title: scRNA_seq_E120

status: Public on Oct 18 2020

type: SRA

city: Qingdao

first: Wei

last: Ge

state: Shandong Province

address: Changcheng Road

department: College of life sciences

country: China

institute: Qingdao Agricultural University

description: The group information is prefixed with E120 in the column of processed data file

library_source: transcriptomic

data_processing:
We used CellRanger count pipeline 3.0.2 to analyze the sequencing data and generated the single cell information. To generate same number of total cells for downstream analysis, we used augments ‘--force-cells=7000 \’.
Genome_build: ARS1
Supplementary_files_format_and_content: tab-delimited text files stores normalized and log-transformed single cell expression value

molecule: total RNA

organism: Capra hircus

source_name: E120 goat skin

extract_protocol:
The goat fetus at desired dates was isolated using cesarean operation when the pregnant goats were anesthetic with the compound ketamine. The skin tissues (0.5 cm × 0.5 cm) were isolated from the fetus back skin and were immediately transferred to the ice-cold DMEM/F12 media (Gibco, Beijing, China) with 50 U/ml penicillin and 50 mg/ml streptomycin (HyClone, Beijing, China).. After washing three times with DMEM/F12 to remove contaminative blood cells, the skin tissues were then dissociated into single cells prior to sequencing. For E60 and E90 skin tissues, the obtained skin tissues were firstly incubated with 2 mg/ml collagenase IV (Sigma, St Louis, MO, USA) for 30 min at 37 °C, and then the skin tissues were mechanically dissociated into single-cell suspensions with a 1ml pipette tip. For E120 skin tissues, the skin tissues were firstly cut into ~3 mm skin pieces and then incubated with 2 mg/ml collagenase IV for 30 min. After incubation, the hair follicles within the skin tissues were isolated with a pair of precise forceps and the pooled hair follicles were further dissociated into single cells with TypLE Express (Gibco, Grand Island, NY, USA) for 30 min at 37 °C. The obtained single-cell suspensions were then washed three times with PBS supplemented with 0.04% BSA (Sigma, St Louis, MO, USA) and were filtered with a 40 μm cell strainer (BD Falcon, BD Biosciences, San Jose, CA, USA) to remove debris and cell aggregations. For each stage, the samples were obtained from at least 2 different goat fetus and for each fetus goat, the single-cell suspension was prepared separately until finally pooled together prior to single-cell barcoding.
Single-cell RNA-seq libraries were prepared using Single Cell 3’ Library Gel Bead Kit V3 (10x Genomics Inc., Pleasanton, CA, USA) following the manufacture’s introduction.

tag: breed

value: Northern Shaanxi White Cashmere Goat

tag: tissue

value: skin

tag: developmental stage


title: scRNA_seq_E90

description: The group information is prefixed with E90 in the column of processed data file

source_name: E90 goat skin


title: scRNA_seq_E60

description: The group information is prefixed with E60 in the column of processed data file

source_name: E60 goat skin


title: pSTK::amiRNACWIN24 (4-3) rep1

status: Public on Feb 29 2020

city: Callaghan

first: Shengjin

last: Liao

state: NSW

address: University Drive

institute: The University of Newcastle, Australia

data_processing:
Raw reads were trimmed using CLC Genomics Workbench 10.1.1 (Qiagen) (Ru et al., 2017). Raw reads were trimmed as following: (1) Removal of reads with quality scores less than 20 (base-calling error probability less than 0.01) and those with ambiguous nucleotides more than 2; (2) Adapter trimming and (3) Removal of reads with sequences length less than 15 nucleotides
To estimate gene expression level, trimmed reads were mapped to the Arabidopsis reference genome sequence (TAIR10) using the CLC Genomics Workbench, which allows unique mapping with a maximum of two mismatches. Reads mapped to unigenes were counted and used for expression analysis. The number of mapped reads per kilobase per million reads (RPKM) was used as a measure of the expression level of each gene
Genome_build: Arabidopsis reference genome sequence (TAIR10)
Supplementary_files_format_and_content: Log2 FoldChange, RPKM

organism: Arabidopsis thaliana

source_name: flower buds

extract_protocol:
RNA was extracted using the Qiagen RNA Plant Mini Kit, followed by an on-column DNase treatment to eliminate gDNA by DNaseI digestion
RNA libraries were prepared for sequencing using standard Illumina protocols
Sequencing of the cDNA libraries was performed using an Illumina Hiseq2500 with 125bp pair-end with an average sequencing depth of 30 million reads.

value: Floral stage 8-10

tag: genotype

value: pSTK::amiRNACWIN24 (4-3)

value: Floral buds


title: pSTK::amiRNACWIN24 (4-3) rep3


title: pSTK::amiRNACWIN24 (4-3) rep4


title: pSTK::amiRNACWIN24 (4-3) rep2


title: WT rep3

value: WT


title: WT rep4


title: WT rep2


title: WT rep1


title: Control-2

city: Auckland

first: Veronika

last: Sander

address: 85 Park Road

department: Molecular Medicine and Pathology

country: New Zealand

institute: University of Auckland

data_processing:
RNA sequencing data were trimmed for quality control using Trim Galore v0.6.4
Reads were aligned to the human genome (GRCh38) using STAR
Transcript quantification was performed with featureCounts
Differential expression analysis was performed using edgeR and limma
Gene set enrichment analysis wad done using clusterProfiler
Genome_build: GRCh38
Supplementary_files_format_and_content: CountMatrix.txt.gz: tab-delimited text file includes count values for each sample

organism: Homo sapiens

source_name: kidney organoids

extract_protocol:
Kidney organoids were grown from MANZ-2-2 iPSCs according to Przepiorski et al., 2018. Quadruplicate samples of >100 organoids per sample were left untreated (= samples 1 – 4) or treated with 5 µM cisplatin (= samples 5 – 8) on day (d) 12, d14, d16 and d18. On d19, organoids were washed in PBS and homogenized in TRIzol. Total RNA was extracted using the GENEzol TriRNA Pure kit (Geneaid). Libraries were prepared using the Collibri™ Stranded RNA Library Kit (Thermo Fisher) and RNA-sequencing was carried out on an Illumina NextSeq 500.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: kidney organoids

tag: cell line

value: MANZ-2-2 iPSC line

value: wild-type

tag: treatment

value: untreated


title: Cisplatin-2

value: 4 x 5 µM cisplatin


title: Cisplatin-1


title: Cisplatin-3


title: Control-4


title: Control-3


title: Cisplatin-4


title: DP-3_15

city: Vienna

first: Sonali

middle: N.

last: Reisinger

state: Vienna

address: Schwarzspanierstraße 17A

department: Center for Physiology and Pharmacology

country: Austria

institute: Medical University of Vienna

data_processing:
fastq generation, bcl2fastq via Basespace
alignment and extraction of counts/gene, STAR aligner (STAR_2.5.0b) via Basespace, parameters: genomeDir /genomes/Mus_musculus/UCSC/mm10/Sequence/STARindex2 outSAMattrRGline ID:1 "SM:DP-3_1" outSAMattributes NH NM MD outSAMtype BAM SortedByCoordinate limitBAMsortRAM 12000000000 outSAMunmapped Within outSAMmapqUnique 50 readFilesIn "/data/scratch/workspace/RunFolder/Analysis/samples/DP-3_1/replicates/DP-3_1/filtered/DP-3_1_S1_L001_R1_001.fastq.gz" readFilesCommand zcat sjdbGTFfile "/genomes/Mus_musculus/UCSC/mm10/Annotation/Archives/archive-2015-07-17-14-33-26/Genes/genes.gtf" outFilterType BySJout outSJfilterCountUniqueMin -1 2 2 2 outSJfilterCountTotalMin -1 2 2 2 outFilterIntronMotifs RemoveNoncanonical twopassMode Basic
differential gene expression analysis, DESeq2 (1.6.3) via Basespace
Genome_build: UCSC mm10
Supplementary_files_format_and_content: plain text, raw counts per gene, one file per sample

organism: Mus musculus

source_name: dorsal raphe tissue

extract_protocol:
Brains were removed and frozen in embedding matrix before dissection of dorsal raphe (DR) from 4 consecutive 300 um-thick coronal sections (Bregma -4.0 mm to Bregma -5.2 mm, area ~ 1.5x1.5 mm2 directly below cerebral aqueduct). Tissue was stored in RNAlater (ThermoFisher Scientific) until further processing. For RNA extraction, Qiagen's miRNEasy Mini kit was used: Tissue was placed into 700 µl Qiazol (Qiagen) and mechanically disrupted until the homogenate was clear. This mix was incubated at room temperature (RT) for 5 min before addition of chloroform, with a further incubaton period of 3 min after agitating the solution vigorously. After centrifugation (15 min, 12000 G, 4 °C), the upper phase was transferred and RNA was precipitated with 1.5 × the sample volume in ethanol (96 %). Provided columns and collection tubes were used to retain the precipitate prior to washing the filter with the provided wash buffers (RWT once, RPE twice). At each of these steps, the flowthrough after a quick centrifugation step was discarded. Finally, RNA was eluted from the column filter using 40 µl of RNAse-free water.
NEBNext® Ultra™ II RNA Library Prep Kit (New England Biolabs, Ipswich, MA, USA)

tag: strain

value: STAT3 KO

tag: Sex

value: male

value: midbrain dorsal raphe


title: DP-3_5

value: female


title: Control-1


title: DP-3_14


title: DP-3_7


title: DP-3_16


title: DP-3_10


title: DP-3_11

value: control


title: DP-3_8


title: DP-3_6


title: MEL_SMC1_ChIAPET_D5R2

city: Irvine

first: Weihua

last: Zeng

state: CA

address: 2300E Bio Sci III

department: Dev & Cell Biology

country: USA

institute: UCIrvine

library_source: genomic

data_processing:
Half linker sequences were removed from reads and only the 20bp tags from each end were used for mapping. Tags were separated into two groups based on the half linker barcode information of the pair-end reads: the AA/BB group that should hold true interactions as well as some non-specific random ligations and the AB chimeric ligation group to estimate the extent of non-specific random ligations.
The tags were mapped to mm9 reference genomes with Bowtie, respectively using the parameters -S -q -v 2 -k 1 -m 1 --best –strata.
petNet pipeline was used to build Chromatin Interaction Graphs (Jansen et al, in preparation)
Genome_build: mm9
Supplementary_files_format_and_content: 1kb vertices are generated from DNase-seq consolidated hotspots, together with the connection edges list and vertice list with edges based on 1kb vertices from day0 and day5 MEL ChIA-PET data

molecule: genomic DNA

growth_protocol: Mouse erythroleukemia cells (MEL, ATCC, Manassas, VA) were grown in RPMI-1640 medium (Life Technologies, Carlsbad, CA) supplemented with penicillin/streptomycin (Life Technologies) and 10% FBS (VWR, Radnor, PA).  Trypan Blue (VWR) staining was performed before harvesting the cells for each assay in order to make sure that at least 90% of the cells were viable. All experiments were done with 2 biological replicates.

extract_protocol:
Biological replicates of anti-SMC1 (subunit of cohesin complex) ChIA-PET libraries for uninduced (MEL) and induced (MEL+DMSO) MEL were essentially constructed as previously described (Li et al. 2012) with additional changes to volume used in circularization (Heidari et al. 2014).
The starting material was from 100-200 million cells and the ChIPs were performed using rabbit anti-SMC1 antibody (catalog number NC0553162, Thermo Fisher Scientific, MA) and Dynabeads M-280 sheep anti-rabbit beads (Thermo Fisher Scientific).

treatment_protocol: MELs grown to a density of 1 million/ml were differentiated using 2% DMSO (VWR) added to the medium and the cells were grown for another 5 days to induce the expression of hemoglobin genes. At least 80-90% of cells expressed hemoglobin based on their color and benzidine/hydrogen peroxide staining result.

value: MEL

tag: cell type

value: Mouse erythroleukemia cells

tag: induced with

value: 2% DMSO for 5 days

tag: antibody

value: rabbit anti-SMC1 (Thermo Fisher Scientific, Cat. # NC0553162)


title: MEL_SMC1_ChIAPET_D5R1


title: DP-3_3


title: DP-3_13


title: MEL_SMC1_ChIAPET_D0R2

value: none (uninduced)


title: MEL_SMC1_ChIAPET_D0R1


title: DP-3_4


title: Sertoli Clone_wildtype_E11.5_miRNA_rep3

type: RNA

city: Tsukuba

first: Kimiko

last: Inoue

state: Ibaraki

address: 3-1-1 Koyadai

department: Bioresource Engineering Division

country: Japan

institute: BRC, RIKEN

description: miRNA expression of E11.5 SCNT placentas

hyb_protocol: Labeled RNA was hybridized to SurePrint G3 Mouse miRNA 8x60K (Agilent) at 55˚C for 20 hrs, according to manufacture's instructions.

scan_protocol: Scanning of microarray slides was performed on a DNA microarray scanner (Agilent) at a 5 um resolution.

data_processing:
Scanned-image files were processed to give signal intensities using the Feature Extraction software (Agilent). All raw data were loaded into Gene Spring GX software (Agilent) and 90 percentile shift was performed.
Raw intensities after 90 percentile shift. Signals under limit of detection were set as 0.1.

source_name: somatic cell nuclear transferred placenta, Sertoli, E11.5, wildtype

label_protocol: Total RNA was labeled with miRNA Complete Labeling and Hyb Kit (Agilent), according to the manufacturer’s instructions.

growth_protocol: 1-cell stage embryos derived from IVF and SCNT were cultured in KSOM medium at 37°C for 16 hours. Cultured embryos were transferred into pseudopregnant ICR females and 11.5 embryos were retrieved from the uterus.

