ice; Add fragmented RNA directly to Hi-RPM Buffer to stop the reaction; Mix well by pipetting up and down (avoid bubbles and do not vortex); Put sample on ice and load onto array as soon as possible; Put clean gasket onto metal hybridization chamber; Add 45 µL of hybridization onto gasket; Place array (Agilent facing down) onto gasket and close the hybridization chamber; Incubate on rotisserie at 65°C for 17 hr

scan_protocol: Labeled RNA was hybridized to Agilent 8x15k microarrays, which were then washed, scanned, and processed using the Agilent Feature Extraction software with default settings and loess dye bias correction.

data_processing: Each microarray has some number of spots (usually 2) for each gene. All microarrays for the GEV experiments had identical probes, likewise for the ZEV experiments. For each spot, we computed ratio = max(red, C) / max(green, C), where C=2 in arbitrary units. This minimum value application only affects 0.3% of spots. Typical genes have red and green channel measurements above 200. These (red, green, ratio) values foreach spot serve as the raw data. For each dataset, we aggregated the data across individual spots. Specifically, for each timecourse, time point, and gene, we aggregated the spot values and measured the minimum value, maximum value, median value, and standard deviation of the values. In the usual case of 2 spots, the median value is equivalent to mean and standard deviation is equivalent to (max-min)/sqrt(2). At this stage we corrected the most extreme outlier observations. First, for a given sample, we examined the case where, for a given gene, the ratio of the spot values, was larger than four. Since the spots values do not agree, we interpolated the value with the geometric mean across bracketing time points (or neighboring time point in the case of first or last time point). The second class of outliers is where the median ratio moves by a factor of at least four between two time points, and then by a factor of four in the opposite direction for the next time point.  In these cases we again replaced the central point with the geometric mean of the bracketing points. These corrections apply to less than 0.2% of the data. In processing gene expression microarrays, crosstalk between red and green channels can occur. When the red channel fluorescence is much larger than the green channel fluorescence, there can be leakage of signal, and the green channel measurement is affected. To identify instances of this occurring,  we first computed the green channel ratio relative to the time zero measurement.  We then measured the 30% quantile of this value within each timecourse (for time points after t = 0), as well as the 30% quantile of the log-ratio.  We then flagged timecourses where the green ratio quantile exceeded a factor of eight, and the log-ratio quantile exceeds a two-fold change.  These represent cases where the green channel is increasing a great deal when it should be constant. For these rare cases, we repaired the red to green ratios by duplicating the time zero green channel across the full timecourse.  This affects about two dozen TF-gene timecourses (out of more than a million). The GEV and ZEV systems both have characteristic gene expression signatures, including a mild stress response. Previously, it has been shown that Singular Value Decomposition (SVD) is one way to remove such signals. Here, we used a slightly different approach. First, we computed the median time series for each gene in each class of experiments (GEV and ZEV).  We then subtracted this median time series, leaving a normalized log-ratio.  Because a given gene is not directly or indirectly affected by a transcription factor in most experiments, the median is an accurate reflection of any background time-dependent behavior.  We refer to the dataset where outliers are removed and the GEV/ZEV signal is removed as the cleaned dataset.

source_name: SMY2605 including HMX1 at the t90 minute timepoint

label_protocol: Crude RNA was purified using either the QIAGEN RNeasy kit or RNAClean Ampure XP beads. 200 ng of cleaned RNA was used as an input to generate dye-labeled cRNA using the Agilent Quick-Amp Labeling Kit. 1) Prepare labeling reaction: Get clean PCR strip tubes ready; Dilute RNA to 57.2 ng/µL; Add 3.5 µl of RNA (200 ng total) to PCR tube; Make T7 Primer Mix (0.8 µL T7, 1 µL water);Add 1.8 µl of T7 Primer Mix to each tube. Each tube now has 5.3 µl; Denature the template and primer by incubating at 65°C for 10 min; Put reactions on ice for 5 min; 2) cDNA synthesis: Heat 5x First Strand Buffer 80°C for 3-4 minutes, vortex, do a quick spin, and keep at room temperature; Make cDNA master mix (2µL 5x First Strand Buffer, 1 µL 0.1M DTT, 0.5 µL 10 mM dNTP mix, 1.2 µL Affinity Script RNase Block Mix); Briefly spin sample and master mix tubes; Add 4.7 µL of cDNA Master Mix to sample tubes and mix by pipetting up and down. Each tube now has 10 µL; Incubate at 40°C for 2 hours; Incubate at 70°C for 15 minutes (inactivates the AffinityScript enzyme); If you don’t continue to next step, freeze samples -80°C; Ice for 5 min. 3) Labeled cRNA synthesis: Keep T7 RNA polymerase (red cap) on ice. Master Mix = 0.75 µL Water, 3.2 µL 5x Transcription Buffer, 0.6 µL 0.1M DTT, 1 µL NTP Mix, .21µL T7 RNA polymerase Blend; 0.24 µL Cy3-CTP or C5-CTP; Add 6 µL of Transcrption Master Mix with Dye to the cDNA. Each tube now contains a total volume of 16 µL; Incubate samples at 40°C for 2 hours. 4) SPRI cleanup of cRNA: Before beginning: Bring RNAClean XP to RT, Make up enough 80% ethanol for >2 200 µL washes per reaction, Set 96 well thermomixer to 37°C; Add 48 µL (3X) of RNAClean XP beads to each reaction and incubate for 10 minutes; Place plate on magnet and allow supernatant to clear (~5 minutes); Remove supernatant carefully, avoiding beads, and discard; Add 200 µL of 80% ethanol to each well and incubate for 30 seconds; Remove ethanol and repeat for a total of two washes; Remove ethanol, cover plate, and spin down for ~1 minute; Place plate back on magnet and use a p20 to remove residual ethanol; Dry beads at 37°C until beads no longer move around when placed on magnet (~4 minutes); Add 42.5 of RNAse-free water and resuspend beads, then incubate for 2-3 minutes; Place plate on magnet and transfer 40 µL to a new well before placing on ice

growth_protocol: All experiments were performed in chemostats (continuous cultures). We chose chemostats, in part, because the steady-state condition of chemostat cultures is a particularly useful feature for mathematical modeling. Under steady-state conditions, the levels of molecules and activities of process are not changing at a culture-wide level. Cells were grown under continuous culturing conditions in 500 mL vessels as previously described with minor adjustments (Saldanha AJ, Brauer MJ, Botstein D. Nutritional homeostasis in batch and steady-state culture of yeast. Mol Biol Cell. 2004;15: 4089–4104). Cultures were aerated with 6 L/min of humidified air at 30C, maintained at 300 mL, and stirred with a magnetic impeller at 400 RPM. For the majority of experiments, cultures were maintained with minimal medium under phosphate limitation (20 mg/L). Nitrogen-limited cultures were maintained at 40 mg/L ammonium sulfate. Methionine-limited cultures (McIsaac et al, 2012) were maintained at 7.5 mg/L methionine. Growth rates were maintained from 0.15-0.17 vol/hour.  Batch growth in the chemostat vessels was initiated from a 1:60 dilution of a saturated overnight culture prior to turning on the chemostat pumps. Cells were grown to steady state, as determined by culture density, prior to the addition of 1 micromolar beta-estradiol to the culture and subsequent sampling. Chemostat experiments were performed with either the Infors Sixfors or Multifors systems.

extract_protocol: RNA was prepared using a standard acid phenol extraction. Lysis buffer: 600 µL of 0.5M EDTA, 1.5 mL of 10% SDS, 300 µL 1M Tris, 27.6 mL Rnase-free water.

treatment_protocol: The t = 0 was taken (between 3 and 5 mL of culture) and vacuum filtered. Estradiol was then added the continuous culture and sampled at various timepoints.

tag: background


title: SMY2605_HMX1_t45

source_name: SMY2605 including HMX1 at the t45 minute timepoint


title: SMY2605_HMX1_t30

source_name: SMY2605 including HMX1 at the t30 minute timepoint


title: TM94

city: Augusta

first: Jingwen

last: Cai

state: GA

address: 1460 Laney Walker Blvd

department: Cellular biology and Anatomy

institute: Augusta University

hyb_protocol: Following the manufacturer’s protocol of Illumina Infinium HumanMethylation450 BeadChips

scan_protocol: Following the manufacturer's protocol of Illumina iScan System.