extract_protocol: Total RNA from E11.5 placentas was extracted from IVF and SCNT placentas using RNeasy Mini kits (QIAGEN).

treatment_protocol: IVF or SCNT embryos were retrieved from the mother’s uterus at E11.5 and placentas without deciduas were used for RNA extraction.

value: placenta

tag: protocol

tag: clone

value: Sertoli

tag: age

value: wildtype


title: Sertoli Clone_wildtype_E11.5_miRNA_rep2

value: somatic cell nuclear transferred placenta


title: Cumulus Clone_Xist KO_E11.5_miRNA_rep1

source_name: somatic cell nuclear transferred placenta, cumulus, E11.5, Xist KO

value: cumulus

value: Xist KO


title: Cumulus Clone_Xist KO_E11.5_miRNA_rep2


title: WT B-1a_4

city: Kalamazoo

first: Momoko

last: Yoshimoto

state: MI

address: 300 Portage St.

department: Investigative Medicine

institute: WMU Homer Stryker MD School of Medicine

description: Gene expression in WT B-1a cells

hyb_protocol: The Cy3-labeled cDNAs were hybridized overnight (17 hours, 65C) to an Agilent Whole Mouse Genome Oligo Microarrays 8x60K using Agilent's recommended hybridization chamber and oven.

scan_protocol: Fluorescebce signals of the hybridized Agilent Microarrays were detected using Agilent's Microarray Scanner Sytem (Agilent Technologies).

data_processing:
The Agilent Feature Extraction Software was used to read out and process the microarray image files. The software detemines feature intensities (including background subtraction), rejects outliers and calculates statistical confidences.
Value=1 that the signal intensity is positive and significant above the background.
Value=0 that the signal intensity is not positive and significant above the back fround.

source_name: Wild type peritoneal B-1a cells sample #WT_4

label_protocol: 250mg of each of the cDNAs were used as template for Cy3 labeling which was performed according to Miltenyi Biotec's undisclosed protocol.

extract_protocol: Total RNA was extracted from each sampl using Rneasy micro kit (QIAGEN)

value: WT


title: Bmi1 KO_3

description: Gene expression in Bmi1 KO B-1a cells

source_name: Bmi1 KO peritoneal B-1a cells sample #KO_3

value: Bmi1 KO


title: Cumulus Clone_wildtype_E11.5_miRNA_rep1

source_name: somatic cell nuclear transferred placenta, cumulus, E11.5, wildtype


title: Cumulus Clone_wildtype_E11.5_miRNA_rep2


title: Bmi1 KO_4

description: Gene expression in Bmi1 KO B-1a cells

source_name: Bmi1 KO peritoneal B-1a cells sample #KO_4


title: WT 3

description: Gene expression in WT B-1a cells

source_name: Wild type peritoneal B-1a cells sample # WT3


title: WT B-1a_3

description: Gene expression in WT B-1a cells

source_name: Wild type peritoneal B-1a cells sample #WT_3


title: IVF_E11.5_miRNA_rep2

description: miRNA expression of E11.5 IVF placentas

source_name: in vitro fertilized placenta, E11.5, wildtype

value: in vitro fertilized placenta


title: IVF_E11.5_miRNA_rep3

description: miRNA expression of E11.5 IVF placentas


title: Sertoli Clone_Xist KO_E11.5_miRNA_rep1

source_name: somatic cell nuclear transferred placenta, Sertoli, E11.5, Xist KO


title: Sertoli Clone_Xist KO_E11.5_miRNA_rep2


title: Sertoli Clone_wildtype_E11.5_miRNA_rep1


title: WT 4

description: Gene expression in WT B-1a cells

source_name: Wild type peritoneal B-1a cells sample # WT4


title: Bmi1 KO_2

description: Gene expression in Bmi1 KO B-1a cells

source_name: Bmi1 KO peritoneal B-1a cells sample # KO_2


title: Bmi1 KO_1

description: Gene expression in Bmi1 KO B-1a cells

source_name: Bmi1 KO peritoneal B-1a cells sample # KO_1


title: Bmi1 KO4

description: Gene expression in Bmi1 KO B-1a cells

source_name: Bmi1 KO peritoneal B-1a cells sample # KO4


title: WT B-1a_2

description: Gene expression in WT B-1a cells

source_name: Wild type peritoneal B-1a cells sample #WT_2


title: Cumulus Clone_wildtype_E11.5_miRNA_rep3


title: WT 2

description: Gene expression in WT B-1a cells

source_name: Wild type peritoneal B-1a cells sample # WT2


title: IVF_E11.5_miRNA_rep4

description: miRNA expression of E11.5 IVF placentas


title: KNU5: APP/PS1+N-AS 1

city: Daegu

first: Hee Kyung

last: Jin

address: 80 Daehakro, Buk-gu

country: South Korea

institute: Kyungpook National University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 whole genome using Tophat
Read count extraction and nomalization were performed using edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: microglia isolated from mice brain

growth_protocol: In brief, the cortex of WT (9-mo-old), APP/PS1 (9-mo-old), APP/PS1 treated with N-AS (9-mo-old) mice were minced in Hibernate A (Gibco)/B27 (Invitrogen) medium and dissociated using papain (Worthington) solution. After tissue trituration, microglia were separated by Optiprep (Sigma-Aldrich) density gradient centrifugation.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). rRNA was removed using Lexogen RIBO COP rRNA depletion kit from each 1ug of total RNA.
RNA libraries were prepared for sequencing using  Clontech SMARTer Stranded RNA-Seq Kit standard protocols.

treatment_protocol: N-AS (30 mg kg-1, Sigma-Aldrich, 01912) was injected daily s.c. for 8 weeks to 7-mo-old APP/PS1 mice until the age of 9 months.

value: microglia

value: Cortex from adult brain


title: KNU7: WT 3

value: Wild type


title: KNU4: APP/PS1 2


title: WT B-1a_1

description: Gene expression in WT B-1a cells

source_name: Wild type peritoneal B-1a cells sample # WT_1


title: KNU3: APP/PS1 1


title: KNU1: WT 1


title: Bmi1 KO3

description: Gene expression in Bmi1 KO B-1a cells

source_name: Bmi1 KO peritoneal B-1a cells sample # KO3


title: KNU2: WT 2


title: IVF_E11.5_miRNA_rep1

description: miRNA expression of E11.5 IVF placentas


title: A549_siTAZ

city: Bunkyo-ku

first: Hideaki

last: Isago

state: Tokyo

department: Department of Respiratory Medicine

institute: The University of Tokyo Graduate School of Medicine

hyb_protocol: Biotin-labeled sense-strand cDNA were hybridized for 16 hours at 45C on GeneChip Human Gene ST 2.0 in the Genechip Hybridization Oven 645. GeneChips were washed and stained in GeneChip Fluidics Station 450.

scan_protocol: Scanning was performed by GeneChip Scanner 3000 7G, according to manufacturer's instruction.

data_processing: CEL files were obtained and normalized to a global intensity by  by Affymetrix GeneChip Command Console (AGCC) 4.0, using the RMA (Robust Multi-array Average) method.

label: biotin

source_name: human lung cancer cell line A549 transfected with siTAZ

label_protocol: Single-stranded cDNA synthesis and labelling were performed using GeneChip WT PLUS Reagent Kit (Affymetrix), using 500ng total RNA.

growth_protocol: Standard A549 growth condition.

extract_protocol: TRIzol reagent (Thermo Fisher Scientific) was used for total RNA extraction.

treatment_protocol: Cells were transfected with siRNA, using Lipofectamine RNAiMAX (Invitrogen), according to the manufacturer's instructions.Total RNA was extracted from A549 cells 48h after transfection.

tag: transfection

value: transfected with siTAZ

value: lung cancer


title: KNU10: APP/PS1+N-AS 3


title: A549_siYAP

source_name: human lung cancer cell line A549 transfected with siYAP

value: transfected with siYAP


title: KNU9: APP/PS1 4


title: A549_siNC

source_name: human lung cancer cell line A549 transfected with siNC

value: transfected with siNC


title: SS2_17_014.DMP1+

city: New York

first: Ruslan

last: Soldatov

state: New York

address: 323 E 61st Street

department: Computational Oncology

institute: Memorial Sloan Kettering Cancer Center

data_processing:
For SmartSeq2 single cell protocol, scRNA-seq reads were aligned to the UCSC mm10 or GRCh38 genome assemblies using STAR aligner. Per-gene read counts in each cell were determined using feature Counts software
CellRanger-2.2.0 or CellRanger-3.0.2 10x Chromium software was used to perform alignment to GRCh38 or mm10 genome assemblies, filtering, barcode counting and UMI counting.
Individual single-cell datasets were pre-processed using PAGODA1/PAGODA2 packages, which includes normalization, clustering of cells, removal of spike-in cells and t-SNE embedding for visualization
Joint analysis of mouse datasets was performed using data integration CONOS R package
Joint analysis of human datasets was performed using scVI deep learning framework
Genome_build: mm10, hg38
Supplementary_files_format_and_content: text files include gene counts matrices for each Smart-seq2 well and 10x Chromium dataset

source_name: incisor

growth_protocol: All animals were kept under standard conditions with 12/12 day/night cycles with food and water ad libitum.

extract_protocol:
Dental pulps from mouse incisor/molars or human molars/apical papillae were dissected under the stereomicroscope, cut to small pieces and dissociated in Collagenase P solution in HBSS (3U/mL, 10-30 min, 37 °C). After the tissue was completely dissolved, a single-cell suspension was prepared using cell-strainer cap tubes and FACS-sorted into 384-well plates.
Library construction was performed as described in (Picelli S. et al., Nat Protoc. 2014)

treatment_protocol: No specific treatment was performed prior to extract preparation.

tag: isolation

tag: phenotype

value: healthy

tag: plate

tag: platform


title: KNU8: APP/PS1 3

tag: tissue


title: SS2_17_014.Col2.3+


title: KNU6: APP/PS1+N-AS 2

tag: genotype


title: AM from uninfected mice_2

city: Shrewsbury

first: Jinhee

last: Lee

state: MA

address: 9 Deerfield Road

institute: Umass Med

description: AM sorted into uninfected or infected cells

hyb_protocol: Following fragmentation, 10 μg of cRNA was hybridized for 16 h at 45°C on Mouse Genome 430 2.0 arrays

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

data_processing: The data were analyzed with Transcription Analysis Console 3  (Affymetrix).

organism: Mycobacterium tuberculosis

source_name: AM uninfected

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

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

treatment_protocol: C57BL/6 mice were infected with Mtb H37Rv expressing YFP, and 3 weeks later the total lung cells were sorted into unfected and infected cells.

tag: disease state

value: uninfected

value: Lung

value: 8-10 weeks


title: AM from uninfected mice_3


title: Bmi1 KO2

description: Gene expression in Bmi1 KO B-1a cells

source_name: Bmi1 KO peritoneal B-1a cells sample # KO2


title: AM from uninfected mice_1


title: RM infected exp2_4

description: RM sorted into uninfected or infected cells

source_name: RM infected

value: infected


title: SS2_17_011.DMP1+


title: SS2_17_395.whole

source_name: molar

value: whole


title: SS2_16_634.PLP/YFP 9 days traced

treatment_protocol: For unilateral denervation (inferior alveolar nerve transection) adult PLP1CreERT2/R26YFP mice were used. Twenty-four hours before denervation tamoxifen (Sigma T5648) dissolved in corn oil (Sigma C8267) in concentration 150 mg/kg was administered intraperitoneally, animals were anesthetised by intraperitoneal injection of ketamine and medetomidinhydrochlorid combination, incision was made through skin and masseter muscle was made and exposed inferior mandibular nerve on right side of mandible was transected with micro-scissors. Wet food was administered during the survival period.

value: PLP/YFP 9 days traced

value: damaged


title: SS2_16_017.Sox10/creERT2-tdTomato (leaking - all pulp)

treatment_protocol: Animals with creERT2 were injected with 150 mg/kg of tamoxifen dissolved in corn oil intraperitoneally for genetic recombination in periods from 3 days up to 6 months.


title: RM uninfected exp2_1

source_name: RM uninfected


title: SS2_16_016.whole


title: SS2_16_254.whole


title: RM infected exp2_2


title: SS2_16_257.PLP/YFP 3 days traced

value: PLP/YFP 3 days traced


title: SS2_17_394.whole


title: RM infected exp2_1


title: WT, replicate 2

city: Orangeburg

first: Sandipkumar

last: Darji

state: NY

address: 140 Old Orangeburg Rd, Bldg 39

department: Center for Dementia Research

institute: Nathan Kline Institute for Psychiatric Research

data_processing:
Basecalling was performed using illumina's bcl2fastq (v1.8.4).
fastq_screen (v0.5.2) was used to quality check fastq reads for contamination by mapping against multiple genomes.
Trimmomatic (v0.36) was used to trim adapters and low quality bases.
STAR aligner (v2.6.0a) was used to align/map processed reads with reference genome.
Quantification of mapped reads were carried out using featureCounts from Subread package (v1.6.3)
Genome_build: mm10 from UCSC
Supplementary_files_format_and_content: countsPerMillion_filt_TMMnorm.txt is a tab-delimited text file which contains abundance mesurement of genes across the samples. The abundance is in the form of number of reads of genes which are filtered for lowly expressed genes using 'filterByExpr' function from R/Biconductor's EdgeR package and further normalized using Trimmed Mean Value (TMM) method -- to account for composition bias -- before converting them into counts per million to account for the library size difference among samples. The columns represent sample names and rows official gene symbols (NCBI).