data_processing: R package RnBeads in Bioconductor. FDb.InfiniumMethylation.hg19 package and Infinium HumanMethylation450K v1.2 product file were used to annotate data.

label: Cy3, Cy5

source_name: Trabecular meshwork

label_protocol: Standard Illumina labelling protocol

growth_protocol: Isolation and culture of primary SC cells was processed according to the established techniques.

extract_protocol: Genomic DNA was extracted using the AllPrep DNA Mini spin column kit.

treatment_protocol: There is no special treatment for these cells.

tag: gender

tag: disease state

value: Normal

value: TM cells


title: SMY2605_HMX1_t20

source_name: SMY2605 including HMX1 at the t20 minute timepoint


title: SMY2605_HMX1_t0

source_name: SMY2605 including HMX1 at the t0 minute timepoint


title: SMY2605_HMX1_t15

source_name: SMY2605 including HMX1 at the t15 minute timepoint


title: SMY2605_HMX1_t10

source_name: SMY2605 including HMX1 at the t10 minute timepoint


title: SMY2605_HMX1_t5

source_name: SMY2605 including HMX1 at the t5 minute timepoint


title: TM126


title: SC57g

source_name: Schlemm's Canal

value: Male

value: 78 years

value: Glaucoma

value: SC cells


title: SMY2611_YGL117W_t90

source_name: SMY2611 including YGL117W at the t90 minute timepoint


title: SC78_2

value: 77 years


title: TM94_1


title: TM94_2


title: SC3

value: 44 years


title: SC80_2

value: 62 years


title: SMY2611_YGL117W_t45

source_name: SMY2611 including YGL117W at the t45 minute timepoint


title: TM93_1


title: SMY2611_YGL117W_t30

source_name: SMY2611 including YGL117W at the t30 minute timepoint


title: TM93


title: SC1_2


title: SC1_1


title: GTM2


title: SMY2611_YGL117W_t15

source_name: SMY2611 including YGL117W at the t15 minute timepoint


title: SC4_2


title: SMY2610_ARN2_t90

source_name: SMY2610 including ARN2 at the t90 minute timepoint


title: SMY2611_YGL117W_t0

source_name: SMY2611 including YGL117W at the t0 minute timepoint


title: SMY2611_YGL117W_t10

source_name: SMY2611 including YGL117W at the t10 minute timepoint


title: TM123_2


title: SC4_1


title: SMY2611_YGL117W_t5

source_name: SMY2611 including YGL117W at the t5 minute timepoint


title: SC64g


title: TM93_2


title: SC2


title: SC78_1


title: SC76_2

value: Female

value: 59 years


title: SMY2611_YGL117W_t20

source_name: SMY2611 including YGL117W at the t20 minute timepoint


title: SC80_1


title: TM123_1


title: SMY2610_ARN2_t15

source_name: SMY2610 including ARN2 at the t15 minute timepoint


title: SMY2610_ARN2_t30

source_name: SMY2610 including ARN2 at the t30 minute timepoint


title: SMY2610_ARN2_t10

source_name: SMY2610 including ARN2 at the t10 minute timepoint


title: SMY2610_ARN2_t0

source_name: SMY2610 including ARN2 at the t0 minute timepoint


title: SMY2610_ARN2_t5

source_name: SMY2610 including ARN2 at the t5 minute timepoint


title: SC76_1


title: SMY2610_ARN2_t20

source_name: SMY2610 including ARN2 at the t20 minute timepoint


title: SMY2609_ANB1_t45

source_name: SMY2609 including ANB1 at the t45 minute timepoint


title: SMY2609_ANB1_t30

source_name: SMY2609 including ANB1 at the t30 minute timepoint


title: SMY2609_ANB1_t20

source_name: SMY2609 including ANB1 at the t20 minute timepoint


title: SMY2609_ANB1_t10

source_name: SMY2609 including ANB1 at the t10 minute timepoint


title: SMY2609_ANB1_t5

source_name: SMY2609 including ANB1 at the t5 minute timepoint


title: SMY2609_ANB1_t0

source_name: SMY2609 including ANB1 at the t0 minute timepoint


title: SMY2607_STP4_t15

source_name: SMY2607 including STP4 at the t15 minute timepoint


title: SMY2607_STP4_t30

source_name: SMY2607 including STP4 at the t30 minute timepoint


title: SMY2607_STP4_t10

source_name: SMY2607 including STP4 at the t10 minute timepoint


title: SMY2607_STP4_t45

source_name: SMY2607 including STP4 at the t45 minute timepoint


title: SMY2607_STP4_t90

source_name: SMY2607 including STP4 at the t90 minute timepoint


title: SMY2607_STP4_t20

source_name: SMY2607 including STP4 at the t20 minute timepoint


title: SMY2607_STP4_t5

source_name: SMY2607 including STP4 at the t5 minute timepoint


title: SMY2608_YGR066c_t90

source_name: SMY2608 including YGR066c at the t90 minute timepoint


title: SMY2613_PHO11_t90

source_name: SMY2613 including PHO11 at the t90 minute timepoint


title: SMY2608_YGR066c_t15

source_name: SMY2608 including YGR066c at the t15 minute timepoint


title: SMY2613_PHO11_t20

source_name: SMY2613 including PHO11 at the t20 minute timepoint


title: SMY2613_PHO11_t30

source_name: SMY2613 including PHO11 at the t30 minute timepoint


title: SMY2608_YGR066c_t10

source_name: SMY2608 including YGR066c at the t10 minute timepoint


title: SMY2608_YGR066c_t0

source_name: SMY2608 including YGR066c at the t0 minute timepoint


title: SMY2608_YGR066c_t5

source_name: SMY2608 including YGR066c at the t5 minute timepoint


title: SMY2608_YGR066c_t45

source_name: SMY2608 including YGR066c at the t45 minute timepoint


title: SMY2613_PHO11_t45

source_name: SMY2613 including PHO11 at the t45 minute timepoint


title: SMY2608_YGR066c_t20

source_name: SMY2608 including YGR066c at the t20 minute timepoint


title: SMY2608_YGR066c_t30

source_name: SMY2608 including YGR066c at the t30 minute timepoint


title: SMY2607_STP4_t0

source_name: SMY2607 including STP4 at the t0 minute timepoint


title: SMY2613_PHO11_t15

source_name: SMY2613 including PHO11 at the t15 minute timepoint


title: SMY2613_PHO11_t10

source_name: SMY2613 including PHO11 at the t10 minute timepoint


title: SMY2609_ANB1_t90

source_name: SMY2609 including ANB1 at the t90 minute timepoint


title: SMY2613_PHO11_t5

source_name: SMY2613 including PHO11 at the t5 minute timepoint


title: SMY2612_PHO5_t5

source_name: SMY2612 including PHO5 at the t5 minute timepoint


title: SMY2612_PHO5_t90

source_name: SMY2612 including PHO5 at the t90 minute timepoint


title: SMY2612_PHO5_t10

source_name: SMY2612 including PHO5 at the t10 minute timepoint


title: SMY2609_ANB1_t15

source_name: SMY2609 including ANB1 at the t15 minute timepoint


title: SMY2613_PHO11_t0

source_name: SMY2613 including PHO11 at the t0 minute timepoint


title: SMY2614_PHM6_t45

source_name: SMY2614 including PHM6 at the t45 minute timepoint


title: SMY2614_PHM6_t90

source_name: SMY2614 including PHM6 at the t90 minute timepoint


title: SMY2612_PHO5_t30

source_name: SMY2612 including PHO5 at the t30 minute timepoint


title: SMY2612_PHO5_t20

source_name: SMY2612 including PHO5 at the t20 minute timepoint


title: SMY2612_PHO5_t15

source_name: SMY2612 including PHO5 at the t15 minute timepoint


title: SMY2612_PHO5_t45

source_name: SMY2612 including PHO5 at the t45 minute timepoint


title: SMY2614_PHM6_t30

source_name: SMY2614 including PHM6 at the t30 minute timepoint


title: SMY2614_PHM6_t20

source_name: SMY2614 including PHM6 at the t20 minute timepoint


title: SMY2614_PHM6_t5