source_name: Blastocysts

growth_protocol: Cells were grown in 35mm dishes in DMEM (Fisher, 11-995-073) supplemented with 15% fetal bovine serum (Hyclone), penicillin/streptomycin (Fisher, 15-140-148), Glutamax (Fisher, 35-050-061), NEAA (Fisher, 11-140-050) and β-mercaptoethanol (Sigma, M3148) at 37 degree celcius in a 5% CO2 atmosphere.

extract_protocol:
Total RNA was extracted using RNeasy Micro kit (Qiagen, 74004) according to manufacturer's specifications. Quality of RNA was assesed using Agilent 2100 Bioanalyzer (NANO).
500 ng of total RNA were used to prepare cDNA library using TruSeq Stranded mRNA Library Prep Kit (Illumina Inc., San Diego, CA, USA) with PolyA selection. The quality of libraries were assessed with Agilent 2200 TapeStation system.

treatment_protocol: Cells from the treatment group were treated with 200 µM Isoproterenol (Sigma, I2760) for 6 hrs before extracting RNA.

value: WT

tag: treatment

value: No treatment

value: Blastocysts


title: WT, replicate 3

tag: strain


title: RM uninfected exp2_3


title: SS2_16_257.whole


title: RM uninfected exp2_2


title: RM infected exp1_1


title: CD11chighMC uninfected exp2_4

description: CD11chighMC sorted into uninfected or infected cells

source_name: CD11chighMC uninfected


title: CD11chighMC infected exp2_2

source_name: CD11chighMC infected


title: CD11chighMC uninfected exp2_3


title: CD11chighMC infected exp2_4


title: RM uninfected exp1_2


title: CD11chighMC uninfected exp2_1


title: SS2_16_256.whole


title: WT, ISO treated, replicate 3

value: Treated with 200 microM ISO for 6 hrs


title: WT, ISO treated, replicate 2


title: RM infected exp1_2


title: WT, ISO treated, replicate 1


title: RM infected exp2_3


title: RM uninfected exp1_1


title: CD11chighMC uninfected exp2_2


title: CD11chighMC infected exp1_4


title: CD11chighMC uninfected exp1_4


title: CD11chighMC infected exp2_1


title: CD11chighMC uninfected exp1_1


title: CD11chighMC infected exp1_1


title: CD11chighMC infected exp1_2


title: SS2_16_015.whole


title: PSEN1 KO, replicate 2

value: PSEN1 knockout


title: WT, replicate 1


title: PSEN1 KO, ISO treated, replicate 1


title: CD11chighMC infected exp1_3


title: RPE1-hTERT_RNA-seq_rep3

city: Amsterdam

first: Fred

last: van Leeuwen

address: Plesmanlaan 121

department: Gene Regulation

country: Netherlands

institute: Netherlands Cancer Institute

data_processing:
The 65 bp single end reads were mapped to the aligned against the human reference genome (hg38) using HISAT2 (version 2.1.0).
Mapped reads were counted using htseq-count (version 0.9.1) and a Gencode v27 (GRCh38) gene gtf file with the following arguments: ‘-m union -s no -f bam’
Genome_build: hg38
Supplementary_files_format_and_content: comma seperated values with one column per sample and one row per gene containing raw counts

growth_protocol: Cells were grown in DMEM/F12 supplemented with 10% fetal bovine serum.

extract_protocol:
Total RNA was isolated using the RNeasy kit (Qiagen). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug total RNA was extracted according to the manufacturer’s protocol. Quality and quantity of the total RNA was assessed by the 2100 Bioanalyzer using a Nano chip (Agilent). Only RNA samples having an RNA Integrity Number (RIN) > 8 were subjected to library generation.
Strand-specific cDNA libraries were generated using the TruSeq Stranded mRNA sample preparation kit (Illumina) according to the manufacturer’s protocol. The libraries were analyzed for size and quantity of cDNAs on a 2100 Bioanalyzer using a DNA 7500 chip (Agilent), diluted and pooled in multiplex sequencing pools. The libraries were sequenced as 65 base single reads on a HiSeq2500 (Illumina).

value: unperturbed RPE1-hTERT


title: RPE1-hTERT_RNA-seq_rep4


title: PSEN1 KO, replicate 3


title: PSEN1 KO, ISO treated, replicate 2


title: PSEN1 KO, ISO treated, replicate 3


title: PSEN1 KO, replicate 1


title: RPE1-hTERT_RNA-seq_rep2


title: RPE1-hTERT_RNA-seq_rep1


title: AM uninfected exp2_4


title: MLO4(Midbrain-like Organoid4)

city: Seoul

first: Seungwon

middle: Thomas

last: Kim

address: Wangsimniro 222

department: Department of Biochemistry and Molecular Biology

institute: Hanyang University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 whole genome using Tophat
Read count extraction and nomalization were performed using edgeR.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: H9 hESC-derived Midbrain Organoid

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

value: H9 hESC-derived NPC


title: R-1

city: Jinan

first: Ming

last: Shao

state: Shandong

address: 27# Shan Da Nan Lu Road

department: School of Lifesciences

institute: Shandong University

description:
Group_R1-VS-WT1_DE_significant_anno.xls
all headcut.rpkm.xls

data_processing:
Base-calling: Bcl2fastq (v2.17.1.14)
Data filtering step: Cutadapt（version 1.9.1）
Allignment: Hisat2(v2.0.1), default parameter
Differential gene expression: DESeq2（V1.6.3）
Gene expression: Htseq software (V 0.6.1)
Genome_build: GRCz11
Supplementary_files_format_and_content: excel file, gene expression level in FPKM
Supplementary_files_format_and_content: excel file, differentially expressed genes

organism: Danio rerio

source_name: head explant

extract_protocol:
Trizol and isopropanol precipitation
The mRNA libraries were constructed by TruSeq RNA Library Preparation Kit, and 100 bp paired end sequencing was performed on Illumina HiSeq 2000. The data obtained from three independent samples were aligned and analysed as described (Shao et al., 2017).

treatment_protocol: the head region of 33 hpf embryos were cut and collected for RNA extraction

tag: dev stage

value: 33 hpf

value: head region cut before otic vesicle

value: AB

tag: genotype/variation

value: -8 bp deletion by TALEN in the 1st exon


title: AM infected exp1_2

source_name: AM infected

value: Lung

value: 8-10 weeks


title: H3.3-FLAG_24h_4OHT

data_processing:
ChIP-seq reads were aligned to the human genome (hg38) using Bowtie2 (version 2.3.4) using default settings.
Aligned reads were filtered for mapping score (MAPQ) greater than 10 using samtools (version 1.2).
Aligned reads from the three datasets were normalized for library size using bamCoverage (version 2.5.0) using 50 bases bin size and effective genome size of 2685511504 bases.
Genome_build: hg38
Supplementary_files_format_and_content: bigWig files represent normalized read densitity

growth_protocol: DMEM/F12 + 10%FBS

extract_protocol:
Chromatin was isolated from formaldehyde cross-linked cells, sonicated and histone-DNA complexes were immunoprecipiated with antibodies.
Libraries were constructed using the KAPA LTP library preparation kit (KAPA Biosystems KR0453-v6.17) according to manufacturer's protocol. After adaptor ligation, 14 PCR cycles were used for library amplification and ~300 bp fragments were size selected using Agencourt AMPure XP beads (Beckman Coulter).  The libraries were sequenced as 65 base single reads on a HiSeq2500 (Illumina).

treatment_protocol: 100 nM 4OHT

tag: chip antibody

value: anti-FLAG M2 (F1804; Sigma)


title: AM infected exp2_2

value: infected


title: CD11chighMC uninfected exp1_3

value: uninfected


title: AM uninfected exp2_2


title: AM infected exp2_4


title: AM infected exp2_1


title: WT-1

description:
AS wildtype vs rbm24a mutant
Group_Wild-type-VS-mutant_DE_significant_anno
all.fpkm_anno

data_processing:
Base-calling: Bcl2fastq (v2.17.1.14)
Data filtering step: Cutadapt（version 1.9.1）
Allignment: Hisat2(v2.0.1), default parameter
Alternative splicing analysis:  ASprofile（V1.0.4）
Differential gene expression: DESeq2（V1.6.3）
Gene expression: Htseq software (V 0.6.1)
Genome_build: GRCz11
Supplementary_files_format_and_content: excel file, gene expression level in FPKM
Supplementary_files_format_and_content: excel file, alternative splicing
Supplementary_files_format_and_content: excel file, differentially expressed genes

source_name: whole embryo wild-type

value: whole embryo


title: AM infected exp1_1


title: AM uninfected exp1_3


title: AM uninfected exp2_1


title: AM infected exp1_4


title: AM uninfected exp1_4


title: CD11chighMC uninfected exp1_2


title: R-3

description:
AS wildtype vs rbm29a mutant
Group_Wild-type-VS-mutant_DE_significant_anno
all.fpkm_anno

source_name: whole embryo rbm24a mutant

value: -8 bp deletion by TALEN in the 3st exon


title: R-2

description:
AS wildtype vs rbm28a mutant
Group_Wild-type-VS-mutant_DE_significant_anno
all.fpkm_anno

value: -8 bp deletion by TALEN in the 2st exon


title: MLO1(Midbrain-like Organoid1)

tag: cell type


title: R-1

description:
AS wildtype vs rbm27a mutant
Group_Wild-type-VS-mutant_DE_significant_anno
all.fpkm_anno


title: H3.3-FLAG_8h_4OHT


title: AM uninfected exp1_2


title: miRNA_Gab1KO_SCNT_E19.5_rep3

data_processing:
Quality check of FASTQ files was performned with FastQC.
All raw reads were loaded into Strand NGS and low-quality reads (QC <20) were removed from further operation.
Passed reads were aligned to the reference mouse genome (mm10), which was downloaded from the UCSC database using the default algorithm of Strand NGS after trimming of the adapter sequence.
Raw values were normalized using DE-seq and a baseline treatment was performed to set the mean value within each gene to the 0 value.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file includes normalized values using DE-seq and baseline treatment for each sample.

extract_protocol:
On day 11.5, embryos were retrieved from the mother’s uterus and placentas without deciduas were used in further experiments. On day 19.5, the pregnant females underwent Caesarian section and placentas were collected. Total RNA from E11.5 and 19.5 placentas was extracted from IVF and SCNT placentas using RNeasy Mini kits.
The transcriptome library was prepared using the SMARTer Stranded Total RNA Sample Prep Kit-HI Mammalian, according to the manufacturer’s instructions.

value: placenta

tag: source

value: somatic cell nuclear transfer

value: miRNA/Gab1 KO


title: miRNA_Gab1KO_SCNT_E19.5_rep1


title: Og-NSC4

source_name: Sporadic Parkinsons Disease patient iPSC Midbrain Organoid derived NPC


title: H3.3-V5_0h_4OHT

value: anti-V5 (R96025; Invitrogen)


title: WT-3

description:
AS wildtype vs rbm26a mutant
Group_Wild-type-VS-mutant_DE_significant_anno
all.fpkm_anno


title: MLO3(Midbrain-like Organoid3)

value: H9 hESC-derived NPC


title: WT-2

description:
AS wildtype vs rbm25a mutant
Group_Wild-type-VS-mutant_DE_significant_anno
all.fpkm_anno

value: 33 hpf


title: wt wnt8a_7.5 rep2

city: Houston

first: Arne

last: Lekven

state: TX

address: 3507 Cullen Blvd

department: Biology and Biochemistry

institute: University of Houston

data_processing:
Qiagen CLC Genomics Workbench 12 was used for basecalling
The Illumina sequencing adaptors were trimmed and reads were mapped to GRCz11 zebrafish reference genome. Read alignment was represented as integer counts by using parameters of mismatch cost 2, insertion cost 3, deletion cost 3, length fraction 0.8, similarity fraction 0.8, max of 10 hits for a read.
Integer read counts were normalized by Trimmed Means of M-values (TMM) algorithm. After normalization, we performed differential gene expression using the EdgeR package (Robinson and Oshlack, 2010)
Genome_build: GRCz11 zebrafish reference genome used for alignment
Supplementary_files_format_and_content: tab-delimited text files include RPKM and TPM values for each Sample

source_name: wt wnt8a_7.5_embryos

growth_protocol: hs:dkk1b/+) were crossed to wild-type fish, and embryos were collected within 15 minutes of spawning. Heat shocks were performed by placing groups of 10 embryos in standard fish water (zfin.org) into PCR tubes, incubating at 37C for 60 minutes, then returning embryos to 29C for recovery to the designated stages. hs:wnt8a/+) were crossed to wild-type fish, and embryos were collected and heat shocked in groups of 10 in PCR tubes at 39°C for 30 minutes, then returned to 29°C for recovery to the designated stage.  Embryos were fixed in 4% paraformaldehyde overnight at 4°C.