source_name: SMY2614 including PHM6 at the t5 minute timepoint


title: SMY2614_PHM6_t15

source_name: SMY2614 including PHM6 at the t15 minute timepoint


title: SMY2614_PHM6_t10

source_name: SMY2614 including PHM6 at the t10 minute timepoint


title: SMY2612_PHO5_t0

source_name: SMY2612 including PHO5 at the t0 minute timepoint


title: SMY2614_PHM6_t0

source_name: SMY2614 including PHM6 at the t0 minute timepoint


title: SMY254c_Z3EV_t90

source_name: SMY254c including Z3EV at the t90 minute timepoint


title: SMY2606_FMP48_t90

source_name: SMY2606 including FMP48 at the t90 minute timepoint


title: SMY2606_FMP48_t45

source_name: SMY2606 including FMP48 at the t45 minute timepoint


title: SMY254c_Z3EV_t45

source_name: SMY254c including Z3EV at the t45 minute timepoint


title: SMY2606_FMP48_t30

source_name: SMY2606 including FMP48 at the t30 minute timepoint


title: SMY2606_FMP48_t0

source_name: SMY2606 including FMP48 at the t0 minute timepoint


title: SMY2606_FMP48_t15

source_name: SMY2606 including FMP48 at the t15 minute timepoint


title: SMY2606_FMP48_t20

source_name: SMY2606 including FMP48 at the t20 minute timepoint


title: SMY254c_Z3EV_t30

source_name: SMY254c including Z3EV at the t30 minute timepoint


title: SMY254c_Z3EV_t10

source_name: SMY254c including Z3EV at the t10 minute timepoint


title: SMY2610_ARN2_t45

source_name: SMY2610 including ARN2 at the t45 minute timepoint


title: SMY2606_FMP48_t10

source_name: SMY2606 including FMP48 at the t10 minute timepoint


title: SMY254c_Z3EV_t15

source_name: SMY254c including Z3EV at the t15 minute timepoint


title: SMY2606_FMP48_t5

source_name: SMY2606 including FMP48 at the t5 minute timepoint


title: SMY254c_Z3EV_t20

source_name: SMY254c including Z3EV at the t20 minute timepoint


title: SMY254a_Z3EV_t30

source_name: SMY254a including Z3EV at the t30 minute timepoint


title: SMY254a_Z3EV_t45

source_name: SMY254a including Z3EV at the t45 minute timepoint


title: SMY254a_Z3EV_t15

source_name: SMY254a including Z3EV at the t15 minute timepoint


title: SMY254a_Z3EV_t20

source_name: SMY254a including Z3EV at the t20 minute timepoint


title: SMY254c_Z3EV_t5

source_name: SMY254c including Z3EV at the t5 minute timepoint


title: SMY254a_Z3EV_t10

source_name: SMY254a including Z3EV at the t10 minute timepoint


title: SMY254c_Z3EV_t0

source_name: SMY254c including Z3EV at the t0 minute timepoint


title: SMY2266c_SWI1_t90

source_name: SMY2266c including SWI1 at the t90 minute timepoint


title: SMY254a_Z3EV_t0

source_name: SMY254a including Z3EV at the t0 minute timepoint


title: SMY2266c_SWI1_t45

source_name: SMY2266c including SWI1 at the t45 minute timepoint


title: SMY254a_Z3EV_t5

source_name: SMY254a including Z3EV at the t5 minute timepoint


title: SMY254a_Z3EV_t90

source_name: SMY254a including Z3EV at the t90 minute timepoint


title: SMY2266b_SWI1_t20

source_name: SMY2266b including SWI1 at the t20 minute timepoint


title: SMY2266b_SWI1_t15

source_name: SMY2266b including SWI1 at the t15 minute timepoint


title: SMY2266b_SWI1_t90

source_name: SMY2266b including SWI1 at the t90 minute timepoint


title: SMY2266c_SWI1_t0

source_name: SMY2266c including SWI1 at the t0 minute timepoint


title: SMY2266c_SWI1_t20

source_name: SMY2266c including SWI1 at the t20 minute timepoint


title: SMY2266b_SWI1_t10

source_name: SMY2266b including SWI1 at the t10 minute timepoint


title: SMY2266b_SWI1_t30

source_name: SMY2266b including SWI1 at the t30 minute timepoint


title: SMY2266c_SWI1_t15

source_name: SMY2266c including SWI1 at the t15 minute timepoint


title: SMY2266c_SWI1_t5

source_name: SMY2266c including SWI1 at the t5 minute timepoint


title: SMY2266b_SWI1_t45

source_name: SMY2266b including SWI1 at the t45 minute timepoint


title: SMY2266c_SWI1_t10

source_name: SMY2266c including SWI1 at the t10 minute timepoint


title: SMY2266c_SWI1_t30

source_name: SMY2266c including SWI1 at the t30 minute timepoint


title: SMY2266a_SWI1_t20

source_name: SMY2266a including SWI1 at the t20 minute timepoint


title: SMY2266b_SWI1_t5

source_name: SMY2266b including SWI1 at the t5 minute timepoint


title: SMY2266b_SWI1_t0

source_name: SMY2266b including SWI1 at the t0 minute timepoint


title: SMY2266a_SWI1_t30

source_name: SMY2266a including SWI1 at the t30 minute timepoint


title: SMY2266a_SWI1_t90

source_name: SMY2266a including SWI1 at the t90 minute timepoint


title: SMY2266a_SWI1_t45

source_name: SMY2266a including SWI1 at the t45 minute timepoint


title: SMY2270_YAP5_t90

source_name: SMY2270 including YAP5 at the t90 minute timepoint


title: SMY2270_YAP5_t15

source_name: SMY2270 including YAP5 at the t15 minute timepoint


title: SMY2270_YAP5_t0

source_name: SMY2270 including YAP5 at the t0 minute timepoint


title: SMY2270_YAP5_t45

source_name: SMY2270 including YAP5 at the t45 minute timepoint


title: SMY2266a_SWI1_t0

source_name: SMY2266a including SWI1 at the t0 minute timepoint


title: SMY2266a_SWI1_t5

source_name: SMY2266a including SWI1 at the t5 minute timepoint


title: SMY2270_YAP5_t5

source_name: SMY2270 including YAP5 at the t5 minute timepoint


title: SMY2270_YAP5_t30

source_name: SMY2270 including YAP5 at the t30 minute timepoint


title: SMY2270_YAP5_t10

source_name: SMY2270 including YAP5 at the t10 minute timepoint


title: SMY2266a_SWI1_t10

source_name: SMY2266a including SWI1 at the t10 minute timepoint


title: SMY2270_YAP5_t20

source_name: SMY2270 including YAP5 at the t20 minute timepoint


title: SMY2266a_SWI1_t15

source_name: SMY2266a including SWI1 at the t15 minute timepoint


title: SMY2264_SPT20_t90

source_name: SMY2264 including SPT20 at the t90 minute timepoint


title: SMY2264_SPT20_t15

source_name: SMY2264 including SPT20 at the t15 minute timepoint


title: SMY2264_SPT20_t45

source_name: SMY2264 including SPT20 at the t45 minute timepoint


title: SMY2264_SPT20_t30

source_name: SMY2264 including SPT20 at the t30 minute timepoint


title: SMY2264_SPT20_t20

source_name: SMY2264 including SPT20 at the t20 minute timepoint


title: SMY2245_ZNF1_t90

source_name: SMY2245 including ZNF1 at the t90 minute timepoint


title: SMY2245_ZNF1_t45

source_name: SMY2245 including ZNF1 at the t45 minute timepoint


title: SMY2245_ZNF1_t20

source_name: SMY2245 including ZNF1 at the t20 minute timepoint


title: SMY2245_ZNF1_t15

source_name: SMY2245 including ZNF1 at the t15 minute timepoint


title: SMY2264_SPT20_t10

source_name: SMY2264 including SPT20 at the t10 minute timepoint


title: SMY2245_ZNF1_t10

source_name: SMY2245 including ZNF1 at the t10 minute timepoint


title: SMY2245_ZNF1_t5

source_name: SMY2245 including ZNF1 at the t5 minute timepoint


title: SMY2245_ZNF1_t0

source_name: SMY2245 including ZNF1 at the t0 minute timepoint


title: SMY2245_ZNF1_t30

source_name: SMY2245 including ZNF1 at the t30 minute timepoint


title: SMY2264_SPT20_t0

source_name: SMY2264 including SPT20 at the t0 minute timepoint