extract_protocol:
hs:dkk1b/+ or hs:wnt8a/+ embryos, identified by fluorescence, and their wild-type siblings were collected from multiple mating fish pairs, then embryos at the desired time points were immediately homogenized in Trizol and RNA was extracted with Direct-zol RNA kits
RNA libraries were prepared for sequencing using standard Illumina protocols

value: genotypically wild type sibling (to wnt8a)

tag: timepoint

value: 7 hpf

value: heat shock

value: embryos


title: WT-1

value: head region cut before otic vesicle

value: AB


title: hs wnt8a_7.5 rep1

source_name: hs wnt8a_7.5_embryos


title: Og-NSC1

source_name: H9 hESC Midbrain Organoid derived NPC


title: miRNAKO_SCNT_E19.5_rep3

tag: age

value: miRNA KO


title: hs wnt8a_7.5 rep3


title: MLO2(Midbrain-like Organoid2)


title: hs wnt8a_7.5 rep2


title: Og-NSC3


title: wt wnt8a_7.5 rep3


title: Og-NSC5


title: miRNA_Gab1KO_SCNT_E19.5_rep2


title: 2D-NSC1

source_name: H9 hESC-derived NPC


title: Og-NSC2


title: hs wnt8a_5.5 rep2

source_name: hs wnt8a_5.5_embryos

value: 5 hpf


title: wt wnt8a_5.5 rep3

source_name: wt wnt8a_5.5_embryos


title: WT_SCNT_E19.5_rep3

value: wildtype


title: AM uninfected exp1_1

source_name: AM uninfected

value: uninfected

value: Lung

value: 8-10 weeks


title: 2D-NSC2


title: hs wnt8a_5.5 rep1


title: IVF_E19.5_rep2

value: placenta

value: in vitro fertilization


title: wt wnt8a_7.5 rep1


title: WT_SCNT_E19.5_rep2

value: somatic cell nuclear transfer


title: miRNAKO_SCNT_E19.5_rep2


title: WT_SCNT_E19.5_rep1


title: miR214KO_Ang_3

city: Glasgow

first: Ryszard

last: Nosalski

address: 126 University Ave

department: 1Institute of Cardiovascular and Medical Sciences

country: United Kingdom

institute: University of Glasgow

data_processing:
Fastq files obtained from GENEWIZ
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The hit counts were summarized and reported using the gene_id feature in the annotation file. Only unique reads that fell within exon regions were counted. Since a strand-specific library preparation was performed, the reads were strand-specifically counted.
Genome_build: GRCm38
Supplementary_files_format_and_content: txt file with raw_counts

source_name: T cell

growth_protocol: T cells isolated from spleen (magnetic negative selection)

extract_protocol:
Total RNA from T cells was isolated using Direct-zol RNA MiniPrep kit (Zymo Research)  according to the manufacturer’s instructions, including on column DNAse digestion. RNA QC was performed using Agilent 2100 Bioanalyzer System. Samples with RIN score between 9.7-10 were used for sequencing
polyA stranded libraries were prepared and sequenced in HiSeq Illumina at an average of 20M paired end reads (2x150bp) per sample by GENEWIZ.

treatment_protocol: WT and miR-214 KO mice  (n=3 in each group) were infused with a vehicle or angiotensin II  (490ng/kg/d)  for 14 days via mini osmotic pumps (model 2002, Alzet).

value: angiotenisn II


title: IVF_E19.5_rep3


title: wt dkk1b_7.5 rep3

source_name: wt dkk1b_7.5_embryos

value: genotypically wild type sibling (to dkk1b)


title: wt wnt8a_5.5 rep1

value: genotypically wild type sibling (to wnt8a)


title: miRNA_Gab1KO_SCNT_E11.5_rep1

value: miRNA/Gab1 KO


title: hs dkk1b_7.5 rep2

source_name: hs dkk1b_7.5_embryos

value: 7 hpf

value: heat shock


title: IVF_E19.5_rep1


title: wt dkk1b_7.5 rep1

value: embryos


title: miR214KO_Ang_2


title: miRNAKO_SCNT_E11.5_rep2


title: hs dkk1b_7.5 rep1


title: miRNA_Gab1KO_SCNT_E11.5_rep2


title: wt wnt8a_5.5 rep2


title: hs dkk1b_7.5 rep3


title: miR214KO_Ang_1


title: miRNAKO_SCNT_E19.5_rep1


title: wt dkk1b_7.5 rep2


title: miR214KO_Sham_3

value: vehicle


title: miR214KO_Sham_2


title: WT_SCNT_E11.5_rep2


title: miRNAKO_SCNT_E11.5_rep3

value: miRNA KO


title: hs dkk1b_5.5 rep3

source_name: hs dkk1b_5.5_embryos

value: 5 hpf


title: miRNAKO_SCNT_E11.5_rep1


title: miR214KO_Sham_1


title: hs dkk1b_5.5 rep1


title: WT_Ang_3

value: wild-type


title: wt dkk1b_5.5 rep3

source_name: wt dkk1b_5.5_embryos


title: WT_SCNT_E11.5_rep1

value: wildtype


title: IVF_E11.5_rep3


title: hs dkk1b_5.5 rep2


title: wt dkk1b_5.5 rep2


title: WT_Ang_1


title: wt dkk1b_5.5 rep1


title: WT_Ang_2


title: IVF_E11.5_rep2


title: IVF_E11.5_rep1


title: WT_Sham_3


title: WT_Sham_2


title: WT_Sham_1


title: S-3

city: Rochester

first: Jin Sung

last: Jang

state: MN

address: 200 First St SW

institute: Mayo Clinic

description:
beta-cell
S-3.FCH5CJNBBXY_L1_R1_IGGCTAC

data_processing:
The STAR (2.6.1d) aligner was used to perform alignment of reads to the rn6 build of the Rattus norvegicus full reference genome. After alignment, the final BAM files were quantified using Partek E/M algorithm by Ensembl annotations (rn6 ensemble release96 v2).
Genome_build: rn6 ensemble release96 v2
Supplementary_files_format_and_content: tab-delimited text files and gene counts

organism: Rattus norvegicus

growth_protocol: INS-1 832/13 cells were grown in RPMI 1640 medium supplemented with 10 mM HEPES, 1 mM sodium pyruvate, 100 IU/mL penicillin, 100 mg/mL streptomycin (Invitrogen), 10% heat-inactivated fetal bovine serum (Gemini), and 50 mM β-mercaptoethanol (Sigma) at 37°C in a humidified 5% CO2 atmosphere.

extract_protocol:
RNA was harvested using Rneasy kit (Qiagen)
200 ng of total RNA from each sample was used. The RNA-Seq libraries were generated using TruSeq Stranded mRNA Library Prep kit (Illumina, CA).

treatment_protocol: TBK1 siGENOME SMARTpool siRNA or negative control non-targeting siRNA were transfected into INS-1 832/13 b-cells using DharmaFECT Transfection Reagent (Dharmacon, Lafayette, CO) for 36 hours.

value: Insulinoma cell

tag: cell line

tag: transfection


title: human_germ_molar_apical_papilla_female_15yo.apical papilla

source_name: growing molar

extract_protocol:
Dental pulps from mouse incisor/molars or human molars/apical papillae were dissected under the stereomicroscope, cut to small pieces and dissociated in Collagenase P solution in HBSS (3U/mL, 10-30 min, 37 °C). After the tissue was completely dissolved, a single-cell suspension was prepared using cell-strainer cap tubes and processed further according to 10x Genomics Chromium manufacturer's instructions.
The following library preparation protocol was used: 10x Genomics Chromium™ Single Cell 3' GEM v3

tag: isolation

value: apical papilla

tag: phenotype

value: healthy

value: 10x Chromium


title: S-2

description:
beta-cell
S-2.FCH5CJNBBXY_L1_R1_ITAGCTT


title: human_molar_healthy_2.whole

source_name: molar

value: whole

tag: plate

tag: platform


title: No5_24_yo_healthy_retained.whole


title: Mouse_molar_pulp_in_MeOH_11_9_9.whole


title: human_molar_pulp.whole


title: C-3

description:
beta-cell
C-3.FCH5CJNBBXY_L1_R1_IACTTGA

value: Scramble-transfected


title: MF183_Dent.whole


title: human_molar_healthy_1.whole


title: human_germinectomy.apical papilla


title: organoid, Ctrl

city: Helsinki

first: Marianne

last: Lähde

address: Haartmaninkatu 8

department: Faculty of Medicine, Translational cancer medicine program

country: Finland

institute: University of Helsinki

description:
ApcMin/+ mouse intestinal adenoma organoids
MinOrganoidsCombi.Rdata

data_processing:
The Cell Ranger v 2.1.1 mkfastq and count pipelines (10x Genomics, Pleasanton, CA) were used to demultiplex and convert Chromium single-cell 3’ RNA-sequencing barcodes and read data to FASTQ files and to generate aligned reads and gene-cell matrices.
Reads were aligned to mouse reference genome mm10
We used the Seurat R package 3.1.1 for quality control, filtering, and analysis of the data
Cells were filtered based on unique feature counts and the percentage of mitochondrial genes
Cells with more than 15% of mitochondrial genes were filtered out
The expression matrix was further filtered by removing genes with expression in less than five cells and cells with less than 500 distinct expressed genes.
Filtered data was combined for CCA and further analysis, and saved as MinOrganoidsCombi.Robj (supplementary file has .Rdata extension)
Genome_build: mm10

source_name: Intestinal adenoma organoid culture

extract_protocol:
In order to obtain single cell solution, itestinal organoids derived from ApcMin/+ mice treated with or without RSPO1-Fc fusion protein were incubated in Hanks' balanced salt solution (HBSS, 14175-053, Gibco) containing 1 mg/mL collagenase type I (LS004196, Worthington), 1 mg/mL collagenase H (11074032001, Roche), 4 mg/mL dispase II (04942078001, Sigma) and 1000 U/mL benzonase (sc-202391, ChemCruz) for 30 min at 37°C with gentle shaking, followed by 10 min incubation with trypsin. Cells were transferred into 0.04% BSA-HBSS for analysis.
Single cells were analyzed using the 10x Chromium Single-Cell 3′RNA-sequencing system (10x Genomics, Pleasanton, CA, USA) with the Reagent Kit v2 as instructed by the manufacturer. Briefly, the cells were first loaded into Chromium Single-Cell Chip v2 (10x Genomics, Pleasanton, CA, USA), followed by generation of Gel beads in EMulsion (GEM) aiming at 5000 cell captures per sample. This was followed by cDNA purification, amplification (12 cycles), and library construction (sample index PCR 14 cycles) as instructed by the manufacturer.
The sample libraries were sequenced on an Illumina NovaSeq 6000 sequencer using read lengths of 26bp (Read 1), 8bp (i7 Index), 0 bp (i5 Index) and 91bp (Read 2),  resulting in an average of following reads per cell: 58 414 (Ctrl), and 131 291 (RSPO1). Chromium single-cell 3’ RNA-sequencing barcodes and read data were demultiplexed and converted to FASTQ files, and aligned reads and gene-cell matrices were generated using Cell Ranger v 2.1.1 mkfastq and count pipelines (10x Genomics, Pleasanton, CA, USA). Reads were aligned to mouse reference genome mm10.

treatment_protocol: Organoids were cultured with or without RSPO1-Fc fusion protein (10 ug/ml)

tag: genotype

value: ApcMin/+

tag: tissue

value: intestinal adenoma

value: 17 weeks

value: control


title: C-2

description:
beta-cell
C-2.FCH5CJNBBXY_L1_R1_ITTAGGC


title: mouse_molar_pulp_S19.whole


title: mouse_incisor_pulp_S18.whole

source_name: incisor


title: organoid, RSPO1

description:
ApcMin/+ mouse intestinal adenoma organoids cultured with 10 mg/ml RSPO1-Fc fusion protein
MinOrganoidsCombi.Rdata

tag: treatment

value: RSPO1-Fc fusion protein


title: siRBM27.B: RNA-Seq of HAP1 cells after knockdown of RBM27, replicate 2

city: Toronto

first: Ulrich

last: Braunschweig

state: Ontario

address: 160 College Street

department: Donnelly Centre

country: Canada

institute: University of Toronto

data_processing:
Reads were trimmed using Trimmomatic 0.33 to remove Illumina adaptor and low-quality bases from the 3'-end.
To quantify gene expression, trimmed reads were pseudo-aligned to the GENCODE human gene annotation version 29 with Salmon 0.14.1.
Transcript-level quantifications were aggregated per gene using the R package tximport, and differential expression between control non-targeting and RBM26- and/or RBM27-knockdown was assessed using the classic mode (exactTest) in edgeR. Genes changing more than 2-fold and with an FDR < 0.05 were deemed significantly different. To compare overlaps in changes between treatments, only genes expressed at > 5 RPKM in at least one treatment were considered.
Genome_build: hg38 (GENCODE v29)
Supplementary_files_format_and_content: All files are in tab-delimited format. RBM26.27_transcReadCounts.tab.gz contains read counts per transcript and effective transcript lengths for each replicate from Salmon. DE.tab.gz contains edgeR-derived reads per million and kb (RPKM), fold-changes and FDR.

molecule: polyA RNA

source_name: Near-haploid human chronic myelogenous leukemia-derived cells

growth_protocol: HAP1 cells were obtained from Horizon Genomics (clone C631, sex: male with lost Y chromosome, RRID: CVCL_Y019). HAP1 cells were maintained in low glucose (10 mM), low glutamine (1 mM) DMEM (Wisent, 319-162-CL) supplemented with 10% FBS (Life Technologies) and 1% Penicillin/Streptomycin (Life Technologies).