title: SMY2244_YRM1_t90

source_name: SMY2244 including YRM1 at the t90 minute timepoint


title: SMY2244_YRM1_t30

source_name: SMY2244 including YRM1 at the t30 minute timepoint


title: SMY2244_YRM1_t45

source_name: SMY2244 including YRM1 at the t45 minute timepoint


title: SMY2244_YRM1_t10

source_name: SMY2244 including YRM1 at the t10 minute timepoint


title: SMY2264_SPT20_t5

source_name: SMY2264 including SPT20 at the t5 minute timepoint


title: SMY2244_YRM1_t15

source_name: SMY2244 including YRM1 at the t15 minute timepoint


title: SMY2243_YOX1_t5

source_name: SMY2243 including YOX1 at the t5 minute timepoint


title: SMY2243_YOX1_t90

source_name: SMY2243 including YOX1 at the t90 minute timepoint


title: SMY2244_YRM1_t0

source_name: SMY2244 including YRM1 at the t0 minute timepoint


title: SMY2243_YOX1_t10

source_name: SMY2243 including YOX1 at the t10 minute timepoint


title: SMY2243_YOX1_t30

source_name: SMY2243 including YOX1 at the t30 minute timepoint


title: SMY2243_YOX1_t0

source_name: SMY2243 including YOX1 at the t0 minute timepoint


title: SMY2243_YOX1_t15

source_name: SMY2243 including YOX1 at the t15 minute timepoint


title: SMY2243_YOX1_t45

source_name: SMY2243 including YOX1 at the t45 minute timepoint


title: SMY2243_YOX1_t20

source_name: SMY2243 including YOX1 at the t20 minute timepoint


title: SMY2242_YLL054C_t45

source_name: SMY2242 including YLL054C at the t45 minute timepoint


title: SMY2242_YLL054C_t15

source_name: SMY2242 including YLL054C at the t15 minute timepoint


title: SMY2242_YLL054C_t90

source_name: SMY2242 including YLL054C at the t90 minute timepoint


title: SMY2242_YLL054C_t30

source_name: SMY2242 including YLL054C at the t30 minute timepoint


title: SMY2244_YRM1_t20

source_name: SMY2244 including YRM1 at the t20 minute timepoint


title: SMY2242_YLL054C_t10

source_name: SMY2242 including YLL054C at the t10 minute timepoint


title: SMY2241_YHP1_t90

source_name: SMY2241 including YHP1 at the t90 minute timepoint


title: SMY2241_YHP1_t45

source_name: SMY2241 including YHP1 at the t45 minute timepoint


title: SMY2242_YLL054C_t20

source_name: SMY2242 including YLL054C at the t20 minute timepoint


title: SMY2241_YHP1_t30

source_name: SMY2241 including YHP1 at the t30 minute timepoint


title: SMY2242_YLL054C_t5

source_name: SMY2242 including YLL054C at the t5 minute timepoint


title: SMY2241_YHP1_t20

source_name: SMY2241 including YHP1 at the t20 minute timepoint


title: SMY2241_YHP1_t10

source_name: SMY2241 including YHP1 at the t10 minute timepoint


title: SMY2241_YHP1_t5

source_name: SMY2241 including YHP1 at the t5 minute timepoint


title: SMY2239_WTM2_t20

source_name: SMY2239 including WTM2 at the t20 minute timepoint


title: SMY2241_YHP1_t15

source_name: SMY2241 including YHP1 at the t15 minute timepoint


title: SMY2241_YHP1_t0

source_name: SMY2241 including YHP1 at the t0 minute timepoint


title: SMY2239_WTM2_t90

source_name: SMY2239 including WTM2 at the t90 minute timepoint


title: SMY2239_WTM2_t45

source_name: SMY2239 including WTM2 at the t45 minute timepoint


title: SMY2239_WTM2_t30

source_name: SMY2239 including WTM2 at the t30 minute timepoint


title: SMY2242_YLL054C_t0

source_name: SMY2242 including YLL054C at the t0 minute timepoint


title: SMY2239_WTM2_t15

source_name: SMY2239 including WTM2 at the t15 minute timepoint


title: SMY2239_WTM2_t10

source_name: SMY2239 including WTM2 at the t10 minute timepoint


title: SMY2239_WTM2_t5

source_name: SMY2239 including WTM2 at the t5 minute timepoint


title: SMY2239_WTM2_t0

source_name: SMY2239 including WTM2 at the t0 minute timepoint


title: SMY2238_WTM1_t90

source_name: SMY2238 including WTM1 at the t90 minute timepoint


title: SMY2238_WTM1_t15

source_name: SMY2238 including WTM1 at the t15 minute timepoint


title: SMY2238_WTM1_t0

source_name: SMY2238 including WTM1 at the t0 minute timepoint


title: SMY2238_WTM1_t10

source_name: SMY2238 including WTM1 at the t10 minute timepoint


title: SMY2129_XBP1_t90

source_name: SMY2129 including XBP1 at the t90 minute timepoint


title: SMY2238_WTM1_t20

source_name: SMY2238 including WTM1 at the t20 minute timepoint


title: SMY2129_XBP1_t45

source_name: SMY2129 including XBP1 at the t45 minute timepoint


title: SMY2238_WTM1_t30

source_name: SMY2238 including WTM1 at the t30 minute timepoint


title: SMY2129_XBP1_t30

source_name: SMY2129 including XBP1 at the t30 minute timepoint


title: SMY2129_XBP1_t15

source_name: SMY2129 including XBP1 at the t15 minute timepoint


title: SMY2238_WTM1_t45

source_name: SMY2238 including WTM1 at the t45 minute timepoint


title: SMY2238_WTM1_t5

source_name: SMY2238 including WTM1 at the t5 minute timepoint


title: SMY2129_XBP1_t20

source_name: SMY2129 including XBP1 at the t20 minute timepoint


title: SMY2069_GCR1_t90

source_name: SMY2069 including GCR1 at the t90 minute timepoint


title: SMY2069_GCR1_t45

source_name: SMY2069 including GCR1 at the t45 minute timepoint


title: SMY2129_XBP1_t5

source_name: SMY2129 including XBP1 at the t5 minute timepoint


title: SMY2069_GCR1_t30

source_name: SMY2069 including GCR1 at the t30 minute timepoint


title: SMY2069_GCR1_t10

source_name: SMY2069 including GCR1 at the t10 minute timepoint


title: SMY2273_OPI1_t45

source_name: SMY2273 including OPI1 at the t45 minute timepoint


title: SMY2069_GCR1_t15

source_name: SMY2069 including GCR1 at the t15 minute timepoint


title: SMY2273_OPI1_t20

source_name: SMY2273 including OPI1 at the t20 minute timepoint


title: SMY2273_OPI1_t15

source_name: SMY2273 including OPI1 at the t15 minute timepoint


title: SMY2129_XBP1_t0

source_name: SMY2129 including XBP1 at the t0 minute timepoint


title: SMY2273_OPI1_t90

source_name: SMY2273 including OPI1 at the t90 minute timepoint


title: SMY2069_GCR1_t0

source_name: SMY2069 including GCR1 at the t0 minute timepoint


title: SMY2273_OPI1_t30

source_name: SMY2273 including OPI1 at the t30 minute timepoint


title: SMY2263_SOK2_t15

source_name: SMY2263 including SOK2 at the t15 minute timepoint


title: SMY2273_OPI1_t10

source_name: SMY2273 including OPI1 at the t10 minute timepoint


title: SMY2263_SOK2_t20

source_name: SMY2263 including SOK2 at the t20 minute timepoint


title: SMY2273_OPI1_t0

source_name: SMY2273 including OPI1 at the t0 minute timepoint


title: SMY2263_SOK2_t90

source_name: SMY2263 including SOK2 at the t90 minute timepoint


title: SMY2263_SOK2_t45

source_name: SMY2263 including SOK2 at the t45 minute timepoint


title: SMY2273_OPI1_t5

source_name: SMY2273 including OPI1 at the t5 minute timepoint


title: SMY2263_SOK2_t0

source_name: SMY2263 including SOK2 at the t0 minute timepoint


title: SMY2240_YAP6_t90

source_name: SMY2240 including YAP6 at the t90 minute timepoint


title: SMY2263_SOK2_t10

source_name: SMY2263 including SOK2 at the t10 minute timepoint


title: SMY2069_GCR1_t20

source_name: SMY2069 including GCR1 at the t20 minute timepoint