extract_protocol:
Total RNA was extracted with the Qiagen RNasy Mini kit.
DNase-treated RNA samples were submitted for RNA-seq at the Donnelly Sequencing Centre at the University of Toronto (http://ccbr.utoronto.ca/donnelly-sequencing-centre). Total RNA was quantified using Qubit RNA BR (cat # Q10211, Thermo Fisher Scientific Inc., Waltham, USA) fluorescent chemistry and 1 ng was used to obtain RNA Integrity Number (RIN) using the Bioanalyzer RNA 6000 Pico kit (cat # 5067-1513, Agilent Technologies Inc., Santa Clara, USA). The lowest RIN was 8.7; median RIN was 9.6.  2.5 ug of total RNA per sample was processed using the MGIEasy Directional RNA Library Prep Set V2.0 (protocol v. A0, cat # 1000006385, Shenzhen MGI Tech Co. Ltd., Shenzhen, China) including mRNA enrichment with Dynabeads mRNA Purification Kit (cat # 61006, Thermo Fisher Scientific Inc.). RNA was fragmented at 87°C for 6 minutes, after adding only 75% of the recommended volume of fragmentation buffer in order to produce longer fragments. Libraries were amplified with 12 cycles of PCR.  1 ul top stock of each purified final library was run on an Agilent Bioanalyzer dsDNA High Sensitivity chip (cat # 5067-4626, Agilent Technologies Inc., Santa Clara, USA) to determine an average library size of 581 bp, and to confirm absence of dimers. The libraries were quantified using the Quant-iT dsDNA High Sensitivity (cat # Q33120, Thermo Fisher Scientific Inc., Waltham, USA) fluorometry kit, pooled equimolar, and libraries in each of 4 replicate pools were then circularized using the MGIEasy Circularization Module (cat # 1000005260, Shenzhen MGI Tech Co. Ltd.).  From each of the 4 pools, 40 fmol of circularized library was sequenced 2x150 bp on a single lane of an FCL flowcell on the MGISEQ-2000 platform (also known as DNBSEQ-G400 platform, Shenzhen MGI Tech Co. Ltd.), for a total of 4 lanes of sequencing.

treatment_protocol: Cells were transfected with 10nM of siGENOME siRNA pools targeting RBM26 and RBM27 (Dharmacon) using RNAiMax (Life Technologies). A non-targeting siRNA pool was used as control. Cells were harvested 48 hours post-transfection for RNA extraction.

tag: knockdown


title: siRBM26.B: RNA-Seq of HAP1 cells after knockdown of RBM26, replicate 2

value: Near-haploid human chronic myelogenous leukemia-derived cells


title: siNT.B: RNA-Seq of HAP1 cells after control non-targeting knockdown, replicate 2

value: siNT


title: Cu-limited rep1

city: Montreal

first: Liangliang

last: Kong

state: Quebec

address: 1205 Docteur Penfield

department: Biology

institute: McGill

data_processing: Raw RNA-seq reads were first processed to remove Illumina adaptors and low-quality reads by Trimmomatic v0.32 (Bolger et al. 2014).  Only high-quality reads with a phred quality score >30 and a minimum length of 48 bp after trimming were retained for subsequent analysis. Processed high-quality reads (~93% of raw reads) from 9 samples (3 cultures × 3 biological replicates) were pooled and submitted to Trinity for de novo transcriptome assembly using the default parameters except for that the minimum k-mer coverage requirement was set to 2 (--min_kmer_cov 2) to exclude the singly occurring k-mers and decrease the complexity of the de Bruijn graph (Haas et al. 2013).  To quantify gene transcription levels, the clean RNA-seq reads from each individual sample were aligned to the assembled transcriptome using the bowtie alignment program (Langmead et al. 2009) and quantified by RSEM (RNA-Seq by Expectation Maximization; Li and Dewey 2011). Transcript abundance of each gene was calculated by counting mRNA fragments aligned to each gene and normalized to gene length, library size and composition of mRNA population by a trimmed mean of M values (TMM) normalization method (Robinson and Oshlack 2010) and described as TMM-normalized FPKM (Fragments Per Kilobase of exon per Million fragments mapped) values.

organism: Thalassiosira oceanica CCMP1005

source_name: single cell

growth_protocol: Semi-continuous cultures were maintained in in Cu-replete (21.4 nM) and Cu-deplete (1 nM) Aquil medium, respectively, at 20°C under continuous illumination of 200 μmol photons · m-2 · s-1 supplied by Phillips cool white fluorescent bulbs

extract_protocol:
Total RNA was isolated from the filtered cells (~8 million cells) using a TRIzol Plus RNA Purification Kit (Thermo Fisher Scientific) with an on-column DNase (TURBO DNase, Thermo Fisher Scientific) digestion step to remove genomic DNA, as per the manufacturer’s recommendation.
Messenger RNA was enriched from 250 ng of total RNA and cDNA libraries were prepared from fragmented mRNA using a TruSeq Stranded mRNA Sample Preparation Kit (Illumina, CA, USA).

treatment_protocol: Thalassiosira oceanica was maintained in exponential growth by semi-continuous culture in Cu-replete or Cu-deplete medium for more than 500 generations prior to sampling.  These cultures were adapted to Cu-replete and Cu-limiting conditions and subsequently referred to as adapted cultures.  A Cu-transient culture was also included in the study to investigate the short-term response of the cells to Cu deficiency.  In these experiments, 2 ml of exponentially growing cells from the Cu-replete, adapted culture was inoculated into 26 ml of Cu-free Aquil medium.  The final concentration of Cu in the transient cultures, after accounting for Cu in the inoculum, was 1.4 nM.  Pulse amplitude modulated (PAM) fluorometry (Fv/Fm, ΦPSII, Ek, rETRmax) was used to monitor the transition of the cells from Cu sufficiency to Cu deficiency.  The adapted, Cu-replete and Cu-limited T. oceanica were harvested in exponential phase. The transient cultures were harvested once the rETRmax was midway between the values observed in adapted, Cu-replete and Cu-deplete cultures, about 4 generations after inoculating Cu-replete cells into Cu-free medium.

value: Cu-limited cells that grow at ~50% of the maximum rate

tag: sample type

value: treatment


title: Clodrosome.whole

value: Clodrosome-treated

value: Clodrosome


title: Cu-limited rep2


title: Cu-limited rep3


title: Cu-transient rep2

value: Cu-transient cells that just experience Cu deficiency


title: Cu-transient rep1


title: siRBM26.27.A: RNA-Seq of HAP1 cells after double knockdown of RBM26 and RBM27, replicate 1


title: Cu-transient rep3


title: Cu-replete rep3

value: Cu-replete cells that grow at the maximum growth rate


title: siRBM27.A: RNA-Seq of HAP1 cells after knockdown of RBM27, replicate 1


title: siNT.A: RNA-Seq of HAP1 cells after control non-targeting knockdown, replicate 1


title: siRBM26.A: RNA-Seq of HAP1 cells after knockdown of RBM26, replicate 1


title: Cu-replete rep2


title: siRBM26.27.B: RNA-Seq of HAP1 cells after double knockdown of RBM26 and RBM27, replicate 2


title: Cu-replete rep1


title: DGRP Line 93 Female Rep 2

status: Public on Feb 28 2020

city: East Lansing

first: Wen

last: Huang

address: 474 S Shaw Ln, Anthony Hall 1205F

department: Animal Science

institute: Michigan State University

data_processing:
Barcoded sequence reads were demultiplexed using the Illumina pipeline v1.9.
Adapter sequences were trimmed using cutadapt v1.642 and trimmed sequences shorter than 50bp were discarded from further analysis.
Trimmed sequences were then aligned to multiple target sequence databases in the following order, using BWA v0.7.10 (MEM algorithm with parameters ‘-v 2 –t 4’):
(1) all trimmed sequences were aligned against a database containing the complete 5S, 18S-5p8S-2S-28S, mt:lrRNA, and mt:srRNA sequences to filter out residual rRNA that escaped depletion during library preparation;
(2) remaining sequences were then aligned against a custom database of potential microbiome component species (see below);
(3) sequences that did not align to either the rRNA or microbiome databases were aligned to all D. melanogaster sequences in RepBase.
The remaining sequences that did not align to any of the databases above were then aligned to the D. melanogaster genome (BDGP5) and known transcriptome (FlyBase v5.57) using STAR v2.4.0e.
Generation of microbiome database: We first performed a preliminary alignment of RNA-seq reads by filtering only rRNA sequences, and then aligning directly to the D. melanogaster genome using the tools and parameters described above. Sequences that did not align to the rRNA database or D. melanogaster reference genome were then analyzed with Trinity v2.1.1 to perform de novo assembly of longer sequences from the short reads. We discarded assembled sequences < 1kb in length, and the remaining sequences were then run through a BLAST search against the refseq_genomic database (downloaded from NCBI on 1/27/16).  We then compiled a list of all refseq genomes that were found as a top BLAST hit for at least two assembled sequences. We compiled all fasta files for each of these refseq genomes into a single database for alignment with BWA.
Genotype validation: To validate the DGRP line assigned to each RNA-seq sample, we identified single nucleotide polymorphisms (SNPs) from the RNA-seq reads that aligned to the D. melanogaster reference genome using STAR as described above. We retained only those SNP calls covered by at least 3 reads and at least 75% of all reads supporting the major genotype (note that DGRP lines are inbred and therefore the majority of SNPs are homozygous). This filtering process produced >400k usable SNPs per sample, primarily located in transcribed regions of the genome. We then performed two validation tests of the DGRP line assigned to each sample X by comparing to the previously published genotype calls for each DGRP line (http://dgrp2.gnets.ncsu.edu/data/website/dgrp2.tgeno).
Inference of novel transcripts: We constructed a de novo transcriptome for each individual sample by inputting the RNA-seq reads aligned to the D. melanogaster reference genome into Cufflinks v2.2.1. We also considered the novel transcribed regions (NTRs) identified in a previous study based on unstranded pooled RNA sequencing of the DGRP lines. However, the previously published data do not provide strand-specific signal, while our current RNA-seq data uses a strand-specific library preparation. Therefore, we reassigned the strand for each of the previously published NTRs that was supported by the greater number of total aligned reads across all samples. We then merged all de novo sample transcriptomes and the previously published NTRs using the cuffmerge tool included with Cufflinks v2.2.1, then removed all merged transcript models with any exon overlapping on the same strand any exon in the known D. melanogaster transcriptome. We defined the known transcriptome here as all gene models in FlyBase v5.57 plus all subsequently added gene models in FlyBase v6.11 to account for recently discovered lncRNA sequences. Thus, the final output of this analysis was a set of NTRs constructed from both our current RNA-seq data and previously published pooled RNA-seq data that do not overlap any known gene exons on the same strand.
Gene expression estimation: Read counts were computed for known and novel gene models using HTSeq-count with the ‘intersection-nonempty’ assignment method. Read counts for each gene were then normalized across all samples using EdgeR as follows. First, genes with low expression overall (<10 aligned reads in >75% of the libraries) were excluded from the analysis by modeling the overall distribution of expression levels as a mixture of background noise and foreground signal to determine an empirical threshold for sufficiently expressed genes. Library sizes were re-computed as the sum of reads assigned to the remaining genes, and further normalized using the Trimmed Mean of M-values (TMM) method. We further adjusted gene expression values by estimating and removing the effect of alignment bias resulting from higher rates of non-reference variants clustering in some lines. We computed the alignment bias score A(g,L) defined as the number of non-reference nucleotides per kb in all exons of gene g in DGRP line L, based on the previous map of genomic variation in the DGRP. We then fit a linear model for each endogenous gene: Y = A + ε, where Y is the normalized expression profile for gene g after the read counting and EdgeR normalization described above. After fitting these linear models, ε represents the alignment bias-corrected expression, and was used as the normalized gene expression in all subsequent analysis.
Genetics of gene expression: For each gene in each sex, we fit mixed-effect models to the gene expression vector across all samples corresponding to: Y = W + L + ε, where Y is the observed log2(normalized read count), W is Wolbachia infection status, L is DGRP line, and ε is the residual error. We identified genetically variable transcripts as those that passed a 5% FDR threshold (based on Benjamini-Hochberg corrected P-values) for the L terms. We computed the broad sense heritabilities (H2) for each gene expression trait separately for males and females as H^2 = V/(V+R), where V and R are, respectively, the among line and within line variance components.
Genome_build: BDGP R5/dm3
Supplementary_files_format_and_content: Tab-delimited text files contain normalized log2 FPKM expression values, variant density correction factors, and within-sex line means for all genes.

organism: Drosophila melanogaster

source_name: DGRP Line 93 Female

growth_protocol: We used 200 inbred, sequenced DGRP lines, established by 20 generations of full sib inbreeding from gravid females collected at the Raleigh, NC USA Farmer’s Market. All lines were reared on cornmeal-molasses-agar medium at 25°C, 60–75% relative humidity and a 12-hr light-dark cycle at equal larval densities. We collected two replicates of 25 females and 30 males per line, for a total of 800 samples. We used a strict randomized experimental design for sample collection. We collected mated 3-5 day old flies between 1-3 pm. We transferred the flies into empty culture vials and froze them over ice supplemented with liquid nitrogen, and sexed the frozen flies. The samples were transferred to 2.0 ml nuclease-free microcentrifuge tubes (Ambion) and stored at -80°C until ready to process.

extract_protocol:
Total RNA was extracted with Trizol using the RNAeasy Mini Kit (Qiagen, Inc.). rRNA was depleted using the Ribo-Zero™ Gold Kit (Epicentre, Inc.) with 5ug total RNA input.
Depleted mRNA was fragmented and converted to first strand cDNA. During the synthesis of second strand cDNA, dUTP instead of dTTP was incorporated to label the second strand cDNA. cDNA from each RNA sample was used to produce barcoded cDNA libraries using NEXTflex™ DNA Barcodes (Bioo Scientific, Inc.) with an Illumina TruSeq compatible protocol. Library size was selected using Agencourt Ampure XP Beads (Beckman Coulter, Inc.) and centered around 250 bp with the insert size ~130 bp. Second strand DNA was digested with Uracil-DNA Glycosylase before amplification to produce directional cDNA libraries. Libraries were quantified using Qubit dsDNA HS Kits (Life Technologies, Inc.) and Bioanalyzer (Agilent Technologies, Inc.) to calculate molarity. Libraries were then diluted to equal molarity and re-quantified. A total of 50 pools of 16 libraries were made, again randomly assigning samples to each pool. Pooled library samples were quantified again to calculate final molarity and then denatured and diluted to 14pM. Pooled library samples were clustered on an Illumina cBot; each pool was sequenced on one lane of Illumina Hiseq2500 using 125 bp single-read v4 chemistry. Libraries with fewer than 5 million reads uniquely aligned to the D. melanogaster reference genome were re-sequenced to achieve sufficient read depth.

treatment_protocol: Not applicable

tag: strain

tag: Sex

value: Female

value: 3-5 days old

tag: medium

value: cornmeal-molasses-agar

value: Whole flies


title: DGRP Line 93 Female Rep 1


title: DGRP Line 93 Male Rep 2

source_name: DGRP Line 93 Male

value: Male


title: DGRP Line 913 Male Rep 2

source_name: DGRP Line 913 Male


title: Rosa26CreERT2KrasG12D 3

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

country: Germany

institute: University clinics Freiburg

hyb_protocol: Labeled fragments were hybridized to Affymetrix Mouse Gene ST 1.0 arrays for 16h at 45°C with 60 rpm in an Affymetrix Hybridization oven 645.

scan_protocol: After washing and staining, the arrays were scanned with the Affymetrix GeneChip Scanner 3000 7G. CEL-files were produced from the raw data with Affymetrix GeneChip Command Console Software.

data_processing: CEL files were analysed using the oligo R package. RMA method, log2 transformed were used to normalized the probe intensities.

label: Biotin

source_name: Bone marrow derived dendritic cells

label_protocol: We used the Affymetrix WT Pico kit for cDNA synthesis, amplification, and second-cycle cDNA synthesis, as well as fragmentation and labeling with Biotin, as described by the manufacturer.

growth_protocol: Rosa26CreERT2KrasG12D and wildtype control littermate mice were treated with Tamoxifen (1mg) to induce oncogenic KrasG12D, and sacrificed 5 weeks after upon successful recombination. Mice were anesthetized using Isoflourane and sacrificed by cervical dislocation. The fur was disinfected by 70% Ethanol. The femur and tibia bones were isolated using forceps and scissors, cleared of muscles and tendons and kept on PBS. Under sterile conditions, the bone marrow (BM) was flushed with cold sterile PBS under the culture hood. The BM solution was homogenised, passed through a 70 µm cell strainer and washed with PBS. Erythrocyte lysis was performed and cells were washed with PBS. The cell pellet was resuspended in BM-dendritic cells (BMDCs) media and counted using hematocytmeter. A total of 6 x 106 BM cells were then plated in 10 cm dishes containing BMDCs media (RPMI + 10% FCS + 1% P/S + 40ng/ml GM-CSF) and incubated at 37°C. The cells were fed with more media on days 3 and 5 post plating. Cells were used on day 7 when a CD11c+ purity of >80% was achieved, as determined by flow cytometry.

extract_protocol: BMDCs were harvested, and RNA was isolated using the miRNeasy Mini kit (Qiagen). RNA quality was assessed by Agilent 2100 Bioanalyzer (Agilent 141 Technologies). RNA samples with an RNA integrity number (RIN) greater than 8 were further processed for Affymetrix microarrays.

tag: tissues

value: Bones (Tibia/femur)

tag: cell type

value: Bone marrow derived dendritic cells

value: 8-12 weeks

value: Cre+ Kras+

tag: agent

value: Tamoxifen (1mg)


title: DGRP Line 91 Female Rep 2

source_name: DGRP Line 91 Female

tag: age


title: Rosa26CreERT2KrasG12D 2

treatment_protocol: Rosa26CreERT2KrasG12D and wildtype control littermate mice were treated with Tamoxifen (1mg)


title: Rosa26CreERT2KrasG12D 4


title: DGRP Line 913 Female Rep 1

source_name: DGRP Line 913 Female


title: DGRP Line 911 Male Rep 2

source_name: DGRP Line 911 Male


title: DGRP Line 913 Female Rep 2


title: DGRP Line 913 Male Rep 1


title: Wildtype (WT) littermate 4

value: Cre- Kras+


title: Wildtype (WT) littermate 5


title: DGRP Line 911 Female Rep 2

source_name: DGRP Line 911 Female


title: Wildtype (WT) littermate 1


title: DGRP Line 91 Male Rep 2

source_name: DGRP Line 91 Male


title: DGRP Line 911 Male Rep 1


title: Rosa26CreERT2KrasG12D 1


title: DGRP Line 91 Male Rep 1


title: DGRP Line 908 Male Rep 2

source_name: DGRP Line 908 Male


title: DGRP Line 908 Male Rep 1


title: DGRP Line 91 Female Rep 1


title: DGRP Line 907 Female Rep 1

source_name: DGRP Line 907 Female


title: DGRP Line 907 Male Rep 2

source_name: DGRP Line 907 Male


title: DGRP Line 908 Female Rep 1

source_name: DGRP Line 908 Female


title: DGRP Line 908 Female Rep 2


title: DGRP Line 907 Male Rep 1


title: DGRP Line 911 Female Rep 1


title: DGRP Line 907 Female Rep 2


title: DGRP Line 900 Male Rep 1

source_name: DGRP Line 900 Male


title: DGRP Line 900 Female Rep 2

source_name: DGRP Line 900 Female


title: DGRP Line 900 Female Rep 1


title: DGRP Line 900 Male Rep 2


title: DGRP Line 897 Male Rep 1

source_name: DGRP Line 897 Male


title: DGRP Line 897 Female Rep 1

source_name: DGRP Line 897 Female


title: DGRP Line 894 Male Rep 2

source_name: DGRP Line 894 Male


title: DGRP Line 892 Male Rep 2

source_name: DGRP Line 892 Male


title: DGRP Line 897 Female Rep 2


title: DGRP Line 894 Female Rep 1

source_name: DGRP Line 894 Female


title: DGRP Line 894 Male Rep 1


title: DGRP Line 894 Female Rep 2


title: DGRP Line 892 Male Rep 1


title: DGRP Line 892 Female Rep 2

source_name: DGRP Line 892 Female


title: DGRP Line 890 Male Rep 2

source_name: DGRP Line 890 Male


title: DGRP Line 890 Male Rep 1


title: DGRP Line 890 Female Rep 1

source_name: DGRP Line 890 Female


title: DGRP Line 890 Female Rep 2


title: DGRP Line 884 Male Rep 2

source_name: DGRP Line 884 Male


title: DGRP Line 884 Female Rep 1

source_name: DGRP Line 884 Female


title: DGRP Line 884 Female Rep 2


title: DGRP Line 884 Male Rep 1


title: DGRP Line 882 Male Rep 1

source_name: DGRP Line 882 Male


title: DGRP Line 882 Female Rep 2

source_name: DGRP Line 882 Female


title: DGRP Line 88 Male Rep 1

source_name: DGRP Line 88 Male


title: DGRP Line 88 Male Rep 2


title: DGRP Line 882 Female Rep 1


title: DGRP Line 897 Male Rep 2


title: DGRP Line 88 Female Rep 1

source_name: DGRP Line 88 Female


title: DGRP Line 88 Female Rep 2


title: DGRP Line 861 Male Rep 2

source_name: DGRP Line 861 Male


title: DGRP Line 861 Female Rep 2

source_name: DGRP Line 861 Female


title: DGRP Line 861 Male Rep 1


title: DGRP Line 892 Female Rep 1


title: Wildtype (WT) littermate 3

source_name: Bone marrow derived dendritic cells


title: DGRP Line 857 Male Rep 1

source_name: DGRP Line 857 Male


title: DGRP Line 857 Female Rep 1

source_name: DGRP Line 857 Female


title: DGRP Line 857 Female Rep 2


title: DGRP Line 855 Male Rep 2

source_name: DGRP Line 855 Male


title: DGRP Line 857 Male Rep 2


title: DGRP Line 855 Male Rep 1


title: DGRP Line 855 Female Rep 1

source_name: DGRP Line 855 Female


title: DGRP Line 855 Female Rep 2


title: DGRP Line 853 Female Rep 1

source_name: DGRP Line 853 Female


title: DGRP Line 852 Male Rep 2

source_name: DGRP Line 852 Male


title: DGRP Line 852 Male Rep 1


title: DGRP Line 853 Male Rep 2

source_name: DGRP Line 853 Male


title: DGRP Line 852 Female Rep 2

source_name: DGRP Line 852 Female


title: DGRP Line 853 Male Rep 1


title: DGRP Line 852 Female Rep 1


title: DGRP Line 853 Female Rep 2


title: DGRP Line 850 Male Rep 2

source_name: DGRP Line 850 Male


title: DGRP Line 850 Male Rep 1


title: DGRP Line 861 Female Rep 1


title: DGRP Line 850 Female Rep 2

source_name: DGRP Line 850 Female


title: DGRP Line 85 Male Rep 2

source_name: DGRP Line 85 Male


title: DGRP Line 850 Female Rep 1


title: DGRP Line 85 Female Rep 2

source_name: DGRP Line 85 Female


title: DGRP Line 85 Male Rep 1


title: DGRP Line 849 Male Rep 2

source_name: DGRP Line 849 Male


title: DGRP Line 849 Male Rep 1


title: DGRP Line 849 Female Rep 2

source_name: DGRP Line 849 Female


title: DGRP Line 843 Male Rep 2

source_name: DGRP Line 843 Male


title: DGRP Line 849 Female Rep 1


title: DGRP Line 882 Male Rep 2

source_name: DGRP Line 882 Male


title: DGRP Line 843 Male Rep 1


title: DGRP Line 837 Male Rep 1

source_name: DGRP Line 837 Male


title: DGRP Line 843 Female Rep 2

source_name: DGRP Line 843 Female


title: DGRP Line 837 Male Rep 2


title: DGRP Line 832 Male Rep 2

source_name: DGRP Line 832 Male


title: DGRP Line 843 Female Rep 1


title: DGRP Line 837 Female Rep 2

source_name: DGRP Line 837 Female


title: DGRP Line 832 Female Rep 1

source_name: DGRP Line 832 Female


title: DGRP Line 837 Female Rep 1


title: DGRP Line 85 Female Rep 1


title: DGRP Line 83 Male Rep 2

source_name: DGRP Line 83 Male


title: DGRP Line 83 Male Rep 1


title: DGRP Line 83 Female Rep 1

source_name: DGRP Line 83 Female


title: DGRP Line 822 Female Rep 1

source_name: DGRP Line 822 Female


title: DGRP Line 83 Female Rep 2


title: DGRP Line 822 Female Rep 2


title: DGRP Line 821 Male Rep 1

source_name: DGRP Line 821 Male


title: DGRP Line 820 Male Rep 2

source_name: DGRP Line 820 Male


title: DGRP Line 821 Male Rep 2


title: DGRP Line 822 Male Rep 1

source_name: DGRP Line 822 Male


title: DGRP Line 821 Female Rep 1

source_name: DGRP Line 821 Female


title: DGRP Line 821 Female Rep 2


title: DGRP Line 820 Female Rep 1

source_name: DGRP Line 820 Female


title: DGRP Line 819 Male Rep 2

source_name: DGRP Line 819 Male


title: DGRP Line 819 Female Rep 2

source_name: DGRP Line 819 Female


title: DGRP Line 832 Female Rep 2


title: DGRP Line 819 Female Rep 1


title: DGRP Line 820 Male Rep 1


title: DGRP Line 818 Male Rep 1

source_name: DGRP Line 818 Male


title: DGRP Line 818 Female Rep 2

source_name: DGRP Line 818 Female


title: DGRP Line 818 Female Rep 1


title: DGRP Line 822 Male Rep 2


title: DGRP Line 812 Male Rep 2

source_name: DGRP Line 812 Male


title: DGRP Line 812 Female Rep 2

source_name: DGRP Line 812 Female


title: DGRP Line 812 Female Rep 1


title: DGRP Line 810 Male Rep 2

source_name: DGRP Line 810 Male


title: DGRP Line 810 Male Rep 1


title: DGRP Line 820 Female Rep 2


title: DGRP Line 810 Female Rep 1

source_name: DGRP Line 810 Female


title: DGRP Line 808 Female Rep 2

source_name: DGRP Line 808 Female


title: DGRP Line 819 Male Rep 1


title: DGRP Line 810 Female Rep 2


title: DGRP Line 805 Male Rep 2

source_name: DGRP Line 805 Male


title: DGRP Line 808 Male Rep 1

source_name: DGRP Line 808 Male


title: DGRP Line 808 Female Rep 1


title: DGRP Line 832 Male Rep 1

source_name: DGRP Line 832 Male


title: DGRP Line 812 Male Rep 1


title: DGRP Line 805 Male Rep 1


title: DGRP Line 805 Female Rep 2

source_name: DGRP Line 805 Female


title: DGRP Line 818 Male Rep 2


title: DGRP Line 804 Male Rep 1

source_name: DGRP Line 804 Male


title: DGRP Line 805 Female Rep 1


title: DGRP Line 802 Male Rep 2

source_name: DGRP Line 802 Male


title: DGRP Line 804 Female Rep 2

source_name: DGRP Line 804 Female


title: DGRP Line 804 Female Rep 1


title: DGRP Line 802 Male Rep 1


title: DGRP Line 802 Female Rep 2

source_name: DGRP Line 802 Female


title: DGRP Line 801 Male Rep 1

source_name: DGRP Line 801 Male


title: DGRP Line 801 Male Rep 2


title: DGRP Line 802 Female Rep 1


title: DGRP Line 93 Male Rep 1

source_name: DGRP Line 93 Male


title: DGRP Line 808 Male Rep 2


title: DGRP Line 801 Female Rep 2

source_name: DGRP Line 801 Female


title: DGRP Line 799 Male Rep 2

source_name: DGRP Line 799 Male


title: DGRP Line 799 Female Rep 2

source_name: DGRP Line 799 Female


title: DGRP Line 799 Female Rep 1


title: DGRP Line 790 Male Rep 1

source_name: DGRP Line 790 Male


title: DGRP Line 796 Male Rep 2

source_name: DGRP Line 796 Male


title: DGRP Line 796 Female Rep 1

source_name: DGRP Line 796 Female


title: DGRP Line 796 Male Rep 1


title: DGRP Line 790 Male Rep 2


title: DGRP Line 804 Male Rep 2


title: DGRP Line 790 Female Rep 2

source_name: DGRP Line 790 Female


title: DGRP Line 796 Female Rep 2


title: DGRP Line 787 Male Rep 2

source_name: DGRP Line 787 Male


title: DGRP Line 790 Female Rep 1


title: DGRP Line 801 Female Rep 1


title: DGRP Line 786 Female Rep 2

source_name: DGRP Line 786 Female


title: DGRP Line 786 Male Rep 2

source_name: DGRP Line 786 Male


title: DGRP Line 787 Male Rep 1


title: DGRP Line 786 Male Rep 1


title: DGRP Line 787 Female Rep 2

source_name: DGRP Line 787 Female


title: DGRP Line 787 Female Rep 1


title: DGRP Line 783 Female Rep 2

source_name: DGRP Line 783 Female


title: DGRP Line 783 Male Rep 2

source_name: DGRP Line 783 Male


title: DGRP Line 786 Female Rep 1


title: DGRP Line 783 Male Rep 1


title: DGRP Line 799 Male Rep 1


title: DGRP Line 783 Female Rep 1


title: DGRP Line 776 Female Rep 2

source_name: DGRP Line 776 Female


title: DGRP Line 776 Male Rep 2

source_name: DGRP Line 776 Male


title: DGRP Line 776 Male Rep 1


title: DGRP Line 776 Female Rep 1


title: DGRP Line 774 Male Rep 2

source_name: DGRP Line 774 Male


title: DGRP Line 765 Female Rep 2

source_name: DGRP Line 765 Female


title: DGRP Line 765 Male Rep 1

source_name: DGRP Line 765 Male


title: DGRP Line 774 Female Rep 1

source_name: DGRP Line 774 Female


title: DGRP Line 765 Male Rep 2


title: DGRP Line 774 Male Rep 1


title: DGRP Line 761 Male Rep 1

source_name: DGRP Line 761 Male


title: DGRP Line 761 Female Rep 2

source_name: DGRP Line 761 Female


title: DGRP Line 765 Female Rep 1


title: DGRP Line 761 Female Rep 1


title: DGRP Line 757 Male Rep 2

source_name: DGRP Line 757 Male


title: DGRP Line 757 Male Rep 1


title: DGRP Line 761 Male Rep 2


title: DGRP Line 75 Male Rep 1

source_name: DGRP Line 75 Male


title: DGRP Line 75 Male Rep 2


title: DGRP Line 757 Female Rep 2

source_name: DGRP Line 757 Female


title: DGRP Line 75 Female Rep 1

source_name: DGRP Line 75 Female


title: DGRP Line 75 Female Rep 2


title: DGRP Line 738 Female Rep 2

source_name: DGRP Line 738 Female


title: DGRP Line 738 Male Rep 1

source_name: DGRP Line 738 Male


title: DGRP Line 748 Female Rep 2

source_name: DGRP Line 748 Female


title: DGRP Line 748 Male Rep 1

source_name: DGRP Line 748 Male


title: DGRP Line 737 Male Rep 2

source_name: DGRP Line 737 Male


title: DGRP Line 748 Female Rep 1


title: DGRP Line 738 Male Rep 2


title: DGRP Line 748 Male Rep 2


title: DGRP Line 774 Female Rep 2


title: DGRP Line 737 Male Rep 1


title: DGRP Line 737 Female Rep 2

source_name: DGRP Line 737 Female


title: DGRP Line 732 Male Rep 2

source_name: DGRP Line 732 Male


title: DGRP Line 737 Female Rep 1


title: DGRP Line 730 Female Rep 2

source_name: DGRP Line 730 Female


title: DGRP Line 732 Female Rep 2

source_name: DGRP Line 732 Female


title: DGRP Line 732 Male Rep 1


title: DGRP Line 730 Male Rep 2

source_name: DGRP Line 730 Male


title: DGRP Line 757 Female Rep 1


title: DGRP Line 73 Male Rep 2

source_name: DGRP Line 73 Male


title: DGRP Line 730 Female Rep 1


title: DGRP Line 73 Male Rep 1


title: DGRP Line 732 Female Rep 1


title: DGRP Line 73 Female Rep 2

source_name: DGRP Line 73 Female


title: DGRP Line 738 Female Rep 1


title: DGRP Line 727 Female Rep 1

source_name: DGRP Line 727 Female


title: DGRP Line 721 Male Rep 2

source_name: DGRP Line 721 Male


title: DGRP Line 714 Male Rep 1

source_name: DGRP Line 714 Male


title: DGRP Line 716 Male Rep 2

source_name: DGRP Line 716 Male


title: DGRP Line 721 Female Rep 1

source_name: DGRP Line 721 Female


title: DGRP Line 716 Female Rep 2

source_name: DGRP Line 716 Female


title: DGRP Line 730 Male Rep 1


title: DGRP Line 712 Male Rep 2

source_name: DGRP Line 712 Male


title: DGRP Line 721 Male Rep 1


title: DGRP Line 714 Female Rep 1

source_name: DGRP Line 714 Female


title: DGRP Line 714 Male Rep 2


title: DGRP Line 707 Male Rep 2

source_name: DGRP Line 707 Male


title: DGRP Line 712 Female Rep 2

source_name: DGRP Line 712 Female


title: DGRP Line 707 Male Rep 1


title: DGRP Line 712 Female Rep 1


title: DGRP Line 727 Male Rep 2

source_name: DGRP Line 727 Male


title: DGRP Line 73 Female Rep 1


title: DGRP Line 705 Male Rep 2

source_name: DGRP Line 705 Male


title: DGRP Line 707 Female Rep 1

source_name: DGRP Line 707 Female


title: DGRP Line 705 Male Rep 1


title: DGRP Line 707 Female Rep 2


title: DGRP Line 705 Female Rep 1

source_name: DGRP Line 705 Female


title: DGRP Line 721 Female Rep 2


title: DGRP Line 716 Male Rep 1


title: DGRP Line 705 Female Rep 2


title: DGRP Line 716 Female Rep 1


title: DGRP Line 703 Male Rep 2

source_name: DGRP Line 703 Male


title: DGRP Line 714 Female Rep 2


title: DGRP Line 712 Male Rep 1


title: DGRP Line 703 Female Rep 2

source_name: DGRP Line 703 Female


title: DGRP Line 69 Male Rep 1

source_name: DGRP Line 69 Male


title: DGRP Line 703 Male Rep 1


title: DGRP Line 69 Male Rep 2


title: DGRP Line 69 Female Rep 2

source_name: DGRP Line 69 Female


title: DGRP Line 703 Female Rep 1


title: DGRP Line 69 Female Rep 1


title: DGRP Line 642 Male Rep 2

source_name: DGRP Line 642 Male


title: DGRP Line 727 Male Rep 1


title: DGRP Line 642 Female Rep 2

source_name: DGRP Line 642 Female


title: DGRP Line 727 Female Rep 2

source_name: DGRP Line 727 Female


title: DGRP Line 642 Female Rep 1


title: DGRP Line 639 Male Rep 1

source_name: DGRP Line 639 Male


title: DGRP Line 639 Female Rep 2

source_name: DGRP Line 639 Female


title: DGRP Line 639 Male Rep 2


title: DGRP Line 634 Male Rep 2

source_name: DGRP Line 634 Male


title: DGRP Line 634 Female Rep 1

source_name: DGRP Line 634 Female


title: DGRP Line 639 Female Rep 1


title: DGRP Line 630 Female Rep 1

source_name: DGRP Line 630 Female


title: DGRP Line 630 Male Rep 1

source_name: DGRP Line 630 Male


title: DGRP Line 634 Male Rep 1


title: DGRP Line 627 Male Rep 2

source_name: DGRP Line 627 Male


title: DGRP Line 630 Male Rep 2


title: DGRP Line 630 Female Rep 2


title: DGRP Line 627 Female Rep 1

source_name: DGRP Line 627 Female


title: DGRP Line 596 Male Rep 2

source_name: DGRP Line 596 Male


title: DGRP Line 595 Female Rep 2

source_name: DGRP Line 595 Female


title: DGRP Line 627 Female Rep 2


title: DGRP Line 596 Female Rep 1

source_name: DGRP Line 596 Female


title: DGRP Line 642 Male Rep 1


title: DGRP Line 595 Male Rep 1

source_name: DGRP Line 595 Male


title: DGRP Line 596 Male Rep 1


title: DGRP Line 59 Male Rep 2

source_name: DGRP Line 59 Male


title: DGRP Line 627 Male Rep 1


title: DGRP Line 596 Female Rep 2


title: DGRP Line 595 Female Rep 1


title: DGRP Line 59 Male Rep 1


title: DGRP Line 59 Female Rep 2

source_name: DGRP Line 59 Female


title: DGRP Line 59 Female Rep 1


title: DGRP Line 634 Female Rep 2


title: DGRP Line 589 Male Rep 1

source_name: DGRP Line 589 Male


title: DGRP Line 589 Female Rep 1

source_name: DGRP Line 589 Female


title: DGRP Line 584 Male Rep 2

source_name: DGRP Line 584 Male


title: DGRP Line 589 Female Rep 2


title: DGRP Line 584 Male Rep 1


title: DGRP Line 584 Female Rep 1

source_name: DGRP Line 584 Female


title: DGRP Line 584 Female Rep 2


title: DGRP Line 57 Male Rep 1

source_name: DGRP Line 57 Male


title: DGRP Line 57 Male Rep 2


title: DGRP Line 57 Female Rep 2

source_name: DGRP Line 57 Female


title: DGRP Line 595 Male Rep 2


title: DGRP Line 57 Female Rep 1


title: DGRP Line 566 Male Rep 1

source_name: DGRP Line 566 Male


title: DGRP Line 563 Male Rep 2

source_name: DGRP Line 563 Male


title: DGRP Line 563 Male Rep 1


title: DGRP Line 566 Female Rep 1

source_name: DGRP Line 566 Female


title: DGRP Line 566 Male Rep 2


title: DGRP Line 559 Male Rep 1

source_name: DGRP Line 559 Male


title: DGRP Line 589 Male Rep 2


title: DGRP Line 563 Female Rep 1

source_name: DGRP Line 563 Female


title: DGRP Line 559 Female Rep 2

source_name: DGRP Line 559 Female


title: DGRP Line 555 Male Rep 2

source_name: DGRP Line 555 Male


title: DGRP Line 559 Female Rep 1


title: DGRP Line 559 Male Rep 2


title: DGRP Line 555 Male Rep 1


title: DGRP Line 563 Female Rep 2


title: DGRP Line 555 Female Rep 2

source_name: DGRP Line 555 Female


title: DGRP Line 551 Male Rep 2

source_name: DGRP Line 551 Male


title: DGRP Line 551 Male Rep 1


title: DGRP Line 555 Female Rep 1


title: DGRP Line 551 Female Rep 1

source_name: DGRP Line 551 Female


title: DGRP Line 535 Male Rep 1

source_name: DGRP Line 535 Male


title: DGRP Line 551 Female Rep 2


title: DGRP Line 535 Male Rep 2


title: DGRP Line 535 Female Rep 1

source_name: DGRP Line 535 Female


title: DGRP Line 535 Female Rep 2


title: DGRP Line 566 Female Rep 2


title: DGRP Line 531 Male Rep 2

source_name: DGRP Line 531 Male


title: DGRP Line 531 Male Rep 1


title: DGRP Line 531 Female Rep 1

source_name: DGRP Line 531 Female


title: DGRP Line 531 Female Rep 2


title: DGRP Line 530 Male Rep 2

source_name: DGRP Line 530 Male


title: DGRP Line 530 Male Rep 1


title: DGRP Line 513 Female Rep 2

source_name: DGRP Line 513 Female


title: DGRP Line 530 Female Rep 2

source_name: DGRP Line 530 Female


title: DGRP Line 528 Female Rep 2

source_name: DGRP Line 528 Female


title: DGRP Line 517 Male Rep 2

source_name: DGRP Line 517 Male


title: DGRP Line 513 Female Rep 1


title: DGRP Line 513 Male Rep 1

source_name: DGRP Line 513 Male


title: DGRP Line 528 Male Rep 1

source_name: DGRP Line 528 Male


title: DGRP Line 528 Male Rep 2


title: DGRP Line 530 Female Rep 1


title: DGRP Line 513 Male Rep 2


title: DGRP Line 509 Male Rep 1

source_name: DGRP Line 509 Male


title: DGRP Line 517 Male Rep 1


title: DGRP Line 509 Male Rep 2


title: DGRP Line 517 Female Rep 1

source_name: DGRP Line 517 Female


title: DGRP Line 509 Female Rep 2

source_name: DGRP Line 509 Female


title: DGRP Line 517 Female Rep 2


title: DGRP Line 508 Male Rep 2

source_name: DGRP Line 508 Male


title: DGRP Line 509 Female Rep 1


title: DGRP Line 505 Male Rep 1

source_name: DGRP Line 505 Male


title: DGRP Line 505 Male Rep 2


title: DGRP Line 528 Female Rep 1


title: DGRP Line 505 Female Rep 2

source_name: DGRP Line 505 Female


title: DGRP Line 505 Female Rep 1


title: DGRP Line 502 Male Rep 2

source_name: DGRP Line 502 Male


title: DGRP Line 508 Female Rep 1

source_name: DGRP Line 508 Female


title: DGRP Line 502 Male Rep 1


title: DGRP Line 502 Female Rep 2

source_name: DGRP Line 502 Female


title: DGRP Line 492 Male Rep 1

source_name: DGRP Line 492 Male


title: DGRP Line 502 Female Rep 1


title: DGRP Line 492 Male Rep 2


title: DGRP Line 491 Male Rep 2

source_name: DGRP Line 491 Male


title: DGRP Line 492 Female Rep 1

source_name: DGRP Line 492 Female


title: DGRP Line 508 Female Rep 2


title: DGRP Line 492 Female Rep 2


title: DGRP Line 508 Male Rep 1


title: DGRP Line 491 Male Rep 1


title: DGRP Line 491 Female Rep 2

source_name: DGRP Line 491 Female


title: DGRP Line 491 Female Rep 1


title: DGRP Line 48 Male Rep 2

source_name: DGRP Line 48 Male


title: DGRP Line 486 Female Rep 2

source_name: DGRP Line 486 Female


title: DGRP Line 49 Female Rep 1

source_name: DGRP Line 49 Female


title: DGRP Line 486 Male Rep 2

source_name: DGRP Line 486 Male


title: DGRP Line 49 Male Rep 2

source_name: DGRP Line 49 Male


title: DGRP Line 486 Male Rep 1


title: DGRP Line 486 Female Rep 1


title: DGRP Line 49 Male Rep 1


title: DGRP Line 48 Female Rep 2

source_name: DGRP Line 48 Female


title: DGRP Line 48 Male Rep 1


title: DGRP Line 49 Female Rep 2


title: DGRP Line 48 Female Rep 1


title: DGRP Line 443 Male Rep 2

source_name: DGRP Line 443 Male


title: DGRP Line 441 Male Rep 1

source_name: DGRP Line 441 Male


title: DGRP Line 443 Female Rep 2

source_name: DGRP Line 443 Female


title: DGRP Line 441 Female Rep 1

source_name: DGRP Line 441 Female


title: DGRP Line 443 Female Rep 1


title: DGRP Line 461 Female Rep 1

source_name: DGRP Line 461 Female


title: DGRP Line 45 Male Rep 2

source_name: DGRP Line 45 Male


title: DGRP Line 45 Male Rep 1


title: DGRP Line 461 Male Rep 2

source_name: DGRP Line 461 Male


title: DGRP Line 461 Female Rep 2


title: DGRP Line 461 Male Rep 1


title: DGRP Line 441 Male Rep 2


title: DGRP Line 45 Female Rep 2

source_name: DGRP Line 45 Female


title: DGRP Line 440 Male Rep 2

source_name: DGRP Line 440 Male


title: DGRP Line 45 Female Rep 1


title: DGRP Line 440 Male Rep 1


title: DGRP Line 440 Female Rep 1

source_name: DGRP Line 440 Female


title: DGRP Line 439 Female Rep 2

source_name: DGRP Line 439 Female


title: DGRP Line 439 Male Rep 1

source_name: DGRP Line 439 Male


title: DGRP Line 437 Female Rep 2

source_name: DGRP Line 437 Female


title: DGRP Line 437 Male Rep 2

source_name: DGRP Line 437 Male


title: DGRP Line 440 Female Rep 2


title: DGRP Line 427 Male Rep 2

source_name: DGRP Line 427 Male


title: DGRP Line 427 Male Rep 1


title: DGRP Line 439 Male Rep 2


title: DGRP Line 439 Female Rep 1


title: DGRP Line 437 Female Rep 1


title: DGRP Line 443 Male Rep 1


title: DGRP Line 427 Female Rep 2

source_name: DGRP Line 427 Female


title: DGRP Line 42 Male Rep 1

source_name: DGRP Line 42 Male


title: DGRP Line 41 Female Rep 1

source_name: DGRP Line 41 Female


title: DGRP Line 42 Female Rep 1

source_name: DGRP Line 42 Female


title: DGRP Line 426 Female Rep 1

source_name: DGRP Line 426 Female


title: DGRP Line 426 Female Rep 2


title: DGRP Line 42 Female Rep 2


title: DGRP Line 441 Female Rep 2

source_name: DGRP Line 441 Female


title: DGRP Line 409 Male Rep 2

source_name: DGRP Line 409 Male


title: DGRP Line 409 Male Rep 1


title: DGRP Line 41 Male Rep 1

source_name: DGRP Line 41 Male


title: DGRP Line 426 Male Rep 1

source_name: DGRP Line 426 Male


title: DGRP Line 409 Female Rep 2

source_name: DGRP Line 409 Female


title: DGRP Line 426 Male Rep 2


title: DGRP Line 41 Male Rep 2


title: DGRP Line 437 Male Rep 1


title: DGRP Line 41 Female Rep 2


title: DGRP Line 42 Male Rep 2


title: DGRP Line 406 Male Rep 2

source_name: DGRP Line 406 Male


title: DGRP Line 405 Male Rep 2

source_name: DGRP Line 405 Male


title: DGRP Line 409 Female Rep 1


title: DGRP Line 405 Male Rep 1


title: DGRP Line 406 Male Rep 1


title: DGRP Line 405 Female Rep 1

source_name: DGRP Line 405 Female


title: DGRP Line 40 Male Rep 2

source_name: DGRP Line 40 Male


title: DGRP Line 405 Female Rep 2


title: DGRP Line 40 Male Rep 1


title: DGRP Line 427 Female Rep 1


title: DGRP Line 40 Female Rep 2

source_name: DGRP Line 40 Female


title: DGRP Line 406 Female Rep 1

source_name: DGRP Line 406 Female


title: DGRP Line 40 Female Rep 1


title: DGRP Line 399 Male Rep 1

source_name: DGRP Line 399 Male


title: DGRP Line 406 Female Rep 2


title: DGRP Line 399 Male Rep 2


title: DGRP Line 399 Female Rep 2

source_name: DGRP Line 399 Female


title: DGRP Line 397 Male Rep 2

source_name: DGRP Line 397 Male


title: DGRP Line 395 Male Rep 2

source_name: DGRP Line 395 Male


title: DGRP Line 397 Male Rep 1


title: DGRP Line 392 Male Rep 2

source_name: DGRP Line 392 Male


title: DGRP Line 392 Male Rep 1


title: DGRP Line 391 Male Rep 1

source_name: DGRP Line 391 Male


title: DGRP Line 390 Male Rep 1

source_name: DGRP Line 390 Male


title: DGRP Line 390 Female Rep 2

source_name: DGRP Line 390 Female


title: DGRP Line 399 Female Rep 1


title: DGRP Line 395 Female Rep 1

source_name: DGRP Line 395 Female


title: DGRP Line 395 Female Rep 2


title: DGRP Line 392 Female Rep 1

source_name: DGRP Line 392 Female


title: DGRP Line 390 Female Rep 1


title: DGRP Line 391 Female Rep 1

source_name: DGRP Line 391 Female


title: DGRP Line 390 Male Rep 2


title: DGRP Line 391 Male Rep 2


title: DGRP Line 386 Male Rep 2

source_name: DGRP Line 386 Male


title: DGRP Line 386 Male Rep 1


title: DGRP Line 386 Female Rep 2

source_name: DGRP Line 386 Female


title: DGRP Line 397 Female Rep 2

source_name: DGRP Line 397 Female


title: DGRP Line 395 Male Rep 1


title: DGRP Line 385 Male Rep 1

source_name: DGRP Line 385 Male


title: DGRP Line 385 Female Rep 1

source_name: DGRP Line 385 Female


title: DGRP Line 383 Male Rep 2

source_name: DGRP Line 383 Male


title: DGRP Line 392 Female Rep 2


title: DGRP Line 391 Female Rep 2


title: DGRP Line 383 Female Rep 1

source_name: DGRP Line 383 Female


title: DGRP Line 397 Female Rep 1


title: DGRP Line 382 Female Rep 2

source_name: DGRP Line 382 Female


title: DGRP Line 385 Female Rep 2


title: DGRP Line 386 Female Rep 1


title: DGRP Line 381 Male Rep 2

source_name: DGRP Line 381 Male


title: DGRP Line 381 Male Rep 1


title: DGRP Line 382 Male Rep 1

source_name: DGRP Line 382 Male


title: DGRP Line 381 Female Rep 1

source_name: DGRP Line 381 Female


title: DGRP Line 381 Female Rep 2


title: DGRP Line 380 Male Rep 2

source_name: DGRP Line 380 Male


title: DGRP Line 383 Female Rep 2


title: DGRP Line 383 Male Rep 1


title: DGRP Line 380 Male Rep 1


title: DGRP Line 380 Female Rep 1

source_name: DGRP Line 380 Female


title: DGRP Line 380 Female Rep 2


title: DGRP Line 38 Male Rep 2

source_name: DGRP Line 38 Male


title: DGRP Line 38 Male Rep 1


title: DGRP Line 38 Female Rep 2

source_name: DGRP Line 38 Female


title: DGRP Line 385 Male Rep 2


title: DGRP Line 38 Female Rep 1


title: DGRP Line 379 Male Rep 1

source_name: DGRP Line 379 Male


title: DGRP Line 379 Male Rep 2


title: DGRP Line 382 Male Rep 2


title: DGRP Line 377 Male Rep 2

source_name: DGRP Line 377 Male


title: DGRP Line 379 Female Rep 2

source_name: DGRP Line 379 Female


title: DGRP Line 379 Female Rep 1


title: DGRP Line 377 Male Rep 1


title: DGRP Line 377 Female Rep 2

source_name: DGRP Line 377 Female


title: DGRP Line 382 Female Rep 1


title: DGRP Line 377 Female Rep 1


title: DGRP Line 375 Male Rep 2

source_name: DGRP Line 375 Male


title: DGRP Line 375 Female Rep 2

source_name: DGRP Line 375 Female


title: DGRP Line 375 Female Rep 1


title: DGRP Line 374 Female Rep 1

source_name: DGRP Line 374 Female


title: DGRP Line 374 Female Rep 2


title: DGRP Line 374 Male Rep 1

source_name: DGRP Line 374 Male


title: DGRP Line 371 Male Rep 2

source_name: DGRP Line 371 Male


title: DGRP Line 373 Male Rep 1

source_name: DGRP Line 373 Male


title: DGRP Line 374 Male Rep 2


title: DGRP Line 373 Female Rep 2

source_name: DGRP Line 373 Female


title: DGRP Line 371 Female Rep 2

source_name: DGRP Line 371 Female


title: DGRP Line 373 Female Rep 1


title: DGRP Line 371 Male Rep 1


title: DGRP Line 371 Female Rep 1


title: DGRP Line 370 Male Rep 1

source_name: DGRP Line 370 Male


title: DGRP Line 370 Male Rep 2


title: DGRP Line 370 Female Rep 1

source_name: DGRP Line 370 Female


title: DGRP Line 370 Female Rep 2


title: DGRP Line 375 Male Rep 1


title: DGRP Line 367 Male Rep 2

source_name: DGRP Line 367 Male


title: DGRP Line 367 Female Rep 2

source_name: DGRP Line 367 Female


title: DGRP Line 367 Male Rep 1


title: DGRP Line 367 Female Rep 1


title: DGRP Line 373 Male Rep 2


title: DGRP Line 365 Male Rep 1

source_name: DGRP Line 365 Male


title: DGRP Line 365 Female Rep 2

source_name: DGRP Line 365 Female


title: DGRP Line 362 Male Rep 2

source_name: DGRP Line 362 Male


title: DGRP Line 362 Male Rep 1


title: DGRP Line 365 Female Rep 1


title: DGRP Line 362 Female Rep 2

source_name: DGRP Line 362 Female


title: DGRP Line 362 Female Rep 1


title: DGRP Line 361 Male Rep 2

source_name: DGRP Line 361 Male


title: DGRP Line 361 Female Rep 2

source_name: DGRP Line 361 Female


title: DGRP Line 361 Male Rep 1


title: DGRP Line 360 Male Rep 1

source_name: DGRP Line 360 Male


title: DGRP Line 359 Male Rep 1

source_name: DGRP Line 359 Male


title: DGRP Line 360 Female Rep 1

source_name: DGRP Line 360 Female


title: DGRP Line 360 Male Rep 2


title: DGRP Line 365 Male Rep 2


title: DGRP Line 359 Female Rep 2

source_name: DGRP Line 359 Female


title: DGRP Line 358 Male Rep 2

source_name: DGRP Line 358 Male


title: DGRP Line 358 Female Rep 1

source_name: DGRP Line 358 Female


title: DGRP Line 359 Female Rep 1


title: DGRP Line 358 Male Rep 1


title: DGRP Line 357 Female Rep 2

source_name: DGRP Line 357 Female


title: DGRP Line 357 Male Rep 1

source_name: DGRP Line 357 Male


title: DGRP Line 357 Male Rep 2


title: DGRP Line 356 Male Rep 1

source_name: DGRP Line 356 Male


title: DGRP Line 357 Female Rep 1


title: DGRP Line 356 Male Rep 2


title: DGRP Line 355 Male Rep 2

source_name: DGRP Line 355 Male


title: DGRP Line 355 Female Rep 2

source_name: DGRP Line 355 Female


title: DGRP Line 355 Female Rep 1